Genetic Analysis of Nitrogen Remobilization and Kernel Compositon in Zea Mays L

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Spring 2015 Genetic Analysis of Nitrogen Remobilization and Kernel Compositon in Zea Mays L. and Sorghum Bicolor (L.) Moench Raymond S Lindsey Purdue University

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GENETIC ANALYSIS OF NITROGEN REMOBILIZATION AND KERNEL COMPOSITION IN ZEA MAYS L. AND SORGHUM BICOLOR (L.) MOENCH

A Dissertation

Submitted to the Faculty

Purdue University

Raymond S Lindsey

In Partial Fulfillment of the

Requirements for the Degree

Doctor of Philosophy

May 2015

Purdue University

West Lafayette, Indiana

To my parents: their love and support have made this possible.

iii

ACKNOWLEDGEMENTS

I would like to take this opportunity to thank my major advisor Dr. Mitch

Tuinstra. His advocacy of hard work and scientific achievement have had an enormous influence on my graduate tenure. I would also like to express appreciation toward my committee members; Drs. Patrick Brown, David Rhodes, Torbert Rocheford, and Tony

Vyn. Their collection of expertise has been a valuable asset throughout my research, and for their willingness to discuss a multitude of topics during my graduate tenure I am indebted.

I would also like to thank those who supported my research at Purdue, particularly our technician Andy Linvill. Without him, our field research would not be possible. I’m also appreciative of his time spent teaching me the intricacies of precision planting, and harvest; experience I am sure to utilize in my career. Data collection for my research in 2012 and 2013 was extremely labor intensive, and I am very grateful to all of

the members of the Tuinstra group, past and present, who assisted in data collection. iii

Field research would not be possible without excellent research stations, and I thank Jim

Beaty and Jon Leuck for their facilitation of my field experiments. Appreciation is also extended to Dr. Alex Lipka for his support in my Genome-Wide Association Mapping.

I am incredibly thankful for the love and support of my parents and brother.

TABLE OF CONTENTS

Page LIST OF TABLES ...... ix LIST OF FIGURES ...... xiii ABSTRACT …………………………………………………………………………………………………………………….. x

CHAPTER 1. LITERATURE REVIEW ...... 1 1.1 Introduction ...... 1 1.2 Nitrogen Use Efficiency ...... 4 1.3 Kernel Composition in Maize ...... 10 1.3.1 Maize Kernel Protein ...... 11 1.3.2 Maize Kernel Oil ...... 15 1.3.3 Maize Kernel Starch ...... 16 1.3.4 Maize Kernel Ash ...... 19 1.3.5 Maize Kernel Fiber ...... 19 1.3.6 Maize Kernel Density ...... 20 1.3.7 Xenia Effects ...... 21 1.4 Kernel Composition in Sorghum ...... 22

1.4.3 Sorghum Kernel Feeding Quality ...... 23 iv

1.4.4 Sorghum Kernel Protein ...... 25 1.4.5 Sorghum Kernel Oil ...... 28 1.4.6 Sorghum Kernel Starch ...... 28 CHAPTER 2. GENOME-WIDE ASSOCIATION STUDY OF LEAF NITROGEN REMOBILIZATION IN ZEA MAYS ...... 31 2.1 Abstract ...... 31

...... Page 2.2 Introduction ...... 32 2.3 Materials and Methods ...... 33 2.3.1 Genetic Material ...... 33 2.3.2 Experimental Design ...... 33 2.3.3 Phenotypic Evaluation ...... 36 2.3.4 Genotypic Information ...... 38 2.3.5 Statistical Analysis ...... 38 2.3.6 Candidate Gene Analysis ...... 40 2.4 Results ...... 40 2.4.1 Genetic Variance and Trait Correlations ...... 40 2.4.2 Heritabilities ...... 42 2.4.3 Genome Wide Association Studies ...... 42 2.4.3.1 Examination of VTR2 Traits ...... 45 2.4.3.2 Examination of VTR4 Traits ...... 49 2.5 Discussion ...... 54 2.5.1 Genetic Variance and Trait Correlation ...... 54 2.5.2 Heritabilities ...... 55 2.5.3 Candidate Genes for Leaf N Remobilization ...... 55

v 2.5.3.1 Senescence Signaling...... 55 2.5.3.2 Senescence Activation/Regulation...... 60 2.5.3.3 Genetic Control of N Remobilization ...... 62 2.6 Conclusions ...... 68 CHAPTER 3. GENETIC MAPPING OF KERNEL COMPOSITION IN A DIVERSE POPULATION OF ZEA MAYS ...... 70 3.1 Abstract ...... 70 3.2 Introduction ...... 71 3.3 Materials and Methods ...... 72 3.3.1 Genetic Material ...... 72

...... Page 3.3.2 Experimental Design ...... 73 3.3.3 Phenotypic Evaluation ...... 73 3.3.4 Genotypic Information ...... 74 3.3.5 Statistical Analysis ...... 74 3.3.6 Candidate Gene Analysis ...... 75 3.3.7 Transcript expression analysis ...... 75 3.4 Results ...... 76 3.4.1 Genetic Variance and Trait Correlations ...... 76 3.4.2 Heritabilities ...... 77 3.4.3 Genome Wide Association Studies ...... 77 3.5 Discussion ...... 83 3.5.1 Genetic Variance and Trait Correlations ...... 83 3.5.2 Heritabilities ...... 85 3.5.3 Candidate genes for kernel composition ...... 85 3.6 Conclusion ...... 89 CHAPTER 4. GENETIC MAPPING OF KERNEL COMPOSITION IN A DIVERSE POPULATION OF SORGHUM BICOLOR ...... 92 4.1 Abstract ...... 92

vi 4.2 Introduction ...... 93 4.3 Materials and Methods ...... 95 4.3.1 Genetic Material ...... 95 4.3.2 Experimental Design ...... 95 4.3.3 Phenotypic Evaluation ...... 96 4.3.4 Genotypic Information ...... 97 4.3.5 Statistical Analysis ...... 97 4.3.6 Candidate Gene Analysis ...... 99 4.4 Results ...... 100 4.4.1 Genetic Variation and Trait Correlations ...... 100

vii

...... Page 4.4.2 Heritabilities ...... 102 4.4.3 Significant SNPs ...... 102 4.5 Discussion ...... 110 4.5.1 Genetic Variance and Trait Correlations ...... 110 4.5.2 Heritabilities ...... 111 4.5.3 Feeding Quality Candidate Genes ...... 111 4.5.4 Protein Kernel Composition Candidate Genes ...... 114 4.6 Conclusion ...... 117 CHAPTER 5. PROSPECTUS ...... 119 5.1 Maize Leaf Nitrogen Remobilization ...... 119 5.2 Maize Kernel Composition ...... 120 5.3 Sorghum Kernel Composition ...... 121 REFERENCES ...... 122 APPENDICES Appendix A Maize Leaf N Remobilization SAS Code for BLUP Analysis ...... 157 Appendix B Maize Leaf N Remobilization R Code for GWAS Analysis...... 161 Appendix C Maize Leaf N Remobilization ANOVA Outputs ...... 172 Appendix D Maize Leaf N Remobilization Candidate Genes ...... 178

vii

D-1 Trait R2HL Candidate Genes ...... 178 D-2 Trait VTR2 Candidate Genes ...... 179 D-3 Trait VTR2H Candidate Genes ...... 181 D-4 Trait VTR2L Candidate Genes ...... 188 D-5 Trait VTR4 Candidate Genes ...... 190 D-6 Trait VTR4H Candidate Genes ...... 239 D-7 Trait VTR4L Candidate Genes ...... 315 Appendix E Maize Kernel Composition NIR Calibration Correlations ...... 350 Appendix F Maize Kernel Composition SAS Code for BLUP Analysis ...... 351 Appendix G Maize Kernel Composition R Code for GWAS Analysis ...... 355

viii

...... Page Appendix H Maize Kernel Composition ANOVA Outputs ...... 366 Appendix I Maize Kernel Composition Candidate Genes ...... 372 I-1 Maize Kernel Density Candidate Genes ...... 372 I-2 Maize Kernel Oil Candidate Genes ...... 387 I-3 Maize Kernel Protein Candidate Genes ...... 392 Appendix J Sorghum Kernel Composition NIR Calibration Correlations ...... 517 Appendix K Sorghum Kernel Composition SAS Code for BLUP Analysis ...... 525 Appendix L Sorghum Kernel Composition R Code for GWAS Analysis ...... 530 Appendix M Sorghum Kernel Composition ANOVA Outputs ...... 533 Appendix N Sorghum Kernel Composition Candidate Genes ...... 539 N-1 Sorghum Kernel Acid Detergent Fiber (ADF) Candidate Genes ...... 539 N-2 Sorghum Kernel Net Energy of Lactation (NEL) Candidate Genes...... 542 N-3 Sorghum Kernel Net Energy of Maintenance (NEM) Candidate Genes ...... 548 N-4 Sorghum Kernel Protein Candidate Genes ...... 556 N-5 Sorghum Kernel Total Digestible Nutrients (TDN) Candidate Genes ...... 558 VITA ...... 560

viii

LIST OF TABLES

Table ...... Page Table 2-1 Basic statistics and trait correlations for RVI greenness characteristics of leaves at different positions on the plant and at different stages of development ...... 41

Table 2-2 Heritabilities of RVI greenness traits for leaves at different positions on the plant and at different stages of development ...... 42

Table 2-3 Summary of GWAS indicating the number of significant SNPs, linkage blocks, candidate genes, and genes with annotations for chlorophyll degradation and remobilization timing traits ...... 43

Table 2-4 Candidate genes of interest for VTR2 senescence signaling ...... 48

Table 2-5 Candidate genes of interest for VTR2 senescence regulation ...... 48

Table 2-6 Candidate genes of interest for VTR4 senescence signaling ...... 52

Table 2-7 Candidate genes of interest for VTR4 senescence regulation ...... 53

Table 2-8 Candidate genes of interest for VTR4 N remobilization ...... 54

Table 3-1 Statistics for moisture values from NIR used for dry basis conversions ...... 74

Table 3-2 Basic statistics and trait correlations for maize kernel traits ...... 76

Table 3-3 Heritabilities of maize kernel traits measured in multilocation trials ...... 77

Table 3-4 Summary GWAS results for maize kernel traits ...... 78

Table 3-5 Candidate Gene of Interest for Kernel Oil Composition ...... 82

Table ...... Page

Table 3-6 Candidate Genes of Interest for Kernel Density ...... 82

Table 3-7 Candidate Genes of Interest for Kernel Protein ...... 83

Table 4-1 Statistics for moisture values from NIR used for dry basis conversions ...... 96

Table 4-2 Basic statistics and trait correlations for sorghum kernel traits ...... 101

Table 4-3 Heritabilities of sorghum kernel traits measured in multilocation trials ...... 102

Table 4-4 Summary GWAS results for sorghum kernel traits ...... 103

Table 4-5 Table of significant SNPs identified GWAS analysis with trait p-values and allelic effects ...... 105

Table 4-6 Candidate Genes of Interest for Kernel Feeding Quality ...... 106

APPENDIX TABLE

C-1Trait VTL ANOVA ...... 172

C-2 Trait VTH ANOVA ...... 173

C-3 Trait R2L ANOVA ...... 174

C-4 Trait R2H ANOVA ...... 175

C-5 Trait R4L ANOVA ...... 176

C-6 Trait R4H ANOVA ...... 177

D-1 Trait R2HL Candidate Genes ...... 178

D-2 Trait VTR2 Candidate Genes ...... 179

D-3 Trait VTR2H Candidate Genes ...... 181

D-4 Trait VTR2L Candidate Genes ...... 188

D-5 Trait VTR4 Candidate Genes ...... 190

Appendix Table ...... Page

D-6 Trait VTR4H Candidate Genes ...... 239

D-7 Trait VTR4L Candidate Genes ...... 315

H-1 Maize Kernel Ash ANOVA ...... 366

H-2 Maize Kernel Density ANOVA ...... 367

H-3 Maize Kernel Fiber ANOVA...... 368

H-4 Maize Kernel Oil ANOVA ...... 369

H-5 Maize Kernel Protein ANOVA ...... 370

H-6 Maize Kernel Starch ANOVA ...... 371

I-1 Maize Kernel Density Candidate Genes ...... 372

I-2 Maize Kernel Oil Candidate Genes ...... 387

I-3 Maize Kernel Protein Candidate Genes ...... 392

M-1 Sorghum Kernel ADF ANOVA ...... 533

M-2 Sorghum Kernel NEG ANOVA ...... 534

M-3 Sorghum Kernel NEL ANOVA ...... 535

M-4 Sorghum Kernel NEM ANOVA ...... 536

M-5 Sorghum Kernel Protein ANOVA ...... 537

M-6 Sorghum Kernel TDN ANOVA ...... 538

N-1 Sorghum Kernel Acid Detergent Fiber (ADF) Candidate Genes ...... 539

N-2 Sorghum Kernel Net Energy of Lactation (NEL) Candidate Genes ...... 542

N-3 Sorghum Kernel Net Energy of Maintenance (NEM) Candidate Genes ...... 548

N-4 Sorghum Kernel Protein Candidate Genes ...... 556

xii

Appendix Table ...... Page

N-5 Sorghum Kernel Total Digestible Nutrients (TDN) Candidate Genes ...... 558

xii

xiii

LIST OF FIGURES

Figure ...... Page Figure 2-1 2012 Precipitation amounts and flowering dates for each maturity group ... 35

Figure 2-2 2013 Precipitation amounts and flowering dates for each maturity group ... 35

Figure 2-3 Manhattan plot of maize leaf chlorophyll content ratio R2HL examining relative differences between the R2 high and low leaf measurements...... 44

Figure 2-4 Manhattan plot of maize leaf chlorophyll content ratio VTR2 examining relative differences between the VT and R2 leaf measurements ...... 46

Figure 2-5 Manhattan plot of maize leaf chlorophyll content ratio VTR2H examining relative differences between the VT and the R2 high leaf measurements ...... 46

Figure 2-6 Manhattan plot of maize leaf chlorophyll content ratio VTR2L examining relative differences between the VT and R2 low leaf measurements...... 47

Figure 2-7 Manhattan plot of maize leaf chlorophyll content ratio VTR4 examining relative differences between the VT and R4 leaf measurements ...... 49

xiii

Figure 2-8 Manhattan plot of maize leaf chlorophyll content ratio VTR4H examining relative differences between the VT and R4 high leaf measurements ...... 50

Figure 2-9 Manhattan plot of maize leaf chlorophyll content ratio VTR4L examining relative differences between the VT and R4 low leaf measurements ...... 50

xiv

Figure ...... Page

Figure 2-10 Proposed Pathway of Leaf N Remobilization and identified genes affecting timing of N remobilization in both sink (NADH-GOGAT) and Source (GS1 and Glutamate

Decarboxylase) and identified genes responsible for transportation of N compounds. . 66

Figure 3-1 Manhattan plot of SNPs associated with maize kernel density ...... 79

Figure 3-2 Manhattan plot of SNPs associated with maize kernel fiber ...... 80

Figure 3-3 Manhattan plot of SNPs associated with maize kernel oil ...... 80

Figure 3-4 Manhattan plot of SNPs associated with maize kernel protein ...... 81

Figure 4-1 Manhattan plot of SNPs associated with sorghum kernel acid detergent fiber

...... 107

Figure 4-2 Manhattan plot of SNPs associated with sorghum kernel net energy of lactation ...... 108

Figure 4-3 Manhattan plot of SNPs associated with sorghum kernel net energy of maintenance ...... 108

Figure 4-4 Manhattan plot of SNPs associated with sorghum kernel total digestible xiv

nutrients ...... 109

Figure 4-5 Manhattan plot of SNPs associated with sorghum kernel protein ...... 109

ABSTRACT

Lindsey, Raymond S. Ph.D., Purdue University, May 2015. Genetic Analysis of Nitrogen Remobilization and Kernel Composition in Zea Mays L. and Sorghum Bicolor (L.) Moench. Major Professor: Mitchell Tuinstra.

Modern maize (Zea mays L.) production relies heavily on nitrogen fertilization for high productivity. Over-application of nitrogen fertilizers in cropping systems can have detrimental economic and environmental effects. For this reason, improving Nitrogen

Use Efficiency (NUE) is a major goal of breeders and producers. Nitrogen Utilization

Efficiency (NUtE) is one component of NUE, and the most important component under

N-limited conditions. In this study we examined the genetic controls of the timing and preferential canopy position of leaf N remobilization during reproductive growth stages.

Utilizing a diversity panel of over 2,400 lines, genome wide association mapping was conducted in 2012 and 2013 to examine leaf chlorophyll content at different growth stages and kernel composition at maturity. Chlorophyll content meters were utilized for measurements of leaf chlorophyll content on two different leaves at VT, R2, and R4

sampling times. Near infrared reflectance spectroscopy (NIRS) was utilized for analysis of kernel composition on whole kernels. NIRS was also utilized for analysis of kernel composition on whole kernels of sorghum (Sorghum bicolor L. Moench) in a diverse panel of 840 accessions; with the goal of applying known genetic controls of maize kernel composition to gain a greater understanding of the controls of sorghum grain

xvi composition. Results from the maize leaf chlorophyll analysis and sorghum kernel composition analysis suggest a role for NADH - Glutamate Synthase as a sink control of

N remobilization from the leaves. Genes identified in these analyses suggest that genetic controls at both the source and sink level affect the timing and rate of N remobilization from the leaves. Knowledge of these genetic controls may be utilized in breeding programs to select lines with improved NUE and NUtE characteristics.

xvi

CHAPTER 1. LITERATURE REVIEW

1.1 Introduction

Zea mays L. and Sorghum bicolor (L.) Moench are important cereal crops utilizing

C4 photosynthesis grown worldwide under a multitude of climates and production systems with uses as food, feed, and fuel. The end uses of these crops largely depend upon the environment and region in which they are grown. Maize and sorghum are primarily grown as grain crops, although sometimes the plant material is used as forage or silage feed for cattle and other ruminant livestock. Greater understanding of how these cereal species manage available soil nutrients, as well as the genetic controls of kernel composition, may lead to improved crop nutrition programs and improved maize and sorghum grains for diverse uses.

Fertilizers are applied in many different production systems to increase growth, production (and subsequently profits), and/or aesthetic appeal. These applications include turf grasses (private lawns and golf courses), ornamental and horticultural crops,

and agricultural production. In most situations, the nutrient applied in the greatest amount is nitrogen. Commercial production of maize in the United States relies heavily on application of nitrogen-based fertilizers. In the U.S. alone, nitrogen consumption

2 amounts to 11,725,000 metric tonnes (“IFADATA”). This amount is equivalent to 18% of total worldwide N production (Heffer 2008).

Historically, synthetic nitrogen fertilizer accounted for a small portion of the total input cost of maize production. In 1960 the cost for N fertilizer was approximately $100 for a ton of actual N. More recently, due to an increase in worldwide demand and the rising cost of production, N prices have reached unprecedented highs. The $300/ton barrier was broken as recently as 2005, and since that time has reached prices as high as

$530/ton N (USDA NASS, 2012).

Historically, the low cost of synthetic N fertilizers and, more recently, the heightened price for corn grain, have allowed farmers to justify high rates of nitrogen application. These large nitrogen applications have not gone without an environmental consequence. In the Midwest region of the United States where a large portion of the land is used for agricultural production, high rates of N fertilizer application have affected ground and surface waters including NO3- leaching into groundwater systems

(Jarvis 1996; Socolow 1999; Castillo et al., 2000; Schilling and Libra 2000; Burkart and

Stoner 2001; Sauer et al., 2008). Once in the streams and rivers, N run-off can lead to eutrophication and algal blooms, disturbing and crippling the aquatic ecosystem (Ryther and Dunstan 1971). These environmental impacts have increased public awareness about agricultural practices and have elevated the need for efficient and responsible applications of N to agricultural soils. With increasing economic and environmental constraints, efficient use of N is gaining in importance and farmers are seeking new ways to use N fertilizers more efficiently.

The commercial maize hybrids grown in the United States in the past five decades have been selected for performance in high input environments. As the rising cost of fertilizers become a burden to farmers, cultivars that can utilize a smaller amount of applied N without a decline in yield have become more important.

Development of these cultivars will not only necessitate the examination of the acquisition of N by the plant, but also the Nitrogen Harvest Index (NHI, fraction of total

N translocated to grain (Moll et al.,, 1982)) in which the plant utilizes and eventually remobilizes plant N into the kernel.

Sorghum is considered a more abiotic stress-tolerant crop than maize, as it is well adapted to environments that experience extremes in both heat and drought

(Maunder 2005). This is evident in the regions where it is largely produced. Of the top

15 sorghum producing countries in 2011, 11 are found on the African continent, where sorghum originated (Top Production, 2011). While these locations often experience extremes in drought and heat, agricultural productivity in these environments are also

limited by deficient fertility management programs. Sorghum is generally better adapted than maize for production under these high-stress and low-input conditions.

Grain sorghum is commonly harvested as either a food or feed source. In the

United States, a large portion of sorghum is grown under dry-land conditions in the High

Plains region of Texas, Oklahoma, Kansas, Nebraska and Missouri (USDA ERS 2010). The

High Plains in recent decades have been converted to irrigated fields as the Ogallala

Aquifer has been tapped for pivot irrigation across this region. This has allowed alternate crops such as maize to be grown in this region, reducing the planted acreage

4 of sorghum. As increasing amounts of farmland in this region have been converted to irrigated agriculture, a tremendous stress has been placed on the Ogallala Aquifer, diminishing the supply of fresh water (Sloggett and Dickason 1986). As the aquifer continues to be drained, more of this irrigated land will be converted back to dry-land within the next few decades (Associates 1982; Hornbeck and Keskin 2011). Once irrigation in this region ceases to be physically or economically viable, it can be hypothesized that much of this irrigated maize ground will return to dry-land sorghum, thereby increasing the importance of yield and grain quality of sorghum in this region of the United States.

1.2 Nitrogen Use Efficiency

Nitrogen Use Efficiency (NUE) is composed of two components; Nitrogen Uptake

Efficiency (NUpE, also referenced as Nitrogen Recovery Efficiency (NRE)) and Nitrogen

Utilization Efficiency (NUtE; also referenced as Nitrogen Internal Efficiency (NIE)) (Moll

et al., 1982). NUpE examines the ability of the plant to acquire N considering the amount of N available in the environment. This trait is broken into two distinct periods, uptake during the vegetative phase and the reproductive growth phase. During vegetative and early reproductive growth periods, accumulated N is stored in vegetative plant parts including the leaves, stalks, and roots. This stored N is then made available to the developing reproductive plant parts during the later stages of growth, measured by NUtE. As breeders have selected for improved lines in optimal environments for decades, selection gains have been made in NUpE values, resulting in adaptation to high

5 nitrogen environments (Castleberry et al., 1984). Many environmental and plant- produced signals affect the accumulation and movement of plant N, and greater understanding of the movement, storage, and reallocation of this vital element within the plant can lead to improvement of NUE.

Improving NRE and NIE is complicated by the many roles that N plays within the plant. The importance of N within the plant has supported many studies examining aspects of assimilation, storage, and final utilization. Genetic studies examining both

NRE and NIE have found a negative correlation between the two traits (Gallais and

Coque 2005; Coque and Gallais 2007a; Coque et al., 2008). Agronomic studies have also been conducted to determine the relationships between NRE, NIE, and grain yield (Reed et al., 1980; Purcino et al., 1998). These studies have revealed genetic variation for these traits, and studies in testcross hybrids have shown a stronger relationship between post-silking N uptake and yield than between NIE and yield (Masclaux et al.,

2001; Gallais et al., 2006; Coque and Gallais 2007b; Gallais et al., 2007). This is likely a

function of selection by breeders under optimal N environments. Although N uptake has a greater correlation to yield, both post-silking uptake of new N and remobilized N (RN) play an important role in grain N accumulation, and the proportion each process contributes also varies greatly with genotype (Beauchamp et al., 1976; Below et al.,

1981; Pan et al., 1984; Pan et al., 1986; Ta and Weiland 1992).

The contributions of NRE and NIE to grain N is dependent on multiple factors, the largest of which is the environment in which the crop is grown. Historically, cultivars have been selected by breeders in programs utilizing optimum field fertilization

6 practices, and this has placed a selection pressure upon the lines for certain NRE and NIE characteristics. Era hybrid studies have shown that more recent hybrids produce a higher yield when grown in high or excess N environments compared to older hybrids, supporting other research showing that NRE is of greater importance at high fertilization levels and NIE is of greater importance to the plant under N-poor environments (Duvick

1977; Uribelarrea et al., 2007). Era studies have also shown that more recent commercial hybrids have a greater yield response per unit fertilizer applied, as well as a greater tolerance to N stresses (based on 0 N treatment yields) (Ciampitti and Vyn 2012;

Ciampitti et al., 2013). These yield differences have been shown to be exacerbated when plants are subjected to stressful growing conditions (McCullough et al., 1994;

Dwyer et al., 1995; Boomsma et al., 2009; Ciampitti et al., 2013). This difference in performance is thought to be related to a Genotype X Environment (G x E) interaction and differential gene expression associated with N partitioning within the plant (Moll et al., 1987; Landbeck 1995; Bertin and Gallais 2000a, b, 2001); although some research

suggests otherwise (Rajcan and Tollenaar 1999). Examination of significant QTL of lines in both high- and low-N environments suggest that variation in NUE performance is largely associated with post-silking NRE in N-abundant environments, while NIE and remobilization have greater genetic variance and importance when N is limited (Muruli and Paulsen 1981; Di Fonzo et al., 1982; Moll et al., 1982; Jackson et al., 1986; Moll et al., 1987; Lafitte and Edmeades 1994; Bertin and Gallais 2000a). If performance is to be maintained at lower levels of N fertilization, NIE must be improved. This runs counter to historical breeding efforts that have improved NRE under high-N environments.

The relationship between N recovery (both during vegetative and reproductive stages) and N internal efficiency is complicated and dependent upon source/sink relationships. A study by Ciampitti et al. (2013) noted a strong relationship between N uptake during vegetative growth and remobilization of stalk N during the reproductive growth in hybrids. This is logical, as N would have to be acquired in the vegetative stages and stored in the stalks in order to be subsequently remobilized to the grain during the reproductive stages of growth. A positive relationship was also observed between reproductive stage N-uptake and both the ear strength (sink strength) and late-season shoot N remobilization (source strength) in hybrids (Ciampitti et al., 2013). Ear strength, whose components of kernel number and weight are also positively related to grain yield, was shown to be associated with total plant N-uptake at both the vegetative and reproductive stages of growth; this trait has also been shown to be associated with late stage N remobilization in hybrids tested under different treatments of plant density and

N rate (Ciampitti et al., 2013). Ear strength (sink strength) appeared to affect

remobilization of vegetative N in the shoot in the later reproductive stages of growth

(Ciampitti et al., 2013).

Plants grown in N limited environments exhibit other physiological differences that affect the yield potential of the crop. Nitrogen deficiencies can limit the number and rate at which leaves are produced, while at the same time reducing the size of the leaves and net photosynthesis of the plant (Muchow and Davis 1988; Wolfe et al., 1988;

Evans 1989; Muchow and Sinclair 1994). Reduced photosynthesis results in less carbon accumulation in the plant, smaller kernel size, and a reduction in yield. Maintaining leaf

8 photosynthetic capabilities in N-limited environments will assist in maintaining grain yields (Borrell 2000a, 2000b).

Nitrogen Utilization Efficiency (NUtE) involves the movement of N within the plant for other uses. The timing at which N is remobilized from the vegetative sources within the plant (stalks, leaves, and roots) to the grain can have a large effect on the total grain yield and is dependent upon the N available in the environment (Ta and

Weiland 1992; Crafts-Brandner et al., 1996; Ono et al., 1999; Masclaux et al., 2000). The switch in the vegetative tissue from N sink to N source is controlled by a multitude of factors (Harrison et al., 2000; Hellmann et al., 2000; Lewis et al., 2000; Masclaux et al.,

2001). Once started, the remobilization of vegetative N begins in the stalks followed by leaf material (Ta and Weiland 1992; Weiland and Ta 1992). This occurs to preserve N in the photosynthetic machinery of the leaves for as long as possible (Evans 1989). Once remobilization reaches the leaves, N is removed from the photosynthetic compounds faster than other leaf stores of N (Weiland and Ta 1990; Rajcan and Tollenaar 1999;

Paponov and Engels 2003). This loss of photosynthetic N decreases overall carbohydrate accumulation, increases rate of senescence, and limits the yield potential of the crop

(Swank et al., 1982; Moll et al., 1994; Matile 1997; Rajcan and Tollenaar 1999). Under low-N conditions, the reduced N reserves of the plant lead to a more quickly remobilized leaf N from photosynthetic compounds (Weiland and Ta 1990). As this occurs, leaf photosynthesis is greatly reduced and less photosynthate is produced, reducing kernel size and yields. In order to develop genotypes that are tolerant to low N conditions, it is important to maintain the N in the leaves so that carbohydrate

9 accumulation can be optimized and yields maintained. Leaf measurement of chlorophyll offers an accurate and quick method to estimate the relative amount of N remaining in the leaves (Ercoli et al., 1993). Field based measurements of leaf chlorophyll content have been used by farmers to determine the desired amount of N fertilizer to add to optimize their production (Schepers et al., 1992; Piekkielek and Fox 1992; Blackmer and

Schepers 1995; Chapman and Barreto 1997; Argenta et al., 2004). Use of chlorophyll content meters at multiple time points during the plant’s reproductive growth can identify lines with unique timing and rates of leaf N remobilization.

While the timing of leaf N remobilization plays an important role in the photosynthetic ability of the plant, the location from which the N is remobilized also has importance in the plant’s potential productivity. Previous research has noted two possible origins of N remobilization from vegetative tissue; remobilization can either begin in the lower leaves and the stalk which maintains the photosynthetic ability of the higher leaves as discussed above, or remobilization of N can more uniformly occur

throughout the plant (Ciampitti et al., 2013). However, premature remobilization of vegetative N from the upper canopy would have a detrimental effect on the ability of the plant to capture light and negatively impact starch accumulation and grain yield.

Examination of genotypic differences in these two patterns of vegetative remobilization may identify genetic controls of this trait for future breeding efforts.

1.3 Kernel Composition in Maize

Zea mays L., a cereal grain native to central Mexico, is thought to have been domesticated in a single event from teosinte approximately 9,000 years ago (Matsuoka et al., 2002). Many traits were altered during domestication for agricultural production including loss of shattering mechanisms, ear number, ear location, and size and number of kernels on each ear. During domestication, it is believed that kernel traits, including those involved with kernel architecture, were subjected to rounds of selection that greatly altered composition (Doebley 2004). As a result of these selections, certain kernel components such as protein have been diminished (Fedak 1985). Testcross hybrids with wild parents can exhibit 50% greater kernel protein production than hybrids of modern maize lines (Perini and Magoja 1988).

Maize grain has many uses as a food, feed, fiber, or fuel. These uses are benefitted by different profiles of protein, oil, starch, ash, fiber, or changes in kernel density; dependent upon the end use desired. Commercial Corn-Belt dent maize

contains approximately 71.7% starch, 9.5% protein, 4.3% oil, 1.4% ash, and 6.2% fiber

(Watson et al., 2003). Genetic variations for these components have been observed in diverse panels of maize inbreds, and utilization of this diversity could be useful in development of lines for specific uses (Flint-Garcia et al., 2009). Increased protein, oil, or starch may improve the value of that crop for a specific use as well as improve processing efficiencies.

1.3.1 Maize Kernel Protein

The grain protein content of maize has declined over past decades. This decline is likely a result of the negative relationship that is observed between grain yield and grain protein content (Rhodes and Jenkins 1978). Kernel protein also exhibits a negative correlation with plant population (Zuber et al., 1954; Genter et al., 1956; Stickler 1964).

With high-yielding maize hybrids being planted at ever increasing populations, modern agronomic practices designed to increase maize yield generally have a secondary effect of simultaneously reducing the concentration of grain protein (Olson and Frey 1987;

Ciampitti and Vyn 2012; Ciampitti and Vyn 2013).

There are four main protein fractions in the maize kernel that can be differentiated based on solubility. These fractions are the albumin, globulin, glutelin, and prolamin (Osborne and Mendel 1914). Maize kernel protein and carbohydrate synthesis has been thoroughly reviewed in recent years (Hannah 1997; Motto et al.,

1997; Coleman and Larkins 1999; James et al., 2003). The prolamins are called zeins and

constitute a major portion of the kernel proteins (Tsai 1983; Prasanna and Sarkar 1991).

The zein fraction provides the major source of N for the kernel during germination

(Anderson and Lamsal 2011). The endosperm accounts for the vast majority of the dry weight in the kernel and contains about 70% of the total protein with zein contributing approximately 60% of the total protein in the endosperm (Hansel et al., 1973).

Zeins have been shown to play an integral role in relation to N uptake and metabolism in the plant. Zeins are thought to be the kernel sink for the nitrogen translocated to the kernel (Tsai et al., 1980). When N is not fixed in zeins, it normally

12 exists in the form of free amino acids (Lee and Tsai 1985; Tsai et al., 1986). When increasing amounts of N fertilizer are added to the soil, kernel protein is observed to increase; largely due to elevated zeins in the kernel (Frey 1951; Schneider et al., 1952;

Sauberlich et al., 1953; Keeney 1970; Tsai et al., 1978a; Rendig and Broadbent 1979; Tsai et al., 1980). These protein compounds are not inherently beneficial for end use, as kernel protein is negatively correlated to yield (Murphy 1980). In fact, many genotypes that have been developed with improved grain quality traits actually contain reduced zein content (Mertz et al., 1964; Nelson et al., 1965; McWhirter 1971; Tsai and Dalby

1974; Ma and Nelson 1975).

While the synthesis of albumin, globumin, and glutelin are fairly stable under differing N environments, the synthesis of zeins have been shown to be quite responsive to N availability (Frey 1951; Schneider et al., 1952; Sauberlich et al., 1953; Keeney 1970;

Rendig and Broadbent 1979; Tsai et al., 1980). Low amounts of zein are produced when

N is limited and zein production increases when N is plentiful. This has led to the

conclusion by various researchers that zeins are the main N sink and storage protein in maize (Tsai et al., 1980; Miflin and Shewry 1978).

Lines selected for increased kernel protein content exhibit altered N metabolic activity including greater N translocation, increased glutamine utilization, higher enzyme activity of tyrosine and phenylalanine synthesis enzymes, and an increased protein accumulation efficiency (Reggiani 1985). Although the content of protein in the kernel is important for some specific end uses such as livestock feed or human food, the specific amino acids contained in the kernel are also of importance (Paulis and Wall 1977). An

13 overall relationship between the kernel total protein and the content of essential amino acids has been observed (Miller et al., 1950). A similar relationship is noted for the amino acid tryptophan and the non-zein proteins, while it is much weaker between tryptophan and total protein content (Frey et al., 1949).

While well adapted for polygastric animals, the amino acid profiles of maize and other cereal grains are not optimized for human and monogastric animal consumption due to low concentrations of lysine and tryptophan in the grain (Tsai 1983). Efforts to improve nutritional quality of cereal grains have been outlined in numerous reviews

(Wall and Paulis 1978; Nelson 1979, 1980; Axtell 1981). In less developed countries where maize serves as a stable food crop, grain high in essential amino acids can increase the dietary value of the grain and supplement diets that are low in these nutritional components. Grain produced in high N environments often exhibit lower lysine and tryptophan content as a percentage of the total kernel protein (Sauberlich et al., 1953; MacGregor et al., 1961; Keeney 1970; Tsai et al., 1978a; Rendig and Broadbent

1979; Tsai et al., 1980). The relative lysine content in the maize kernel has been improved through the utilization of mutations, such as the opaque-2 mutant (Mertz et al., 1964). Opaque-2 increases the kernel lysine concentration through a decrease in zein synthesis to levels as low as 20% of the original amount. Other mutations have also been shown to increase the concentration of lysine in the kernel including floury-2, opaque-7, opaque-6, and floury-3 (Mertz et al., 1964; Nelson et al., 1965; Misra et al.,

1972; Dalby and Tsai 1975; Ma and Nelson 1975). Further research into these mutations has not shown a direct link to any particular zein polypeptide synthesis, suggesting that

14 these genes are not directly involved in zein synthesis but in fact may be regulatory factors (Nelson 1969; Ma and Nelson 1975; Fonzo et al., 1980).

Maize mutants such as opaque-2 have shown promise in lowering the concentration of zeins and therefore increasing the lysine relative concentration in the kernel. However, opaque-2 can have a negative effect on grain yield and certain functional traits. The lower kernel weight and density associated with opaque-2 maize has resulted in lower yields than conventional maize varieties (Alexander et al., 1969;

Lambert et al., 1969; Nass and Crane 1970; Paez et al., 1970; Salamini et al., 1970;

Sreeramulu and Bauman 1970; Glover 1976). End-use quality can also be impacted with the opaque-2 mutants as these kernels often have an increased occurrence of insect damage, ear diseases and rots, and subsequent yield and quality reduction (Lambert et al., 1969; Ortega et al., 1975; Singh and Asnani 1975; Warren 1978; Toro et al., 2003).

These end-use quality issues combined with depressed yield have largely held back large scale implementation of opaque-2 mutants in maize production (Lauderdale 2002).

Other research efforts to select for improved tryptophan and lysine content of the kernel not related to opaque-2 have also been conducted (Frey et al., 1949; Zuber and Helm 1975). Researchers were able to find success in selection for high lysine content due to the relatively high heritability of this trait (Choe et al., 1976). Although these selections have shown promise, the lack of an efficient and affordable assay and the multiple years required to conduct multiple generations of selection have proven difficult obstacles to overcome (Pollak and Scott 2005).

Transgenic modifications have also been attempted to increase kernel lysine content (Mertz et al., 1964; Villegas et al., 1992). In one case, a high lysine gene from potato was successfully used to increase kernel lysine and total protein content in maize

(Yu et al., 2004). Although successful, this and other attempts at transgenic modification for increased kernel lysine content have not been commercialized.

1.3.2 Maize Kernel Oil

Maize grain can be used as an important component of livestock feed. High-oil content maize varieties are desirable for feeding uses in swine and poultry (Adams and

Jensen 1987; Han et al., 1987; Mišević and Alexander 1989). In swine, it has been found that maize with high oil content increases the return on feed by increasing the weight gain per pound of feed (Lambert and Hallauer 1994; Lambert et al., 2004). A high oil maize diet also circumvents feeding animal fats to livestock in order to increase oil intake (Thomison et al., 2003). Oil content of maize kernels is largely determined by embryo size and composition (Watson and Ramstad 1987). The embryo is comprised of

nearly one-third oil and accounts for approximately 80% of the total oil content of the kernel (Val et al., 2009). Kernel oil composition has shown a negative correlation with yields in previous studies (Lambert and Hallauer 1994). Therefore, selection for high oil content often results in reduced yields in the crop.

The consumption of certain fatty acids can provide health benefits in humans

(Diet 1989). Oils derived from maize kernels are generally high in unsaturated fats and low in cholesterol (Weber et al., 1987). Genetic variation has been shown for linolenic, palmitic, oleic, and linoleic fatty acid composition (Poneleit and Alexander 1965; Jellum

1966; Poneleit and Bauman 1970; De la Roche et al., 1971; Widstrom and Jellum 1975).

These traits are highly heritable and efforts are being made to breed for oil quality to improve end use value (Alexander and Creech 1977; Alexander 1988; Hallauer et al.,

2010). Diverse maize populations of both temperate and exotic germplasm have shown vast variation in fatty oil composition (Jellum 1970; Dunlap et al., 1995a, 1995b).

Genetic variation for oil composition has been used to develop genotypes with altered oil profiles (Dudley and Lambert 1992). Many oil traits have been shown to fall under single-gene inheritance with the involvement of modifier genes (Poneleit and

Alexander 1965; Wright 1995; Balconi et al., 2007). Multiple QTLs have been identified in various studies of kernel oil concentration (Goldman et al., 1994; Berke and

Rocheford 1995; Mangolin et al., 2004; Wilson et al., 2004; Cook et al., 2012). Several studies have shown that acyl-CoA: diaglycerol acytransgerase (DGAT1-2) is a large-effect gene controlling oil content (Zheng et al., 2008; Cook et al., 2012). These studies have shown that kernel oil content and composition can be altered to meet specific food and

feed uses.

1.3.3 Maize Kernel Starch

The starch biosynthesis pathway has been well examined through the utilization of mutant lines, and starch biosynthesis in the kernel is better understood than protein biosynthesis (Boyer et al., 1994). There are many possible external controls of starch biosynthesis including genetics, physiology, and environmental effects (Boyer et al.,

1994; Hannah 1997).

The starch mutants of maize have been shown to affect starch content and composition in dramatic ways such as waxy which is completely devoid of kernel amylose (Sprague et al., 1943). The waxy mutants had a large economic significance during WWII as a replacement to tapioca starch which at the time was not available

(Pollak and Scott 2005). Since then, the private sector has placed some effort into the development of new waxy lines (Fergason 1994, 2001). Other mutations in maize such as amylose extender (ae) have been shown to increase the ratio of amylose to amylopectin while maintaining the same overall amount of starch in the kernel

(Vineyard and Bear 1952). Although ae has been shown to alter the starch ratio and improve the amount of amylose, breeding for this trait has proven to be difficult due to the complexity of the genetic controls of amylose and amount of modifiers within the genome (Fergason 1994, 2001). Numerous other starch mutations in maize including dull-1, sugary-1, and sugary-2 have been found to increase the amount of kernel amylose (Dunn et al., 1953; Creech 1965; Inouchi et al., 1984; Brockett et al., 1988;

Sanders et al., 1990; Wang et al., 1992; Wang et al., 1993a; Wang et al., 1993b; Wang et al., 1993c). These mutations show that amylose and amylopectin biosynthetic pathways are independent (Nelson and Rines 1962).

The use of maize grain for ethanol production is rising in the United States and other developed countries. During the fermentation process, sugars are derived from starch so grain high in starch is ideal (Clark et al., 2006). Although starches have an important relationship to ethanol yield, they are not the sole contributing factor. Kernel

18 hardness and density are two other factors contributing to a variation in commercial maize ethanol yields (Singh et al., 2004).

Kernel concentrations of protein, oil, starch, and other components have been found to be correlated. The relationship between starch and protein content is negative

(Hannah 1997; Motto et al., 1997; Coleman and Larkins 1999; James et al., 2003). While this is not a new development, it is important when considering optimal kernel composition. High starch is desired for ethanol and biofuel production, but increased protein and oil concentrations are ideal when grain is used for livestock feed. Due to the large concentration of starch in the endosperm of the kernel, the yield potential of a line is also affected by the concentration of starch in the kernel (Boyer et al., 1994).

A number of studies have been conducted examining the genetic, epigenetic, and cytological basis for variation in timing and rate of kernel development (Chaudhury et al., 2001; Olsen 2001). During early development, the kernel is primarily comprised of sugars. As the kernel matures, oil, protein, and starch are accumulated (Boyer and

Shannon 1983). The rapid accumulation of proteins begins about 12 days after fertilization (Tsai et al., 1978a; Watson et al., 2003). Zein synthesis follows a gradient, beginning around 12 days after fertilization with a peak from 16 to 35 days post- pollination (Tsai and Dalby 1974; Tsai et al., 1978b; Oaks et al., 1979). Hybrids examined under different densities and N treatments have exhibited a consistent N concentration in the ear across reproductive growth stages, independent of ear mass; suggesting this is a conservative trait (Ciampitti et al., 2013). Examination of enzymes associated with kernel starch accumulation found that peak accumulation occurred around 22 days after

19 the flowering event (Tsai et al., 1970). This is a time when environmental stresses such as heat and drought can play an important role in kernel composition.

1.3.4 Maize Kernel Ash

The germ fraction has been shown to contain the highest portion of ash in the kernel with an average of 10% (Hopkins 1903; Ockerman 1978). Kernel ash composition averages 1.4% in the whole kernel (Watson et al., 2003). Ash content has been shown in several cereal crop species to correspond to photosynthetic and remobilization characteristics during grain fill stages (Febrero et al., 1994; Araus et al., 1998; Voltas et al., 1998; Araus et al., 2001; Cabrera-Bosquet et al., 2009). The phloem is responsible for the mineral translocation to the kernels (Nonogaki et al., 2007). This translocation system is involved in nutrient remobilization from leaves to the grain. Although the ash component does not directly benefit the nutritional value of the kernel, the interaction between ash content and plant photosynthesis may have an effect on kernel carbohydrate and starch accumulation by effecting translocation through the phloem.

1.3.5 Maize Kernel Fiber

Corn fiber is the residual endosperm and seed coat proportions that remain after processing of the raw grain (Akin and Rigsby 2008). With increasing production of ethanol, the byproducts of fermentation have also increased. Over four million tons of corn fiber are produced in the U.S. annually (Doner and Hicks 1997; Hicks et al., 2003;

Rose et al., 2010). One issue with ethanol production is the need to find markets for the byproducts such as fiber (Rausch and Belyea 2006). The high fiber concentration in ethanol byproducts has relegated these products for use in ruminant animal feed

(Rausch and Belyea 2006). Although these byproducts are mostly considered a low- value commodity, the aromatic compounds and carbohydrates in this material offer potential for new value added products to be developed (Schell et al., 2004). Corn fiber is composed of seven main components including hemicellulose (38-57%), starch (10-

30%), protein (15%), cellulose (15%), oil (3.7%), and lignin and ash (3%) (Osborn and

Chen 1984; Gáspár et al., 2007).

Corn fiber is a general term and includes both the coarse and fine fiber components. Coarse fiber largely contains the kernel pericarp and tip cap, while fine fiber contains the kernel endosperm (Singh et al., 2000; Yadav et al., 2007a). Coarse and fine fiber products are used in the production of corn fiber gum, which has an industrial use as an emulsifier in beverage systems (Yadav et al., 2006; Yadav et al., 2007b).

Although corn fiber gums created from course and fine fibers are very similar in carbohydrate composition, they largely differ in phenolic acid, lipid, and protein contents (Singh et al., 2000; Yadav et al., 2007c). Studies of emulsification gums have

shown that protein and lipid concentrations can have substantial effects on the emulsification qualities (Randall et al., 1988; Yadav et al., 2006; Yadav et al., 2007d).

Recent studies have also shown that these gums have greater emulsification ability than the commonly used acacia gum (Yadav et al., 2009).

1.3.6 Maize Kernel Density

Kernel characteristics such as low breakability are crucial to maintaining the quality of the grain through transport to export markets (Hill 1982). Hardness and density have been shown to be correlated to kernel breakage therefore kernel density

21 and hardness are important traits (Wichser 1961; Thompson and Isaacs 1967; Freeman

1973; Stroshine et al., 1981, 1982; Ellis et al., 1983). The physical properties of the kernel also affect the industrial uses of maize grain as extraction efficiencies of starch components may be affected (Kniep and Mason 1989). Starch and protein concentrations can affect kernel density (Ortega and Bates 1983; Larkins et al., 1984;

Dombrink-Kurtzman and Bietz 1993; Dombrink-Kurtzman 1994; Pratt et al., 1995;

Eyherabide et al., 1996; Mestres and Matencio 1996; Robutti et al., 1997;

Chandrashekar and Mazhar 1999; Robutti et al., 2000; Gupta et al., 2003; Zhang et al.,

2003; Holding and Larkins 2006; Lee et al., 2006; Loerger et al., 2007; Sanchez et al.,

2007; Fox and Manley 2009).

Unlike barley and wheat, maize does not contain specific genes related to hardness and density, rather they are considered quantitative traits (Morris 2002; Fox et al., 2007). Kernel breakability has also been found to be affected by characteristics such as kernel density (Bauer and Carter 1986; Moes and Vyn 1988; Vyn and Moes 1988).

Improved kernel density profiles will also add value to the grain for improved stability during storage and transportation.

1.3.7 Xenia Effects

The composition of the kernel can be impacted by the parent lines used in hybrid combination (Perini and Magoja 1988). In maize, it has been observed that the maternal plant has a particularly large effect on the kernel composition (Wyss et al., 1991). The xenia effect is the change in composition caused by the source of pollination. Xenia effects for oil, protein, and starch have been examined. Protein content has not been

22 found to have any effect from pollen source in multiple studies examining different populations of maize (Pixley and Bjarnason 1994; Letchworth and Lambert 1998). It was also found that self-pollinated ears contained higher protein content than open pollinated ears (Letchworth and Lambert 1998). Analyses of reciprocal crosses of maize for starch composition revealed that paternal parent had no effect on final content

(Letchworth and Lambert 1998). Unlike protein and starch, the pollen parent has been shown to affect the content of oil in the kernel (Miller and Brimhall 1951; Curtis et al.,

1956; Letchworth and Lambert 1998; Tanaka and Maddonni 2008). The xenia effect on kernel composition has attracted the attention of commercial seed research programs.

In 2001, DeKalb began a program to examine the effect of pollen source on high oil maize production (Bullant and Gallais 1998).

1.4 Kernel Composition in Sorghum

Sorghum is an ancient C4 cereal diverged from other cereal species 50-70 million

years ago (Paterson et al., 2003). Domestication of sorghum began in Central Africa about 7,000 years ago. The adaption of sorghum to drought and heat stress makes it an important agronomic crop in many areas of the world (Watson et al., 1970; Murty and

Kumar 1995). Sorghum is used for food, feed, fiber, and fuel production (Obizoba 1988;

Brannan et al., 2001). Over the past half century, grain sorghum production has increased by 60% worldwide and yields have increased 233% (Maunder 2005). Grain sorghum is produced primarily for animal feed (51%) but is also used for food and fuel

(Carter et al., 1989; Maunder 2002). Grain sorghum is a staple crop for millions of

23 people in Asia and Africa (Yousif and El Tinay 2001). In recent years, sorghum has demonstrated an increase in food use within the developed world, gaining in popularity as a substitute for wheat for those afflicted with celiac disease (Fenster 2003). The end use of the sorghum grain can largely be affected by the composition of the grain. The commercial value of sorghum as a bioenergy crop has led to an increase in forage and sweet sorghum production (Edwards 1943; Barham et al., 1946; Horan and Heider 1946;

Karper and Quinby 1947; Cannon et al., 1952; Watson and Hirata 1955; Rooney et al.,

2006; Sauer et al., 2008).

1.4.3 Sorghum Kernel Feeding Quality

Sorghum constitutes a major source of energy and nutrition for people and livestock (Klopfenstein and Hoseney 1995; Maunder 2002). Sorghum grain serves as a major source of feed for cattle in finishing operations throughout the U.S. even though the large variability in sorghum composition has resulted in a lower potential feeding value when compared to maize (Hibberd et al., 1982; Rooney and Pflugfelder 1986).

These variations in kernel composition have been shown to impact livestock growth when different sorghum varieties are fed to cattle, making variety selection and analysis crucial to profitable cattle production. However, some studies suggest that corn and sorghum are completely equal in feeding values and may be interchangeable in livestock production (Aubel 1955; Menzies and Richardson 1961; Koch 1962; Deyoe and

Shellenberger 1965; Waldroup et al., 1967; Session 1974; Baterii et al., 1979; Hibberd et al., 1979; Cullison 1987; Streeter et al., 1990; Wester et al., 1992; Streeter et al., 1993;

Subramanian and Metta 2000; Maunder 2002). In non-ruminant animals, the feeding

24 values of sorghum are estimated to be 90-95% of maize (Cousins 1979; Hulan and

Proudfoot 1982). In poultry, the replacement of corn with sorghum has been shown to result in no change in growth or production of layers and broilers (Sharma et al., 1979;

Gualtieri and Rapaccini 1990; Dean 2000). In swine, sorghum grain without tannins has been shown to have similar feeding qualities as maize (Lin et al., 1987).

Sorghum grain is ground for cattle feed; the small size of sorghum grains allow it to be fed whole to other species (McDonald et al., 1987; Carter et al., 1989; Atteh 2002).

Larger seeds have been shown to have a greater protein and a lower starch content, but kernel weight has not been shown to have any effect on the feeding quality of the grain

(Hicks et al., 2002). Sorghum kernel composition has been examined in multiple studies, but the relationship between kernel composition and digestibility is still unclear

(Hibberd et al., 1979; Hibberd et al., 1982; Streeter et al., 1993).

Various components of feeding quality have been examined. Acid Detergent

Fiber (ADF) is the fibrous portion of the kernel that is least likely to be digested and

generally associated with reduced grain feeding quality (Saha et al., 2010). In sorghum, it has been shown that ADF is higher than in corn kernels (Douglas et al., 1990). An interaction has also been noted between ADF and kernel protein (Bach-Knudsen and

Munck 1985). ADF is an important component in the calculation of Net Energy of

Lactation (NEL), Net Energy Maintenance (NEM), Net Energy Gain (NEG), and Total

Digestible Nutrients (TDN). Total Digestible Nutrients (TDN) is a measurement used to determine the potential energy value of a feed source. This trait has been used for decades and a range of values have been reported across regions (Saha et al., 2010).

Sorghum is thought to contain 95% of the TDN value of maize (Dowling et al., 2002).

Proximates such as starch, oil, protein, and ash also play an import role in determining feed value. Ash is the inorganic residue remaining from the sample once all of the organic material is burned away (Saha et al., 2010).

1.4.4 Sorghum Kernel Protein

The composition of sorghum grain has been known for decades (Miller 1958;

Goswami et al., 1969; Sharma and Goswami 1969; Goswami et al., 1970; Reddy 2000).

Substantial variation in grain protein content has been reported with values ranging from 8.73% to 12.81% (Connor et al., 1976; Vannalli et al., 2007). Sorghum generally has slightly higher protein content than maize (Bressani and Rios 1962; Oyenuga 1968;

Bolton and Blair 1977; Hulan and Proudfoot 1982; Douglas et al., 1990; Aduku 1993;

Tacon 1995; Aletor 1999; Etuk 2008). Maize and sorghum have the same limiting amino acids in the grain with particularly low concentrations of lysine, methionine, and tryptophan (Shelton et al., 1951; Purseglove 1972; Badi et al., 1990; Olomu 1995;

McDonald 2002). Significant genetic variation has been reported for kernel protein content (Deosthale et al., 1972).

The prolamins of sorghum are the major storage protein of the kernel. These proteins are named kafirins in sorghum as opposed to zeins in maize, and contribute

70% to 80% of total endosperm protein (Watterson et al., 1993; Hamaker et al., 1995).

Multiple studies have examined differences in kafirins in the sorghum kernel (Shull et al., 1991; Shull et al., 1992; Watterson et al., 1993; Bean et al., 2001). Kafirins are the component of kernel protein that are increased in lines that exhibit a higher protein

26 content (Virupaksha and Sastry 1968). Kafirins are also categorized in three different classifications: α, β, and γ. These classifications vary in molecular weight, structure, and solubility (Esen 1987; Watterson et al., 1993). Of the kafirins, the α-kafirins constitute over 70% of the total kernel kafirins (Paulis and Wall 1979; Oria et al., 2000).

Kernel protein digestibility is largely determined by the structure of kernel protein (Hamaker et al., 1995; Oria et al., 2000). Due to their structure, kafirins are more difficult to digest than other proteins and are actually the last to be digested by consumers (Hamaker et al., 1986; Oria et al., 2000). The fact that the majority of kernel proteins are kafirins means that increased protein content does not implicitly imply a greater protein digestibility. Genotypic differences in the composition and amount of kernel protein have been identified in sorghum (Hamaker et al., 1995). Sorghum breeders have worked to select for improved protein quantity and quality within their breeding programs (Liang et al., 1969; Sastry et al., 1986); however, these efforts have been plagued with difficulties (Bramel-Cox et al., 1990).

Protein accumulation and synthesis are crucial to feeding quality of sorghum.

Protein digestibility is crucial when the sorghum grain is used as a food or feed.

Exogenous factors that affect protein digestibility include tannin content, phytic acid content, starch content, and the grain organizational structure (Duodu et al., 2003).

Endogenous factors that affect protein digestibility include protein structure, hydrophobicity, and sulphide bonds (Duodu et al., 2003). Cooking can negatively impact protein digestibility of sorghum (Axtell 1981; Duodu et al., 2003). The digestibility of sorghum proteins is also highly dependent upon the form in which the grain will be

27 utilized (Chibber et al., 1980; Axtell 1981; Mertz et al., 1984; Hamaker et al., 1986;

Duodu et al., ; Bookwalter et al., 1987; Hamaker et al., 1987; Rom et al., 1992; Oria et al., 1995a; Oria et al., 1995b; Weaver et al., 1998).

The polyphenols of sorghum have been shown to impact composition and availability of nutrients in sorghum grain (Vohra et al., 1966; Rostagno et al., 1973;

Nelson et al., 1975; Guillaume and Bellec 1977; Sibbald 1977; Elkin et al., 1978; Hahn et al., 1984). The sorghum polyphenols, tannins, serve insecticidal and fungicidal purposes

(Serna-Saldivar and Rooney 1995). High tannin sorghums have low food and feed value and are frequently selected against in breeding programs. Tannins can also have a large impact on amino acid availability of the grain (Bornstein and Bartov 1967; Stephenson et al., 1971; Rostagno et al., 1973). Tannins can bind with up to 12 times their mass of grain protein, meaning a small amount of tannin can bind the majority of kernel protein making it unavailable for processing and utilization (Butler et al., 1984). Other kernel polyphenols such as flavonoids and phenolic acid have not been shown to have the

same detrimental effects on the digestibility of kernel protein (Serna-Saldivar and

Rooney 1995; Bravo 1998).

Fertilization of sorghum fields can impact kernel composition of sorghum.

Nitrogen fertilization has been shown to increase total kernel protein and the levels of

17 amino acids (Waggle et al., 1967; Deosthale et al., 1972; Warsi and Wright 1973).

Lysine is unfortunately not one of the amino acids that exhibited a positive relationship with N fertilization (Campbell and Pickett 1968). Under moderate N applications, the

28 prolamin portion of kernel protein shows the most direct response, and under high levels of N applications other protein components also increase (Salunkhe et al., 1977).

1.4.5 Sorghum Kernel Oil

The majority of oils stored in sorghum kernel are in the germ (Rooney 1978;

Rooney and Serna-Saldivar 1991; Vannalli et al., 2007). Almost 70% of kernel oil content is found in the germ fraction, and these lipids are largely unsaturated (Rooney 1978).

Sorghum oil shares many characteristics with maize oil, making it a reasonable alternative for industrial applications (Rooney 1978). In animal feeding, sorghum oil content may affect the feeding ability of the grain and, therefore, fatty acid profiles may be useful as a selection tool. With such a large portion of sorghum consumed in developing countries, alterative profiles containing more health friendly oils may be desirable.

1.4.6 Sorghum Kernel Starch

Kernel carbohydrates are stored in the form of starches and represent

approximately 70% of kernel weight (Jambunathan and Subramanian 1988). Sorghum starches are largely composed of amylopectin, with mutant lines available that contain either exclusively amylopectin (waxy mutants) or high amylose content in the kernels

(Boyer and Liu 1983). Sorghum mutant lines have been identified that contain floury, sugary, and waxy endosperms (Anglani 1998). In addition to these endosperm types common to maize and sorghum, sorghum additionally has basmati and vani endosperm types (Murty et al., 1982; Murty et al., 1985). Starch composition has been shown to

29 have a direct effect on food quality, giving this trait large importance in those areas of the world where sorghum is a main food source (Beta and Corke 2001).

The sugars found in the sorghum kernel endosperm include glucose, fructose, raffinose, sucrose, and maltose; although glucose and fructose are found in the highest concentrations (Watson and Hirata 1960). Disagreement exists as to whether the major sugar in sorghum is sucrose or a combination of fructose and glucose (Watson and

Hirata 1960; Neucere and Sumrell 1980; Subramanian et al., 1980; Anglani 1998).

Kernel composition of sorghum grain may be influenced by a variety of factors; including climate, soil factors, and fertilization (Aduku 1993; Tacon 1995; Ngoka 1997;

Etuk and Ukaejiofo 2007; Etuk 2008). Climatic changes can affect some composition components of the kernel. Under optimal growth conditions, kernel starches are accumulated in greater quantities than protein (Bewley and Black 1994).

The composition of grain sorghum greatly influences its quality in food products

(Bello et al., 1990; Fliedel 1994; Taylor et al., 1997). Genetic studies to understand the

controls of kernel composition have been conducted in sorghum through genome mapping efforts (Lin et al., 1995; Pereira et al., 1995; Pereira and Lee 1995). Multiple resources including genetic, physical, and comparative maps of the sorghum genome are available for use in examining genetic factors of kernel composition (Menz et al.,

1980;2002; Bowers et al., 2003; Paterson et al., 2004). This has presented the opportunity for transgenic approaches to be attempted to increase vital kernel components such as lysine (Zhao et al., 2003).

Near Infrared Spectroscopy (NIRS) is increasingly utilized as a tool to examine the composition of kernel grains, including attempts to understand the genetic architecture of kernel composition (Rosales et al., 2011; Cook et al., 2012). The results from one such study support future research with diverse association populations, and the potential use of NIRS on sorghum kernels to determine kernel composition (Sukumaran et al.,

2012).

The Sorghum Conversion Program was initiated to convert diverse tropical sorghum varieties into genotypes with temperate adaptation (Stephens et al., 1967).

This program resulted in a diverse population of dwarf, photoperiod-insensitive, sorghum lines. These materials exhibit diverse kernel compositions and may provide a unique genetic resource to study kernel composition in temperate environments.

CHAPTER 2. GENOME-WIDE ASSOCIATION STUDY OF LEAF NITROGEN REMOBILIZATION IN ZEA MAYS

2.1 Abstract

Nitrogen Use Efficiency (NUE) is a major concern of maize breeders and producers. Nitrogen Utilization Efficiency (NUtE, the efficiency by which N absorbed is utilized to produce grain (Moll et al., 1982)) is one component of NUE, and the most important component under N-limited conditions. In this study, 2,400 maize genotypes from the Ames Association Panel were grown in 2012 and 2013 and were evaluated for chlorophyll concentrations of one leaf above and two leaves below the developing ear at different stages of reproductive development. These phenotypes were used to examine differences in timing or canopy location of leaf N remobilization among genotypes. Genome-Wide Association Study (GWAS) methodologies identified genetic markers for N remobilization traits and linked candidate genes associated with senescence signaling (auxin, wrky, and map kinase related genes), senescence

31 regulation (senescence associated genes (SAGs)), and N remobilization (NADH-

Dependent Glutamate Synthase, Glutamine Synthetase, and aminotransferases).

Identification of these candidate genes allows for further studies to confirm function and utilize these genes in selection of more N-efficient cultivars.

2.2 Introduction

Maize production relies heavily on N applications to maintain current yields and field productivity. Grain yields are highly correlated with N application rates (Castleberry et al., 1984). This has promoted high N applications on agricultural soils. The cost of N fertilizers has drastically increased in recent years, jeopardizing economic returns on maize production (USDA NASS, 2012). Additionally, over-application of N has negatively affected ground and surface waters, causing concern over the environmental sustainability of current production systems (Jarvis 1996; Socolow 1999; Castillo et al.,

2000; Schilling and Libra 2000; Burkart and Stoner 2001; Sauer et al., 2008). Sustainable production of maize will rely on adjustments to current production systems to allow high production potential while limiting degradation of the environment.

NUE has been utilized to study the efficiency of the plant to acquire and utilize applied nitrogen. NUE is composed of two components, Nitrogen Uptake Efficiency

(NUpE, N acquired by the plant / N made available to the plant) and Nitrogen Utilization

Efficiency (NUtE, grain produced per unit of whole-plant N acquired in the biomass).

Nitrogen Uptake Efficiency has been improved through selection in breeding programs in optimal or high-N environments, while NUtE has been shown to be more important in

N-limited environments (Duvick 1977; Uribelarrea et al., 2007). NUtE may be improved by the remobilization of N acquired during vegetative growth and stored in vegetative tissues including leaves and stalks (Muruli and Paulsen 1981; Di Fonzo et al., 1982; Moll et al., 1982; Jackson et al., 1986; Moll et al., 1987; Lafitte and Edmeades 1994; Bertin and Gallais 2000a). Nitrogen remobilization is instigated by multiple factors signaling the

33 switch of vegetative tissues from N sinks to sources (Harrison et al., 2000; Hellmann et al., 2000; Lewis et al., 2000; Masclaux et al., 2001).

In this study, GWAS was used to examine genetic controls of timing and canopy location of leaf N remobilization during the grain fill period to identify genetic controls of NUtE in a panel of diverse maize lines. Identification of genes and allelic variants controlling leaf senescence and N remobilization may provide useful resource for enhancing selection for improved NUtE characteristics in breeding programs.

2.3 Materials and Methods

2.3.1 Genetic Material

The Ames Association Panel is a collection of over 2,400 tropical and temperate maize lines held at the North Central Regional Plant Introduction Station (NCRPIS) in

Ames, Iowa. The panel was used as the genetic population for GWAS studies and includes popcorn, sweet, dent, flint, tropical, temperate, and ex-PVP (elite temperate) corn accessions, and includes the 26 founder parents of the Nested Association Mapping

(NAM) population (Yu et al., 2008).

2.3.2 Experimental Design

The Ames Association Panel was grown in 2012 and 2013 at Purdue University’s

Agronomy Center for Research and Education (ACRE) in West Lafayette, Indiana in fields with a mixture of Chalmers Silty Clay Loam and Raub - Brenton Complex soil types. The genotypes were grown in 1-row plots 3.048 m long with 0.762 m alleys between plots and 0.76 m between rows. Plots were planted at a population of 54,340 plants per hectare; final stands varied due to differences in germination and emergence amongst

34 the plots. The experiments were 120 field rows wide and 24 ranges deep for a total of

2,880 plots. The plots were arranged using an augmented incomplete block design split into six maturity blocks to account for variation in maturity among genotypes (Federer

2005). Maturity block 1 represented genotypes with the earliest flowering time and included mostly popcorn and sweet corn types. Maturity blocks 2 through 5 represented genotypes with increasingly later flowering times with maturity block 5 representing many tropical varieties. Maturity block 6 consisted of ex-PVP material and was largely elite temperate material found in elite US corn inbreds. Within each maturity block, each range of 20 plots was considered a statistical block and contained two maturity- block check genotypes and a field-wide check genotype. The maturity checks used in

2012 were the NAM founder parents P39, Mo17, B97, NC358, Mo18W, and CML247 in maturities 1-6, respectively. Due to poor seed yield for some of these checks (Chapter

3), the maturity checks used in 2013 were adjusted to the ex-PVP lines PHJ40, Mo17,

PHG35, PHG39, CML 247, and DK3IIH6 in maturity blocks 1-6, respectively. The field-

wide check used in both 2012 and 2013 was B73 with one plot in each statistical block in every maturity. Accessions were randomized within each maturity block.

Plots were planted on May 14th, 2012 and May 20th, 2013. Due to the extreme drought that affected much of the Midwest in 2012, drip irrigation was applied to the field. Precipitation amounts and silking dates for each maturity group are shown for

West Lafayette, IN in 2012 (Figure 2.1) and 2013 (Figure 2.2). In both years, 202 kg per hectare of N as NH3 was applied with N-Serve™ in the spring prior to planting.

50 Maturity 1 40 Maturity 2 30 Maturity 3

Precipitation(mm) 20 Maturity 4 Maturity 5 10

0 6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 Date

Figure 2-1 2012 Precipitation amounts and flowering dates for each maturity group.

60 35

50 Maturity 1 40 Maturity 2 30 Maturity 3

Precipitation(mm) 20 Maturity 4 Maturity 5 10

0 6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 Date

Figure 2-2 2013 Precipitation amounts and flowering dates for each maturity group.

2.3.3 Phenotypic Evaluation

Relative Vegetative Index (RVI) of individual leaves and plants were measured using Opti-Science CCM-200+ Chlorophyll Content Meters (Hudson, NH) to quantify leaf chlorophyll content and thus estimate leaf N concentration. CCM-200+ instruments are similar to Minolta SPAD meters, but offer the advantages of a larger measurement surface (0.71 cm2 vs. 0.06 cm2) and a lower cost (Knighton and Bugbee 2004). Leaves were measured at the midpoint of the leaf slightly off of the midrib. Four plants per plot were measured at 3 growth stages (VT, R2, and R4). For the maturity groups 4 and 5, leaf chlorophyll measurements were halted following the first frost during the R2 and R4 measurement stages. At each time point, measurements were taken on two plant positions, the leaf above the top ear (High leaf (H)) and the leaf two leaves below the top ear (Low leaf (L)). Differences in leaf N timing and rate of remobilization were quantified based on changes in chlorophyll content between the measured leaves.

Ratios were calculated to measure the differences in timing or location of leaf N

remobilization among genotypes and were calculated below.

Traits measured to calculate ratios for GWAS

VTL = Value of low leaf at VT time point

VTH = Value of high leaf at VT time point

VT = Average of VT high (VTH) and low (VTL) leaf measurements

R2L = Value of low leaf at R2 time point

R2H = Value of high leaf at R2 time point

R2 = Average of R2 high (R2H) and low (R2L) leaf measurements

R4L = Value of low leaf at R4 time point

R4H = Value of high leaf at R4 time point

R4 = Average of R4 high (R4H) and low (R4L) leaf measurements

Ratios Used to Examine Differences in Leaf N Remobilization Timing

푉푇 − 푅2 푉푇 − 푅4 푉푇푅2 = 푉푇푅4 = 푉푇 푉푇

푉푇 − 푅2퐻 푉푇 − 푅4퐻 푉푇푅2퐻 = 푉푇푅4퐻 =

푉푇 푉푇 37

푉푇 − 푅2퐿 푉푇 − 푅4퐿 푉푇푅2퐿 = 푉푇푅4퐿 = 푉푇 푉푇

Ratios Used to Examine Differences in Leaf N Remobilization Location

푅2퐻 − 푅2퐿 푅4퐻 − 푅4퐿 푅2퐻퐿 = 푅4퐻퐿 = 푅2퐻 푅4퐻

2.3.4 Genotypic Information

Genotypic information used for the Genome Wide Association Study (GWAS) was acquired through GBS sequencing (Romay et al., 2013). Romay et al., (2013) sequenced a total of 2,813 maize accessions stored at NCRPIS. A total of 681,000 SNPs were developed in this sequencing across the entire genome, including many rare alleles

(Romay et al., 2013). A set of 2,400 of these accessions were available in the required quantity from the NCRPIS and were grown and used in this GWAS study.

2.3.5 Statistical Analysis

SAS statistical software (SAS Version 9.2 for Windows, SAS Institute Inc., Cary,

NC, USA) was used to examine the RVI chlorophyll measurements for potential errors or extraneous data points. PROC GLM was used to test for significant variation between examined lines. The model used to analyze these variations in PROC GLM was:

Chlorophyll Content at Specific Growth Stage = Genotype + Location + Block(Location)

Where location and block(location) were treated as random variables.

Variance components from PROC GLM were used to calculate broad-sense heritabilities (H) as follows:

푉 H= 퐺 푉퐺+푉퐸

Best Linear Unbiased Predictors (BLUPs) were calculated on the combined 2012 and 2013 datasets using SAS PROC MIXED. The common B73 field-wide check was utilized in these BLUP calculations as described by Wolfinger et al., (1997) with year,

39 block nested within year, and the individual line identifier treated as random effects.

BLUP values were calculated using the formula below:

Line BLUP Value = Grand Mean + Individual Est. + 2012 Block Est. + 2013 Block Est.

The SAS PROC TRANS procedure was utilized to determine the necessity of transformation on the BLUPs. Normality was the main criteria used for transformation and traits were transformed as needed.

A Genome Wide Association Study was conducted to identify SNP markers associated with ratios used to measure the differences in timing or location of leaf N remobilization among genotypes. The analysis was performed with the compressed mixed linear model method (Zhang et al., 2010) implemented in the GAPIT R package

(Lipka et al., 2012). Although compressed mixed linear models and kinship grouping were utilized, completion of GWAS using over 2,400 lines and 681,000 SNPs proved computationally daunting. To accomplish this, random-access memory (RAM) was increased to 32 Gb in an HP Compaq 8200 Desktop Convertible Minitower (Hewlett-

Packard, Palo Alto, California). With this increase in RAM, GAPIT GWAS analysis could be conducted through the RStudio R interface (RStudio, Boston, MA) on a chromosome-by- chromosome basis on each trait separately. A minor allele frequency threshold of 0.05 was used. Kinships and covariates were calculated on 50% of the total SNPs.

Compressed mixed models were used to shorten the time required for each trait analysis. For each trait, clustering selection was used to determine the ideal kinship clustering to maximize genetic variance and heritability while reducing the residual variance and -2log likelihood during the chromosome 1 analysis. This cluster value was

40 then used for the remaining chromosomes for that trait. Compilation code was utilized through GAPIT to combine the GWAS results from each individual chromosome and recalculate the p-values using the False Discovery Rate (FDR)-controlling method

(Benjamini and Hochberg 1995).

Linkage disequilibrium was examined for each of the SNPs found to be significant in the GWAS analysis to identify the size of potential linkage blocks. This was conducted through the Trait Analysis by Association, Evolution, and Linkage (TASSEL) software

(Bradbury et al., 2007).

2.3.6 Candidate Gene Analysis

SNPs that exhibited an FDR corrected p-value < 0.05 for a trait were evaluated as markers for potential candidate genes. A window of 10 Kb adjacent to each significant

SNP was examined for candidate genes. Candidate genes and annotations were identified through the Maize Genetics and Genomics Datatbase (Andorf et al., 2010).

2.4 Results

2.4.1 Genetic Variance and Trait Correlations

The combined analysis indicated significant variation for RVI greenness of leaves at different positions on the plant and at different stages of development. Basic statistics for each trait are shown in Table 2-1. Between 3,480 (R4) and 4,169 (VT) phenotypes were analyzed for each trait. The average values for each trait exhibited a consistent decline from the VT to R4 time points in both leaf positions from 49.64 (VTH) to 23.43 (R4L).

Table 2-1 Basic statistics and trait correlations for RVI greenness characteristics of leaves at different positions on the plant and at different stages of development Traits VTL VTH R2L R2H R4L R4H N 4169 4169 3973 3974 3480 3480

Mean 49.64 43.87 39.42 39.58 23.43 25.45 Std Dev 12.28 10.99 14.52 13.92 15.88 15.02

Statistics Min 6.40 9.68 0.00 3.00 0.00 3.00 Max 99.78 89.85 97.75 89.15 76.00 88.60 VTL VTH R2L R2H R4L R4H VTL - 0.79*** 0.64*** 0.60*** 0.39*** 0.44***

VTH 0.79*** - 0.57*** 0.62*** 0.32*** 0.41*** R2L 0.64*** 0.57*** - 0.79*** 0.53*** 0.55*** Traits R2H 0.60*** 0.62*** 0.79*** - 0.44*** 0.56*** R4L 0.39*** 0.32*** 0.53*** 0.44*** - 0.79*** R4H 0.44*** 0.41*** 0.55*** 0.56*** 0.79*** -

* = 0.05 Significance

** = 0.01 Significance

*** = 0.001 Significance

Trait correlations were positive and no lower than 0.32 for all pairwise

comparisons (Table 2-1). At each growth stage, the RVI values for the higher and lower 41

leaves were highly correlated (VTH/L = 0.79, R2H/L = 0.79, and R4H/L = 0.79).

Correlations were generally higher for traits measured at similar time points. R2, as the middle time point, exhibited moderate and similar correlations (R2= 0.44-0.64) with all traits. The weakest correlations were noted between the VT and R4 traits, which had the greatest time between measurements.

2.4.2 Heritabilities

Broad-sense heritabilities were calculated for traits utilizing variance values obtained from ANOVA (Appendix C) provided through SAS PROC GLM (Table 2-2).

Heritabilities were low to moderate for all traits, ranging from 0.44-0.64. Trait heritabilities were lower for observations later in the season from a peak of 0.64 for VT traits to 0.44 for R4 measurements.

Table 2-2 Heritabilities of RVI greenness traits for leaves at different positions on the plant and at different stages of development

Trait H VTL 0.64 VTH 0.60 R2L 0.59 R2H 0.58 R4L 0.47 R4H 0.44

2.4.3 Genome Wide Association Studies

To examine the genetic controls of RVI greenness of leaves at different positions on the plant and at different stages of development ratios were calculated from the

BLUPs for individual traits (VT (average of VTH and VTL), VTH, VTL, R2 (average of R2H and R2L), R2H, R2L, R4 (average of R4H and R4L), R4H, and R4L). GWAS was conducted on the following ratios to examine genetic controls responsible for chlorophyll degradation and remobilization timing: VTR2, VTR2H, VTR2L, VTR4, VTR4H, and VTR4L.

Analysis of these ratios resulted in identification of 0-699 significant SNPs, which fell into

0-195 significant linkage blocks (Table 2-3). Examination of significant SNPs for these N remobilization ratios identified multiple candidate genes for each trait (See Appendix D).

Table 2-3 Summary of GWAS indicating the number of significant SNPs, linkage blocks, candidate genes, and genes with annotations for chlorophyll degradation and remobilization timing traits

TRAIT R2HL R4HL VTR2 VTR2H VTR2L VTR4 VTR4H VTR4L

Significant SNPs 4 0 9 61 12 345 699 313 Linkage Blocks 2 0 9 33 10 155 195 141 Candidate Genes 10 0 26 167 41 1113 2276 1019 Candidate Genes with 7 0 15 161 20 469 961 396 Annotations

Significant SNPs were analyzed for potential candidate genes utilizing a window of 10Kb on either side of significant SNPs. Further analysis of these candidates identified those that have annotated functions in either maize or Arabidopsis thaliana. Complete lists of significant SNPs and associated annotated candidate genes are shown in

Appendix D.

We analyzed R2HL and R4HL to examine genetic controls of the particular leaf 43

locations of N remobilization between high and lower leaves on the plant. Two significant loci were observed for the R2HL trait, one on chromosome 7 with one significant SNP and the other on chromosome 8 with three significant SNPs (Figure 2-3).

Seven candidate genes with annotations were linked to the significant SNPs identified for R2HL but there were no obvious relationships with apparent N remobilization (Table

2-3). There were no significant SNPs identified for R4HL (Table 2-3). For this reason, only

44 the ratios related to chlorophyll degradation and N remobilization timing were further considered.

Figure 2-3 Manhattan plot of maize leaf chlorophyll content ratio R2HL examining relative differences between the R2 high and low leaf measurements

Candidate genes linked to SNPs associated with the chlorophyll degradation

44 timing ratios (VTR2, VTR2H, VTR2L, VTR4, VTR4H, and VTR4L) were examined. These analyses indicated 15 annotated candidate genes for VTR2, 161 annotated candidate genes for VTR2H, 20 annotated candidate genes for VTR2L, 469 annotated candidate genes for VTR4, 961 annotated candidate genes for VTR4H, and 396 annotated candidate genes for VTR4L (Table 2-3). From the full list of candidate genes identified for each trait (Appendix D), a combination of genes related to senescence and

45 remobilization were identified for the VTR4 traits, while candidates related to leaf senescence were identified for the VTR2 traits.

2.4.3.1 Examination of VTR2 Traits

The comparison of the VT and R2 measurements using the VTR2 ratio, identified significant loci on chromosomes 1, 2, 4, 7, and 8 for a total of 9 significant loci containing

9 significant SNPs (Figure 2-4 and Table 2-3). The most significant SNP was observed on chromosome 1 with a significance level slightly under –Log 10(p) = 7 (Figure 2-4). The trait VTR2H identified 61 significant SNPs across 33 linkage blocks on chromosomes 3, 4,

5, 6, and 9; although the only peak identified with multiple SNPs was identified on chromosome 3 (Figure 2-5 and Table 2-3). Fewer SNPs were identified for VTR2L than

VTR2H; 12 significant SNPs across 10 different linkage blocks (Figure 2-6 and Table 2-3).

These 10 loci were located on chromosomes 1, 2, 4, 5, and 7.

Figure 2-4 Manhattan plot of maize leaf chlorophyll content ratio VTR2 examining relative differences between the VT and R2 leaf measurements

Figure 2-5 Manhattan plot of maize leaf chlorophyll content ratio VTR2H examining relative differences between the VT and the R2 high leaf measurements

Figure 2-6 Manhattan plot of maize leaf chlorophyll content ratio VTR2L examining relative differences between the VT and R2 low leaf measurements.

Many of the candidate genes identified for the VTR2 ratios were related to leaf senescence; the majority of which related to signaling of senescence. Two auxin-related genes were identified in GWAS analysis for VTR2 traits; an auxin efflux carrier protein

(GRMZM2G064941; Traits: VTR2, VTR2H, and VTR2L) and an auxin response factor 2

(GRMZM2G378580; Traits: VTR2, VTR2H) (Table 2-4).

Table 2-4 Candidate genes of interest for VTR2 senescence signaling SNPs w/in 20 q- Effect Gene Annotation Chr maf Kb Value* Direction GRMZM2G335814 GRAS family S1_248676101 1 0.09 0.033 - transcription factor GRMZM2G064941 Auxin efflux carrier S2_212641128 2 0.43 0.032 + family protein: (ATPIN4,PIN4) GRMZM2G378580 Auxin response S4_23529175 4 0.17 0.048 - factor 2:(ARF1- BP,ARF2,HSS,ORE14 ) * FDR Corrected p-value (Benjamini and Hochberg 1995)

Two other genes were also identified with potential roles in senescence activation or regulation: SAG24 (GRMZM2G087233; Trait: VTR2H) and CPR5

(GRMZM2G158811; Traits: VTR2 and VTR2H) (Table 2-5). SAG24, is thought to serve a function in the senescence pathway and CPR5 is thought to function in the senescence processes of the leaf.

Table 2-5 Candidate genes of interest for VTR2 senescence regulation SNPs w/in 20 q- Effect

Gene Annotation Kb Chr maf Value* Direction 48

GRMZM2G158811 CPR5 protein: S4_178040254 4 0.19 0.049 + (CPR5,HYS1) GRMZM2G087233 Senescence S5_19441400 5 0.30 0.030 + Associated Gene S5_19441434 5 0.27 0.030 - 24: S5_19441469 5 0.25 0.017 - (RPL10C,SAG24) S5_19448689 5 0.31 0.030 - S5_19441435 5 0.27 0.030 - * FDR Corrected p-value (Benjamini and Hochberg 1995)

2.4.3.2 Examination of VTR4 Traits

Many significant SNPs were identified for the VTR4 traits. GWAS for VTR4 identified 345 SNPs representing 155 significant loci. Significant loci were located on chromosomes 1, 3, 6, 7, and 9 (Figure 2-7). VTR4H identified the highest number of significant markers with 699 significant SNPs organized in 195 loci on chromosomes 1, 3,

7, 8, and 9 (Figure 2-8). GWAS for VTR4L identified 313 significant SNPs across 141 linkage blocks. These significant loci were located across the genome, on all chromosomes except for chromosomes 4 and 10 (Figure 2-9).

Figure 2-7 Manhattan plot of maize leaf chlorophyll content ratio VTR4 examining relative differences between the VT and R4 leaf measurements

Figure 2-8 Manhattan plot of maize leaf chlorophyll content ratio VTR4H examining relative differences between the VT and R4 high leaf measurements

Figure 2-9 Manhattan plot of maize leaf chlorophyll content ratio VTR4L examining relative differences between the VT and R4 low leaf measurements

The analysis of candidate genes for the VTR4 traits identified many genes involved in senescence signaling. Candidate genes involved in senescence signaling included auxin-related genes; although different than those identified in the VTR2 analyses (Table 2-6). Other candidates for VTR4 included numerous mitogen-activated protein kinases (MPKs) and WRKY transcription factors (Table 2-6).

Table 2-6 Candidate genes of interest for VTR4 senescence signaling SNPs w/in 20 q- Effect Gene Annotation Chr maf Kb Value* Direction Auxin GRMZM2G331638 Auxin-responsive family S1_24743247 1 0.07 0.036 + protein GRMZM2G030465 Auxin-induced protein 13: S5_214404494 5 0.09 0.047 + (IAA13) GRMZM2G066202 Auxin-responsive family S7_137514390 7 0.24 0.025 - protein:(AIR12) GRMZM2G086949 Auxin-responsive factor S10_147122400 10 0.30 0.039 - AUX/IAA-related: (ARF5,IAA24,MP) Map Kinase GRMZM2G020216 Mitogen-activated protein S9_18880032 9 0.06 0.045 + kinase 6: (MAPK6,MPK6) GRMZM2G374088 Mitogen-activated protein S4_239436102 4 0.14 0.038 - kinase 9: (MPK9) GRMZM2G173965 Mitogen-activated protein S8_153018091 8 0.25 0.046 - kinase kinase kinase 15: (MAPKKK15) GRMZM2G173965 Mitogen-activated protein S8_153018099 8 0.25 0.046 - kinase kinase kinase 15: (MAPKKK15) GRMZM2G165099 Mitogen-activated protein S3_205364922 3 0.13 0.035 - kinase kinase kinase 16: S3_205364934 3 0.13 0.035 - (MAPKKK16) S3_205364946 3 0.13 0.035 - GRMZM2G041774 S3_205364933 3 0.13 0.035 - Mitogen-activated protein S3_205364934 3 0.13 0.035 - kinase kinase kinase 16: (MAPKKK16) S3_205364946 3 0.13 0.035 - S3_205364922 3 0.13 0.035 - GRMZM2G131334 Mitogen-activated protein S8_145846703 8 0.13 0.029 - 52 kinase 20: (MPK20) WRKY GRMZM2G120320 WRKY DNA-binding protein S5_92802848 5 0.31 0.025 + 40: (ATWRKY40,WRKY40) GRMZM2G125653 WRKY DNA-binding protein S7_115310293 7 0.11 0.040 - 40: (ATWRKY40,WRKY40) GRMZM2G065290 WRKY DNA-binding protein S3_184948734 3 0.16 0.006 - 46: (ATWRKY46,WRKY46) GRMZM2G382350 WRKY DNA-binding protein S3_185026390 3 0.16 0.038 + 64: (ATWRKY64,WRKY64) S3_185026412 3 0.18 0.043 + GRMZM5G812272 WRKY DNA-binding protein S8_149078078 8 0.14 0.027 - 71: (ATWRKY71,WRKY71) * FDR Corrected p-value (Benjamini and Hochberg 1995)

Four other candidate genes for VTR4 were related to senescence activation and regulation including SAG12 (GRMZM2G095265; Traits: VTR4 and VTR4H) and SAG29

(GRMZM2G368827; Trait: VTR4L) (Table 2-7). Two other candidate genes associated with senescence regulation included a response regulator (GRMZM2G099797; Trait:

VTR4L) and ethylene-insensitive-like 3 genes (AC234203.1 FG011; Trait: VTR4L) (Table 2-

7).

Table 2-7 Candidate genes of interest for VTR4 senescence regulation SNPs w/in 20 q- Effect Gene Annotation Kb Chr maf Value* Direction GRMZM2G095265 Senescence- S8_19968068 8 0.06 0.036 + Associated Gene S8_19961897 8 0.11 0.035 + 12: (SAG12) S8_19968068 8 0.06 0.030 + GRMZM2G368827 Senescence- S2_194937752 2 0.05 0.039 - Associated Gene 29: (SAG29) GRMZM2G099797 Response S1_28424547 1 0.28 0.028 + Regulator 2: S1_28424548 1 0.28 0.028 - (ARR2,RR2) AC234203.1_FG011 Ethylene- S1_188064698 1 0.14 0.049 + Insensitive3-like3: (AtEIL3,ATSLIM,EI

L3,SLIM1) 53

* FDR Corrected p-value (Benjamini and Hochberg 1995)

Five candidate genes for VTR4 have roles in either amino acid metabolism or transportation through the plant including Glutamate Decarboxylase 2

(GRMZM2G355906; Trait: VTR4L), CYP89A9 (GRMZM2G344903; Trait: VTR4), NADH- dependent Glutamate Synthase 1 (GRMZM2G077054; Trait: VTR4H), Glutamine

Synthetase 1 (GRMZM2G098290; Trait: VTR4H), and an Amino Acid Permease 3

(GRMZM2G157168; Trait: VTR4H) (Table 2.8).

Table 2-8 Candidate genes of interest for VTR4 N remobilization q- Effect Gene Annotation SNPs w/in 20 Kb Chr maf Value* Direction GRMZM2G355906 Glutamate S2_44719146 2 0.06 0.039 - Decarboxylase 2: (GAD2) GRMZM2G344903 Cytochrome P450, S3_228983258 3 0.38 0.048 - family 89, subfamily A, polypeptide 9: (CYP89A9) GRMZM2G077054 NADH-dependent S8_151221458 8 0.20 0.043 - Glutamate S8_151221492 8 0.20 0.043 + Synthase 1: (GLT1) GRMZM2G098290 Glutamine S10_146474711 10 0.07 0.046 - Synthetase 1: (ATGSL1,GLN2,GS2 ) GRMZM2G157168 Amino Acid S10_11315679 10 0.50 0.040 - Permease 3: (AAP3,ATAAP3) * FDR Corrected p-value (Benjamini and Hochberg 1995)

2.5 Discussion

2.5.1 Genetic Variance and Trait Correlation

Genetic variances and trait correlations were calculated before GWAS was

conducted to ensure significant variation for mapping and to examine relatedness among traits before ratio calculation. ANOVA analysis confirmed that significant genetic variation existed in the Ames Association Panel for the chlorophyll degradation and apparent remobilization timing traits measured in this study.

Trait correlations demonstrated there was a stronger relationship when less temporal separation existed between traits. Traits measured on the same day on different leaves had a stronger correlation than those measured at other times during

55 the growing season. Logically, the VT measurements had a weaker correlation with the

R4 traits than the R2 traits. Moderate to high correlations were noted between all traits; this may in part be due to the consistency in field measurements taken.

2.5.2 Heritabilities

Broad sense heritabilities for the leaf greenness traits measured in this study were low to moderate, ranging from 0.44-0.64. One possible reason for these low values could be the large differences in maturities within the Ames Panel; the lines in Maturity

1 flowered on average 40 days sooner than the tropical lines found in Maturity 5

(Figures 2-1 and 2-2). The data from 2012 and 2013 were combined for heritability calculations, and the large differences in seasonal weather in these two growing seasons may also have contributed to variations in expression of these traits from year-to-year.

Although drought stress was managed via drip irrigation, heat and drought stress were still prevalent. Another possible cause for the low heritabilities may be the time required to measure each trait. Even with multiple phenotyping crews, several hours

were required to collect trait data in any maturity group and this time may have had an effect on trait expression.

2.5.3 Candidate Genes for Leaf N Remobilization

2.5.3.1 Senescence Signaling

Leaf senescence is a programmed plant process in annual and perennial plants including cellular death and remobilization of nutrients found in the photosynthetic

56 machinery. While programmed within the plant, both biotic and abiotic stresses can affect the timing of leaf senescence. Research studies on senescence under abiotic stresses have identified genes controlling stay-green in sorghum (Borrell et al., 2000).

While delaying senescence under abiotic stresses such as drought offers the ability to increase yields in these environments, senescence delayed too long also has the detrimental effects of reducing the amount of nutrients remobilized from vegetative tissues to the grain, thereby decreasing nutritional value of the crop (Mi et al., 2002;

Gong et al., 2005). For this reason, we sought to identify genes controlling the timing of leaf senescence and N remobilization to better understand the signaling and degradation genes involved in these processes.

The experimental population in this study experienced heat stress in the summer of 2012, while 2013 was an average summer for Indiana. As drip irrigation was applied in 2012 and consistent rainfall fell throughout the growing season in 2013, drought stress was lessened as a factor in the onset of senescence in this population. The lack of

abiotic and biotic stress in both years suggests that candidate genes identified in this study are involved with normal senescence processes.

2.5.3.1.1 Candidate genes for VTR2 traits

Candidate genes linked to SNPs associated with the chlorophyll degradation timing ratios indicated roles related to senescence and N remobilization (Tables 2-4 and

2-5). Previous analyses of signaling elements have identified auxin with a role in cellular signaling of senescence (Addicott 1982; Sexton and Roberts 1982; Thompson et al.,

1988; Buchanan‐Wollaston et al., 2003; Lim et al., 2003; Buchanan‐Wollaston et al.,

2005). Previous studies also demonstrated that there is a delay in the initialization of senescence when auxin is applied (Shoji et al., 1951; Sacher 1957). Auxin Response

Factor 2 (ARF2) has also been observed to be expressed in senescing leaves of

Arabidopsis thaliana (Ellis et al., 2005). The hormone auxin has been observed to affect many plant processes, and ARF2 is a transcription factor controlled by the presence of auxin. The ARF2 protein has been shown to have a repressive effect on auxin signaling in

Arabidopsis thaliana, and mutations in ARF2 delay senescence (Ellis et al., 2005; Lim et al., 2010). This suggests that auxin is involved in repressing senescence (Tiwari et al.,

2003). Allelic variants of ARF2 may exhibit different sensitivities to auxin, thereby altering the initiation of senescence. Also identified in our analysis was an auxin efflux carrier protein. This protein serves a function in the plant transporting auxin; and may be responsible for the transportation of auxin to or from ARF2 along the auxin- senescence pathway. This gene is in the PIN4 family, and PIN genes have been shown to

affect the auxin gradient in the cell (Forestan and Varotto 2012). Identification of both a carrier and a response auxin protein in this study suggest that auxin metabolism and signaling may contribute to senescence in the Ames Association Panel.

A GRAS transcription factor was also identified as a candidate gene for the

VTR2H trait (GRMZM2G335814; Trait VTR2H). Previous research identified the potential of this transcription factor in signaling senescence within the cell (Buchanan‐Wollaston et al., 2005). With auxin and GRAS related genes identified in the VTR2 analysis, this

58 suggests that these two signaling elements may be activated earlier in the senescence process than other plant signaling molecules.

2.5.3.1.2 Candidate genes for VTR4 traits

Candidate genes associated with VTR4 traits indicated a combination of genes related to senescence and N remobilization (Tables 2-6, 2-7, and 2-8). Two auxin response proteins were identified for the VTR4 trait; GRMZM2G331638 (VTR4 and

VTR4H) and GRMZM2G066202 (VTR4H). Although research on these particular genes has been limited, these genes may function in the auxin-signaling pathway. Additionally, an auxin response factor 5 (GRMZM2G086949) was identified for the VTR4H trait.

Studies have shown this particular response factor is very similar to ARF1, binding with auxin responsive elements. ARF5 encodes an indole 3-acetic acid (IAA-24) transcription factor in the senescence signaling pathway. Identification of these auxin responsive genes, in addition to the IAA auxin induced protein 13 (GRMZM2G030465; Trait: VTR4H), further strengthens the potential relationship of auxin in the inhibition of senescence in

58 maize (Gan and Amasino 1997; van der Graaff et al., 2006; Mashiguchi et al., 2011; Won et al., 2011).

The WRKY genes have been identified to serve a function in plant cellular processes in many studies (Buchanan‐Wollaston et al., 2003; Guo and Gan 2005;

Gregersen and Holm 2007; Balazadeh et al., 2008). The WRKY53 and WKRY70 transcription factors have been identified to have positive and negative regulatory effect on senescence; respectively (Miao et al., 2004; Ülker et al., 2007). We identified

59 five other WRKY elements with potential functions in plant signaling processes; WRKY

40 (GRMZM2G120320; Trait: VTR4H), WRKY 41 (GRMZM2G324999; Trait: VTR4H), WRKY

46 (GRMZM2G065290; Traits: VTR4H and VTR4L), WRKY 64 (GRMZM2G382350; Trait:

VTR4H), and WRKY 71 (GRMZM2G812272; Traits: VTR4 and VTR4H). Although these

WRKY transcription factors have not been determined to have a specific role in senescence, their roles have been examined in other plant processes. Both WRKY40 and

WRKY46 have been found in response to abiotic stresses; heat stress increases expression of WRKY40 and drought increases expression of WRKY46 (Dang et al., 2013;

Ding et al., 2014). It may be possible that our identification of WRKY40 is due to the heat stress in the 2012 field season. Notably, WRKY40 has shown negative involvement with abscisic-acid (ABA) signaling; another transcription factor with potential effect on senescence activation (Yan et al., 2013). WRYK64 and WRKY71 are associated with other hormone signaling pathways. WRKY64 has a proposed function in jasmonate signaling, while WRKY71 seems to play a role in the gibberellin signaling pathway, activated by

ABA (Xie et al., 2006; Schluttenhofer et al., 2014).

Map kinases including mapk 6 (GRMZM2G020216; Trait: VTR4L), mapkk 9

(GRMZM2G374088; Trait: VTR4H), mapkkk 15 (GRMZM2G173965; Trait: VTR4H), mapkkkk 16 (GRMZM2G165099; Trait: VTR4H), and mapk 20 (GRMZM2G131334; Traits:

VTR4 and VTR4H) were also identified in this analysis suggesting a potential function of these genes in the signaling cascades associated with senescence (Table 2-6). There is still much to be learned about the role of mapk transcription factors in cascade signaling, although two of these map kinases have been shown to exhibit an important

60 role in leaf senescence cascades. Map Kinase 6 (MPK6) has been shown to function in the leaf senescence signaling cascade with a direct relationship to Map Kinase Kinase 9

(MKK9) (Zhou et al., 2009). Zhou et al., (2009) determined that activation of both MPK6 and MKK9 are required for senescence to occur regularly. Knockout mutants of these genes exhibit delayed senescence. Map kinases have shown wide roles in plant processes, and further evaluation of these kinases may elucidate additional roles in senescence signaling pathways.

2.5.3.2 Senescence Activation/Regulation

In addition to the signaling genes identified in our GWAS analysis, genes with roles in activation and regulation of leaf senescence were also identified (Tables 2-7 and

2-8). These genes exhibit functions in the activation or regulation of senescence.

2.5.3.2.1 Candidate genes VTR2 traits

Senescence Associated Genes (SAGs) have been shown to play a key role in

senescence (Buchanan‐Wollaston et al., 2003; Lim et al., 2007; Li et al., 2012). In this 60

study, SAG24 was associated with VTR2 suggesting a potential role in early senescence regulation within the plant. CPR5 has beneficial functions in early plant development. As the plant ages, CPR5 transcripts increase and appear to stimulate the activation of senescence (Jing et al., 2007). Allelic variations in this gene may exhibit differences in the timing of senescence. As these genes are involved in early activation of senescence, it can be postulated that these genes play a significant role in the R2 stages of growth.

2.5.3.2.2 Candidate genes for VTR4 traits

SAG12 has been shown to have multiple functions in relation to leaf senescence, including the cytokinin signaling pathway, promoting senescence as cytokinin levels decrease in the plant (Gan and Amasino 1995; Ori et al., 1999; McCabe et al., 2001).

Other researchers have suggested that SAG12 has a chloroplast degradation role as a protease (Martínez et al., 2008). Still other researchers have suggested that SAG12 may play a regulatory role in N remobilization that occurs during leaf senescence (Hollmann et al., 2014). Although multiple functions are proposed, a role for SAG12 in leaf senescence is strongly supported. Less is known about SAG29, but this gene has been identified as a protein on the ABA signaling pathway, furthering the evidence of ABA’s role in later stages of senescence signaling (Li et al., 2012).

An ARR2 (GRMZM2G099797; Trait: VTR4L) gene was identified as a candidate for

VTR4L (Table 2.7). In Arabidopsis thaliana, ARR2 is necessary for leaf longevity (Lim et al., 2007). Transcript analysis has found that overexpression of ARR2 delayed

senescence; suggesting that allelic variants in ARR2 may delay senescence (Kim et al.,

2006). As ARR2 is phosphorylated by cytokinin to delay senescence, this is further evidence of the inhibitive role cytokinins play in leaf senescence (Gan and Amasino

1997).

An Ethylene Insensitve 3 (EIN3) gene (AC234203.1_FGP011; Trait: VTR4L) identified in this study was also shown to have significant effect on ethylene signaling of senescence in Arabidopsis (Li et al., 2013a). Li et al., (2013) observed EIN3 to repress the transcription of miR164, and therefore signal regulated senescence activation under

62 both normal and stressed conditions. Transgenic overexpression of EIN3 had a positive effect on the rate of senescence in Arabidopsis thaliana.

2.5.3.3 Genetic Control of N Remobilization

Many cellular processes occur during senescence including the remobilization of nutrients from the senescing tissue (Himelblau and Amasino 2001; Masclaux-Daubresse et al., 2010). One of the nutrients remobilized from these tissues to the grain is N.

Phosphoenolpyruvate carboxylase (PEPc), Glutamine Synthetase, and Ribulose- 1,5- bisphosphate carboxylase/oxygenase (Rubisco) constitute a significant portion of the stored N in vegetative tissues of the plant (Good and Beatty 2011; Kant et al., 2011). In addition to the transcription factors and senescence-related genes identified in our

GWAS analysis, genes with functions in both conversion and transportation of N were also identified. Identification of these specific genes suggests that allelic differences may affect the N remobilization rate and NIE of the plant.

2.5.3.3.1 Candidate genes for VTR4 traits 62

The candidate genes identified for VTR2 were related to signaling and activation of senescence; none were identified in relation to N remobilization. This may show that while signaling and preliminary steps in senescence are induced at the R2 stage, photosynthetic materials have not been metabolized yet to allow for remobilization of

During leaf senescence, chlorophyll is catabolized in the chloroplasts to mitigate any potential phototoxic effects of free movement within the cell (Hörtensteiner and

Kräutler 2011). The catabolism of chlorophyll includes multiple steps starting with conversion of chlorophyll a and b molecules through multiple steps to fluorescent chlorophyll catabolites (FCC) and finally non-flourescent chlorophyll catabolites (NCC)

(Mach 2013). Recent research has identified a slight variation to this pathway where

FCCs are converted to fluorescent dioxobilin-type chlorophyll catabolites (FDCC) via

CYP89A9 (GRMZM2G344903; VTR4). In Arabidopsis thaliana, chlorophyll catabolism contributes to the production of non-flourescent dioxobilin-type chlorophyll catabolites

(NDCC) as the final product on the FDCC pathway (Christ et al., 2013). CYP89A9 is a fluorescent chlorophyll catabolite deformylase and converts FCC components to FDCC.

The high NDCC content in the plant following chlorophyll degradation suggests that

CYP89A9 has an important function in chlorophyll degradation and nutrient remobilization. This cytochrome p450 enzyme may also serve a role in maize chlorophyll

catabolism (Table 2-8). Allelic variants of CYP89A9 may affect the catabolism cascade of chlorophyll.

GDC2 and AAP3 were identified in a GWAS for VTR4 N remobilization (Table 2-8).

Glutamate decarboxylase 2 (GDC2) (GRMZM2G355906; VTR4L) is an enzyme in the glutamate metabolism pathway that is responsible for the conversion of glutamate to 4- aminobutanoate (GABA). GABA has been noted to respond to both biotic and abiotic stresses (Shelp et al., 1999; Bouche and Fromm 2004). GABA concentration is positively correlated with plant senescence (Masclaux et al., 2000; Diaz et al., 2005). Although the

64 function of GABA during plant senescence has not been fully elucidated, it has been suggested that GABA functions in C and N metabolism (Ansari et al., 2005; Weigelt et al.,

2008; Tegeder and Rentsch 2010). The proposed role of GABA in plant senescence and N remobilization is supported by the identification of Amino Acid Permease 3 (AAP3)

(GRMZM2G157168; Trait: VTR4H) (Table 2-8). AAP3 is a known transporter of GABA

(Breitkreuz et al., 1999). Identification of the enzymes responsible for the synthesis and transportation of GABA suggests a possible role of GABA and further research is needed to determine the specific role and effect GABA has on N remobilization.

Nitrate-N is taken up by the plant, reduced and stored in many forms including the amino acid glutamate. Although glutamate is a major storage form of N, transportation of N through the plant is more efficient via other amino acids. Glutamine and Asparagine are two such forms that are more efficiently transported through phloem (Simpson et al., 1983; Hayashi and Chino 1990; Atkins 2000; Fisher 2000; Tilsner et al., 2005). Glutamine Synthetase 1 (GS1) was associated with VTR4 in this study (Table

2-8). GS1 converts glutamate to glutamine in the cytosol (Brugière et al., 2000;

Masclaux-Daubresse et al., 2010). In maize, GS1 is found in the cytoplasm and GS2 is found in the chloroplast. GS activity has been observed to decrease during leaf senescence, attributed largely to the decrease in GS2 activity during chloroplast degradation (Streit and Feller 1983; Kamachi et al., 1991; Mitsuhashi and Feller 1992;

Masclaux et al., 2000; Diaz et al., 2008). Identification of GS1 as a candidate gene in our analysis of leaf chlorophyll remobilization further supports that GS1 is the enzyme responsible for glutamate conversion to glutamine during N remobilization (Habash et

65 al., 2001; Miflin and Habash 2002; Tercé-Laforgue et al., 2004; Martin et al., 2005). Prior studies have noted the role of GS1 in grain filling, kernel number, and grain N (Martin et al., 2006; Habash et al., 2007; Hirel et al., 2007). Reduction of kernel number induced by changes in GS1 activity suggest an influence on plant sink and subsequent accumulation of carbon molecules in the leaves of lines with reduced GS activity (Amiour et al., 2014).

With effects on kernel number and subsequent carbon allocation to the grain, it has been suggested that GS is the rate limiting step for incorporation of inorganic N into organic molecules within the plant (Broyart et al., 2009; Amiour et al., 2014).

Identification of GS1 as a candidate in our analysis suggests allelic variations may metabolize glutamate with different efficiencies, affecting the ability to remobilize N.

After glutamine reaches the reproductive sink, from both remobilized vegetative sources and directly from reproductive N acquisition, it must then be metabolized back to glutamate for conversion to other amino acids in the grain. This process is completed with NADH-dependent Glutamate Synthase (NADH-GOGAT) (GRMZM2G077054; Trait:

VTR4H). NADH GOGAT converts the glutamine transported to the sink into glutamate; and from glutamate to other amino acids such as arginine and proline. There are two forms of GOGAT; an NADH–dependent form (as identified in our analysis), and a ferredoxin-dependent (FD) form. It has been noted that FD-GOGAT is largely found in photosynthetic tissue, whereas NADH-GOGAT is relegated more towards non- photosynthetic tissue; although some discrepancy exists (Coruzzi and Last 2000). NADH-

GOGAT has been hypothesized as a major candidate in cereal NUE (Quraishi et al.,

2011). The association of NADH-GOGAT with VTR4 N remobilization in our analysis

66 suggests activity in the sink may have an effect on the rate of N remobilization and

NADH-GOGAT may play a role as previous analyses have indicated (Obara et al., 2001;

Yamaya et al., 2002).

2.5.3.3.1.1 Proposed enzymatic pathway

Figure 2-10 Proposed Pathway of Leaf N Remobilization and identified genes affecting timing of N remobilization in both sink (NADH-GOGAT) and Source (GS1 and Glutamate Decarboxylase) and identified genes responsible for transportation of N compounds.

We propose a model for N remobilization where candidate enzymes are localized in both the leaf and reproductive tissues (Figure 2-10). This further supports a hypothesized relationship between source tissues and sink tissues controlling the rate of

N remobilization in the leaves (Seebauer et al., 2004; Cañas et al., 2010; Cañas et al.,

2012) . GS1 and NADH-GOGAT have exemplified coordinated expression during leaf senescence and nutrient remobilization (Coschigano et al., 1998). GS1 activity in the leaves is crucial to N remobilization as vegetatively-stored glutamate is converted to the more mobile glutamine. High activity allelic variants of the GS1 gene allow for more efficient conversion of glutamate, ensuring this step in the pathway is not the limiting factor. Signaling of GS1 may be completed by a multitude of factors, possibly including

GABA, metabolized by GDC2 and transported through the plant by AAP3, both identified in this analysis of VTR4 traits. Allelic variation for metabolism and transport of GABA may affect the signaling and activation of GS1 (this signaling portion of the pathway is speculative, and further research must be conducted to confirm). Once glutamine enters

the reproductive tissue, it must be metabolized back to glutamate for conversion to other forms of amino acids in the grain. NADH-GOGAT may convert the incoming glutamine into glutamate in non-photosynthetic tissue such as the grain. Differences in

NADH-GOGAT activation energies affect the speed at which glutamine is metabolized and less efficient enzymes may result in a buildup of glutamine in the grain. Highly active forms of NADH-GOGAT may utilize glutamine as a transportation mechanism and allow delivery to the grain, thereby increasing efficiency of the N remobilization process.

Candidate genes for enzymes involved in N remobilization in both the source and sink

68 tissues were identified in this study. Once validated, this would support the theory that

N remobilization from maize leaves is a process controlled by both the ‘push’ of the source vegetative tissues as well as the ‘pull’ from the sink reproductive tissues (Cañas et al., 2009).

2.6 Conclusions

GWAS was conducted on a diverse population of maize lines in an effort to examine genetic controls of the timing of leaf N remobilization. Candidate genes associated with leaf senescence and N remobilization were detected. Comparison of candidate genes for VTR2 and VTR4 traits suggest that leaf senescence signaling began at R2, but not protein degradation or N remobilization under this N fertilization level.

Conversely, a multitude of genes were noted with functions in both leaf senescence and

N remobilization in the VTR4 analysis.

Evidence in support of both potential sink and source activity on the level of N remobilization is further indicated by the genes identified in our analysis of VTR4. GS1, a

known enzyme in the conversion of amino acids within senescing vegetative tissues was noted; as was NADH-GOGAT, found within non-photosynthetic tissues. Significant enzymes found in both source and sink tissues are consistent with the theory that N remobilization from the leaves is a complex process under source and sink controls.

This analysis identified potential candidate genes controlling both the timing of senescence and N remobilization. The size of this population provided statistical power to identify candidates but further research must be conducted to elucidate the specific agronomic and physiological effects of these identified candidates - such as yield, and

69 disease and insect susceptibility. Identification of lines with allelic variation for these genes of interest will allow for more detailed analysis of gene function. Implementation of selected alleles into a breeding program will contribute to increased NUE; allowing growers to maintain productivity with lower N inputs.

CHAPTER 3. GENETIC MAPPING OF KERNEL COMPOSITION IN A DIVERSE POPULATION OF ZEA MAYS

3.1 Abstract

Maize grain has many end-uses including food, feed, fiber, and fuel. The composition of the maize kernel for ash, density, fiber, oil, protein, and starch has a large effect on the processing quality and final use efficiencies of the grain. Breeding efforts for these traits have been in progress for decades, but the implementation of genetic marker technologies offer the opportunity to expedite this and other key processes. Near Infrared Spectroscopy (NIRS) can also be used to non-destructively analyze the kernel compositions of lines; allowing sampled seed to be planted the following season. A Genome Wide Association (GWAS) analysis was conducted on a diverse population of more than 2,400 maize lines to identify genetic controls of kernel composition. Significant markers for kernel density, oil, and protein were identified.

Candidate genes located near the significant loci for kernel density identified a heavy

70 metal transporter gene (GRMZM2G031528) and a transketolase gene

(GRMZM2G033208), both activated under the presence of cadmium; suggesting a relationship between heavy metal content and kernel density. GWAS for kernel oil content showed an association with acyl-CoA:diacylglycerol acyltransferase-2 (DGAT-2,

GRMZM2G169089), an oil biosynthesis gene in the Kennedy Pathway. These results

71 suggest that DGAT-2 may contribute to a rate limiting step for oil accumulation, which would allow for breeding of improved DGAT-2 activity to potentially increase kernel oil content. Analyses of kernel protein showed an association with a transmembrane amino acid transporter (GRMZM2G137161) and an amino acid permease (GRMZM2G145989).

Utilization of these markers and genes in breeding programs may allow for selection of maize lines with optimized kernel composition.

3.2 Introduction

Maize grain has many uses as food, feed, fiber, or fuel. These applications are benefitted by specific profiles of protein, oil, starch, ash, fiber, or differences in kernel density depending on the specific end use. Commercial dent maize varieties typically contain approximately 71.7% starch, 9.5% protein, 4.3% oil, 1.4% ash, and 6.2% fiber

(Watson et al., 2003). Genetic variations for these components have been observed in diverse panels of maize inbred lines, and exploitation of this diversity could be useful in development of lines for specific uses (Flint-Garcia et al., 2009). Increased protein, oil, or

starch can improve the value of the grain for a specific use. Differences in kernel density can affect the processing quality of the grain since kernels with different hardness profiles must be processed using different methods, altering the time and effort required to obtain a final product.

Breeding efforts to improve grain quality have been conducted by many programs and the results have been previously outlined (Wall and Paulis 1978; Nelson

1979, 1980; Axtell 1981). Typically these efforts involved creation of a breeding population and selection of lines based upon destructive laboratory analysis following

72 harvest. This process was both time and labor consuming as the samples were usually ground for analysis, and selected lines must rely on non-sampled seed for propagation.

Utilization of NIRS allows researchers to quickly sample whole kernels, and then use those same kernels as seed if the line is selected to advance. As this process is more time efficient for both sample preparation and analysis, larger populations can be analyzed with the same amount of effort, saving time and resources within a breeding program and allowing potentially for greater gain per cycle of selection. NIRS technology is also developing rapidly and declining in price. As such, there is potential to increase efficiency and efficacy of breeding programs in the developing world.

In this study, a large population of diverse maize inbred lines was characterized for variations in kernel composition (ash, density, fiber, oil, protein, and starch) using

NIRS. GWAS was then performed to identify the genetic controls of these kernel composition traits. Significant markers for kernel density, oil, and protein were detected and used to identify possible candidate genes controlling these composition traits.

3.3 Materials and Methods

3.3.1 Genetic Material

Analyses of kernel composition were conducted for association mapping utilizing the same population of diverse maize inbred lines as described in Chapter 2 Genetic

Material. Ears from more than 2,400 genotypes were harvested for kernel composition analyses.

3.3.2 Experimental Design

This study utilized the same experimental design as Chapter 2, an augmented design separated into six maturity groups with each range in a maturity treated as a block. Further details on experimental design and plot handling in both 2012 and 2013 can be found in Chapter 2 Experimental Design.

3.3.3 Phenotypic Evaluation

Four self-pollinations were completed for each plot in the experiment, including the check varieties. From these self-pollinations, the three best ears were selected at physiological maturity (R6; Hanway 1966). Ears were harvested into mesh bags by plot, placed onto a forced air dryer at 35°C and shelled into one bulk sample per plot using an

Agriculex SCS-2 single ear corn sheller (Agriculex Inc. Guelph, Ontario, Canada).

NIRS was conducted on whole kernels with a Perten DA 7250 NIR analyzer

(Perten Instruments, Hagersten, Sweden). NIRS calibration information can be found in

Appendix E. A concave mirrored sampling dish (breeder cup) was utilized to measure a sample of 15 kernels from each bulk sample. Reflectance analysis was conducted on these samples, measuring the wavelength of light returning to the sensor from the sample. This system is not a transmittance analysis, and the portion of the kernel which reflects the light emitted may have an effect on the composition analysis. To account for this variability, and potentially reduce error attributed to machine measurement variability, each sample was run in replicates of two and samples were repositioned

74 three times in the breeder cup, for a total of six separate measurements which were averaged into a final plot mean by the NIRS internal software.

Kernel samples exhibited slightly different moisture values at the time of measurement. To account for this variation, all trait values were converted to a dry basis

(db) value using a grain moisture conversion ratio (Extension 2006). Basic statistics for the moisture values, separated by maturity group, are shown in Table 3.1.

Table 3-1 Statistics for moisture values from NIR used for dry basis conversions Mean Std Dev Min Max Maturity 1 8.04 1.76 4.09 14.54 Maturity 2 8.14 1.30 3.76 11.67 Maturity 3 7.74 1.16 3.56 11.02 Maturity 4 7.82 1.09 2.14 11.08 Maturity 5 8.47 1.09 2.14 11.08 Maturity 6 8.40 1.32 3.34 11.72

3.3.4 Genotypic Information

Genotyping-By-Sequencing (GBS) data were utilized for GWAS analysis from

Romay et al., (2013), the same as used for Chapter 2 Genotypic Information. In total,

680,000 Single Nucleotide Polymorphism (SNP) markers were utilized in this analysis.

3.3.5 Statistical Analysis

Dry basis trait values were used for statistical analyses including: examination for outlying data points, testing for significant genetic variation, calculation of trait heritabilities, calculation of Best Linear Unbiased Predictors (BLUPs), GWAS analysis, and examination of maize linkage blocks as described in Chapter 2 Statistical Analysis.

Statistical Analysis Software (SAS) (SAS Version 9.2 for Windows, SAS Institute Inc., Cary,

NC, USA) was utilized for examination of outlying data points, genetic variation testing, heritability and BLUP calculations. R statistical analysis software was used for GWAS analysis utilizing the compressed mixed linear model method (Zhang et al., 2010) in the

GAPIT package (Lipka et al., 2012). Linkage block analysis was conducted in TASSEL V 5.0

(Bradbury et al., 2007). BLUP spatial correction and GWAS statistical codes are presented in Appendices F and G, respectively. A minor allele frequency (MAF) of 0.05 was utilized in the GWAS analysis. SNP markers that do not meet this threshold were removed. Candidate genes for each trait were identified by searching within a 20 Kb window of significant SNPs.

3.3.6 Candidate Gene Analysis

Significant SNPs were examined for candidate genes as described in Chapter 2

Candidate Gene Analysis. A 20 Kb window surrounding each significant SNP was examined through the B73 v2 annotation on MaizeGDB (Lawrence et al., 2005). Genes within that window were recorded along with their annotated functions (Appendix I).

3.3.7 Transcript expression analysis

Maize transcript analysis was conducted to examine expression profiles of candidate genes throughout the plant in different phases of the growth cycle. This was accomplished on candidate genes through the maize eFP browser (Winter et al., 2007).

Candidate genes were examined in the browser for relative expression in kernels compared to average plant expression.

3.4 Results

3.4.1 Genetic Variance and Trait Correlations

Trait correlation analyses were conducted using SAS PROC CORR on the grain composition traits measured using the Perten NIRS. Between 2,100 and 4,904 data points were collected for each trait from the association panel of over 2,400 maize inbred lines grown in 2012 and 2013. Significant genetic variation (p<0.05) was observed for ash, density, fiber, oil, protein, starch (Appendix H; Table 3.2). The standard deviations for these traits ranged from 0.07 to 4.77.

Table 3-2 Basic statistics and trait correlations for maize kernel traits Traits Ash Density Fiber Oil Protein Starch N 2160 4903 2611 4884 4904 4704

Mean 1.11 1.46 1.92 4.63 14.92 59.43 Std Dev 0.09 0.07 0.69 1.20 2.00 4.77

Statistics Min 1.01 1.16 1.10 2.17 9.11 48.30 Max 1.62 1.72 5.43 11.02 23.29 73.64

Ash Density Fiber Oil Protein Starch 76

Ash - -0.19*** 0.06*ss 0.08*** 0.09*** -0.08*** Density -0.19*** - -0.25*** 0.25*** 0.23*** -0.41*** Fiber 0.06*dd -0.25*** - -0.28*** NS -0.14***

Correlations Oil 0.08*** 0.25*** -0.28*** - 0.36*** -0.35*** Protein 0.09*** 0.23*** NS 0.36*** - -0.69*** Traits Starch -0.08*** -0.41*** -0.14*** -0.35*** -0.69*** -

* = 0.05 Significance

** = 0.01 Significance

*** = 0.001 Significance

NS = No Significance

Correlations between the kernel traits were significant for all pairwise relationships, except fiber and protein. With the exception of ash and fiber (p = 0.05), all correlations are significant at the p = 0.001 level. Ash levels were weakly correlated with all traits and negatively correlated with density and starch. Kernel density exhibited low to moderate correlations with all traits (R2=-0.41 to 0.25). Fiber exhibited weak negative correlations with density, oil, and starch but was poorly correlated with ash (R2=0.06).

Oil exhibited a moderate positive correlation with protein content (R2=0.36) and a moderate negative correlation with starch (R2=-0.35); starch is negatively correlated to protein with a moderate strength (R2=0.69).

3.4.2 Heritabilities

Broad-sense heritabilities were calculated using PROC GLM to estimate the variance components (Table 3.3). The lowest observed heritability was observed for kernel ash (0.11), and the highest heritability for kernel oil (0.66).

Table 3-3 Heritabilities of maize kernel traits measured in multilocation trials

77 Trait H

Ash 0.11 Density 0.57 Fiber 0.24 Oil 0.66 Protein 0.60 Starch 0.40

3.4.3 Genome Wide Association Studies

Genome wide association analyses were conducted to identify SNPs associated with variation in kernel composition. Between 0 and 819 significant SNPs were

78 identified for each trait; falling within 0 to 242 linkage blocks (Table 3.4). Multiple genes were often identified for each SNP and the total number of candidate genes for each trait ranged from 0 to 2,787. Further examination of these associated genes for known annotations resulted in 0 to 1,232 annotated genes (Appendix 3.5). In decreasing order, the kernel traits with the most annotated genes are protein (1,232), density (155), oil

(43), fiber (2), ash (0), and starch (0) (Table 3.4).

Table 3-4 Summary GWAS results for maize kernel traits

TRAIT Ash Density Fiber Oil Protein Starch

Significant SNPs 0 114 1 27 819 0 Linkage Blocks 0 45 1 14 242 0 Associated Genes 0 334 3 83 2787 0 Candidate Genes 0 155 2 43 1232 0 with Annotations

Manhattan plots were created to demonstrate SNP associations for kernel 78

composition traits. Significance thresholds for SNP markers ranged from -Log10(p) = 5 to

6.75 (Figures 3.1-3.4). For kernel density and oil (Figures 3.1 & 3.3), pronounced and distinct peaks were noted on chromosomes 3 and 9 (density) and 5 and 6 (oil). Kernel fiber exhibited a significant SNP on chromosome 5 (Figure 3.2). For kernel protein, significant SNPs were observed but distinct peaks were more difficult to identify (Figure

3.4). The kernel density trait has by far the most significant SNPs, with a –log10(p) value

> 13 on chromosome 9 (Figure 3.1). Oil and protein traits both exhibit significant peaks near –log10(p) = 7 (Figures 3.3 & 3.4).

Figure 3-1 Manhattan plot of SNPs associated with maize kernel density

Figure 3-2 Manhattan plot of SNPs associated with maize kernel fiber

Figure 3-3 Manhattan plot of SNPs associated with maize kernel oil

Figure 3-4 Manhattan plot of SNPs associated with maize kernel protein Analysis of maize kernel fiber identified one significant SNP on chromosome 5,

S5_6133336. Subsequent analysis of candidate genes within 10 kb of this SNP identified

3 associated genes, 2 of which had annotations. Although two candidates were identified, neither warranted further examination.

GWAS analysis of kernel oil resulted in the identification of 27 significant SNPs located in 14 linkage blocks. Candidate genes were examined within a 10 Kb of these

SNPs, and 83 candidate genes were identified. 43 of these genes have known annotations (Appendix I-2). Of the 43 annotated genes identified, an acyl-

CoA:diacylglycerol acyltransferase-2 (DGAT-2) gene was identified on chromosome 6

(GRMZM2G169089; Table 3-5).

Table 3-5 Candidate Gene of Interest for Kernel Oil Composition

q- Effect Gene Annotation SNP w/in 20Kb Chr maf Value* Direction acyl-CoA: diacylglycerol GRMZM2G169089 S6_104858735 6 0.15 .0010 + acyltransferase- 2 (DGAT-2) * FDR Corrected p-value (Benjamini and Hochberg, 1995)

GWAS analysis of maize kernel density identified 114 significant SNPs on 45 linkage blocks. 334 genes were found to be located within 10 kb of these 114 SNPs.

Analyses of candidate genes identified 155 genes with known annotations (Appendix I-

1). On chromosome 3, a gene encoding a heavy metal transport and detoxification protein was identified near significant marker S3_156795071 (GRMZM2G031528; Table

3-6). Also identified in maize kernel density analysis was a transketolase

(GRMZM2G033208) found near S9_22781026 on chromosome 9.

Table 3-6 Candidate Genes of Interest for Kernel Density q- Effect Gene Annotation SNP w/in 20 Kb Chr maf Value* Direction Heavy metal transport/ GRMZM2G031528 S3_156795071 3 0.13 .0017 - detoxification superfamily protein GRMZM2G033208 Transketolase S9_22781026 9 0.09 .0018 + * FDR Corrected p-value (Benjamini and Hochberg, 1995)

Maize kernel protein was analyzed through GWAS analysis. 819 significant SNPs were identified across 242 loci. Analysis of candidate genes within 10kb of these significant SNPs identified 2,787 genes, of which 1,232 were annotated (Appendix I-3).

On chromosome 2 an amino acid transporter was identified near the SNP S2_42001237

(GRMZM2G137161; Table 3-7). Also identified on chromosome 9 near SNP S9_73922636 was amino acid permease 1 (GRMZM2G145989).

Table 3-7 Candidate Genes of Interest for Kernel Protein SNP w/in q- Effect Gene Annotation 20Kb Chr maf Value* Direction Amino Acid Permease GRMZM2G145989 S9_73922636 9 0.26 0.047 + 1 (AAP1,NAT2) Transmembrane GRMZM2G137161 amino acid S2_42001237 2 0.16 0.008 +

transporter * FDR Corrected p-value (Benjamini and Hochberg, 1995) 3.5 Discussion

3.5.1 Genetic Variance and Trait Correlations

The kernel composition traits examined in this study exhibited significant genetic 83

variation. The two kernel composition traits with the lowest number of samples were ash and fiber with 2,160 and 2,611 samples, respectively. Compared to the other traits which utilized between 4,704 to 4,904 data points, the sample number for ash and fiber were considerably less. When NIRS was conducted, all kernel traits were acquired from the same sampling run. Variation in the number of samples for each kernel trait was the result of the removal of values which lie outside of the range of the calibration population for each respective trait. The maize calibration for the NIR was created using

84 commercial maize samples. In the association panel some diverse lines are significantly different for the measured trait than commercial U.S. maize. Ash and fiber had a much greater number of sampled values outside of the calibration range (both high and low) than the other kernel composition traits examined, thus explaining the lower number of observations for these traits.

Trait correlations were significant for all relationships except for protein and fiber. Weak relationships were noted between ash and all other measured components with density and starch displaying negative relationships. Moderate correlations were noted for density with other components (R2=0.19 to 0.41) with oil and protein exhibiting positive relationships. The majority of kernel oil is found in the embryo, a small and dense portion of the kernel. It is therefore reasonable that increases in kernel oil, and subsequently the relative size or density of kernel embryo, may have an overall effect on kernel density. Conversely, the negative relationship between kernel density and starch content (R2=-0.41) may be an effect of the larger relative size of the less-

dense kernel endosperm in high-starch lines of maize. The correlation of fiber to other traits was consistently small (R2=-0.28 to -0.06), and negative with all traits except ash

(R2=0.06). Kernel oil, as expected, was found to share a moderate (R2=0.36) positive correlation with kernel protein (Coleman and Moore 2003) and a moderate (R2=-0.35) negative correlation with starch (Motto et al., 1997). As reported in many earlier studies

(Murphy 1980; Hannah 1997; Motto et al., 1997; Coleman and Larkins 1999; James et al., 2003), kernel protein and starch exhibited a high negative correlation (R2=-0.69).

3.5.2 Heritabilities

Broad-sense heritabilities for the kernel composition traits ranged from 0.08 (for ash) to 0.57 (for oil). The lower heritabilities of the ash and fiber traits (0.08 and 0.18, respectively) suggest that GWAS for these traits with the current NIR calibration may not be useful. Broad-sense heritabilities were moderate for the other kernel composition traits included in this study including density (0.47), oil (0.57), and protein

(0.50). These heritabilities are lower than those in previous studies (Cook et al., 2012), and are most likely the result of different heritability calculation methodology, population size, and/or experimental design.

3.5.3 Candidate genes for kernel composition

Candidate genes were identified near SNPs associated with maize kernel density, oil, and protein (See Appendix I for a complete list of candidates). Examination of SNPs associated with kernel oil content identified significant loci on chromosomes 1, 3, 5, 6, 7,

8, and 9. The most significant association was for a SNP mapped to chromosome 6

(Table 3.5). Examination of genes near this loci identified an acyl-CoA:diacylglycerol acyltransferase-2 (DGAT-2, GRMZM2G169089) gene. DGAT-2 was implicated with variations in kernel content in previous QTL and GWAS studies for kernel oil (Dudley et al., 1977; Goldman et al., 1993; Goldman et al., 1994; Berke et al 1995; Dudley 2007;

Dudley et al., 2007; Cook et al., 2012; Li et al., 2013b).

Further analyses of DGAT-2 was conducted to examine transcription profiles in the B73 referenced genome across different growth stages employing the Maize eFP

Browser (Winter et al., 2007). The candidate gene DGAT-2 was examined for an

86 informative expression pattern (Sekhon et al., 2011). The expression of DGAT-2 was 6.4 fold greater in the kernel embryo than average across the plant for this gene. Expression profiles of DGAT-2 in other kernel portions (endosperm and pericarp) were near average. These results are consistent with DGAT-2 playing an important role in kernel oil biosynthesis since the majority of kernel oil is found in the embryo.

The oil biosynthetic pathway to which DGAT-2 belongs produces a final product of triacylglycerol (TAG). In many plants, this lipid serves as a storage lipid in the seed for germination and provides a reduced form of carbon that can be utilized for germination and early seedling growth (Lung and Weselake 2006). The TAG biosynthesis pathway, also known as the Kennedy Pathway (Kennedy 1961), is largely located in the endoplasmic reticulum, although some scientific debate has existed surrounding the potential additional locations in oil bodies throughout the cell (Appelqvist 1975;

Mukherjee 1986; Stobart et al., 1986; Murphy and Mukherjee 1987; Stymne and Stobart

1987; Garcia et al., 1988; Murphy 1988; Bernerth and Frentzen 1990; Browse and

Somerville 1991; Oo and Chew 1992; Kamisaka and Nakahara 1994; Lacey and Hills

1996;). The Kennedy Pathway contains 4 enzymes; glycerol-3-phosphate acyltransferase

(GPAT), lyso-phosphatidic acid acyltransferase (LPAT), phosphatidate phosphohydrolase

(PAPase), and diacylglycerol acyltransferase (DGAT).

Examination of the transcription profiles of DGAT-2 support its function in oil biosynthesis during seed development, as increases in DGAT-2 activity correlated with oil accumulation (Aymé et al., 2014). DGAT activity has been observed to increase rapidly concurrently with the origination of oil accumulation in the seed, and then

87 decreases to almost no activity once oil accumulation is complete (Tzen et al., 1993;

Weselake et al., 1993; Jako et al., 2001). In addition to enzymatic profiles showing the increases in DGAT activity during seed oil accumulation, analysis of DGAT-2 activity relative to the other enzymes in the TAG pathway has been conducted. Results indicate that of the four enzymes involved, DGAT exhibits the lowest activity (Stobart et al.,

1986; Perry et al., 1999). This suggests that DGAT-2 may in fact be the limiting step in oil accumulation in the seed. Furthering this theory, analysis of TAG intermediates has noted diacyl-glycerol (DAG), the intermediate molecule utilized by DGAT-2 to form TAG, is the intermediate in highest accumulation in the cell (Ichihara and Noda 1980; Ichihara et al., 1988; Perry and Harwood 1993; Settlage et al., 1995). This evidence suggests the importance of DGAT-2 in kernel oil biosynthesis, and allelic variants for DGAT-2 may support higher activity level, thereby utilizing the DAG currently exhibited to be in excess with a resulting increase in overall oil accumulation in the kernel.

For kernel density, highly significant SNPs were identified on chromosomes 1, 3,

and 9. Potential candidate genes were examined for activity levels in the kernel. Several candidates with above-average expression in the kernel were identified (Table 3.6). On chromosome 3, a significant SNP peak was located near a heavy metal transport protein,

GRMZM2G031528 (Table 3.6). Annotations of this gene in Arabidopsis thaliana

(AT2G35730) have shown responsiveness to cadmium and function as a binding and transporting protein of heavy metals. In maize, this gene has shown increased activity through all stages of kernel development in the embryo relative to overall plant expression. The speculative relationship between heavy metal activity (in particular

88 cadmium) and kernel density gains further support when examining other loci significant for this trait. A transketolase (GRMZM2G033208) gene was identified in close proximity to a significant locus on chromosome 9 (Table 3.6). In Arabidopsis thaliana, this transketolase gene (AT3G60750) has been shown to be expressed in the seed, and activated under cadmium and salinity stresses. These results suggest there may be an association between kernel heavy metal content and density. A reduction in expression

(relative to mean expression) was noted for kernel endosperm beginning at the R3 growth stage (Winter et al., 2007).

GWAS analysis of kernel protein content identified significant loci on multiple chromosomes (1, 2, 3, 5, 8, and 9). On chromosome 2, a transmembrane amino acid transporter (GRMZM2G137161) was identified near a significant locus for this trait.

Expression analysis demonstrated high levels of expression for this gene in developing kernel embryos and decreasing activity in leaves during remobilization stages of growth.

The annotated function of the orthologous gene in Arabidopsis thaliana (AT5G15240)

suggests a role in movement of amino acids into the seed during N remobilization.

Previous research identified the role of this amino acid transporter gene in movement of N into and throughout the seed in the form of amino acids (Masclaux‐Daubresse et al., 2008). Allelic variants of this transporter-encoding gene may increase the movement of amino acids into the seed, providing more available N to amino acid biosynthesis pathways within the seed.

Analysis of significant loci on chromosome 9 revealed a gene encoding Amino

Acid Permease 1/Neutral Amino Acid Transporter 2 (AAP1/NAT2). In maize, expression

89 of AAP1/NAT2 has been shown to be highest in the embryo, but average in the rest of the kernel; suggesting a role in amino acid movement into the embryo portion of the seed. In Arabidopsis thaliana, there are six known AAP genes, with different affinities to the transport of different amino acids (Fischer et al., 2002). AAP1 has been shown to have lower efficiencies of movement for the amino acids tryptophan, phenylalanine, threonine, valine, and cyclic amino acids (Fischer et al., 2002). It has also been shown to have a low affinity towards the common forms of amino acids (Asparagine, Glutamine, and Glutamate) by which N is remobilized from other plant tissues to the seed. This suggests that AAP1 proteins may be utilized in the transport of amino acids formed in the seed (pericarp and endosperm) to other locations within the seed (germ), although they must work in conjunction with other transporters that initially supply N to the seed. Results indicating significance in both AAP1 and the transmembrane amino acid transporter indicate that differences in protein content are a result of source strength, supplying N to the seed, as opposed to metabolism within the seed.

3.6 Conclusion

A diverse maize population of over 2,400 inbred lines was examined for kernel composition characteristics in 2012 and 2013. A Perten DA 7250 NIRS analyzer measured ash, density, fiber, oil, protein, and starch on 15-kernel samples. Genotypic information of over 680,000 SNP markers provided resolution of the mapping results and allowed for identification of candidate genes in relation to the kernel density, oil, and protein traits.

Examination of kernel oil identified a significant relationship with DGAT-2. DGAT-

2 serves an important function in the kernel oil biosynthesis pathway. Examination of prior literature and transcription expression of this gene provides further support of its importance in oil biosynthesis (Dudley et al., 1977; Goldman et al., 1993; Goldman et al.,

1994; Berke 1995; Dudley 2007; Dudley et al., 2007; Winter et al., 2007; Cook et al.,

2012; Li et al., 2013b;). GWAS analyses of kernel density identified a heavy metal transport gene (GRMZM2G031528) and a transketolase (GRMZM2G033208) gene. Both of these genes have been found to be activated with the presence of cadmium, and their significance in GWAS analysis allows us to propose a relationship between cadmium and kernel density. Examination of kernel protein identified two candidate genes related to amino acid transport, a transmembrane amino acid transporter

(GRMZM2G137161) and an amino acid permease (GRMZM2G145989). Expression profile analysis suggests that the transmembrane amino acid transporter,

GRMZM2G137161, is utilized in movement of remobilized N to the grain, and the amino

acid permease is responsible for movement of N in the form of certain amino acids into the embryo.

This study identified five candidate genes of interest associated with kernel oil

(1), density (2), and protein (2). Further research is needed to confirm these relationships. Future research may identify allelic variants of these candidates for functional genomic studies to confirm an effect on the examined phenotype. With the large population of the Ames Diversity Panel at our disposal, the potential exists for identification of these allelic variants and utilization in future confirmation studies.

Confirmation of the effects of these genes and identification of lines with unique alleles will benefit a breeding program aimed at improved kernel characteristics. Breeders would then have access to this germplasm and SNP markers, allowing for more efficient selection of optimal kernel profiles.

CHAPTER 4. GENETIC MAPPING OF KERNEL COMPOSITION IN A DIVERSE POPULATION OF SORGHUM BICOLOR

4.1 Abstract

Sorghum grain is utilized globally for food, feed, fiber, and fuel. In parts of the developing world, particularly in Africa, sorghum is a large portion of the daily diet of the local population. In the United States, sorghum grain is a livestock feed in the western Midwest and Great Plains regions. The composition of the grain has a large effect on the nutritional and feed values of the crop. Increasing the understanding of the genetic controls involved in kernel development will assist breeders in selecting the best lines for the desired end use. In this study, we utilized a diverse panel of sorghum lines from the Sorghum Conversion Program in 3 locations in 2013 to conduct a GWAS study to identify genetic controls of kernel composition. A sample of whole kernels from each genotype was analyzed using Near Infrared Reflectance Spectroscopy (NIRS) for

92 grain composition analysis. Phosphoenolpyruvate Carboxylase (PEPC) and K+

Transporter genes were located near significant SNPs for the sorghum grain feeding quality traits. A glutamate synthase gene was identified near a significant SNP for kernel protein. Results from this study will allow further analysis for potential use in breeding programs for improved kernel characteristics and nutritional value.

4.2 Introduction

Sorghum bicolor (L.) Moench is grown worldwide for forage and grain.

Originating in Africa, sorghum has greater tolerance to both heat and drought stresses than other cereal crops including maize (Watson et al., 1970; Murty and Kumar 1995;

Maunder 2005). This adaptation to high stress environments has resulted in large production acreages in the high plains of the U.S. and throughout Africa. With the increased installation of irrigation systems in the western plains, sorghum acreage has decreased as maize production has increased in these regions. More recently, water shortages in these regions, moratoriums on new wells, and a decline in the Ogallala

Aquifer water level have prompted growers to reconsider their farming strategies. It is possible that maize production may no longer be economically feasible or reliable for these regions in the long term, leading to increased production and utilization of sorghum once again.

Sorghum grain is utilized for human food and animal feed, dependent upon the

region of the world in which it is grown (Obizoba 1988; Brannan et al., 2001). While the majority of sorghum grain is used for feed worldwide, it also serves as an important food source (Maunder 2002). In developing countries, sorghum grain constitutes a major portion of the caloric intake of the population, while in the U.S. sorghum is an important and gluten-free wheat substitute for those with celiac disease (Yousif and El

Tinay 2001; Fenster 2003). The efficiency of feeding and nutritional values of sorghum are largely dependent upon the composition of the kernel.

When fed to livestock, sorghum grain is usually analyzed for feeding quality to control the nutritional value of the feed for optimal livestock growth. These feeding traits include Acid Detergent Fiber (ADF), Net Energy of Gain (NEG), Net Energy of

Lactation (NEL), Net Energy of Maintenance (NEM), and Total Digestible Nutrients (TDN).

Combined, these measurements give a value of the fibrous portion of the grain (ADF), energy value (NEG, NEL, and NEM), and the overall nutritional value of the crop (TDN).

Protein composition of the grain is also of importance for both animal and human consumption. NIRS can be used to measure these grain quality parameters. NIRS offers the advantage of measuring these traits on small amounts of whole grain allowing for non-destructive line selection and advancement.

GWAS was used in this study to characterize a panel of diverse Sorghum bicolor lines to identify the genetic controls of these kernel quality traits. More than 100,000

Single Nucleotide Polymorphism (SNP) markers were evaluated, allowing for the identification of candidate genes across three chromosomes (2, 3, and 4) for feeding

quality traits; a glutamate synthase candidate gene was also identified on Chromosome

9 for kernel protein content. The role of glutamate synthase in kernel protein biosynthesis has been well researched, and results from this study suggest a relationship between glutamate synthase and kernel protein.

4.3 Materials and Methods

4.3.1 Genetic Material

Sorghum bicolor lines selected for use in this study were a collection of 840 diverse lines from the Sorghum Conversion Program; converted from photoperiod sensitive to photoperiod insensitive types (Stephens et al., 1967). This material includes tropical sorghums and representative lines from caudatum, kafir, guinea, and durra families. These lines were acquired by the P.J. Brown Lab (University of Illinois,

Champaign/Urbana, IL) from the United States Department of Agriculture - Agriculture

Research Service - Plant Genetic Resources Conservation Unit (USDA-ARS-PGRCU) in

Griffin, GA. Also included in this panel were BTx623, the reference genome, and Macia as checks.

4.3.2 Experimental Design

The association panel was grown in three locations in 2013; Purdue University’s

Agronomy Center for Research and Education (ACRE; 4540 US 52 West, West Lafayette,

IN) and through collaboration with P.J. Brown at the University of Illinois’s Northwestern

Illinois Agricultural Research and Demonstration Center (NIARDC; 321 210th Ave,

Monmouth, IL) and the Energy Biosciences Institute (EBI) Energy farm (4110 S Race St,

Urbana, IL). Lines were evaluated in an augmented design at each location, with 20 blocks of 15 lines each. One each of BTx623 and Macia were assigned to each block randomly as checks. Plots were planted at a population of 242,060 plants per hectare.

At the ACRE location, lines were grown in 3.81 m long plots with 0.762 m alleys in a field of Chalmers silty-clay loam designed as 45 rows and 20 ranges for a total of 900 plots.

The 48 rows at NIARDC were grown 20 ranges deep in 3.65 m plots with 1.22 m alleys into Muscatune and Osco silt loams. At the EBI Energy farm, 3.65 m plots with 1.22 m alleys were placed into the same 48 rows by 20 range design as the NIARDC location.

The Drummer silty clay loam soil type at the EBI Energy Farm promoted strong growth, but the location of the plots in the field near a drainage way and abnormally high rainfall in May 2013 subjected some plots at this location to flooding stress.

4.3.3 Phenotypic Evaluation

Three panicles per plot were self-pollinated in experiments at each location. These heads were mechanically threshed and bulked into a single sample per plot. Near Infrared Reflectance Spectroscopy (NIRS) was conducted on whole kernels with a Perten DA 7250 NIR analyzer (Perten Instruments, Hagersten, Sweden). Seed samples of 2.46 milliliter (ml) were analyzed using a concave mirrored breeder cup. As this machine conducts reflectance analysis instead of transmittance analysis, the position of the kernels in the mirror cup may have an effect on measured values. To

account for variability in the sampling and analysis methods used, each sample was run in duplicate and samples were repositioned three times in the breeder cup, for a total of six measurements that were averaged into a final plot mean by the NIRS internal software. Basic statistics for the moisture values, to calculate the dry basis (db) values, are shown in Table 3.1.

Table 4-1 Statistics for moisture values from NIR used for dry basis conversions Mean Std Dev Min Max 9.51 0.91 7.67 12.90

The DA 7250 NIR reports final values based on internal calibrations. An existing calibration based on commercial sorghum samples was augmented with the addition of samples representing 100 diverse sorghum lines to increase the range of the calibration to measure diverse lines found in the association panel (See Appendix J for calibration correlation values). Calibrations with a high correlation coefficient were developed for the following traits: Protein (R2=93.06%), Acid Detergent Fiber (ADF) (R2=66.56%), Total

2 2 Digestible Nutrients (TDN) (R =67.58%), Net Energy Main (NEM) (R =67.70%), Net Energy

2 2 Lactation (NEL) (R =65.78%), and Net Energy Gain (NEG) (R =67.98%). Oil and Starch, two other major kernel proximates, did not have a high enough correlation between the NIR measured values and the wet lab calibration (R2=0.29 for both traits) to add useful information to this study.

4.3.4 Genotypic Information

Genotyping By Sequencing (GBS) was conducted by the P.J. Brown Lab at the

University of Illinois using an Illumina HiSeq2000 at the W.M. Keck Center (Thurber et al., 2013). The Single Nucleotide Polymorphism (SNP) dataset used for GWAS analysis in this study were called from Illumina output through the GBS pipeline in TASSEL

(Bradbury et al., 2007).

4.3.5 Statistical Analysis

Plot means for kernel proximates were first analyzed for outlying values. Values which fell out of the range of the calibration were discarded. The data was placed into

SAS statistical software (SAS Version 9.2 for Windows, SAS Institute Inc., Cary, NC, USA)

98 to complete this examination. Remaining values were then analyzed using PROC GLM to test for significant genotypic variation between the lines. The model used to analyze these variations in PROC GLM was:

Kernel Trait = Genotype + Location + Block(Location)

Where location and block(location) were treated as random variables.

Broad-sense heritabilities (H) were calculated in PROC GLM through the identification of the variance components via ANOVA analysis. Using the error variance

(VE) and genotypic variance (VG), heritabilities were calculated with the following calculation:

푉 H= 퐺 푉퐺+푉퐸

Plot mean values were then corrected for spatial variability within and between the locations grown. Best Linear Unbiased Predictors (BLUPs) were calculated on the genotypes using all three locations (See Appendix K for SAS Code). The PROC MIXED function was used, for which the location, blocks nested within location, and genotypes

98 were treated as random variables as described by Wolfinger et al., (1997) to retrieve information across blocks and genotypes (Wolfinger et al., 1997). Estimates were combined in SAS to calculate a single BLUP value for each line and trait combination using the model below:

Line BLUP Value = Grand Mean + Line Estimate + ACRE Block Estimate +

NIARDC Block Estimate + EBI Block Estimate

Following the calculation of BLUP values, PROC TRANS was utilized to determine the necessity of BLUP transformation, using normality as the main criteria in this determination. Traits were transformed as indicated necessary.

GWAS was conducted using the phenotypic BLUPs and the genotypic data.

Utilizing a mixed linear model (Yu et al., 2005), GWAS was conducted using the GAPIT R package (Lipka et al., 2012) (Appendix L for R code). SNPs that did not meet the 0.05 minor allele threshold were removed from the data set. For GWAS computation, a HP

Compaq 8200 Desktop Convertible Minitower was upgraded to 32 GB RAM (Hewlett-

Packard, Palo Alto, California). The RStudio R browser was used in all GWAS analyses to increase flexibility and allow for better visualization of the R program (RStudio 2012).

Selection of significant SNPs relied on a False Discovery Rate (FDR)-controlled p-value threshold of 0.05 (Benjamini and Hochberg 1995).

4.3.6 Candidate Gene Analysis

Significant SNPs were selected from the GWAS runs to examine potential

candidate genes. Using a FDR-corrected p-value of 0.05, a 200 kb window was used to identify candidate genes near the SNPs identified as significant. This larger window for candidate gene analysis was utilized because of the larger LD blocks in this self- pollinating specie. The Phytozome Comparison Platform allowed comparison of SNPs against the sorghum reference genome and was used in this analysis to identify candidate genes (Goodstein et al., 2012). The candidate genes were recorded for the significant SNPs and evaluated for confirmed annotations in other crop species. Genes identified in sorghum were then analyzed for orthologous genes across Oryza sativa,

100

Arabidopsis thaliana, and Zea mays utilizing the Rice Genome Annotation Project funded by the NSF grant DBI-0321538/DBI-0834043 (rice.plantbiology.msu.edu).

4.4 Results

4.4.1 Genetic Variation and Trait Correlations

Genetic variation was examined via PROC GLM in SAS to ensure satisfactory variation for all traits before conducting any genetic studies. Significant genetic variation

(p-value = 0.05) was observed for all traits examined (ADF, NEG, NEL, NEM, Protein, TDN)

(See Appendix M for ANOVA outputs). Significant variation was also observed for locations and for blocks nested within locations for all traits with a significance of p<0.001.

Trait correlations were calculated between the traits using PROC CORR in SAS.

Table 4.2 shows the output from the correlation analysis, including the number of genotypes, mean, standard deviation (std dev), minimum, and maximum values for each

100

trait. There were between 2,483 and 2,549 data points for each trait. BLUPs were calculated based on all of the locations in the study, so a missing genotype in one location resulted in a missing BLUP value for that genotype. Lines that had proximate values outside of the range in the calibration of the NIRS were also removed, as confidence is lost in the accuracy of those values outside the calibrated range.

101

Table 4-2 Basic statistics and trait correlations for sorghum kernel traits Traits Protein ADF(%) NEG(%) NEL(%) NEM(%) TDN(%) (%) N 2517 2485 2526 2541 2483 2549 Mean 6.09 60.33 88.91 91.86 83.48 12.89 Std Dev 1.22 1.94 0.32 2.55 1.96 1.62

Statistics Min 3.20 54.02 88.03 84.30 77.72 7.80 Max 9.52 66.85 89.68 97.94 87.34 17.18

ADF NEG NEL NEM TDN Protein ADF - -0.55 *** -0.99*** -0.95 *** -0.96 *** 0.10 ***

NEG -0.55 *** - 0.57 *** 0.58 *** 0.41 *** -0.32 *** NEL -0.99 *** 0.57 *** - 0.97 *** 0.97 *** -0.12 *** Traits NEM -0.95 *** 0.58 *** 0.97 *** - 0.95 *** -0.23 *** TDN -0.96 *** 0.41 *** 0.97 *** 0.95 *** - -0.11 *** Protein 0.10 *** -0.32 *** -0.12 *** -0.23 *** -0.11 *** -

* = 0.05 Significance

** = 0.01 Significance

*** = 0.001 Significance

ADF = Acid Detergent Fiber; NEG = Net Energy Gain; NEL = Net Energy Lactation; NEM = Net Energy Maintenance; TDN = Total Digestible Nutrients

Significant correlations were observed between all pairwise comparisons of 101

traits, where kernel protein had the weakest correlations with feed quality traits and only exhibited a positive correlation with the ADF trait. Among the energy feeding traits

(NEG, NEL, and NEM) correlations were high and significant at the p< 0.001 level. In fact, all correlations were significant at the 0.001 level except; ADF and Protein (p-value <

0.05) and NEG and Protein (p-value < 0.01).

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4.4.2 Heritabilities

SAS PROC GLM was used to calculate variance components and broad sense heritabilities. For the traits analyzed, the lowest heritability was 0.58 for protein, where the highest was 0.73 for NEM (Table 4.3).

Table 4-3 Heritabilities of sorghum kernel traits measured in multi-location trials

Trait H Protein 0.58 ADF 0.67 TDN 0.70

NEL 0.69 NEG 0.63 NEM 0.73

4.4.3 Significant SNPs

GWAS was conducted on all six traits independently and the results summarized

(Table 4.4). Significant SNPs were identified for all traits except NEG. Traits ranged from

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one significant SNP (for TDN) to eight significant SNPs (for NEM). Following completion of

GWAS and identification of significant SNPs using the FDR-controlling p-value for multiple testing, candidate genes were identified within a 200 Kb window of significant

SNPs. With the exception of NEG, a range of 29-146 candidates were identified through the Phytozome genome analysis tool (Goodstein et al., 2012). NEM returned the greatest number of candidates (146) and following in decreasing order were NEL (85),

ADF (43), Protein (30), and TDN (29). Examination of gene annotations for these

103 candidates was conducted in other plant species (mainly Arabidopsis thaliana and Oryza sativa) (See Appendix N for complete significant SNP and candidate lists). In decreasing order of annotated candidates are: NEM (99), NEL (67), ADF (36), TDN (26), and Protein

(22) (Table 4.4).

Table 4-4 Summary GWAS results for sorghum kernel traits TRAIT

ADF NEG NEL NEM Protein TDN

Significant SNPs 2 0 5 8 2 1 Associated Genes 43 0 85 146 30 29 Candidate Genes 36 0 67 99 22 26 w/Annotations

The same significant SNP Chr4:59095899 was identified for the feeding traits

ADF, NEL, NEM, and TDN (Table 4.5). With the exception of TDN, all of the feeding traits also shared the SNP Chr2:57617151. In addition to these significant SNPs, NEL had significant SNPs on chromosome 3 (63184638, 63184681). SNPs for NEM were also observed on chromosome 2 (57649504, 570604889, 57649529, 57649520, 57582078,

103 and 57649524).

A significant locus was identified on chromosome 9 for kernel protein composition and localized near the SNP pstl_9_56910830 (Table 4.5). Examining a 200 kb window around this SNP revealed multiple genes with annotated functions. There were 27 total genes identified within this 200 kb window, of which 20 have annotated functions (Appendix N-4).

Multiple candidate genes were found within the 200 Kb window surrounding identified SNPs. These candidate genes have annotated functions in Sorghum bicolor,

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Arabidopsis thaliana, or Oryza sativa. Annotated candidates for each trait are located in

Appendix N-4.

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105

Table 4-5 Table of significant SNPs identified GWAS analysis with trait p-values and allelic effects

value value value value value value value

------

ADF NE

TDN

Effect

Allelic Allelic Allelic Allelic Allelic Allelic Allelic

Protein

q q q q q q

Protein

Effect NE

Effect ADF

Effect NE SNP Effect TDN pstI_2_57582078 NS ------NS ----- NS ------0.007 0.005 NS ---- NS ----- pstI_2_57604889 NS ------NS ----- NS ------0.004 0.005 NS ---- NS ----- pstI_2_57617151 0.02 -0.22 NS ----- 0.02 0.05 0.001 0.006 NS ---- NS ----- pstI_2_57649504 NS ------NS ----- NS ------0.004 0.005 NS ---- NS ----- pstI_2_57649520 NS ------NS ----- NS ------0.006 0.005 NS ---- NS ----- pstI_2_57649524 NS ------NS ----- NS ------0.007 0.005 NS ---- NS ----- pstI_2_57649529 NS ------NS ----- NS ------0.004 0.005 NS ---- NS ----- pstI_3_63184638 NS ------NS ----- 0.02 -0.1 NS ------NS ---- NS ----- pstI_3_63184681 NS ------NS ----- 0.02 -0.1 NS ------NS ---- NS ----- pstI_4_59095899 0.04 -0.24 NS ----- 0.02 0.06 0.015 0.006 NS ---- 0.05 0.39 pstI_9_56910830 NS ------NS ----- NS ------NS ------0.03 0.4 NS ----- * FDR Corrected p-value (Benjamini and Hochberg 1995)

105

106

Manhattan plots from the GWAS analysis indicate a similar significance threshold near –log10(p) = 5.4. The peak on chromosome 2, as evident in the ADF, NEL, and NEM traits is quite pronounced and consistent across traits (Figures 4.1-4.3). The single peak on chromosome 9 for kernel protein content exhibited a –log10(p) of 6.2 (Figure 4.5).

Eight significant SNPs were identified in GWAS analysis of kernel feeding quality traits (ADF, NEG, NEL, NEM, and TDN). Examination of candidate genes within a 200 Kb window surrounding significant SNPs identified 333 genes. These genes encompass many plant functions and general cell maintenance, but two of these genes are of particular interest; phosphoenolpyruvate carboxylase (PEPC) and a K+ potassium transporter (Table 4.6). Both candidates have been shown to exhibit effects on specific kernel characteristics.

Table 4-6 Candidate Genes of Interest for Kernel Feeding Quality

SNPs w/in 200 q- Effect

Gene Annotation Chr maf 106 Kb Value* Direction Phosphoenolpyruvate pstI_3_63184638 3 0.25 0.022 - Sb03g035090.1 carboxylase pstI_3_63184681 3 0.25 0.022 - K+ potassium + Sb04g029030.1 pstI_4_59095899 4 0.34 0.047 transporter

* FDR Corrected p-value (Benjamini and Hochberg 1995)

Kernel protein content is an important component of grain quality for both food and feed use. The nitrogen utilized in kernel amino acid biosynthesis may come from newly accumulated N, or may be remobilized from senescing plant tissues, including the

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leaves. Although a variety of pathways may be utilized for N remobilization, the

glutamine synthetase/glutamate synthase (GS/GOGAT) pathway plays a key role in this

process. Genetic analyses of the sorghum association panel identified a NADH-

Glutamate Synthase gene (Sb09g027910) in close proximity to the significant SNP

located on chromosome 9 (Table 4.7).

Table 4-7 Candidate Gene of Interest for Kernel Protein Composition Effect Gene Annotation SNPs w/in 200 Kb Chr maf q-Value* Direction NADH-Glutamate Sb09g027910 pstI_9_56910830 9 0.08 0.034 + Synthase 2 * FDR Corrected p-value (Benjamini and Hochberg 1995)

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Figure 4-1 Manhattan plot of SNPs associated with sorghum kernel acid detergent fiber

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Figure 4-2 Manhattan plot of SNPs associated with sorghum kernel net energy of lactation

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Figure 4-3 Manhattan plot of SNPs associated with sorghum kernel net energy of maintenance

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Figure 4-4 Manhattan plot of SNPs associated with sorghum kernel total digestible nutrients

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Figure 4-5 Manhattan plot of SNPs associated with sorghum kernel protein

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4.5 Discussion

4.5.1 Genetic Variance and Trait Correlations

The sorghum kernel composition and feed value traits examined in this study exhibited significant genetic variation. Trait correlations were examined, with significant correlations found between all of the traits (p-value < 0.01 minimum) (Table 4.2).

Between feeding traits (ADF, NEG, NEL, NEM, and TDN), all pairwise correlations were

2 high and significant (R > 0.70). The NEG, NEL, and NEM traits were significantly correlated, a rational result as these traits are energy measurements of the feeding value for specific animal functions (gain, maintenance + lactation, maintenance). NEG is a measure of the feedstuff value for animal weight gain above maintenance and NEM is the value of a feed source for animal metabolic maintenance, making it reasonable that

2 a positive and strong correlation would be exhibited between the two at R = 0.81. NEL is the summation of both the energy required for animal maintenance and the additional energy required for lactation. This trait also demonstrated a significant and

110 2

positive correlation to NEM (R = 0.96). ADF, the fibrous portion of the grain that is negatively associated with the feeding value of the grain, was negatively correlated with

2 2 2 2 all of the other feeding traits (NEG R = -0.80, NEL R = -0.98, NEM R = -0.95, TDN R = -

0.96). Although selections for feeding quality in grain seek to improve NEG, NEL, and

NEM, a simultaneous reduction in kernel ADF may improve grain quality even further.

TDN is the portion of the kernel that provides digestible nutrients to livestock. An increase in nutrient amounts made available through feeding would increase the value of the grain as a feed source for livestock and reduce the need for feed supplements.

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Similar positive correlations were observed between TDN and energy grain

2 2 2 measurements (NEG R = 0.70 NEL R = 0.97, and NEM R = 0.95). These correlations suggest that in our analysis, these five feeding values were very similar, and therefore were examined together.

4.5.2 Heritabilities

The heritabilities for the sorghum kernel composition and feed quality traits ranged from 0.58-0.73, with the lowest value for kernel protein and highest value for

NEM. Previously reported heritabilities for kernel composition traits in a recombinant inbred line (RIL) population of Sorghum bicolor indicated a narrow-sense heritability of

0.68 for kernel protein, slightly higher than our broad-sense estimate of 0.58 (Rami et al., 1998). This may be explained by differences in protein measurement methods, but the most probable cause of the difference is the structure of the population. A RIL population is developed from a limited number of individuals and may have artificially inflated the estimates of heritability.

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4.5.3 Feeding Quality Candidate Genes

PEPC has been found in most plant tissues, including the seed, and more specifically in the embryo (González et al., 1998). There are two main functions of PEPC in plants, and both have an effect on kernel composition and grain feeding quality. In C4 photosynthesis, PEPC serves an important role in converting PEP to oxaloacetate (OAA) for utilization in the TCA cycle, protecting tissues from the effects of photorespiration and maintaining productivity under hot, dry conditions. PEPC plays a vital role in yield and grain quality for C4 plants through maintenance of photosynthesis and resultant

112 carbon sequestration and starch accumulation under stressful conditions. As delayed senescence qualities in both corn and sorghum increase the starch accumulation in the plant, higher activities of the PEPC enzyme may ensure that the conversion of PEP to

OAA is not the limiting step in the starch accumulation pathway. Alternatively, additional accumulation of starch in the leaves may negatively affect photosynthesis during grain fill as the sink strength may be poor.

In addition to its photosynthetic functions, PEPC serves a role in the anaplerotic pathway, stabilizing citric acid cycle intermediates in the mitochondrion (Huppe and

Turpin 1994; Lebouteiller et al., 2007). In this role, PEPC activity has been shown to fluctuate with the protein and oil biosynthesis activities in the seed (Sangwan et al.,

1992; Singal et al., 1995; King et al., 1998; Blonde and Plaxton 2003; Sebei et al., 2006;

Lebouteiller et al., 2007; Murmu and Plaxton 2007). PEPC serves as the mediator of the partitioning of photosynthate in the grain, allocating carbon to either the leucoplast for fatty acid biosynthesis or to the mitochondria for amino acid biosynthesis as required

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(Brendan et al., 2011). In protein biosynthesis, PEPC is crucial in the assimilation of N as it provides the OAA necessary in amino acid biosynthesis (Rolletschek et al., 2004;

Weber et al., 2005; Radchuk et al., 2007). Although N is commonly transported to the cell as amino acids such as glutamine and alanine, additional carbon is required as an energy source for these amino acids to be deaminated and converted to other amino acids or for integration into the TCA cycle within the seed (Brendan et al., 2011). In other cereal crops, PEPC activity in the seed coincide with the peak biosynthetic production of kernel oil and protein, and are largely controlled by the availability of

113 photosynthate (Sangwan et al., 1992; Singal et al., 1995; King et al., 1998; Blonde and

Plaxton 2003; Rolletschek et al., 2004; Weber et al., 2005; Sebei et al., 2006;

Lebouteiller et al., 2007; Murmu and Plaxton 2007; Radchuk et al., 2007).

PEPC activity in other parts of the plant may also have an effect on kernel protein composition. During leaf senescence at physiological maturity, N is remobilized from the leaf photosynthetic machinery to the grain. During this process, enzymes involved with N and amino acid transport, catabolism, and synthesis including PEPC are utilized to facilitate this movement of N (Taylor et al., 2010). Transgenic alteration of model species such as Arabidopsis thaliana has also provided some insight into the role

PEPC may play in kernel composition. Analysis of Arabidopsis transformed with a construct of a Sorghum PEPC cDNA suggests that the level and subsequent functioning of PEPC in the anaplerotic leaf pathway has a significant impact on seed protein levels

(Lebouteiller et al., 2007). Seed protein was increased by 30% when expression of PEPC was increased (Lebouteiller et al., 2007).

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Potassium (K+) transporters serve a number of functions within the plant and many of these have a significant effect on kernel composition and feeding quality.

Multiple studies have shown that K+ plays a critical role for the transport of NO-3 throughout the plant (Minotti et al., 1968; Blevins et al., 1978a; Blevins et al., 1978b;

Pan et al., 1986). Increasing the efficiency of nitrate transport though the plant and into the seed may subsequently increase the overall protein content of the grain. Specific evidence showing the increase of amino acid transport into the seed and its relationship to K+ coupling has been shown in castor bean (Mengel 1980). Although not directly

114 involved in starch, oil, or protein biosynthesis, K+ may influence the pathways that ensure the requisite source materials (NO3-) are transported to the biosynthesis sites of the kernel.

An enzymatic regulation function of K+ has also been shown. Asparaginase, a key enzyme in N metabolism, has been shown to be activated by K+ in maize, a closely related C4 cereal crop, thus warranting further examination of the role in sorghum

(Sodek et al., 1980). An increase in the expression of K+ transporters is likely to increase the concentration of K+ in the seed. Since asparaginase is activated by K+, higher K+ concentrations may impact asparaginase activity, removing it as a limiting step in kernel

N metabolism.

4.5.4 Protein Kernel Composition Candidate Genes

In plants, two forms of glutamate synthase have been identified, differing in the form of electron donor utilized. The ferredoxin-dependent (fd) is one form of the enzyme, and the nicotinamide adenine dinucleotide-dependent (NADH) is the other

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(Forde and Lea 2007). The NADH accepting glutamate synthase enzyme is capable of utilizing NADPH as an electron donor. While the fd-glutamate synthase form is most commonly found in photosynthetic tissues, the NADH-Glutamate synthase enzyme is largely found in non-photosynthetic tissues (Bowsher et al., 2007). An NADH-glutamate synthase gene was identified as a candidate gene in our GWAS analysis for kernel protein composition. Glutamate synthase is responsible for the synthesis of glutamate utilizing both glutamine and 2-oxoglutarate. Through this process, glutamine is reduced

115 and with 2-oxoglutarate subsequently forms two molecules of glutamate (Ireland and

Lea 1999).

Glutamate and glutamine serve as intermediary stores of N. Subsequent amino acid synthesis is more directly achieved using glutamate as a substrate for intermediary storage (Alburquerque et al., 2006; Amarante et al., 2006; Forde and Lea 2007).

Glutamate is a major storage amino acid of N in vegetative tissues and a product of vegetative N uptake in the leaves (Kamachi et al., 1991). Despite its advantages as a N storage molecule, transport of glutamate through the plant is a complex process. N remobilized from the vegetative tissues of the leaf during senescence relies on other amino acids such as glutamine, asparagine, or arginine (Lea et al., 2007). During leaf remobilization, glutamate in the leaf tissue is converted to glutamine via Glutamine

Synthetase to allow transportation to sinks within the plant, including the grain (Lea et al., 1990; Sechley et al., 1992; Ireland and Lea 1999; Hörtensteiner and Feller 2002; Lea et al., 2007). Glutamine and asparagine have been shown to be the largest pool of N

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entering the kernel (Pate et al., 1974; Atkins et al., 1975; Lewis 1975). Once glutamine reaches the grain, it must be converted back to glutamate so it has been theorized that

NADH-Glutamate Synthase in the grain serves this function (Hayakawa et al., 1994).

Studies examining the direct effect of NADH- Glutamate Synthase in the sorghum kernel on protein composition are not found in the literature though studies have been conducted to examine the effect of glutamate synthase in maize kernels (Sodek and da

Silva 1977). Sodek and daSilva (1977) identified changes in activity of kernel glutamate synthase, and noted that peak kernel glutamate synthase activity corresponded to peak

116 kernel N accumulation. During peak N remobilization, increased activity of kernel glutamate synthase is indicative of its role as an intermediary step before utilization in other amino acids in the grain. Identification of the orthologous gene in sorghum suggests that NADH-glutamate synthase may play a role in utilization and conversion of

N into amino acids during grain fill (Table 4.8). Identification of this gene in this GWAS analysis supports future research to examine the effect of alternative alleles to achieve a desired kernel protein profile. Increased NADH-Glutamate Synthase activity may affect more efficient utilization of N entering the kernel.

Table 4-8 Orthologous Genes to NADH-Glutamate Synthase in other plant species

Species Orthologous genes Putative Role Sorghum Sb09g027910 NADH-glutamate synthase 2 Ferredoxin-dependent glutamate synthase, Sorghum Sb02g041740 chloroplastic Sorghum Sb03g031310 NADH dependent Glutamate Synthase Rice LOC_Os01g48960 glutamate synthase, chloroplast precursor Rice LOC_Os05g48200 glutamate synthase, chloroplast precursor Rice LOC_Os07g46460 precursor Arabidopsis AT2G41220 glutamate synthase 2

116 Arabidopsis AT5G04140 glutamate synthase 1 Arabidopsis AT5G53460 NADH-dependent glutamate synthase 1 Ferredoxin-dependent glutamate synthase, Maize GRMZM2G036609 chloroplastic Maize GRMZM2G077054 Glutamate synthase 1 [NADH], chloroplastic Maize GRMZM2G085078 Glutamate synthase 1 [NADH], chloroplastic Maize GRMZM2G375064 Glutamate synthase 2 [NADH], chloroplastic

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4.6 Conclusion

An association mapping study was conducted for kernel composition traits in a panel of 840 diverse sorghum lines from the sorghum conversion program. The GWAS analyses identified 8 significant SNPs on chromosomes 2, 3, and 4 for kernel feeding quality. Among the genes identified within a 200 kb interval of significant SNPs were a

PEPC and K+ Transporter. PEPC has been shown to control the allocation of carbon arriving to the kernel, thereby controlling the photosynthate availability for kernel amino acid biosynthesis. K+ is a preferred cation for attachment to NO3- during transport and may activate other key enzymes in allocation pathways, such that the K+ transporter identified in this study may exhibit an effect on the K+ availability for such roles.

NIRS analysis for kernel protein composition identified a significant SNP on chromosome 9 in close proximity to an NADH-glutamate synthase gene. Within the kernel, this enzyme regulates metabolism of N entering the kernel as glutamine.

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Glutamine entering the kernel is converted to glutamate, and this glutamate is subsequently converted to amino acids such as proline, alanine, and lysine for N storage within the kernel. As noted in Table 4-7, the NADH Glutamate Synthase 2 identified in this study of sorghum kernel protein is orthologous to NADH Glutamate Synthase 1, the gene identified in our analysis of leaf N remobilization. Higher glutamate synthase activity within the kernel ensures that conversion of glutamine to glutamate is not the limiting factor in kernel N metabolism and amino acid biosynthesis.

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NIRS on whole kernels was utilized in this study with success to determine kernel composition. The speed and affordability of this technology offer the opportunity for these systems to be utilized on a large scale in a breeding program, affording the breeder one more rather simple and potentially instructive phenotypic measurement in their breeding selection process.

Future research should seek to identify lines with allelic variants for these genes as their unique enzymatic activity may be beneficial in a number of breeding programs.

Analyses of mutant lines disrupted at these genes may also shed some insight into the physiological effect of allelic variations on final kernel composition. Utilizing genetic markers for these identified alleles presents breeders with an additional tool for utilization in improving sorghum kernel composition.

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CHAPTER 5. PROSPECTUS

5.1 Maize Leaf Nitrogen Remobilization

Genome Wide Association Mapping (GWAS) of ratios measuring the timing and location of leaf N remobilization identified multiple genes for ratios related to leaf N remobilization timing. Ratios were examined in two groups, VTR2 traits (VTR2, VTR2H, and VTR2L) and VTR4 traits (VTR4, VTR4H, and VTR4L). Analysis of VTR2 ratios identified genes related to both the signaling and regulation of senescence; including auxin family genes and SAG 24. Identification of multiple genes related to auxin suggests a signaling role in early stages of senescence; further research could validate this hypothesized function.

Analysis of VTR4 traits identified genes with roles in signaling and regulation of senescence, as well as N remobilization processes. Genes in the auxin, mapk, and wrky families were all identified with potential roles in senescence signaling at the R4 stage of growth. Further research is warranted to confirm the function of identified candidates 119

which have not previously been noted with a direct annotation to senescence signaling within these gene families. VTR4 analysis also identified genes related to the remobilization of N from vegetative tissues of the plant; NADH-Glutamate Synthase 1

(NADH-GOGAT) and a Glutamine Synthetase 1 (GS1). Found in the cytosol, GS1 converts

120 stored glutamate in the leaves to glutamine for transport to the sinks in the reproductive tissues. Once the glutamine reaches the sink tissues, NADH-GOGAT converts glutamine to glutamate, from which it can be metabolized in the formation of other amino acids. These two genes are of interest in further research, as allelic variation identified in this population may be allowed to be utilized in the selection of lines with improved NUE characteristics. Identification of a gene located in the vegetative source (GS1), and the reproductive sink (NADH-GOGAT) confirms the suggestion that remobilization of vegetative N is controlled by both the source and sink.

5.2 Maize Kernel Composition

Maize kernel composition was examined via GWAS for kernel density, oil, and protein. Analysis of kernel density identified a heavy metal transporter and a tranketolase. Annotated function of these genes has suggested a link between kernel density and the presence of cadmium, as it has been observed in other species that the

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presence of cadmium may activate both of these genes. Further analysis is required to elucidate the relationship between kernel density and cadmium.

Kernel protein analysis also identified a transmembrane amino acid transporter, with a suggested function in movement of N into the reproductive sink, as well as an amino acid permease 1 moving N through the grain. In the population examined, this suggests that transportation of N is an important determinant of variation in kernel protein composition. GWAS for maize kernel oil also identified DGAT-2, a rate limiting step on the Kennedy Pathway. Previously identified in other genetic studies of kernel oil

121 composition, it has been largely suggested that selection for this rate limiting gene may be useful in efforts to increase kernel oil content.

5.3 Sorghum Kernel Composition

Sorghum kernel composition for protein and feeding quality was analyzed via

GWAS. Feeding quality analysis identified PEPC and a K+ transporter. While serving a role in C4 photosynthesis, it has also been suggested that PEPC may also serve a function in the allocation of C to amino acid and lipid biosynthesis pathways. Additional research is necessary to examine this further, but if this hypothesis is proven, this secondary role of PEPC may have a large role in kernel composition. Allelic variants for

PEPC may increase the C allocated for lipid and amino acid biosynthesis.

Sorghum kernel analysis identified NADH-Glutamate Synthase, a gene orthologous to the one identified in analysis of leaf N remobilization. This further suggests the role of kernel sink in the movement of N from source to sink during

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reproductive growth in multiple cereal species, and suggests that genetic controls of kernel composition in C4 cereal species may be similar.

REFERENCES

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REFERENCES

"USDA ERS - Feed Grains: Yearbook Tables". USDA. Adams, KL, and AH Jensen. 1987. "High-fat maize in diets for pigs and sows." Animal Feed Science and Technology 17 (3):201-212. Addicott, FT. 1982. Abscission. Berkeley. University of California Press. Aduku, AO. 1993. "Tropical feedstuff analysis table." ABU Zaria. Akin, DE, and LL Rigsby. 2008. "Corn fiber: structure, composition, and response to enzymes for fermentable sugars and coproducts." Applied Biochemistry and Biotechnology 144 (1):59-68. Alburquerque, N, J Egea, L Burgos, D MartÍnez‐Romero, D Valero, and M Serrano. 2006. "The influence of polyamines on apricot ovary development and fruit set." Annals of Applied Biology 149 (1):27-33. Aletor, VA. 1999. "Anti-nutritional Factors as Nature's Paradox in Food and Nutrition Securities." Alexander, DE. 1988. "Breeding special nutritional and industrial types." Corn and Corn Improvement (cornandcornimpr):869-880. Alexander, DE, and RG Creech. 1977. "Breeding special industrial and nutritional types." Corn and corn improvement. Madison: American Society of Agronomy:363-386. Alexander, DE, RJ Lambert, and JW Dudley. 1969. "Breeding problems and potentials of modified protein of maize." Panel New Approaches Breed Impr Plant Protein Proc. Amarante, L do, JD Lima, and L Sodek. 2006. "Growth and stress conditions cause similar changes in xylem amino acids for different legume species." Environmental and Experimental Botany 58 (1):123-129. Amiour, Nardjis, Sandrine Imbaud, Gilles Clément, Nicolas Agier, Michel Zivy, Benoît Valot, Thierry Balliau et al., "An integrated." BMC genomics 15, no. 1 (2014): 122 1005. Anderson, TJ, and BP Lamsal. 2011. "Review: Zein extraction from corn, corn products, and coproducts and modifications for various applications: A review." Cereal Chemistry 88 (2):159-173. Andorf, CM, CJ Lawrence, LC Harper, ML Schaeffer, DA Campbell, and TZ Sen. 2010. "The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps." Bioinformatics 26 (3):434-436.

123

Anglani, C. 1998. "Sorghum carbohydrates–a review." Plant foods for human nutrition 52 (1):77-83. Ansari, MI, RH Lee, and SC Grace Chen. 2005. "A novel senescence‐associated gene encoding γ‐aminobutyric acid (GABA): pyruvate transaminase is upregulated during rice leaf senescence." Physiologia Plantarum 123 (1):1-8. Appelqvist, LA. 1975. "Biochemical and structural aspects of storage and membrane lipids in developing oil seeds." Recent Adv Chem & Biochem Plant Lipids Proc Symp Arranged by Phytochem Soc & Lipid Group of the Biochem Soc. Araus, JL, T Amaro, J Casadesus, A Asbati, and MM Nachit. 1998. "Relationships between ash content, carbon isotope discrimination and yield in durum wheat." Functional Plant Biology 25 (7):835-842. Araus, JL, J Casadesus, and J Bort. 2001. "Recent tools for the screening of physiological traits determining yield. Application of Physiology in Wheat Breeding." Argenta, G, PRF da Silva, and L Sangoi. 2004. "Leaf relative chlorophyll content as an indicator parameter to predict nitrogen fertilization in maize." Ciência Rural 34 (5):1379-1387. Associates, High Plains. 1982. Six-State High Plains Ogallala Aquifer Regional Resources Study: Summary: a Report to the US Department of Commerce and the High Plains Study Council: High Plains Associates. Atkins, CA. 2000. "Biochemical aspects of assimilate transfers along the phloem path: N- solutes in lupins." Functional Plant Biology 27 (6):531-537. Atkins, CA, JS Pate, and PJ Sharkey. 1975. "Asparagine metabolism—key to the nitrogen nutrition of developing legume seeds." Plant Physiology 56 (6):807-812. Atteh, JO. 2002. "Principles and practice of livestock feed manufacturing." Adlek Printers, Ilorin, Nigeria:52-58. Aubel, CE. 1955. "Kansas Agricultural Expt." Sta., Circ 320. Axtell, JD. 1981. "Breeding for improved nutritional quality [Food crops]."

Aymé, L, S Baud, B Dubreucq, F Joffre, and T Chardot. "Function and localization of the 123

Arabidopsis thaliana diacylglycerol acyltransferase DGAT2 expressed in yeast." PloS one 9, no. 3 (2014): e92237. Bach-Knudsen, KE, and L Munck. 1985. "Dietary fibre contents and compositions of sorghum and sorghum-based foods." Journal of Cereal Science 3 (2):153-164. Badi, S, B Pedersen, L Monowar, and BO Eggum. 1990. "The nutritive value of new and traditional sorghum and millet foods from Sudan." Plant Foods for Human Nutrition 40 (1):5-19. Balazadeh, S, DM Riaño‐Pachón, and B Mueller‐Roeber. 2008. "Transcription factors regulating leaf senescence in Arabidopsis thaliana." Plant Biology 10 (s1):63-75. Balconi, C, H Hartings, M Lauria, R Pirona, V Rossi, and M Motto. 2007. "Gene discovery to improve maize grain quality traits." Maydica 52 (3):357. Barham, HN, JA Wagoner, CL Campbell, and EH Harclerode. 1946. "The chemical composition of some sorghum grains and the properties of their starches." The chemical composition of some sorghum grains and the properties of their starches.

124

Baterii, O, A Dexamir, GH Spiridon, Elena Inculet, I Visan, Angela Popescu, and Victoria Ciupercescu. 1979. "Influenta Nutreturilor Combinate Cu Proportie Diferita De Porumb Si Sorg Aspura Productiei De." Lucrari stiintifice. Seria D. Zootehnie 20:105. Bauer, PJ, and PR Carter. 1986. "Effect of seeding date, plant density, moisture availability, and soil nitrogen fertility on maize kernel breakage susceptibility." Crop Science 26 (6):1220-1226. Bean, SR, C Hicks, M Tuinstra, and GL Lookhart. 2001. "Use of SDS to Extract Sorghum and Maize Proteins for Free Zone Capillary Electrophoresis (FZCE) Analysis 1." Cereal Chemistry 78 (1):84-87. Beauchamp, EG, LW Kannenberg, and RB Hunter. 1976. "Nitrogen accumulation and translocation in corn genotypes following silking." Agronomy Journal 68 (2):418- 422. Bello, AB, LW Rooney, and RD Waniska. 1990. "Factors affecting quality of sorghum tô, a thick porridge." Cereal Chem 67:20-25. Below, FE, LE Christensen, AJ Reed, and RH Hageman. 1981. "Availability of reduced N and carbohydrates for ear development of maize." Plant Physiology 68 (5):1186- 1190. Benjamini, Y, and Y Hochberg. 1995. "Controlling the false discovery rate: a practical and powerful approach to multiple testing." Journal of the Royal Statistical Society. Series B (Methodological):289-300. Berke, TG, and TR Rocheford. 1995. "Quantitative trait loci for flowering, plant and ear height, and kernel traits in maize." Crop Science 35 (6):1542-1549. Bernerth, R, and M Frentzen. 1990. "Utilization of erucoyl-CoA by acyltransferases from developing seeds of Brassica napus (L.) involved in triacylglycerol biosynthesis." Plant Science 67 (1):21-28. Bertin, P, and A Gallais. 2000a. "Genetic variation for nitrogen use efficiency in a set of

recombinant maize inbred lines. I. Agrophysiological results." Maydica 45 (1):53- 124

66. Bertin, P, and A Gallais. 2000b. "Physiological and genetic basis of nitrogen use efficiency in maize. I. Agrophysiological results." Maydica 45 (1-4):53-66. Bertin, P, and A Gallais. 2001. "Physiological and genetic basis of nitrogen use efficiency in maize. II. QTL detection and coincidences." Maydica 46:53-68. Beta, T, and H Corke. 2001. "Genetic and environmental variation in sorghum starch properties." Journal of Cereal Science 34 (3):261-268. Bewley, JD, and M Black. 1994. Seeds : physiology of development and germination. 2nd ed, The language of science. New York: Plenum Press. Blackmer, TM, and JS Schepers. 1995. "Use of a chlorophyll meter to monitor nitrogen status and schedule fertigation for corn." Journal of Production Agriculture 8 (1):56-60. Blevins, DG, NM Barnett, and WB Frost. 1978. "Role of potassium and malate in nitrate uptake and translocation by wheat seedlings." Plant Physiology 62 (5):784-788.

125

Blevins, DG, AJ Hiatt, RH Lowe, and JE Leggett. 1978. "Influence of K on the uptake, translocation, and reduction of nitrate by barley seedlings." Agronomy Journal 70 (3):393-396. Blonde, JD, and WC Plaxton. 2003. "Structural and kinetic properties of high and low molecular mass phosphoenolpyruvate carboxylase isoforms from the endosperm of developing castor oilseeds." Journal of Biological Chemistry 278 (14):11867- 11873. Bolton, W., & Blair, R. 1982. “Poultry nutrition (Ministry of agriculture, fisheries and food reference book 174).”Her Majesty’s Stationery Office, London, 115-121. Bookwalter, GN, AW Kirleis, and ET Mertz. 1987. "In Vitro Digestibility of Protein in Milled Sorghum and Other Processed Cereals With and Without Soy‐Fortification." Journal of Food Science 52 (6):1577-1579. Boomsma, C. R., Santini, J. B., Tollenaar, M., & Vyn, T. J. 2009. “Maize morphophysiological responses to intense crowding and low nitrogen availability: An analysis and review.” Agronomy Journal, 101(6), 1426-1452. Bornstein, S, and I Bartov. 1967. "Comparisons of sorghum grain (Milo) and maize as the principal cereal grain source in poultry rations: 1. Their relative feeding value for broilers 1." British Poultry Science 8 (3):213-221. Borrell, AK, GL Hammer, and Andrew CL Douglas. 2000. "Does maintaining green leaf area in sorghum improve yield under drought? I. Leaf growth and senescence." Crop Science 40 (4):1026-1037. Bouche, N, and H Fromm. 2004. "GABA in plants: just a metabolite?" Trends in Plant Science 9 (3):110-115. Bowers, JE, C Abbey, S Anderson, C Chang, X Draye, AH Hoppe, R Jessup, C Lemke, J Lennington, and Z Li. 2003. "A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses." Genetics 165 (1):367-

386. 125

Bowsher, CG, AE Lacey, GT Hanke, DT Clarkson, LR Saker, I Stulen, and MJ Emes. 2007. "The effect of Glc6P uptake and its subsequent oxidation within pea root plastids on nitrite reduction and glutamate synthesis." Journal of Experimental Botany 58 (5):1109-1118. Boyer, CD, LC Hannah, and AR Hallauer. 1994. "Kernel mutants of corn." Specialty corns.:1-28. Boyer, CD, and JC Shannon. 1983. "The use of endosperm genes for sweet corn improvement." In Plant Breeding Reviews, 139-161. Springer. Boyer, CD, and KC Liu. 1983. "Starch and water-soluble polysaccharides from sugary endosperm of sorghum." Phytochemistry 22 (11):2513-2515. Bradbury, PJ., Z Zhang, DE. Kroon, TM. Casstevens, Y Ramdoss, and ES Buckler. 2007. "TASSEL: software for association mapping of complex traits in diverse samples." Bioinformatics 23 (19):2633-2635. Bramel-Cox, PJ, MA Lauver, and ME Witt. 1990. "Potential gain from selection in grain sorghum for higher protein digestibility." Crop Science 30 (3):521-524.

126

Brannan, GL, CS Setser, KE Kemp, PA Seib, and K Roozeboom. 2001. "Sensory Characteristics of Grain Sorghum Hybrids with Potential for Use in Human Food 1." Cereal Chemistry 78 (6):693-700. Bravo, L. 1998. "Polyphenols: chemistry, dietary sources, metabolism, and nutritional significance." Nutrition Reviews 56 (11):317-333. Breitkreuz, KE, BJ Shelp, WN Fischer, R Schwacke, and D Rentsch. 1999. "Identification and characterization of GABA, proline and quaternary ammonium compound transporters from Arabidopsis thaliana." FEBS letters 450 (3):280-284. Bressani, R, and BJ Rios. 1962. "The chemical and essential amino acid composition of twenty-five selections of grain sorghum." Cereal Chem 39:50-58. Brockett, E, D Thompson, T Davis, and C Boyer. 1988. "Gelatinization Characteristics of Starch from du, wx, ae, and ae wx Endosperm of Sweet Corn Inbred la5125." Starch‐Stärke 40 (5):175-177. Browse, J, and C Somerville. 1991. "Glycerolipid synthesis: biochemistry and regulation." Annual review of plant biology 42 (1):467-506. Broyart, C., Fontaine, J. X., Molinié, R., Cailleu, D., Tercé‐Laforgue, T., Dubois, F., Mesnard, F. 2010. “Metabolic profiling of maize mutants deficient for two glutamine synthetase isoenzymes using 1H‐NMR‐based metabolomics.” Phytochemical Analysis, 21(1), 102-109. Brugière, N, F Dubois, C Masclaux, RS Sangwan, and B Hirel. 2000. "Immunolocalization of glutamine synthetase in senescing tobacco (Nicotiana tabacum L.) leaves suggests that ammonia assimilation is progressively shifted to the mesophyll cytosol." Planta 211 (4):519-527. Buchanan‐Wollaston, V, S Earl, E Harrison, E Mathas, S Navabpour, T Page, and D Pink. 2003. "The molecular analysis of leaf senescence–a genomics approach." Plant Biotechnology Journal 1 (1):3-22. Buchanan‐Wollaston, V, T Page, E Harrison, E Breeze, PO Lim, HG Nam, JF Lin, SH Wu, J

Swidzinski, and K Ishizaki. 2005. "Comparative transcriptome analysis reveals 126

significant differences in gene expression and signalling pathways between developmental and dark/starvation‐induced senescence in Arabidopsis." The Plant Journal 42 (4):567-585. Bullant, C, and A Gallais. 1998. “Xenia Effects In Maize With Normal Endosperm: I Importance and Stability." Crop Science 39:1517-1525. Burkart, MR, and JD Stoner. 2001. Nitrogen in groundwater associated with agricultural systems: Elsevier. Butler, LG, DJ Riedl, DG Lebryk, and HJ Blytt. 1984. "Interaction of proteins with sorghum tannin: mechanism, specificity and significance." Journal of the American Oil Chemists’ Society 61 (5):916-920. Cabrera-Bosquet, L, C Sánchez, and JL Araus. 2009. "How yield relates to ash content, Δ13C and Δ18O in maize grown under different water regimes." Annals of Botany 104 (6):1207-1216.

127

Campbell, AR, and RC Pickett. 1968. "Effect of nitrogen fertilization on protein quality and quantity and certain other characteristics of 19 strains of Sorghum bicolor (L.) Moench." Crop Science 8 (5):545-547. Cañas, Rafael A., Isabelle Quilleré, André Gallais, and Bertrand Hirel. 2012. "Can genetic variability for nitrogen metabolism in the developing ear of maize be exploited to improve yield?." New Phytologist 194, no. 2: 440-452. Cañas, R. A., Quilleré, I., Christ, A., & Hirel, B. 2009. “Nitrogen metabolism in the developing ear of maize (Zea mays): analysis of two lines contrasting in their mode of nitrogen management.” New Phytologist, 184(2), 340-352. Cañas, Rafael A., Isabelle Quilleré, Peter J. Lea, and Bertrand Hirel. 2010. "Analysis of amino acid metabolism in the ear of maize mutants deficient in two cytosolic glutamine synthetase isoenzymes highlights the importance of asparagine for nitrogen translocation within sink organs."Plant biotechnology journal, no. 9: 966-978. Cannon, JA, MM MacMasters, MJ Vqolf, and CE Rist. 1952. "Chemical composition of the mature corn kernel." Trans. Am. Assoc. Cereal Chem 10:74. Carter, PR, DR Hicks, ES Oplinger, JD Doll, LG Bundy, RT Schuler, and BJ Holmes. 1989. "Grain Sorghum (Milo). Alternative field crops manual. University of Wisconsin- Extension, Cooperative Extension." Online publication. Available, email: yyang2@ unl. edu, or http://www. hort. purdue. edu/newcrop/afcm/, accessed 4 (19):2008. Castillo, MM, JD Allan, and S Brunzell. 2000. "Nutrient concentrations and discharges in a Midwestern agricultural catchment." Journal of Environmental Quality 29 (4):1142-1151. Castleberry, RM, CW Crum, and CF Krull. 1984. "Genetic yield improvement of US maize cultivars under varying fertility and climatic environments." Crop Science 24 (1):33-36.

Chandrashekar, A, and H Mazhar. 1999. "The biochemical basis and implications of grain 127

strength in sorghum and maize." Journal of Cereal Science 30 (3):193-207. Chapman, SC, and HJ Barreto. 1997. "Using a chlorophyll meter to estimate specific leaf nitrogen of tropical maize during vegetative growth." Agronomy Journal 89 (4):557-562. Chaudhury, AM, A Koltunow, T Payne, ML, MR Tucker, ES Dennis, and WJ Peacock. 2001. "Control of early seed development." Annual review of cell and developmental biology 17 (1):677-699. Chibber, BAK, ET Mertz, and JD Axtell. 1980. "In vitro digestibility of high-tannin sorghum at different stages of dehulling." Journal of agricultural and food chemistry 28 (1):160-161. Choe, BH, MS Zuber, GF Krause, and ES Hilderbrand. 1976. "Inheritance of high lysine in maize." Crop Science 16 (1):34-38.

128

Christ, B, I Süssenbacher, S Moser, N Bichsel, A Egert, T Müller, B Kräutler, and S Hörtensteiner. 2013. "Cytochrome P450 CYP89A9 is involved in the formation of major chlorophyll catabolites during leaf senescence in Arabidopsis." The Plant Cell Online 25 (5):1868-1880. Ciampitti, IA, ST Murrell, JJ Camberato, M Tuinstra, Y Xia, P Friedemann, and TJ Vyn. 2013. "Physiological Dynamics of Maize Nitrogen Uptake and Partitioning in Response to Plant Density and Nitrogen Stress Factors: II. Reproductive Phase." Crop Science 53 (6):2588-2602. Ciampitti, IA, and TJ Vyn. 2012. "Physiological perspectives of changes over time in maize yield dependency on nitrogen uptake and associated nitrogen efficiencies: A review." Field Crops Research 133:48-67. Ciampitti, I. A., & Vyn, T. J. (2014). “Nutrient Sufficiency Concepts for Modern Corn Hybrids: Impacts of Management Practices and Yield Levels.” Crop Management, 13(1). Clark, D, JW Dudley, TR Rocheford, and JR LeDeaux. 2006. "Genetic analysis of corn kernel chemical composition in the random mated 10 generation of the cross of generations 70 of IHO× ILO." Crop science 46 (2):807-819. Coleman, CE, and BA Larkins. 1999. "The prolamins of maize." In seed Proteins, 109-139. Springer. Coleman, SW, and JE Moore. 2003. "Feed quality and animal performance." Field Crops Research 84 (1):17-29. Connor, JK, AR Neill, and KM Barram. 1976. "The metabolizable energy content for the chicken of maize and sorghum grain hybrids grown at several geographical regions." Animal Production Science 16 (82):699-703. Cook, JP, MD McMullen, JB Holland, F Tian, P Bradbury, J Ross-Ibarra, ES Buckler, and SA Flint-Garcia. 2012. "Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels." Plant Physiology

158 (2):824-834. 128

Coque, M, and A Gallais. 2007a. "Genetic variation for N-remobilization and postsilking N-uptake in a set of maize recombinant inbred lines. I. Evaluation by 15N- labeling, heritabilities and correlations among traits for testcross performance." Crop Science 47:1787-1796. Coque, M, and A. Gallais. 2007b. "Genetic variation for nitrogen remobilization and postsilking nitrogen uptake in maize recombinant inbred lines: heritabilities and correlations among traits." Crop Science 47 (5):1787-1796. Coque, M, A Martin, JB Veyrieras, B Hirel, and A Gallais. 2008. "Genetic variation for N- remobilization and postsilking N-uptake in a set of maize recombinant inbred lines. 3. QTL detection and coincidences." TAG Theoretical and Applied Genetics 117 (5):729-747. Coruzzi, G, and R Last. 2000. "Amino Acids." In Biochemistry and Molecular Biology of Plants, edited by B. Buchanan, W. Gruissem and R. Jones, Rockville, MD: American Society of Plant Physiologists. 358-410.

129

Coschigano, KT, R Melo-Oliveira, J Lim, and GM Coruzzi. 1998. "Arabidopsis gls mutants and distinct Fd-GOGAT genes: implications for photorespiration and primary nitrogen assimilation." The Plant Cell Online 10 (5):741-752. Cousins, BW. 1979. "The Effect of Polyphenolic Concentration in Sorghum on Nutrient Digestibility in Swine." Thesis/Dissertation, Texas A & M University. Crafts-Brandner, SJ, RR Klein, P Klein, R Hölzer, and U Feller. 1996. "Coordination of protein and mRNA abundances of stromal enzymes and mRNA abundances of the Clp protease subunits during senescence of Phaseolus vulgaris (L.) leaves." Planta 200 (3):312-318. Creech, RG. 1965. "Genetic control of carbohydrate synthesis in maize endosperm." Genetics 52 (6):1175. Cullison, EA. 1987. Air-dry energy feeds. Feeds and feeding. Reston Publishing Company Inc. Curtis, JJ, AM Brunson, JE Hubbard, and FR Earle. 1956. "Effect of the pollen parent on oil content of the corn kernel." Agronomy Journal 48 (12):551-555. Dalby, A, and CY Tsai. 1975. "Comparisons of lysine and zein and nonzein protein contents in immature and mature maize endosperm mutants." Crop Science 15 (4):513-515. Dang, FF, YN Wang, L Yu, T Eulgem, Y Lai, ZQ Liu, X Wang, AL Qiu, TX Zhang, and J Lin. 2013. "CaWRKY40, a WRKY protein of pepper, plays an important role in the regulation of tolerance to heat stress and resistance to Ralstonia solanacearum infection." Plant, Cell & Environment 36 (4):757-774. De la Roche, IA, DE Alexander, and EJ Weber. 1971. "Inheritance of oleic and linoleic acids in Zea mays L." Crop Science 11 (6):856-859. Dean, DW. 2000. "Processing characteristics and nutritional value of food-grade sorghum and the effects of sorghum ergot in diets for swine and poultry." Kansas State University.

Deosthale, YG, V Nagarajan, and K Viswesware Rao. 1972. "Some factors influencing the 129

nutrient composition of sorghum grain." Indian J Agr Sci. Deyoe, CW, and JA Shellenberger. 1965. "Nutritive value of grains, amino acids and proteins in sorghum grain." Journal of Agricultural and Food Chemistry 13 (5):446-450. Di Fonzo, N, M Motto, T Maggiore, R Sabatino, and F Salamini. 1982. "N-uptake, translocation and relationships among N-related traits in maize as affected by genotype." Agronomie 2 (9):789-796. Diaz, C, T Lemaître, A Christ, M Azzopardi, Y Kato, F Sato, JF Morot-Gaudry, FL Dily, and C Masclaux-Daubresse. 2008. "Nitrogen recycling and remobilization are differentially controlled by leaf senescence and development stage in Arabidopsis under low nitrogen nutrition." Plant Physiology 147 (3):1437-1449. Diaz, C, S Purdy, A Christ, JF Morot-Gaudry, A Wingler, and C Masclaux-Daubresse. 2005. "Characterization of markers to determine the extent and variability of leaf senescence in Arabidopsis. A metabolic profiling approach." Plant Physiology 138 (2):898-908.

130

Ding, Zhong Jie, Jing Ying Yan, Xiao Yan Xu, Di Qiu Yu, Gui Xin Li, Shu Qun Zhang, and Shao Jian Zheng. 2014. "Transcription factor WRKY46 regulates osmotic stress responses and stomatal movement independently in Arabidopsis." The Plant Journal. Doebley, J. 2004. "The genetics of maize evolution." Annu. Rev. Genet. 38:37-59. Dombrink-Kurtzman, MA. 1994. "Examination of Opaque Mutants of Maize by Reversed-phase High-performance liquid Chromatography and Scanning Electron Microscopy." Journal of Cereal Science 19 (1):57-64. Dombrink-Kurtzman, MA, and JA Bietz. 1993. "Zein composition in hard and soft endosperm of maize." Cereal Chemistry 70:105-105. Doner, LW, and KB Hicks. 1997. "Isolation of hemicellulose from corn fiber by alkaline hydrogen peroxide extraction." Cereal Chemistry 74 (2):176-181. Douglas, JH, TW Sullivan, PL Bond, FJ Struwe, JG Baier, and LG Robeson. 1990. "Influence of grinding, rolling, and pelleting on the nutritional value of grain sorghums and yellow corn for broilers." Poultry Science 69 (12):2150-2156. Dowling, LF, C Arndt, and BR Hamaker. 2002. "Economic viability of high digestibility sorghum as feed for market broilers." Agronomy Journal 94 (5):1050-1058. Dudley, JW. 2007. "From means to QTL: The Illinois long-term selection experiment as a case study in quantitative genetics." Crop Science 47 (Supplement_3):S-20-S-31. Dudley, JW, D Clark, TR Rocheford, and JR LeDeaux. 2007. "Genetic analysis of corn kernel chemical composition in the random mated 7 generation of the cross of generations 70 of IHP× ILP." Crop Science 47 (1):45-57. Dudley, JW, and RJ Lambert. 1992. "Ninety generations of selection for oil and protein in maize." Maydica. Dudley, JW, RJ Lambert, and IA De La Roche. 1977. "Genetic analysis of crosses among corn strains divergently selected for percent oil and protein." Crop Science 17 (1):111-117.

Dunlap, FG, PJ White, and LM Pollak. 1995. "Fatty acid composition of oil from exotic 130

corn breeding materials." Journal of the American Oil Chemists’ Society 72 (9):989-993. Dunlap, FG, PJ White, LM Pollak, and TJ Brumm. 1995. "Fatty acid composition of oil from adapted, elite corn breeding materials." Journal of the American Oil Chemists’ Society 72 (9):981-987. Dunn, GM, HH Kramer, and RL Whistler. 1953. "Gene dosage effects on corn endosperm carbohydrates." Agronomy Journal 45 (3):101-104. Duodu, KG, A Nunes, I Delgadillo, ML Parker, ENC Mills, PS Belton, and JR Taylor. "Effect of grain structure and cooking on sorghum and maize in vitro protein digestibility." Journal Cereal Science 35:161-174. Duodu, KG, JRN Taylor, PS Belton, and BR Hamaker. 2003. "Factors affecting sorghum protein digestibility." Journal of Cereal Science 38 (2):117-131. Duvick, DN. 1977. "Genetic rates of gain in hybrid maize yields during the past 40 years." Maydica 22.

131

Dwyer, LM, AM Anderson, DW Stewart, BL Ma, and M Tollenaar. 1995. "Changes in maize hybrid photosynthetic response to leaf nitrogen, from pre-anthesis to grain fill." Agronomy Journal 87 (6):1221-1225. Edwards, WM. 1943. Grain sorghums, their products and uses: US Department of Agriculture, Bureau of Agricultural Chemistry and Engineering. Elkin, RG, JC Rogler, and WR Featherston. 1978. "Influence of sorghum grain tannins on methionine utilization in chicks." Poultry Science 57 (3):704-710. Ellis, CM, P Nagpal, JC Young, G Hagen, TJ Guilfoyle, and JW Reed. 2005. "AUXIN RESPONSE FACTOR1 and AUXIN RESPONSE FACTOR2 regulate senescence and floral organ abscission in Arabidopsis thaliana." Development 132 (20):4563- 4574. Ellis, EB, PD Friedmann, and LO Mehlberg. 1983. "Grain quality for food processing." Proc. Ann. Corn Sorghum Ind. Res. Conf. Ercoli, L, M Mariotti, A Masoni, and F Massantini. 1993. "Relationship between nitrogen and chlorophyll content and spectral properties in maize leaves." European Journal of Agronomy 2. Esen, A. 1987. "A proposed nomenclature for the alcohol-soluble proteins (zeins) of maize (Zea mays L.)." Journal of Cereal Science 5 (2):117-128. Etuk, EB. 2008. "Nutrient composition and feeding value of sorghum for turkeys." PhD Thesis, Federal University of Technology, Owerri, Nigeria. Etuk, EB, and UR Ukaejiofo. 2007. "Tannin content and dietary effects of brown coat coloured sorghum on the performance of young local turkey." Anim. Prod. Res. Adv 3 (2):86-90. Evans, JR. 1989. "Partitioning of nitrogen between and within leaves grown under different irradiances." Functional Plant Biology 16 (6):533-548. Eyherabide, GH, JL Robutti, and FS Borras. 1996. "Effect of near-infrared transmission- based selection on maize hardness and the composition of zeins." Cereal

Chemistry 73 (6):775-778. 131

Febrero, A, J Bort, J Catala, P Marzabal, J Voltas, and JL Araus. 1994. "Grain yield, carbon isotope discrimination and mineral content in mature kernels of barley under irrigated and rainfed conditions." Agronomie 14 (2):127-132. Fedak, G. 1985. "Alien species as sources of physiological traits for wheat improvement." Euphytica 34 (3):673-680. Federer, WT. 2005. "Augmented split block experiment design." Agronomy Journal 97 (2):578-586. Fenster, C. 2003. "White food sorghum in the American diet." US Grains Council 43rd Board of Delegates’ Meeting. Fergason, V. 1994. "High amylose and waxy corns." In Specialty Corns, edited by A.r. Hallauer, 55-77. Boca Raton, FL: CRC Press. Fergason, V. 2001. "High amylose and waxy corns." In Specialty Corns, edited by A.R. Hallauer, 63-84. Boca Raton, FL: CRC Press.

132

Fischer, WN, DDF Loo, U Ludewig, KJ Boorer, M Tegeder, D Rentsch, EM Wright, and WB Frommer. 2002. "Low and high affinity amino acid H+‐cotransporters for cellular import of neutral and charged amino acids." The Plant Journal 29 (6):717-731. Fisher, DB. 2000. "Long-distance transport." Biochemistry and molecular biology of plants:730-784. Fliedel, G., Ollitrault, P., & Erwin, T. (1995). Appraisal of sorghum quality for making tô. Agriculture et développement, (DEC), 34-42. Flint-Garcia, SA, AL Bodnar, and MP Scott. 2009. "Wide variability in kernel composition, seed characteristics, and zein profiles among diverse maize inbreds, landraces, and teosinte." TAG Theoretical and Applied Genetics 119 (6):1129-1142. Fonzo, N, E Fornasari, F Salamini, R Reggiani, and C Soave. 1980. "Interaction of maize mutants floury-2 and opaque-7 with opaque-2 in the synthesis of endosperm proteins." Journal of Heredity 71 (6):397-402. Forde, BG, and PJ Lea. 2007. "Glutamate in plants: metabolism, regulation, and signalling." Journal of Experimental Botany 58 (9):2339-2358. Forestan, C, and S Varotto. 2012. "The role of PIN auxin efflux carriers in polar auxin transport and accumulation and their effect on shaping maize development." Molecular plant 5 (4):787-798. Fox, G, and M Manley. 2009. "Hardness methods for testing maize kernels." Journal of agricultural and food chemistry 57 (13):5647-5657. Fox, GP, L Nguyen, J Bowman, D Poulsen, A Inkerman, and RJ Henry. 2007. "Relationship between hardness genes and quality in barley (Hordeum vulgare)." Journal of the Institute of Brewing 113 (1):87-95. Freeman, JE. 1973. "Quality factors affecting value of corn for wet milling." Transactions of the ASAE 16 (4):671. Frey, KJ. 1951. "The interrelationships of proteins and amino acids in corn." Cereal Chem 28:123-132.

Frey, KJ, B Brimhall, and GF Sprague. 1949. "The effects of selection upon protein quality 132

in the corn kernel." Agronomy Journal 41 (9):399-403. Gallais, A, and M Coque. 2005. "Genetic variation and selection for nitrogen use efficiency in maize: a synthesis." Maydica 50 (3/4):531. Gallais, A, M Coque, J Le Gouis, JL Prioul, B Hirel, and I Quillere. 2007. "Estimating the proportion of nitrogen remobilization and of postsilking nitrogen uptake allocated to maize kernels by nitrogen-15 labeling." Crop science 47 (2):685-691. Gallais, A, M Coque, I Quilléré, JL Prioul, and B Hirel. 2006. "Modelling postsilking nitrogen fluxes in maize (Zea mays) using 15N‐labelling field experiments." New Phytologist 172 (4):696-707. Gan, S, and RM Amasino. 1995. "Inhibition of leaf senescence by autoregulated production of cytokinin." Science 270 (5244):1986-1988. Gan, S, and RM Amasino. 1997. "Making Sense of Senescence (Molecular Genetic Regulation and Manipulation of Leaf Senescence)." Plant Physiology 113 (2):313. Garcia, JM, LC Quintero, and M Mancha. 1988. "Oil bodies and lipid synthesis in developing soybean seeds." Phytochemistry 27 (10):3083-3087.

133

Genter, CF, JF Eheart, and WN Linkous. 1956. "Effects of location, hybrid, fertilizer, and rate of planting on the oil and protein contents of corn grain." Agronomy Journal 48 (2):63-67. Glover, DV. 1976. "Improvement of protein quality in maize." Washington, DC: US Agency for International Development. Goldman, IL, TRR Rocheford, and JW Dudley. 1993. "Quantitative trait loci influencing protein and starch concentration in the Illinois long term selection maize strains." Theoretical and Applied Genetics 87 (1-2):217-224. Goldman, IL, TR Rocheford, and JW Dudley. 1994. "Molecular markers associated with maize kernel oil concentration in an Illinois high protein× Illinois low protein cross." Crop Science 34 (4):908-915. Gong, YH, J Zhang, JF Gao, JY Lu, and JR Wang. 2005. "Slow Export of Photoassimilate from Stay‐green Leaves during Late Grain‐Filling Stage in Hybrid Winter Wheat (Triticum aestivum L.)." Journal of Agronomy and Crop Science 191 (4):292-299. González, MC, L Osuna, C Echevarrıá , J Vidal, and FJ Cejudo. 1998. "Expression and localization of phosphoenolpyruvate carboxylase in developing and germinating wheat grains." Plant Physiology 116 (4):1249-1258. Good, AG, and PH Beatty. 2011. "Biotechnological approaches to improving nitrogen use efficiency in plants: alanine aminotransferase as a case study." The Molecular and Physiological Basis of Nutrient Use Efficiency in Crops:165-191. Goodstein, DM, S Shu, R Howson, R Neupane, RD Hayes, J Fazo, T Mitros, W Dirks, U Hellsten, and N Putnam. 2012. "Phytozome: a comparative platform for green plant genomics." Nucleic acids research 40 (D1):D1178-D1186. Goswami, AK, KL Sehgal, and BK Gupta. 1970. "Chemical composition of bajra grains. 3. Indian inbreds." Indian Journal of Nutrition and Dietetics 7:5-9. Goswami, AK, KL Sehgal, and KP Sharma. 1969. "Chemical composition of bajra grains-1 African entries." J. Nutr. Diet 6:287.

Gregersen, PL, and PB Holm. 2007. "Transcriptome analysis of senescence in the flag leaf 133

of wheat (Triticum aestivum L.)." Plant Biotechnology Journal 5 (1):192-206. Gualtieri, M, and S Rapaccini. 1990. "Sorghum grain in poultry feeding." World's Poultry Science Journal 46 (03):246-254. Guillaume, J, and R Bellec. 1977. "Use of field beans (Vicia faba L) in diets for laying hens." British Poultry Science 18 (5):573-583. Guo, Y, and S Gan. 2005. "Leaf senescence: signals, execution, and regulation." Current topics in developmental biology 71:83-112. Gupta, HO, A Sachdev, RP Johari, and RP Singh. 2003. "Storage protein and its impact on nutritional quality in quality protein maize." Indian J. Agric. Biochem 16:67-71. Gáspár, M, G Kálmán, and K Réczey. 2007. "Corn fiber as a raw material for hemicellulose and ethanol production." Process Biochemistry 42 (7):1135-1139. Habash, DZ, S Bernard, J Schondelmaier, J Weyen, and SA Quarrie. 2007. "The genetics of nitrogen use in hexaploid wheat: N utilisation, development and yield." Theoretical and Applied Genetics 114 (3):403-419.

134

Habash, DZ, AJ Massiah, HL Rong, RM Wallsgrove, and RA Leigh. 2001. "The role of cytosolic glutamine synthetase in wheat." Annals of Applied Biology 138 (1):83- 89. Hahn, DH, LW Rooney, and CF Earp. 1984. "Tannins and phenols of sorghum." Cereal foods world (USA). Hallauer, A. R., Carena, M. J., & Miranda Filho, J. D. (2010). Quantitative genetics in maize breeding (Vol. 6). Springer Hamaker, BR, AW Kirleis, LG Butler, JD Axtell, and ET Mertz. 1987. "Improving the in vitro protein digestibility of sorghum with reducing agents." Proceedings of the National Academy of Sciences 84 (3):626-628. Hamaker, BR, AA Mohamed, JE Habben, CP Huang, and BA Larkins. 1995. "Efficient procedure for extracting maize and sorghum kernel proteins reveals higher prolamin contents than the conventional method." Cereal Chemistry 72 (6):583- 588. Hamaker, BR, AW Kirleis, ET Mertz, and JD Axtell. 1986. "Effect of cooking on the protein profiles and in vitro digestibility of sorghum and maize." Journal of Agricultural and Food Chemistry 34 (4):647-649. Han, Y, CM Parsons, and DE Alexander. 1987. "Nutritive value of high oil corn for poultry." Poultry science 66 (1):103-111. Hannah, LC. 1997. "Starch synthesis in the maize seed." In Cellular and Molecular Biology of Plant Seed Development, 375-405. Springer. Hansel, LW, CY Tsai, and OE Nelson. 1973. "Effect of the floury-2 gene on the distribution of protein fractions and methionine in maize endosperm." Cereal chemistry. Hanway, JJ. 1966. "How a corn plant develops." Spec. Rep. 48 Iowa State Univ. Sci. Technol. Harrison, J, N Brugière, B Phillipson, S Ferrario-Mery, T Becker, A Limami, and B Hirel.

2000. "Manipulating the pathway of ammonia assimilation through genetic 134

engineering and breeding: consequences to plant physiology and plant development." Plant and Soil 221 (1):81-93. Hayakawa, T, T Nakamura, F Hattori, T Mae, K Ojima, and T Yamaya. 1994. "Cellular localization of NADH-dependent glutamate-synthase protein in vascular bundles of unexpanded leaf blades and young grains of rice plants." Planta 193 (3):455- 460. Hayashi, H, and M Chino. 1990. "Chemical composition of phloem sap from the uppermost internode of the rice plant." Plant and Cell Physiology 31 (2):247- 251. Heffer, P. 2006/07 - 2007/08. Assessment of Fertilizer Use by Crop at the Global Level. Paris, France: International Fertilizer Industry Asociation. Hellmann, H, L Barker, D Funck, and WB Frommer. 2000. "The regulation of assimilate allocation and transport." Functional Plant Biology 27 (6):583-594. Hibberd, CA, ED Mitchell, DG Wagner, and RL Hintz. 1979. "Seed Characteristics of Different Varieties ofGrain Sorghum."

135

Hibberd, CA, DG Wagner, RL Schemm, ED Mitchell, RL Hintz, and DE Weibel. 1982. "Nutritive characteristics of different varieties of sorghum and corn grains." Journal of Animal Science 55 (3):665-672. Hicks, C, MR Tuinstra, JF Pedersen, FE Dowell, and KD Kofoid. 2002. "Genetic analysis of feed quality and seed weight of sorghum inbred lines and hybrids using analytical methods and NIRS." Euphytica 127 (1):31-40. Hicks, KB, RA Moreau, DB Johnston, LW Doner, ML Fishman, and BS Dien. 2003. "Nutraceuticals and novel food ingredients from corn milling by-products." Abstracts of Papers of the Maerican Chemical Society. Hill, L D. 1982. "Quality problems in exporting US corn." Proceedings of the... annual corn and sorghum industry research conference-American Seed Trade Association, Corn and Sorghum Division, Corn and Sorghum Research Conference (USA). Himelblau, E, and RM Amasino. 2001. "Nutrients mobilized from leaves of Arabidopsis thaliana during leaf senescence." Journal of Plant Physiology 158 (10):1317- 1323. Hirel, Bertrand, Jacques Le Gouis, Bertrand Ney, and André Gallais. "The challenge of improving nitrogen use efficiency in crop plants: towards a more central role for genetic variability and quantitative genetics within integrated approaches." Journal of Experimental Botany 58, no. 9 (2007): 2369-2387. Holding, DR, and BA Larkins. 2006. "The development and importance of zein protein bodies in maize endosperm." Maydica 51 (2):243. Hollmann, J, PL Gregersen, and K Krupinska. 2014. "Identification of predominant genes involved in regulation and execution of senescence-associated nitrogen remobilization in flag leaves of field grown barley." Journal of Experimental Botany: 094. Hopkins, CJ. 1903. "The structure of the corn kernel and the composition of its different

parts." 135

Horan, FE, and MF Heider. 1946. "A study of sorghum and sorghum starches." Cereal Chem 23:492. Hulan, HW, and FG Proudfoot. 1982. "Nutritive value of sorghum grain for broiler chickens." Canadian Journal of Animal Science 62 (3):869-875. Huppe, HC, and DH Turpin. 1994. "Integration of carbon and nitrogen metabolism in plant and algal cells." Annual review of plant biology 45 (1):577-607. Hornbeck, R., & Keskin, P. 2011.”The evolving impact of the Ogallala Aquifer: Agricultural adaptation to groundwater and climate”(No. w17625). National Bureau of Economic Research. Hörtensteiner, S, and U Feller. 2002. "Nitrogen metabolism and remobilization during senescence." Journal of Experimental Botany 53 (370):927-937. Hörtensteiner, S, and B Kräutler. 2011. "Chlorophyll breakdown in higher plants." Biochimica et Biophysica Acta (BBA)-Bioenergetics 1807 (8):977-988.

136

Ichihara, K, T Takahashi, and S Fujii. 1988. "Diacylglycerol acyltransferase in maturing safflower seeds: its influences on the fatty acid composition of triacylglycerol and on the rate of triacylglycerol synthesis." Biochimica et Biophysica Acta (BBA)-Lipids and Lipid Metabolism 958 (1):125-129. Ichihara, K, and M Noda. 1980. "Fatty acid composition and lipid synthesis in developing safflower seeds." Phytochemistry 19 (1):49-54. Inouchi, N, DV Glover, Y Sugimoto, and H Fuwa. 1984. "Developmental changes in starch properties of several endosperm mutants of maize." Starch‐Stärke 36 (1):8-12. Ioerger, B, SR Bean, MR Tuinstra, Jeffrey F Pedersen, J Erpelding, KM Lee, and TJ Herrman. 2007. "Characterization of polymeric proteins from vitreous and floury sorghum endosperm." Journal of Agricultural and Food Chemistry 55 (25):10232- 10239. Iowa State University Extension. 2006. Moisture Basis Conversions for Grain Composition Data. http://www.store.extension.iastate.edu: ISU University Extension. Ireland, RJ, and PJ Lea. 1999. "The enzymes of glutamine, glutamate, asparagine, and aspartate metabolism." Plant amino acids. Biochemistry and biotechnology:49- 109. Jackson, WA, WL Pan, RH Moll, and EJ Kamprath. 1986. "Uptake, translocation and reduction of nitrate." Biochemical basis of plant breeding 2:73-108. Jako, C, A Kumar, Y Wei, J Zou, DL Barton, EM Giblin, PS Covello, and DC Taylor. 2001. "Seed-specific over-expression of an Arabidopsis cDNA encoding a diacylglycerol acyltransferase enhances seed oil content and seed weight." Plant Physiology 126 (2):861-874. Jambunathan, R, and V Subramanian. 1988. "Grain quality and utilization of sorghum and pearl millet." International Biotechnology Workshop, Patancheru, AP (India), 12-15 Jan 1987.

James, MG, K Denyer, and AM Myers. 2003. "Starch synthesis in the cereal endosperm." 136

Current Opinion in Plant Biology 6 (3):215-222. Jarvis, SC. 1996. "Future trends in nitrogen research." In Progress in Nitrogen Cycling Studies, 1-10. Springer. Jellum, MD. 1970. "Plant introductions of maize as a source of oil with unusual fatty acid composition." Journal of agricultural and food chemistry 18 (3):365-370. Jellum, MD. 1966. "Fatty acid composition of corn oil of parental inbreds and reciprocal crosses." Journal of Heredity 57 (6):243-244. Jing, HC, L Anderson, MJG Sturre, J Hille, and PP Dijkwel. 2007. "Arabidopsis CPR5 is a senescence-regulatory gene with pleiotropic functions as predicted by the evolutionary theory of senescence." Journal of Experimental Botany 58 (14):3885-3894. Kamachi, K, T Yamaya, T Mae, and K Ojima. 1991. "A role for glutamine synthetase in the remobilization of leaf nitrogen during natural senescence in rice leaves." Plant Physiology 96 (2):411-417.

137

Kamisaka, Y, and T Nakahara. 1994. "Characterization of the diacylglycerol acyltransferase activity in the lipid body fraction from an oleaginous fungus." Journal of Biochemistry 116 (6):1295-1301. Kant, S, YM Bi, and SJ Rothstein. 2011. "Understanding plant response to nitrogen limitation for the improvement of crop nitrogen use efficiency." Journal of Experimental Botany 62 (4):1499-1509. Karper, RE, and JR Quinby. 1947. "Sorghum—Its production, utilization and breeding." Economic Botany 1 (4):355-371. Keeney, DR. 1970. "Protein and amino acid composition of maize grain as influenced by variety and fertility." Journal of the Science of Food and Agriculture 21 (4):182- 184. Kennedy, EP. 1961. "Biosynthesis of complex lipids." Federation proceedings. Kim, HJ, H Ryu, SH Hong, HR Woo, PO Lim, IC Lee, J Sheen, HG Nam, and I Hwang. 2006. "Cytokinin-mediated control of leaf longevity by AHK3 through phosphorylation of ARR2 in Arabidopsis." Proceedings of the National Academy of Sciences of the United States of America 103 (3):814-819. King, SP, MR Badger, and RT Furbank. 1998. "CO2 refixation characteristics of developing canola seeds and silique wall." Functional Plant Biology 25 (3):377- 386. Klopfenstein, CF, and RC Hoseney. 1995. "Nutritional properties of sorghum and the millets." Sorghum and millets: chemistry and technology:125-168. Kniep, KR, and SC Mason. 1989. "Kernel breakage and density of normal and opaque-2 maize grain as influenced by irrigation and nitrogen." Crop Science 29 (1):158- 163. Knighton, N, and B Bugbee. 2004. A Comparison of Opti-sciences CCM-200 Chlorophyll Meter and the Minolta SPAD 502 Chlorophyll Meter. Koch, BA. 1962. "Kansas. 4gricultural Expt." Sta., Bull 447.

Lacey, DJ, and MJ Hills. 1996. "Heterogeneity of the endoplasmic reticulum with respect 137

to lipid synthesis in developing seeds of Brassica napus L." Planta 199 (4):545- 551. Lafitte, HR, and GO Edmeades. 1994. "Improvement for tolerance to low soil nitrogen in tropical maize II. Grain yield, biomass production, and N accumulation." Field Crops Research 39 (1):15-25. Lambert, RJ, DE Alexander, and JW Dudley. 1969. "Relative performance of normal and modified protein (opaque-2) maize hybrids." Crop Science 9 (2):242-243. Lambert, RJ, DE Alexander, and IJ Mejaya. 2004. "Single kernel selection for increased grain oil in maize synthetics and high-oil hybrid development." Plant Breeding Reviews 24 (1):153-176. Lambert, RJ, and AR Hallauer. 1994. "High-oil corn hybrids." Specialty Corns.:123-145. Landbeck, MV. 1995. "Untersuchungen zur genetischen Verbesserung der Anbaueignung von Körnermais unter Produktionsbedingungen mit verringerter Stickstoffversorgung." Universität Hohenheim.

138

Larkins, BA, K Pedersen, MD Marks, and DR Wilson. 1984. "The zein proteins of maize endosperm." Trends in Biochemical Sciences 9 (7):306-308. Lauderdale, J. 2002. Issues regarding targeting and adoption of quality protein maize. CIMMYT working paper. Lawrence, CJ, TE Seigfried, and V Brendel. 2005. ”The maize genetics and genomics database. The community resource for access to diverse maize data." Plant Physiology 138, no. 1: 55-58. Lea, PJ, SA Robinson, and GR Stewart. 1990. "The enzymology and metabolism of glutamine, glutamate, and asparagine." The Biochemistry of Plants 16:121-159. Lea, PJ, L Sodek, MAJ Parry, PR Shewry, and NG Halford. 2007. "Asparagine in plants." Annals of Applied Biology 150 (1):1-26. Lebouteiller, B, A Gousset-Dupont, JN Pierre, J Bleton, A Tchapla, M Maucourt, A Moing, D Rolin, and J Vidal. 2007. "Physiological impacts of modulating phosphoenolpyruvate carboxylase levels in leaves and seeds of Arabidopsis thaliana." Plant science 172 (2):265-272. Lee, KM, SR Bean, S Alavi, TJ Herrman, and RD Waniska. 2006. "Physical and biochemical properties of maize hardness and extrudates of selected hybrids." Journal of agricultural and food chemistry 54 (12):4260-4269. Lee, L, and CY Tsai. 1985. "Effect of sucrose accumulation on zein synthesis in maize starch-deficient mutants." Phytochemistry 24 (2):225-229. Letchworth, MB, and RJ Lambert. 1998. "Pollen parent effects on oil, protein, and starch concentration in maize kernels." Crop Science 38 (2):363-367. Lewis, CE, G Noctor, D Causton, and CH Foyer. 2000. "Regulation of assimilate partitioning in leaves." Functional Plant Biology 27 (6):507-519. Lewis, QAM. 1975. "An 15N—14C Study of the Role of the Leaf in the Nitrogen Nutrition of the Seed of Datura Stramonium L." Journal of Experimental Botany 26 (3):361-366.

Li, H, Z Peng, X Yang, W Wang, J Fu, J Wang, Y Han, Y Chai, T Guo, and N Yang. 2013. 138

"Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels." Nature genetics 45 (1):43-50. Li, Z, J Peng, X Wen, and H Guo. 2012. "Gene Network Analysis and Functional Studies of Senescence‐associated Genes Reveal Novel Regulators of Arabidopsis Leaf SenescenceF." Journal of integrative plant biology 54 (8):526-539. Li, Z, J Peng, X Wen, and H Guo. 2013. "Ethylene-insensitive3 is a senescence-associated gene that accelerates age-dependent leaf senescence by directly repressing miR164 transcription in Arabidopsis." The Plant Cell Online 25 (9):3311-3328. Liang, GHL, TL Walter, CD Nickell, and YO Koh. 1969. "Heritability estimates and interrelationships among agronomic traits in grain sorghum, Sorghum bicolor (L.) Moench." Canadian Journal of Genetics and Cytology 11 (1):199-208. Lim, PO, HJ Kim, and HG Nam. 2007. "Leaf senescence." Annu. Rev. Plant Biol. 58:115- 136.

139

Lim, PO, IC Lee, J Kim, HJ Kim, JS Ryu, HR Woo, and HG Nam. 2010. "Auxin response factor 2 (ARF2) plays a major role in regulating auxin-mediated leaf longevity." Journal of Experimental Botany. Lim, PO, HR Woo, and HG Nam. 2003. "Molecular genetics of leaf senescence in Arabidopsis." Trends in plant science 8 (6):272-278. Lin, FD, DA Knabe, and TD Tanksley Jr. 1987. "Apparent digestibility of amino acids, gross energy and starch in corn, sorghum, wheat, barley, oat groats and wheat middlings for growing pigs." Journal of Animal Science 64 (6):1655. Lin, YR, KF Schertz, and AH Paterson. 1995. "Comparative analysis of QTLs affecting plant height and maturity across the Poaceae, in reference to an interspecific sorghum population." Genetics 141 (1):391. Lipka, AE, F Tian, Q Wang, J Peiffer, ML, Peter J Bradbury, Michael A Gore, Edward S Buckler, and Zhiwu Zhang. 2012. "GAPIT: genome association and prediction integrated tool." Bioinformatics 28 (18):2397-2399. Lung, SC, and RJ Weselake. 2006. "Diacylglycerol acyltransferase: a key mediator of plant triacylglycerol synthesis." Lipids 41 (12):1073-1088. Ma, Y, and OE Nelson. 1975. "Amino acid composition and storage proteins in two new high-lysine mutants in maize." Cereal Chemistry. MacGregor, JM, LT Taskovitch, and WP Martin. 1961. "Effect of nitrogen fertilizer and soil type on the amino acid content of corn grain." Agronomy journal 53 (4):211- 214. Mach, J. 2013. "Chlorophyll Breakdown Branches Out: Identification of a Major Catabolic Route Involving Cytochrome P450 CYP89A9." The Plant Cell Online 25 (5):1486-1486. Mangolin, CA, CL de Souza Jr, AAF Garcia, AF Garcia, ST Sibov, and AP de Souza. 2004. "Mapping QTLs for kernel oil content in a tropical maize population." Euphytica 137 (2):251-259.

Martin, A, X Belastegui‐Macadam, I Quilleré, M Floriot, MH Valadier, B Pommel, B 139

Andrieu, I Donnison, and Bertrand Hirel. 2005. "Nitrogen management and senescence in two maize hybrids differing in the persistence of leaf greenness: agronomic, physiological and molecular aspects." New Phytologist 167 (2):483- 492. Martin, A, JL, T Kichey, D Gerentes, M Zivy, C Tatout, F Dubois, T Balliau, B Valot, and M Davanture. 2006. "Two cytosolic glutamine synthetase isoforms of maize are specifically involved in the control of grain production." The Plant Cell Online 18 (11):3252-3274. Martínez, DE, ML Costa, and JJ Guiamet. 2008. "Senescence‐associated degradation of chloroplast proteins inside and outside the organelle." Plant Biology 10 (s1):15- 22. Masclaux, C, I Quillere, A Gallais, and B Hirel. 2001. "The challenge of remobilisation in plant nitrogen economy. A survey of physio‐agronomic and molecular approaches." Annals of Applied Biology 138 (1):69-81.

140

Masclaux, C, MH Valadier, N Brugière, JF Morot-Gaudry, and B Hirel. 2000. "Characterization of the sink/source transition in tobacco (Nicotiana tabacum L.) shoots in relation to nitrogen management and leaf senescence." Planta 211 (4):510-518. Masclaux-Daubresse, C, F Daniel-Vedele, J Dechorgnat, F Chardon, L Gaufichon, and A Suzuki. 2010. "Nitrogen uptake, assimilation and remobilization in plants: challenges for sustainable and productive agriculture." Annals of Botany:028. Masclaux‐Daubresse, C, M Reisdorf‐Cren, and M Orsel. 2008. "Leaf nitrogen remobilisation for plant development and grain filling." Plant Biology 10:23-36. Mashiguchi, K, K Tanaka, T Sakai, S Sugawara, H Kawaide, M Natsume, A Hanada, T Yaeno, K Shirasu, and H Yao. 2011. "The main auxin biosynthesis pathway in Arabidopsis." Proceedings of the National Academy of Sciences 108 (45):18512- 18517. Matile, Ph. 1997. "The vacuole and cell senescence." Advances in botanical research 25:87-112. Matsuoka, Y, Y Vigouroux, MM Goodman, J Sanchez, E Buckler, and J Doebley. 2002. "A single domestication for maize shown by multilocus microsatellite genotyping." Proceedings of the National Academy of Sciences 99 (9):6080-6084. Maunder, B. 2005. "Sorghum: The global grain of the future." National Grain Sorghum Producers, Lubbock, TX. McCabe, MS, LC Garratt, F Schepers, WJRM Jordi, GM Stoopen, E Davelaar, JH A van Rhijn, JB Power, and MR Davey. 2001. "Effects of PSAG12-IPT gene expression on development and senescence in transgenic lettuce." Plant Physiology 127 (2):505-516. McCullough, DE, M Mihajlovic, A Aguilera, M Tollenaar, and Ph Girardin. 1994. "Influence of N supply on development and dry matter accumulation of an old and a new maize hybrid." Canadian Journal of Plant Science 74 (3):471-477.

McDonald, P, RA Edwards, and JFD Greenhalgh. 1987. Animal Nutrition. ELBS. Longman. 140

McDonald, P. 2002. Animal nutrition: Pearson education. McWhirter, KS. 1971. "A floury endosperm, high lysine locus on chromosome 10." Maize Genet. Coop. News Letter 45:184. Mengel, K. 1980. "Effect of potassium on the assimilate conduction to storage tissue." Berichte der Deutschen Botanischen Gesellschaft 93 (1):353-362. Menz, MA, RR Klein, JE Mullet, JA Obert, NC Unruh, and PE Klein. 2002. "A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLP®, RFLP and SSR markers." Plant molecular biology 48 (5-6):483-499. Menzies, CS, and D Richardson. 1961. "Cox, RR, Kansas Agricultural Expt." Experimental Station Circular 383. Mertz, ET, LS Bates, and OE Nelson. 1964. "Mutant gene that changes protein composition and increases lysine content of maize endosperm." Science 145 (3629):279-280.

141

Mertz, ET, MM Hassen, C Cairns-Whittern, AW Kirleis, L Tu, and JD Axtell. 1984. "Pepsin digestibility of proteins in sorghum and other major cereals." Proceedings of the National Academy of Sciences 81 (1):1-2. Mestres, C, and F Matencio. 1996. "Biochemical basis of kernel milling characteristics and endosperm vitreousness of maize." Journal of Cereal Science 24 (3):283-290. Mi, G, L Tang, F Zhang, and J Zhang. 2002. "Carbohydrate storage and utilization during grain filling as regulated by nitrogen application in two wheat cultivars." Journal of plant nutrition 25 (2):213-229. Miao, Y, T Laun, P Zimmermann, and U Zentgraf. 2004. "Targets of the WRKY53 transcription factor and its role during leaf senescence in Arabidopsis." Plant molecular biology 55 (6):853-867. Miflin, BJ, and DZ Habash. 2002. "The role of glutamine synthetase and glutamate dehydrogenase in nitrogen assimilation and possibilities for improvement in the nitrogen utilization of crops." Journal of Experimental Botany 53 (370):979-987. Miflin, BJ, and PR Shewry. 1978. "The biology and biochemistry of cereal seed prolamins." Miller, DF. 1958. Composition of cereal grains and forages. Vol. 585: National Academies. Miller, PA, and B Brimhall. 1951. "Factors influencing the oil and protein content of corn grain." Agronomy Journal 43 (7):305-311. Miller, RC, LW Aurand, and WR Flach. 1950. "Amino acids in high and low protein corn." American Association for the Advancement of Science. Science 112:57-58. Minotti, PL, DC Williams, and WA Jackson. 1968. "Nitrate uptake and reduction as affected by calcium and potassium." Soil Science Society of America Journal 32 (5):692-698. Misra, PS, R Jambunathan, ET Mertz, DV Glover, HM Barbosa, and KS McWhirter. 1972. "Endosperm protein synthesis in maize mutants with increased lysine content."

Science 176 (4042):1425-1427. 141

Mitsuhashi, W, and U Feller. 1992. "Effects of light and external solutes on the catabolism of nuclear-encoded stromal proteins in intact chloroplasts isolated from pea leaves." Plant Physiology 100 (4):2100-2105. Mišević, D, and DE Alexander. 1989. "Twenty-four cycles of phenotypic recurrent selection for percent oil in maize. Per se and test-cross performance." Crop Science 29 (2):320-324. Moes, J, and TJ Vyn. 1988. "Management effects on kernel breakage susceptibility of early maturing corn hybrids." Agronomy Journal 80 (4):699-704. Moll, RH, WA Jackson, and RL Mikkelsen. 1994. "Recurrent selection for maize grain yield: dry matter and nitrogen accumulation and partitioning changes." Crop Science 34 (4):874-881. Moll, RH, EJ Kamprath, and WA Jackson. 1982. "Analysis and interpretation of factors which contribute to efficiency of nitrogen utilization." Agronomy Journal 74 (3):562-564.

142

Moll, RH, EJ Kamprath, and WA Jackson. 1987. "Development of nitrogen-efficient prolific hybrids of maize." Crop Science 27 (2):181-186. Morris, CF. 2002. "Puroindolines: the molecular genetic basis of wheat grain hardness." Plant Molecular Biology 48 (5-6):633-647. Motto, M, R Thompson, and F Salamini. 1997. "Genetic regulation of carbohydrate and protein accumulation in seeds." In Cellular and Molecular Biology of Plant Seed Development, 479-522. Springer. Muchow, RC, and R Davis. 1988. "Effect of nitrogen supply on the comparative productivity of maize and sorghum in a semi-arid tropical environment II. Radiation interception and biomass accumulation." Field Crops Research 18 (1):17-30. Muchow, RC, and TR Sinclair. 1994. "Nitrogen response of leaf photosynthesis and canopy radiation use efficiency in field-grown maize and sorghum." Crop Science 34 (3):721-727. Mukherjee, KD. 1986. "Glycerolipid synthesis by homogenate and oil bodies from developing mustard (Sinapis alba L.) seed." Planta 167 (2):279-283. Murmu, J, and WC Plaxton. 2007. "Phosphoenolpyruvate carboxylase protein kinase from developing castor oil seeds: partial purification, characterization, and reversible control by photosynthate supply." Planta 226 (5):1299-1310. Murphy, DJ. 1988. "A highly active soluble diacylglycerol synthesizing system from developing rapeseed, Brassica napus L." Lipids 23 (3):157-163. Murphy, DJ, and KD Mukherjee. 1987. "Acyltransferases in subcellular fractions of developing seeds of rape (Brassica napus L.)." Lipids 22 (5):293-298. Murphy, TC. 1980. Root ammonium assimilation enzyme activities, grain storage protein and grain yield response to high ammonium fertilizer among maize hybrids. West Lafayette, IN: Purdue University. Murty, DS, and KA Kumar. 1995. "Traditional uses of sorghum and millets." Sorghum

and Millets: Chemistry and Technology:185-221. 142

Murty, DS, KD Nicodemus, and LR House. 1982. "Inheritance of basmati and dimpled seed in sorghum." Crop Science 22 (5):1080-1082. Murty, DS, U Singh, S Suryaprakash, and KD Nicodemus. 1985. "Soluble sugars in five endosperm types of sorghum." Cereal Chem 62 (2):l50-I52. Muruli, BI, and GM Paulsen. 1981. "Improvement of nitrogen use efficiency and its relationship to other traits in maize." Maydica 26. Nass, HG, and PL Crane. 1970. "Effects of endosperm genes on dry matter accumulation and moisture loss in corn (Zea mays L.)." Crop Science 10 (3):276-280. National Research Council Committee on Diet. 1989. Diet and health: Implications for reducing chronic disease risk: National Academies Press. Nelson, OE. 1979. "Inheritance of amino acid content in cereals." In Seed Protein Improvement in Cereals and Grain Legumes. Nelson, OE. 1980. "Genetic control of polysaccharide and storage protein synthesis in the endosperms of barley, maize, and sorghum." Advances in Cereal Science and Technology 3:41-71.

143

Nelson, OE. 1969. "Genetic modification of protein quality in plants." Adv. Agron 21:171-194. Nelson, OE, ET Mertz, and LS Bates. 1965. "Second mutant gene affecting the amino acid pattern of maize endosperm proteins." Science 150 (3702):1469-1470. Nelson, OE, and HW Rines. 1962. "The enzymatic deficiency in the waxy mutant of maize." Biochemical and Biophysical Research Communications 9 (4):297-300. Nelson, TS, EL Stephenson, A Burgos, J Floyd, and JO York. 1975. "Effect of tannin content and dry matter digestion on energy utilization and average amino acid availability of hybrid sorghum grains." Poultry Science 54 (5):1620-1623. Neucere, NJ, and G Sumrell. 1980. "Chemical composition of different varieties of grain sorghum." Journal of Agricultural and Food Chemistry 28 (1):19-21. Ngoka, DA. 1997. "Crop production in the Tropics: Theory and Practice." Owerri, Alphabet Publishers. Nonogaki, H, F Chen, and KJ Bradford. 2007. "Mechanisms and genes involved in germination sensu stricto." Annual Plant Reviews Volume 27: Seed Development, Dormancy and Germination:264-304. Oaks, A, KE Jones, DW Ross, I Boesel, D Lenz, and S Misra. 1979. "Enzyme of nitrogen assimilation in developing seeds of Zea mays L." Seed Protein Improvement in Cereals and Grain Legumes 1:179-186. Obara, M, M Kajiura, Y Fukuta, M Yano, M Hayashi, T Yamaya, and T Sato. 2001. "Mapping of QTLs associated with cytosolic glutamine synthetase and NADH‐glutamate synthase in rice (Oryza sativa L.)." Journal of Experimental Botany 52 (359):1209-1217. Obizoba, IC. 1988. "Nutritive value of malted, dry-or wet-milled sorghum and corn." Cereal chemistry. Ockerman, HW. 1978. "Source book for food scientists." O'Leary,B, P Joonho, and CP William. 2011. "The remarkable diversity of plant PEPC

(phosphoenolpyruvate carboxylase): recent insights into the physiological 143

functions and post-translational controls of non-photosynthetic PEPCs." Biochemical Journal 436 (1):15-34. Olomu, JM. 1995. "Monogastric animal nutrition: Principles and practice." Benin, NG: A Jachem Publication. Olsen, OA. 2001. "Endosperm development: cellularization and cell fate specification." Annual Review of Plant Biology 52 (1):233-267. Olson, RA, and KJ Frey. 1987. "Modification of nutritional quality by environment and production practices." Ono, K, K Ishimaru, N Aoki, and R Ohsugi. 1999. "Transgenic rice with low sucrose- phosphate synthase activities retain more soluble protein and chlorophyll during flag leaf senescence." Plant Physiology and Biochemistry 37 (12):949-953. Oo, ZC, and YH Chew. 1992. "Diacylglycerol acyltransferase in microsomes and oil bodies of oil palm mesocarp." Plant and Cell Physiology 33 (2):189-195.

144

Ori, N, MT Juarez, D Jackson, J Yamaguchi, GM Banowetz, and S Hake. 1999. "Leaf senescence is delayed in tobacco plants expressing the maize homeobox gene knotted1 under the control of a senescence-activated promoter." The Plant Cell 11 (6):1073-1080. Oria, MP, BR Hamaker, JD Axtell, and CP Huang. 2000. "A highly digestible sorghum mutant cultivar exhibits a unique folded structure of endosperm protein bodies." Proceedings of the National Academy of Sciences 97 (10):5065-5070. Oria, MP, BR Hamaker, and JM Shull. 1995. "Resistance of Sorghum .alpha.-, .beta.-, and .gamma.-Kafirins to Pepsin Digestion." Journal of Agricultural and Food Chemistry 43 (8):2148-2153. doi: 10.1021. Oria, MP, BR Hamaker, and JM Schull. 1995. "In vitro protein digestibility of developing and mature sorghum grain in relation to α-, β-, and γ-kafirin disulfide crosslinking." Journal of Cereal Science 22 (1):85-93. Ortega, A, C De Leon, G Granados, and SK Vasal. 1975. "Disease-insect interactions in quality protein maize." High quality protein maize. Dowden, Hutchinson and Ross, Inc., Stroudsburg, Pa:173-192. Ortega, EI, and LS Bates. 1983. "Biochemical and agronomic studies of two modified hard-endosperm opaque-2 maize (Zea mays L.) populations [Cultivars, protein components]." Cereal Chemistry. Osborn, D, and LF Chen. 1984. "Corn hull hydrolysis using glucoamylase and sulfuric acid." Starch‐Stärke 36 (11):393-395. Osborne, TB, and LB Mendel. 1914. "Amino-acids in nutrition and growth." Journal of Biological Chemistry 17 (3):325-349. Oyenuga, VA. 1968. Nigeria's food and feeding-stuffs: their chemistry and nutritive value: Ibadan University Press Ibadan. Paez, AV, JL Helm, and MS Zuber. 1970. "Dosage effects of opaque-2 and floury-2 on lysine, protein and light transmission of maize endosperm." Zeitschrift fur

Pflanzenzuchtung 63:119-24. 144

Pan, WL, JJ Camberato, WA Jackson, and RH Moll. 1986. "Utilization of Previously Accumulated and Concurrently Absorbed Nitrogen during Reproductive Growth in Maize Influence of Prolificacy and Nitrogen Source." Plant Physiology 82 (1):247-253. Pan, WL, EJ Kamprath, RH Moll, and WA Jackson. 1984. "Prolificacy in corn: Its effects on nitrate and ammonium uptake and utilization." Soil Science Society of America Journal 48 (5):1101-1106. Patancheru, AP. 1980. “ICRISAT Annual Report 1978-1979.” India: International Crops research Institute for the Semi-Arid Tropics. Paponov, IA, and C Engels. 2003. "Effect of nitrogen supply on leaf traits related to photosynthesis during grain filling in two maize genotypes with different N efficiency." Journal of Plant Nutrition and Soil Science 166 (6):756-763. Pate, JS, PJ Sharkey, and OAM Lewis. 1974. "Phloem bleeding from legume fruits—a technique for study of fruit nutrition." Planta 120 (3):229-243.

145

Paterson, AH, JE Bowers, and BA Chapman. 2004. "Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics." Proceedings of the National Academy of Sciences of the United States of America 101 (26):9903-9908. Paterson, AH, JE Bowers, DG Peterson, JC Estill, and BA Chapman. 2003. "Structure and evolution of cereal genomes." Current Opinion in Genetics & Development 13 (6):644-650. Paulis, JW, and JS Wall. 1977. "Comparison of the protein compositions of selected corns and their wild relatives, teosinte and Tripsacum." Journal of Agricultural and Food Chemistry 25 (2):265-270. Paulis, JW, and JS Wall. 1979. "Distribution and electrophoretic properties of alcohol- soluble proteins in normal and high-lysine sorghums." Cereal Chemistry 56 (1):20-23. Pereira, MG, D Ahnert, M Lee, and K Klier. 1995. "Genetic mapping of quantitative trait loci for panicle characteristics and seed weight in sorghum." Revista Brasileira De Genetica 18:249-249. Pereira, MG, and M Lee. 1995. "Identification of genomic regions affecting plant height in sorghum and maize." Theoretical and Applied Genetics 90 (3-4):380-388. Perini, LA, and JL Magoja. 1988. "Effect of perennial teosinte introgression in maize on kernel protein content." Maize Genet Coop Newsl 62:80. Perry, HJ, R Bligny, E Gout, and JL Harwood. 1999. "Changes in Kennedy pathway intermediates associated with increased triacylglycerol synthesis in oil-seed rape." Phytochemistry 52 (5):799-804. Perry, HJ, and JL Harwood. 1993. "Radiolabelling studies of acyl lipids in developing seeds of Brassica napus: Use of [1-14C] acetate precursor." Phytochemistry 33 (2):329-333. Piekkielek, WP, and RH Fox. 1992. "Use of a chlorophyll meter to predict sidedress

nitrogen." Agronomy Journal 84 (1):59-65. 145

Pixley, KV, and MS Bjarnason. 1994. "Pollen-parent effects on protein quality and endosperm modification of quality protein maize." Crop Science 34 (2):404-409. Pollak, LM, and MP Scott. 2005. "Breeding for grain quality traits." Maydica 50 (3/4):247. Poneleit, CG, and LF Bauman. 1970. "Diallel analyses of fatty acids in corn (Zea mays L.) oil." Crop Science 10 (4):338-341. Poneleit, CG, and DE Alexander. 1965. "Inheritance of linoleic and oleic acids in maize." Science 147 (3665):1585-1586. Prasanna, B, and K Sarkar. 1991. "Coordinate genetic regulation of maize endosperm." Maize genetics Perspectives ICAR:74-86. Pratt, RC, JW Paulis, K Miller, T Nelsen, and JA Bietz. 1995. "Association of zein classes with maize kernel hardness." Cereal Chemistry 72 (2):162-166. Purcino, AAC, C Arellano, GS Athwal, and SC Huber. 1998. "Nitrate effect on carbon and nitrogen assimilating enzymes of maize hybrids representing seven eras of breeding." Maydica 43.

146

Purseglove, JW. 1972. Tropical crops–monocotyledons Longman. London. Quraishi, UM, M Abrouk, F Murat, C Pont, S Foucrier, G Desmaizieres, C Confolent, N Rivière, G Charmet, and E Paux. 2011. "Cross‐genome map based dissection of a nitrogen use efficiency ortho‐metaQTL in bread wheat unravels concerted cereal genome evolution." The Plant Journal 65 (5):745-756. Radchuk, R, V Radchuk, KP Götz, H Weichert, A Richter, RJ Emery, W Weschke, and H Weber. 2007. "Ectopic expression of phosphoenolpyruvate carboxylase in Vicia narbonensis seeds: effects of improved nutrient status on seed maturation and transcriptional regulatory networks." The Plant Journal 51 (5):819-839. Rajcan, I, and M Tollenaar. 1999. "Source: sink ratio and leaf senescence in maize:: II. Nitrogen metabolism during grain filling." Field Crops Research 60 (3):255-265. Rami, JF, P Dufour, G Trouche, G Fliedel, C Mestres, F Davrieux, P Blanchard, and P Hamon. 1998. "Quantitative trait loci for grain quality, productivity, morphological and agronomical traits in sorghum (Sorghum bicolor L. Moench)." Theoretical and Applied Genetics 97 (4):605-616. Randall, RC, GO Phillips, and PA Williams. 1988. "The role of the proteinaceous component on the emulsifying properties of gum arabic." Food Hydrocolloids 2 (2):131-140. Rausch, KD, and RL Belyea. 2006. "The future of coproducts from corn processing." Applied Biochemistry and Biotechnology 128 (1):47-86. Reddy, M. 2000. "Influence of process variables and flour characteristics of sorghum cultivars on rheological properties of dough and roti." M.H.Sc, University of Agricultural Sciences. Reed, AJ, FE Below, and RH Hageman. 1980. "Grain protein accumulation and the relationship between leaf nitrate reductase and protease activities during grain development in maize (Zea mays L.) I. Variation between genotypes." Plant Physiology 66 (1):164-170.

Reggiani, RS, C Di Fonzo, N Gentinetta, E Salamini. 1985. “Factors affecting starch and 146

protein content in developing endosperms of high and low protein strains of maize.” Genetica Agricultruae. Rendig, VV, and FE Broadbent. 1979. "Proteins and amino acids in grain of maize grown with various levels of applied N." Agronomy Journal 71 (3):509-512. Rhodes, AP, and G Jenkins. 1978. "Improving the protein quality of cereals, grain legumes and oilseeds by breeding." Norton G. Butterworth, London, UK:207-266. Robutti, JL, FS Borras, and GH Eyherabide. 1997. "Zein Compositions of Mechanically Separated Coarse and Fine Portions of Maize Kernels 1." Cereal Chemistry 74 (1):75-78. Robutti, JL, FS Borras, ME Ferrer, and JA Bietz. 2000. "Grouping and identification of Argentine maize races by principal component analysis of zein reversed-phase HPLC data." Cereal chemistry 77 (2):91-95.

147

Rolletschek, H, L Borisjuk, R Radchuk, M Miranda, U Heim, U Wobus, and H Weber. 2004. "Seed‐specific expression of a bacterial phosphoenolpyruvate carboxylase in Vicia narbonensis increases protein content and improves carbon economy." Plant Biotechnology Journal 2 (3):211-219. Rom, DL, JM Shull, A Chandrashekar, and AW Kirleis. 1992. "Effects of cooking and treatment with sodium bisulfite on in vitro protein digestibility and microstructure of sorghum flour." Cereal Chem 69 (1):178-181. Romay, MC, MJ Millard, JC Glaubitz, JA Peiffer, KL Swarts, TM Casstevens, RJ Elshire, CB Acharya, SE Mitchell, and SA Flint-Garcia. 2013. "Comprehensive genotyping of the USA national maize inbred seed bank." Genome Biol 14:R55. Rooney, LW, and SO Serna-Saldivar. 1991. "Sorghum." In Handbook of cereal science and technology, edited by VF Rasper, KJ Lorenz and K Kulp, 233-269. New York: Marcel Dekker. Rooney, LW. 1978. "Sorghum and pearl millet lipids." Cereal Chemistry 55 (584):1. Rooney, LW, and RL Pflugfelder. 1986. "Factors affecting starch digestibility with special emphasis on sorghum and corn." Journal of Animal Science 63 (5):1607-1623. Rooney, W, J Mullet, S Kresovich, D Ware, and P Klein. 2006. "Sorghum biomass/feedstock genomics research for bioenergy.". USDOE Office of Science. Rosales, A, L Galicia, E Oviedo, C Islas, and N Palacios-Rojas. 2011. "Near-infrared reflectance spectroscopy (NIRS) for protein, tryptophan, and lysine evaluation in quality protein maize (QPM) breeding programs." Journal of Agricultural and Food Chemistry 59 (20):10781-10786. Rose, D. J., Inglett, G. E., & Liu, S. X. 2010. “Utilisation of corn (Zea mays) bran and corn fiber in the production of food components.”Journal of the Science of Food and Agriculture,90(6), 915-924. Rostagno, HS, JC Rogler, and WR Featherston. 1973. "Studies on the Nutritional Value of Sorghum Grains with Varying Tannin Contents for Chicks 2. Amino Acid

Digestibility Studies." Poultry Science 52 (2):772-778. 147

RStudio Version 0.98.501. http://www.rstudio.org/, Boston, MA. Ryther, JH, and WM Dunstan. 1971. "Nitrogen, phosphorus, and eutrophication in the coastal marine environment." Science 171 (3975):1008-1013. Sacher, JA. 1957. "Relationship between auxin and membrane-integrity in tissue senescence and abscission." Science 125 (3259):1199-1200. Saha, UK, LS Sonon, DW Hancock, NS Hill, L Stewart, GL Heusner, and DE Kissel. 2010. "Common terms used in animal feeding and nutrition." Salamini, F, B Borghi, and C Lorenzoni. 1970. "The effect of the opaque-2 gene on yield in maize." Euphytica 19 (4):531-538. Salunkhe, DK, SS Kadam, and JK Chavan. 1977. "Nutritional quality of proteins in grain sorghum." Qualitas Plantarum 27 (2):187-205. Sanchez, FC, MY Salinas, CM Vázquez, CG Velázquez, and GN Aguilar. 2007. "Effect of the prolamins in maize (Zea mays L.) grain on tortilla texture." Archivos Latinoamericanos de Nutricion 57 (3):295-301.

148

Sanders, EB, DB Thompson, and CD Boyer. 1990. "Thermal behavior during gelatinization and amylopectin fine structure for selected maize genotypes as expressed in four inbred lines." Cereal Chemistry 67 (6):594-602. Sangwan, RS, N Singh, and WC Plaxton. 1992. "Phosphoenolpyruvate carboxylase activity and concentration in the endosperm of developing and germinating castor oil seeds." Plant Physiology 99 (2):445-449. Sastry, LVS, JW Paulis, JA Bietz, and JS Wall. 1986. "Genetic variation of storage proteins in sorghum grain: Studies by isoelectric focusing and high-performance liquid chromatography." Cereal Chem 63 (5):420-427. Sauberlich, HE, WY Chang, and WD Salmon. 1953. "The Amino Acid and Protein Content of Corn as Related to Variety and Nitrogen Fertilization Two Figures." The Journal of Nutrition 51 (2):241-250. Sauer, TJ, RB Alexander, JV Brahana, and RA Smith. 2008. ". The Importance and Role of Watersheds in the Transport of Nitrogen." Nitrogen in the Environment:203. Schell, DJ, CJ Riley, N Dowe, J Farmer, KN Ibsen, MF Ruth, ST Toon, and RE Lumpkin. 2004. "A bioethanol process development unit: initial operating experiences and results with a corn fiber feedstock." Bioresource Technology 91 (2):179-188. Schepers, JS, DD Francis, M Vigil, and FE Below. 1992. "Comparison of corn leaf nitrogen concentration and chlorophyll meter readings." Communications in Soil Science & Plant Analysis 23 (17-20):2173-2187. Schilling, KE, and RD Libra. 2000. "The relationship of nitrate concentrations in streams to row crop land use in Iowa." Journal of Environmental Quality 29 (6):1846- 1851. Schluttenhofer, C, S Pattanaik, B Patra, and L Yuan. 2014. "Analyses of Catharanthus roseus and Arabidopsis thaliana WRKY transcription factors reveal involvement in jasmonate signaling." BMC Genomics 15 (1):502. Schneider, EO, EB Earley, and EE DeTurk. 1952. "Nitrogen fractions of the component

parts of the corn kernel as affected by selection and soil nitrogen." Agronomy 148

Journal 44 (4):161-169. Sebei, K, Z Ouerghi, H Kallel, and S Boukhchina. 2006. "Evolution of phosphoenolpyruvate carboxylase activity and lipid content during seed maturation of two spring rapeseed cultivars (Brassica napus L.)." Comptes Rendus Biologies 329 (9):719-725. Sechley, KA, T Yamaya, and A Oaks. 1992. "Compartmentation of nitrogen assimilation in higher plants." Int Rev Cytol 134:85-163. Seebauer, Juliann R., Stephen P. Moose, Bradon J. Fabbri, Lyle D. Crossland, and Frederick E. Below. 2004. "Amino acid metabolism in maize earshoots. Implications for assimilate preconditioning and nitrogen signaling."Plant Physiology 136, no. 4 (2004): 4326-4334. Sekhon, RS, H Lin, KL Childs, CN Hansey, CR Buell, N de Leon, and SM Kaeppler. 2011. "Genome‐wide atlas of transcription during maize development." The Plant Journal 66 (4):553-563.

149

Serna-Saldivar, S, and LW Rooney. 1995. "Structure and chemistry of sorghum and millets." Sorghum and Millets: Chemistry and Technology:69-124. Session, IV. 1974. "Poultry Nutrition in Latin America with Special Reference to Scientific Poultry Raising." Animal production in the tropics: proceedings of the International Symposium on Animal Production in the Tropics. Settlage, SB, RF Wilson, and P Kwanyuen. 1995. "Localization of diacylglycerol acyltransferase to oil body associated endoplasmic reticulum." Plant Physiology and Biochemistry 33 (4):399-407. Sexton, R, and JA Roberts. 1982. "Cell biology of abscission." Annual Review of Plant Physiology 33 (1):133-162. Sharma, BD, VR Sadagopan, and VR Reddy. 1979. "Utilisation of different cereals in broiler diets." British Poultry Science 20 (4):371-378. Sharma, KP, and AK Goswami. 1969. "Chemical constants of lipid content of high yielding varieties and hybrids of bajra (Pennisetum typhoideum) flour." J. Nutr. Diet 6:316. Shelp, BJ, AW Bown, and MD McLean. 1999. "Metabolism and functions of gamma- aminobutyric acid." Trends in Plant Science 4 (11):446-452. Shelton, M, JR Couch, F Hole, JF Joher, RE Leighton, CM Lyman, and JK Briggs. 1951. "Grain sorghum by-product feeds farm animal." Texas Agricultural Experiment Station Bulletin:743. Shoji, K, FT Addicott, and WA Swets. 1951. "Auxin in relation to leaf blade abscission." Plant Physiology 26 (1):189. Shull, JM, JJ Watterson, and AW Kirleis. 1991. "Proposed nomenclature for the alcohol- soluble proteins (kafirins) of Sorghum bicolor (L. Moench) based on molecular weight, solubility, and structure." Journal of Agricultural and Food Chemistry 39 (1):83-87. Shull, JM, JJ Watterson, and AW Kirleis. 1992. "Purification and immunocytochemical

localization of kafirins inSorghum bicolor (L. Moench) endosperm." Protoplasma 149

171 (1-2):64-74. Sibbald, IR. 1977. "The true metabolizable energy values of some feeding stuffs." Poultry Science 56 (1):380-382. Simpson, RJ, H Lambers, and MJ Dalling. 1983. "Nitrogen redistribution during grain growth in wheat (Triticum aestivum L.) IV. Development of a quantitative model of the translocation of nitrogen to the grain." Plant Physiology 71 (1):7-14. Singal, HR, G Talwar, A Dua, and R Singh. 1995. "Pod photosynthesis and seed dark CO2 fixation support oil synthesis in developing Brassica seeds." Journal of Biosciences 20 (1):49-58. Singh, J, and VL Asnani. 1975. "Present status and future prospects of breeding for better protein quality in maize through opaque-2." High-Quality Protein Maize:85-101. Singh, V, GS Murthy, JV Graeber, and ME Tumbleson. 2004. "Grain quality issues related to corn dry grind processing." International Quality Grains Conference, Indianapolis, IN.

150

Singh, V, LW Doner, DB Johnston, KB Hicks, and SR Eckhoff. 2000. "Comparison of coarse and fine corn fiber for corn fiber gum yields and sugar profiles." Cereal Chemistry 77 (5):560-561. Sloggett, G, and C Dickason. 1986. “Ground-water mining in the United States. Agricultural economic report.” Economic Research Service, Washington, DC (USA). Natural Resource Economics Div. Socolow, RH. 1999. "Nitrogen management and the future of food: lessons from the management of energy and carbon." Proceedings of the National Academy of Sciences 96 (11):6001-6008. Sodek, L, and WJ da Silva. 1977. "Glutamate synthase: a possible role in nitrogen metabolism of the developing maize endosperm." Plant Physiology 60 (4):602- 605. Sodek, L, PJ Lea, and BJ Miflin. 1980. "Distribution and properties of a potassium- dependent asparaginase isolated from developing seeds of Pisum sativum and other plants." Plant Physiology 65 (1):22-26. Sprague, GF, B Brimhall, and RM Hixon. 1943. "Some effects of the waxy gene in corn on properties of the endosperm starch." Agronomy Journal 35 (9):817-822. Sreeramulu, C, and LF Bauman. 1970. "Yield components and protein quality of opaque- 2 and normal diallels of maize." Crop Science 10 (3):262-265. Stephens, JC, FR Miller, and DT Rosenow. 1967. "Conversion of alien sorghums to early combine genotypes." Crop Science 7 (4):396-396. Stephenson, EL, JO York, DB Bragg, and CA Ivy. 1971. "The amino acid content and availability of different strains of grain sorghum to the chick." Poultry Science 50 (2):581-584. Stickler, FC. 1964. "Row width and plant population studies with corn." Agronomy Journal 56 (4):438-441. Stobart, AK, S Stymne, and S Höglund. 1986. "Safflower microsomes catalyse oil

accumulation in vitro: a model system." Planta 169 (1):33-37. 150

Streeter, MN, GM Hill, DG Wagner, CA Hibberd, and FN Owens. 1993. "Chemical and physical properties and in vitro dry matter and starch digestion of eight sorghum grain hybrids and maize." Animal Feed Science and technology 44 (1):45-58. Streeter, MN, DG Wagner, CA Hibberd, and FN Owens. 1990. "The effect of sorghum grain variety on site and extent of digestion in beef heifers." Journal of Animal Science 68 (4):1121-1132. Streit, L, and U Feller. 1983. "Changing activities and different resistance to proteolytic activity of two forms of glutamine synthetase in wheat leaves during senescence." Physiologie Végétale. Stroshine, R, A Emam, J Tuite, F Cantone, A Kirleis, L Bauman, and M Okos. 1981. "Comparison of drying rates and quality parameters for selected corn inbreds/hybrids." Am. Soc. Agric. Engrs, Paper (81-3529). Stroshine, R, A Emam, J Tuite, F Cantone, A Kirleis, L Bauman, and M Okos. 1982. Comparison of drying rates and quality parameters for selected corn inbreds. hybrids. (No. 82-3529). ASAE Paper.

151

Stymne, S, and AK Stobart. 1987. "Triacylglycerol biosynthesis." Biochemistry of Plants 9:175-214. Subramanian, V, R Jambunathan, and S Suryaprakash. 1980. "Note on the soluble sugars of sorghum." Cereal Chemistry 57 (6):440-441. Subramanian, V, and VC Metta. 2000. "Sorghum Grain for Poultry Feed." In Technical and institutional options for sorghum grain mold management. Proceedings of an international consultation, edited by Arun Chandrashekar, Ranajit Bandyopadhyay and Andrew J Hall, 242-247. Patancheru, India: ICRISAT. Sukumaran, S, W Xiang, SR Bean, JF Pedersen, S Kresovich, MR Tuinstra, TT Tesso, MT Hamblin, and J Yu. 2012. "Association mapping for grain quality in a diverse sorghum collection." The Plant Genome 5 (3):126-135. Swank, JC, FE Below, RJ Lambert, and RH Hageman. 1982. "Interaction of carbon and nitrogen metabolism in the productivity of maize." Plant Physiology 70 (4):1185- 1190. Ta, C T, and RT Weiland. 1992. "Nitrogen partitioning in maize during ear development." Crop Science 32 (2):443-451. Tacon, AG. 1995. "Fishmeal replacers: Review of antinurients within oilseeds and pulses." A limiting factor for the aquafeed green revolution. Feed Ingredients, Asia, Singapore. Tanaka, W, and GA Maddonni. 2008. "Pollen source and post-flowering source/sink ratio effects on maize kernel weight and oil concentration." Crop Science 48 (2):666- 677. Taylor, JRN, J Dewar, J Taylor, and RF Von Ascheraden. 1997. "Factors affecting the porridge-making quality in South African sorghums." Taylor, L, A Nunes‐Nesi, K Parsley, A Leiss, G Leach, S Coates, A Wingler, AR Fernie, and JM Hibberd. 2010. "Cytosolic pyruvate, orthophosphate dikinase functions in nitrogen remobilization during leaf senescence and limits individual seed growth

and nitrogen content." The Plant Journal 62 (4):641-652. 151

Tegeder, M, and D Rentsch. 2010. "Uptake and partitioning of amino acids and peptides." Molecular Plant 3 (6):997-1011. Tercé-Laforgue, T, F Dubois, S Ferrario-Méry, MA Pou de Crecenzo, R Sangwan, and B Hirel. 2004. "Glutamate dehydrogenase of tobacco is mainly induced in the cytosol of phloem companion cells when ammonia is provided either externally or released during photorespiration." Plant physiology 136 (4):4308-4317. Thomison, PR, AB Geyer, LD Lotz, HJ Siegrist, and TL Dobbels. 2003. "TopCross High Oil Corn Production." Agronomy Journal 95 (1):147-154. Thompson, JE, LD Nooden, and AC Leopold. 1988. "Senescence and aging in plants." Senescence and Aging in Plants. Thompson, RA, and GW Isaacs. 1967. "Porosity determination of grains and seeds with air comparison pycnometer." Transactions of the ASAE 10 (5):693-696. Thurber, CS, JM Ma, RH Higgins, and PJ Brown. 2013. "Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production." Genome Biology 14 (6):1-12.

152

Tilsner, J, N Kassner, C Struck, and G Lohaus. 2005. "Amino acid contents and transport in oilseed rape (Brassica napus L.) under different nitrogen conditions." Planta 221 (3):328-338. Tiwari, SB, G Hagen, and T Guilfoyle. 2003. "The roles of auxin response factor domains in auxin-responsive transcription." The Plant Cell Online 15 (2):533-543. Toro, AA, LO Medici, L Sodek, PJ Lea, and RA Azevedo. 2003. "Distribution of soluble amino acids in maize endosperm mutants." Scientia Agricola 60 (1):91-96. Tsai, CY, DM Huber, and HL Warren. 1980. "A proposed role of zein and glutelin as N sinks in maize." Plant Physiology 66 (2):330-333. Tsai, CY. 1983. "Genetics of storage protein in maize." In Plant Breeding Reviews, 103- 138. Springer. Tsai, CY, and A Dalby. 1974. "Comparison of the effect of shrunken-4, opaque-2, opaque-7, and floury-2 genes on the zein content of maize during endosperm development." Cereal Chem 51 (825):I974. Tsai, CY, DM Huber, and HL Warren. 1978. "Relationship of the kernel sink for N to maize productivity." Crop Science 18 (3):399-404. Tsai, CY, DM Huber, HL Warren, and CL Tsai. 1986. "Sink regulation of source activity by nitrogen utilization." Tsai, CY, BA Larkins, and DV Glover. 1978. "Interaction of the opaque-2 gene with starch- forming mutant genes on the synthesis of zein in maize endosperm." Biochemical Genetics 16 (9-10):883-896. Tsai, CY, F Salamini, and OE Nelson. 1970. "Enzymes of carbohydrate metabolism in the developing endosperm of maize." Plant Physiology 46 (2):299-306. Tzen, JTC, YZ Cao, P Laurent, C Ratnayake, and AHC Huang. 1993. "Lipids, proteins, and structure of seed oil bodies from diverse species." Plant Physiology 101 (1):267- 276. Ülker, B, MS Mukhtar, and IE Somssich. 2007. "The WRKY70 transcription factor of

Arabidopsis influences both the plant senescence and defense signaling 152

pathways." Planta 226 (1):125-137. Uribelarrea, M, SP Moose, and FE Below. 2007. "Divergent selection for grain protein affects nitrogen use in maize hybrids." Field Crops Research 100 (1):82-90. Val, LD, SH Schwartz, MR Kerns, and J Deikman. 2009. "Development of a high oil trait for maize." In Molecular Genetic Approaches to Maize Improvement, 303-323. Springer. van der Graaff, E, R Schwacke, A Schneider, M Desimone, UI Flügge, and R Kunze. 2006. "Transcription analysis of Arabidopsis membrane transporters and hormone pathways during developmental and induced leaf senescence." Plant Physiology 141 (2):776-792. Vannalli, S, BK, R Naik, and N Yenagi. 2007. "Nutritive value and quality characteristics of sorghum genotypes." Karnataka Journal of Agricultural Sciences 20 (3):586. Villegas, E, SK Vasal, M Bjarnason, and ET Mertz. 1992. "Quality protein maize–what is it and how was it developed." Quality protein maize:27-48.

153

Vineyard, ML, and RP Bear. 1952. "Amylose content." Maize Genet Coop News Lett 26 (5). Virupaksha, TK, and LVS Sastry. 1968. "Protein content and amino acid composition of some varieties of grain sorghum." Journal of Agricultural and Food Chemistry 16 (2):199-203. Vohra, P, FH Kratzer, and MA Joslyn. 1966. "The growth depressing and toxic effects of tannins to chicks." Poultry Science 45 (1):135-142. Voltas, J, I Romagosa, P Muñoz, and JL Araus. 1998. "Mineral accumulation, carbon isotope discrimination and indirect selection for grain yield in two-rowed barley grown under semiarid conditions." European Journal of Agronomy 9 (2):147- 155. Vyn, TJ, and J Moes. 1988. "Breakage susceptibility of corn kernels in relation to crop management under long growing season conditions." Agronomy Journal 80 (6):915-920. Waggle, DH, CW Deyoe, and FW Smith. 1967. "Effect of nitrogen fertilization on the amino acid composition and distribution in sorghum grain." Crop Science 7 (4):367-368. Waldroup, PW, DE Greene, RH Harris, JF Maxey, and EL Stephenson. 1967. "Comparison of corn, wheat, and milo in turkey diets." Poultry Science 46 (6):1581-1585. Wall, JS, and JW Paulis. 1978. "Corn and sorghum grain proteins." Advances in Cereal Science and Technology 11 (3):135-219. Wang, YJ, P White, and L Pollak. 1992. "Thermal and gelling properties of maize mutants from the OH43 inbred line." Cereal Chemistry 69 (3):328-334. Wang, YJ, P White, and L Pollak. 1993. "Physicochemical properties of starches from mutant genotypes of the Oh43 inbred line." Cereal chemistry 70:199-199. Wang, YJ, P White, L Pollak, and J Jane. 1993a. "Amylopectin and intermediate materials in starches from mutant genotypes of the Oh43 inbred line." Cereal chemistry 70

(5):521-525. 153

Wang, YJ, P White, L Pollak, and J Jane. 1993b. "Characterization of starch structures of 17 maize endosperm mutant genotypes with Oh43 inbred line background." Cereal Chemistry 70:171-171. Warren, HL. 1978. "Comparison of normal and high-lysine maize inbreds for resistance to kernel rot caused by Fusarium moniliforme." Phytopathology 68 (9):1331- 1335. Warsi, AS, and BC Wright. 1973. "Effects of Rates and Methods of Nitrogen Application on Quality of Sorghum Grain." Indian Journal of Agricultural Sciences 43 (7):722- 726. Watson, SA, PJ White, and LA Johnson. 2003. "Description, development, structure, and composition of the corn kernel." Corn: Chemistry and Technology (Ed. 2):69-106. Watson, SA, and Y Hirata. 1960. "Carbohydrates in grain sorghum kernels." Sorghum Newsl 3 (7). Watson, SA, and Y Hirata. 1955. "The wet milling properties of grain sorghums." Agronomy Journal 47 (1):11-15.

154

Watson, SA, JS Wall, and WM Ross. 1970. "Wet-milling process and products." Sorghum Production and Utilization.:602-26. Watson, Stanley A, and PE Ramstad. 1987. "Structure and composition." Corn: Chemistry and Technology.:53-82. Watterson, JJ, JM Shull, and AW Kirleis. 1993. "Quantitation of α-, β-, and γ-kafirins in vitreous and opaque endosperm of Sorghum bicolor." Cereal Chemistry 70 (4):452-457. Weaver, CA, BR Hamaker, and JD Axtell. 1998. "Discovery of Grain Sorghum Germ Plasm with High Uncooked and Cooked In Vitro Protein Digestibilities 1." Cereal Chemistry 75 (5):665-670. Weber, EJ, SA Watson, and PE Ramstad. 1987. "Lipids of the kernel." Corn: Chemistry and Technology.:311-349. Weber, H, L Borisjuk, and U Wobus. 2005. "Molecular physiology of legume seed development." Annu. Rev. Plant Biol. 56:253-279. Weigelt, K, H Küster, R Radchuk, M Müller, H Weichert, A Fait, AR Fernie, I Saalbach, and H Weber. 2008. "Increasing amino acid supply in pea embryos reveals specific interactions of N and C metabolism, and highlights the importance of mitochondrial metabolism." The Plant Journal 55 (6):909-926. Weiland, RT, and TC Ta. 1990. "Maize use of 15N applied prior to, at, or after anthesis." Agronomy 82:133. Weiland, RT, and TC Ta. 1992. "Allocation and retranslocation of 15N by maize (Zea mays L.) hybrids under field conditions of low and high N fertility." Functional Plant Biology 19 (1):77-88. Weselake, RJ, MK Pomeroy, TL Furukawa, JL Golden, DB Little, and A Laroche. 1993. "Developmental profile of diacylglycerol acyltransferase in maturing seeds of oilseed rape and safflower and microspore-derived cultures of oilseed rape." Plant physiology 102 (2):565-571.

Wester, TJ, SM Gramlich, RA Britton, and RA Stock. 1992. "Effect of grain sorghum 154

hybrid on in vitro rate of starch disappearance and finishing performance of ruminants." Journal of Animal Science 70 (9):2866-2876. Wichser, WR. 1961. "The world of corn processing." Am. Miller Process 89 (4):29-31. Widstrom, NW, and MD Jellum. 1975. "Inheritance of kernel fatty acid composition among six maize inbreds." Crop Science 15 (1):44-46. Wilson, LM, SR Whitt, AM Ibáñez, TR Rocheford, MM Goodman, and ES Buckler. 2004. "Dissection of maize kernel composition and starch production by candidate gene association." The Plant Cell Online 16 (10):2719-2733. Winter, D, B Vinegar, H Nahal, R Ammar, GV Wilson, and NJ Provart. 2007. "An “Electronic Fluorescent Pictograph” browser for exploring and analyzing large- scale biological data sets." PloS one 2 (8):e718. Wolfe, DW, DW Henderson, TC Hsiao, and A Alvino. 1988. "Interactive water and nitrogen effects on senescence of maize. I. Leaf area duration, nitrogen distribution, and yield." Agronomy Journal 80 (6):859-864.

155

Wolfinger, R, WT Federer, and O Cordero-Brana. 1997. "Recovering information in augmented designs, using SAS PROC GLM and PROC MIXED." Agronomy Journal 89 (6):856-859. Won, C, X Shen, K Mashiguchi, Z Zheng, X Dai, Y Cheng, H Kasahara, Y Kamiya, J Chory, and Y Zhao. 2011. "Conversion of tryptophan to indole-3-acetic acid by Tryptophan aminotransferases of Arabidopsis and Yuccas in Arabidopsis." Proceedings of the National Academy of Sciences 108 (45):18518-18523. Wright, A. 1995. "A gene conditioning high oleic maize oil-Olc1." Maydica (Italy). Wyss, CS, JR Czyzewicz, and FE Below. 1991. "Source-sink control of grain composition in maize strains divergently selected for protein concentration." Crop Science 31 (3):761-766. Xie, Z, ZL Zhang, X Zou, G Yang, S Komatsu, and QJ Shen. 2006. "Interactions of two abscisic‐acid induced WRKY genes in repressing gibberellin signaling in aleurone cells." The Plant Journal 46 (2):231-242. Yadav, MP, DB Johnston, and KB Hicks. 2007. "Structural characterization of corn fiber gums from coarse and fine fiber and a study of their emulsifying properties." Journal of Agricultural and Food Chemistry 55 (15):6366-6371. Yadav, MP, DB Johnston, and KB Hicks. 2009. "Corn fiber gum: New structure/function relationships for this potential beverage flavor stabilizer." Food Hydrocolloids 23 (6):1488-1493. Yadav, MP, DB Johnston, KB Hicks, and EA Nothnagel. 2006. "The role of lipid and protein components in the emulsification properties of gum Arabic and corn fiber gum." Foods and Food Ingredients Journal of Japan 211 (3):243. Yadav, MP, DB Johnston, AT Hotchkiss Jr, and KB Hicks. 2007. "Corn fiber gum: a potential gum arabic replacer for beverage flavor emulsification." Food Hydrocolloids 21 (7):1022-1030. Yadav, MP, JM Igartuburu, Y Yan, and EA Nothnagel. 2007. "Chemical investigation of

the structural basis of the emulsifying activity of gum arabic." Food 155

Hydrocolloids 21 (2):297-308. Yadav, MP, RA Moreau, and KB Hicks. 2007. "Phenolic acids, lipids, and proteins associated with purified corn fiber arabinoxylans." Journal of Agricultural and Food chemistry 55 (3):943-947. Yamaya, T, M Obara, H Nakajima, S Sasaki, T Hayakawa, and T Sato. 2002. "Genetic manipulation and quantitative‐trait loci mapping for nitrogen recycling in rice." Journal of Experimental Botany 53 (370):917-925. Yan, L, ZQ Liu, YH Xu, K Lu, XF Wang, and DP Zhang. 2013. "Auto-and cross-repression of three Arabidopsis WRKY transcription factors WRKY18, WRKY40, and WRKY60 negatively involved in ABA signaling." Journal of Plant Growth Regulation 32 (2):399-416. Yousif, NE, and AH El Tinay. 2001. "Effect of fermentation on sorghum protein fractions and in vitro protein digestibility." Plant Foods for Human Nutrition 56 (2):175- 182.

156

Yu, J, JB Holland, MD McMullen, and ES Buckler. 2008. "Genetic design and statistical power of nested association mapping in maize." Genetics 178 (1):539-551. Yu, J, G Pressoir, WH Briggs, IV Bi, M Yamasaki, JF Doebley, MD McMullen, BS Gaut, DM Nielsen, and JB Holland. 2005. "A unified mixed-model method for association mapping that accounts for multiple levels of relatedness." Nature Genetics 38 (2):203-208. Yu, J, P Peng, X Zhang, Q Zhao, D Zhy, X Sun, J Liu, and G Ao. 2004. "Seed-specific expression of a lysine rich protein sb401 gene significantly increases both lysine and total protein content in maize seeds." Molecular Breeding 14 (1):1-7. Zhang, Y, H Darlington, HD Jones, NG Halford, JA Napier, MR Davey, PA Lazzeri, and PR Shewry. 2003. "Expression of the gamma-zein protein of maize in seeds of transgenic barley: effects on grain composition and properties." Theoretical and Applied Genetics 106 (6):1139-1146. Zhang, Z, E Ersoz, CQ Lai, RJ Todhunter, HK Tiwari, MA Gore, PJ Bradbury, J Yu, DK Arnett, and JM Ordovas. 2010. "Mixed linear model approach adapted for genome-wide association studies." Nature Genetics 42 (4):355-360. Zhao, ZY, K Glassman, V Sewalt, N Wang, M Miller, S Chang, T Thompson, S Catron, E Wu, D Bidney, Y Kedebe, and R Jung. 2003. "Nutritionally Improved Transgenic Sorghum." In Plant Biotechnology 2002 and Beyond : Proceedings of the 10th IAPTC&B Congress, June 23-28, 2002, Orlando, Florida, U.S.A, edited by I. K. Vasil, 413-416. Dordrecht ; Boston: Kluwer Academic Publishers. Zheng, P, WB Allen, K Roesler, ME Williams, S Zhang, J Li, K Glassman, J Ranch, D Nubel, and W Solawetz. 2008. "A phenylalanine in DGAT is a key determinant of oil content and composition in maize." Nature Genetics 40 (3):367-372. Zhou, C, Z Cai, Y Guo, and S Gan. 2009. "An Arabidopsis mitogen-activated protein kinase cascade, MKK9-MPK6, plays a role in leaf senescence." Plant Physiology 150 (1):167-177.

Zuber, MS, and JL Helm. 1975. "Approaches to improving protein quality in maize 156

without the use of specific mutants." High Quality Protein Maize. Dowden, Hutchinson, and Ross, Stroudsburg, PA:241-252. Zuber, MS, GE Smith, and CW Gehrke. 1954. "Crude protein of corn grain and stover as influenced by different hybrids, plant populations, and nitrogen levels." Agronomy Journal 46 (6):257-261.

APPENDICES

157

Appendix A Maize Leaf N Remobilization SAS Code for BLUP Analysis

Below is BLUP SAS code for the trait R2H, all other traits use similar code for BLUP calculations

/****** For Combined analysis of 2012 and 2013 for R2HAVG*/ data AMES12; infile 'U:\Research Projects\Leaf N Movement\2013\Compiled Final File AMES 2012.csv' dsd firstobs=2 missover; input Plot Range Row GROUPID$ MaturityGroup ITEM$ ACCESSION$ DTA DTS VTL1 VTH1 VTL2 VTH2 VTL3 VTH3 VTL4 VTH4 R2L1 R2H1 R2L2 R2H2 R2L3 R2H3 R2L4 R2H4 R4L1 R4H1 R4L2 R4H2 R4L3 R4H3 R4L4 R4H4 treatn$ new; Year = '1'; VTLAVG= (mean(VTL1,VTL2,VTL3,VTL4)); VTHAVG= (mean(VTH1,VTH2,VTH3,VTH4)); R2LAVG= (mean(R2L1,R2L2,R2L3,R2L4)); R2HAVG= (mean(R2H1,R2H2,R2H3,R2H4)); R4LAVG= (mean(R4L1,R4L2,R4L3,R4L4)); R4HAVG= (mean(R4H1,R4H2,R4H3,R4H4)); if GroupID= 'C1' then delete; if GroupID= 'C2' then GroupID= '4000'; Data AMES12AVG; set AMES12; keep Plot Range Row GROUPID MaturityGroup ITEM ACCESSION DTA DTS VTLAVG VTHAVG R2LAVG R2HAVG R4LAVG R4HAVG treatn new year; proc sort; by maturitygroup plot; run; Data AMES12AVG1; set AMES12; keep Range GROUPID MaturityGroup ITEM ACCESSION treatn new R2HAVG;

157 rename range =range12;

rename R2HAVG = R2HAVG12; proc sort; by GroupID ; run; data AMES13; infile 'U:\Research Projects\Leaf N Movement\2013\Compiled Final File AMES 2013.csv' dsd firstobs=2 missover; input Plot Range Row GROUPID$ MaturityGroup ITEM$ ACCESSION$ DTA DTS VTL1 VTH1 VTL2 VTH2 VTL3 VTH3 VTL4 VTH4 R2L1 R2H1 R2L2 R2H2 R2L3 R2H3 R2L4 R2H4 R4L1 R4H1 R4L2 R4H2 R4L3 R4H3 R4L4 R4H4 treatn$ new; Year = '2'; VTLAVG= (mean(VTL1,VTL2,VTL3,VTL4)); VTHAVG= (mean(VTH1,VTH2,VTH3,VTH4)); R2LAVG= (mean(R2L1,R2L2,R2L3,R2L4)); R2HAVG= (mean(R2H1,R2H2,R2H3,R2H4)); R4LAVG= (mean(R4L1,R4L2,R4L3,R4L4)); R4HAVG= (mean(R4H1,R4H2,R4H3,R4H4));

158

if GroupID= 'C1' then delete; if GroupID= 'C2' then GroupID= '4000'; Data AMES13AVG; set AMES13; keep Plot Range Row GROUPID MaturityGroup ITEM ACCESSION DTA DTS VTLAVG VTHAVG R2LAVG R2HAVG R4LAVG R4HAVG treatn new year; proc sort; by maturitygroup plot; run; Data AMES13AVG1; set AMES13; keep Range GROUPID MaturityGroup ITEM ACCESSION treatn new R2HAVG; rename range =range13; rename R2HAVG= R2HAVG13; proc sort; by GroupID ; run; Data AmesComb; set AMES12AVG AMES13AVG; run; proc sort; by maturitygroup plot; run; Data AmesComb1; merge AMES12AVG1 AMES13AVG1; by GroupID; keep range12 range13 MaturityGroup GroupID ITEM ACCESSION treatn new R2HAVG12 R2HAVG13; run; proc sort; by maturitygroup; run;

/* To run an ANOVA on R2HAVG*/

proc glm data=AMESComb; 158 class GroupID year range; model R2HAVG=groupid year range(year); random year range(year); run;

/*To calculate BLUP*/ proc mixed data=AMESComb; by MaturityGroup; class year range GroupID treatn; model R2HAVG = treatn /solution; random year range(year) GroupID*New/ solution; lsmeans treatn; ods listing exclude solutionr; ods output solutionr=sr LSMeans=lsm; run; proc sort data = sr; by effect maturityGroup year;

159

/* Attempt to combine the Estimates for the different traits with the original data to compute BLUPs*/ Data LS; set lsm; rename Estimate=R2HuMean; proc sort Data=LS; By MaturityGroup treatn; run; proc sort data=AMESComb1; By MaturityGroup treatn; run; Data R2HREP; merge LS AMESComb1; By MaturityGroup treatn; keep range12 range13 treatn GROUPID MaturityGroup ITEM ACCESSION R2HuMean R2HAVG12 R2HAVG13; Data R2HRan; set sr; if Effect= 'Year' then delete; if GroupID= " " then R2HRan=Estimate; else delete; Data R2HEST; set sr; if GroupID= '' then delete; keep MaturityGroup GroupID Estimate; rename Estimate=R2HEst; run; Data R2HRan12; set R2HRan; if Year=1 then R2HRan12=R2HRan; else delete; keep MaturityGroup Effect Range R2HRan12; rename Range=Range12; Proc sort data=R2HRan12; by MaturityGroup Range12;

run; 159 Data R2HRan13; set R2HRan; if year=2 then R2HRan13=R2HRan; else delete; keep MaturityGroup Effect Range R2HRan13; rename Range=Range13; Proc Sort data=R2HRan13; by MaturityGroup Range13; run; proc sort data=AmesComb1; by MaturityGroup Range12; run; data R2HRan12Comb; merge AmesComb1 R2HRan12; by MaturityGroup Range12; keep range12 range13 treatn GroupID MaturityGroup Item Accession R2HRan12 R2HAVG12 R2HAVG13;

160 proc sort data=AmesComb1; by MaturityGroup Range13; run; data R2HRan13Comb; merge AmesComb1 R2HRan13; by MaturityGroup Range13; keep range12 range13 treatn GROUPID MaturityGroup ITEM ACCESSION R2HRan13 R2HAVG12 R2HAVG13; proc sort data=R2HRan12Comb; by MaturityGroup GroupID; run; proc sort data=R2HRan13Comb; by MaturityGroup GroupID; run; data R2HRanComb; merge R2HRan12Comb R2HRan13Comb; by MaturityGroup GroupID; keep range12 range13 treatn GroupID MaturityGroup Item Accession R2HRan12 R2HRan13 R2HAVG12 R2HAVG13; data combranrep; merge R2HRanComb R2HRep; by MaturityGroup; run; proc sort data=combranrep; by MaturityGroup GroupID; run; proc sort data=R2HEst; by MaturityGroup GroupID; run; Data CombinedR2H; merge CombRanRep R2HEST; by MaturityGroup GroupID; R2HBLUP= (R2HEST + R2HRan12 + R2HRan13 + R2HuMean); if R2HAVG12='.' then R2HBLUP='.'; if R2HAVG13='.' then R2HBLUP='.';

keep Range12 Range13 treatn GROUPID MaturityGroup ITEM ACCESSION 160 R2HAVG12 R2HAVG13 R2HEST R2HRan12 R2HRan13 R2HuMean R2HBLUP; run; proc univariate data=AmesComb; qqplot R2HAVG ;run; proc univariate data=combinedR2H; qqplot R2HBLUP ;run; proc print data=CombinedR2H;run; proc export DATA= CombinedR2H outfile="U:\Research Projects\Leaf N Movement\2013\BLUPs Calculated\Proc Mixed TO KEEP\CombinedR2H.csv" dbms=CSV; run;

161

Appendix B Maize Leaf N Remobilization R Code for GWAS Analysis

Below is R GWAS code for the trait R2HL, all other traits use similar code for GWAS analysis

rm(biocLite) source("http://www.bioconductor.org/biocLite.R") biocLite("multtest") install.packages("gplots") install.packages("LDheatmap") install.packages("genetics") library("multtest") library("gplots") library("LDheatmap") library("genetics") library("compiler") #this library is already installed in R source("http://www.maizegenetics.net/images/stories/bioinformatics/GAPIT/gapit_fun ctions.txt") source("http://www.maizegenetics.net/images/stories/bioinformatics/GAPIT/emma.txt ")

161 setwd("U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL") myY <- read.table("R2HL.txt",sep="", head = TRUE) head(myY) setwd("U:/Research Projects/GAPIT/diagrid") myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c1.hmp.txt ",sep= "", head = FALSE) head(myG)[,1:20] setwd("U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/") myKI <- read.table("Ames_50%SNPs_Comprehensive_K_JanuaryGBS_Names.txt", sep = "", head = FALSE) head(myKI)[,1:20]

162 is.numeric(myKI[,2]) myCV <- read.table("GAPIT.PCA_Ames2012_JanuaryGBS_names_50%SNP_estimated_short.txt", sep = "", head = TRUE) head(myCV)

#moving to dir to dump GAPIT results #setwd("/results") setwd("U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr1")

#Step 2: Run GAPIT for Chromosome 1 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV, group.from = 1500, group.to = 1717, group.by=10, #group.by = c(seq(1,1817,by=200),1817), G=myG, Model.selection=TRUE )

162

setwd("U:/Research Projects/GAPIT/diagrid") myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c2.hmp.txt ",sep= "", head = FALSE) setwd("U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr2")

#Step 2: Run GAPIT for Chromosome 2 myGAPIT <- GAPIT( Y=myY, KI=myKI,

163

CV=myCV, group.from = 1560, group.to = 1560, G=myG, Model.selection=TRUE ) setwd("U:/Research Projects/GAPIT/diagrid") myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c3.hmp.txt ",sep= "", head = FALSE) setwd("U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr3")

#Step 2: Run GAPIT for Chromosome 3 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV, group.from = 1560, group.to = 1560, G=myG, Model.selection=TRUE )

163 setwd("U:/Research Projects/GAPIT/diagrid") myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c4.hmp.txt ",sep= "", head = FALSE) setwd("U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr4")

#Step 2: Run GAPIT for Chromosome 4 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV,

164

group.from = 1560, group.to = 1560, G=myG, Model.selection=TRUE ) setwd("U:/Research Projects/GAPIT/diagrid") myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c5.hmp.txt ",sep= "", head = FALSE) setwd("U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr5")

#Step 2: Run GAPIT for Chromosome 5 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV, group.from = 1560, group.to = 1560, G=myG, Model.selection=TRUE )

164 setwd("U:/Research Projects/GAPIT/diagrid") myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c6.hmp.txt ",sep= "", head = FALSE) setwd("U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr6")

#Step 2: Run GAPIT for Chromosome 6 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV, group.from = 1560,

165

group.to = 1560, G=myG, Model.selection=TRUE ) setwd("U:/Research Projects/GAPIT/diagrid") myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c7.hmp.txt ",sep= "", head = FALSE) setwd("U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr7")

#Step 2: Run GAPIT for Chromosome 7 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV, group.from = 1560, group.to = 1560, G=myG, Model.selection=TRUE ) setwd("U:/Research Projects/GAPIT/diagrid")

165 myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c8.hmp.txt ",sep= "", head = FALSE) setwd("U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr8")

#Step 2: Run GAPIT for Chromosome 8 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV, group.from = 1560, group.to = 1560,

166

G=myG, Model.selection=TRUE ) setwd("U:/Research Projects/GAPIT/diagrid") myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c9.hmp.txt ",sep= "", head = FALSE) setwd("U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr9")

#Step 2: Run GAPIT for Chromosome 9 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV, group.from = 1560, group.to = 1560, G=myG, Model.selection=TRUE ) setwd("U:/Research Projects/GAPIT/diagrid") myG <-

166 read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c10.hmp.t xt",sep= "", head = FALSE) setwd("U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr10")

#Step 2: Run GAPIT for Chromosome 10 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV, group.from = 1560, group.to = 1560, G=myG,

167

Model.selection=TRUE )

##################################################################### To Combine all the runs into 1 analysis #Step 0: In your working directory, create three folders, and name them "Results_1", #"Results_2", and "Results_Combined". Put all of the GAPIT output files from one set up SNPs in # "Results_1", and all of the GAPIT output files from the second set of SNPs in "Results_2". # Finally, suppose that two traits named "trait1" and "trait2" are being analyzed ######################################################################## ############### library('MASS') library(multtest) library(gplots) setwd("U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL") #Import the source code source("http://www.maizegenetics.net/images/stories/bioinformatics/GAPIT/emma.txt ") source("http://www.maizegenetics.net/images/stories/bioinformatics/GAPIT/gapit_fun

167 ctions.txt") #Step 1: Set data directory and import files ######################################################################## ############### mydataPath.Results.1="U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr1/" mydataPath.Results.2="U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr2/" mydataPath.Results.3="U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr3/" mydataPath.Results.4="U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr4/"

168 mydataPath.Results.5="U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr5/" mydataPath.Results.6="U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr6/" mydataPath.Results.7="U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr7/" mydataPath.Results.8="U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr8/" mydataPath.Results.9="U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr9/" mydataPath.Results.10="U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Chr10/" name <- c("R2HL") #Step 2: Set the result directory to where the combined data will go ######################################################################## ############### setwd("U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/Combined_Traits/R2HL/Results_Combined") for(i in 1:length(name)){ #Read in the GWAS and Allelic effect estimates GWAS.Results.1 <- read.csv(paste(mydataPath.Results.1,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE)

168 GWAS.Results.2 <- read.csv(paste(mydataPath.Results.2,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE) GWAS.Results.3 <- read.csv(paste(mydataPath.Results.3,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE) GWAS.Results.4 <- read.csv(paste(mydataPath.Results.4,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE) GWAS.Results.5 <- read.csv(paste(mydataPath.Results.5,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE)

169

GWAS.Results.6 <- read.csv(paste(mydataPath.Results.6,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE) GWAS.Results.7 <- read.csv(paste(mydataPath.Results.7,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE) GWAS.Results.8 <- read.csv(paste(mydataPath.Results.8,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE) GWAS.Results.9 <- read.csv(paste(mydataPath.Results.9,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE) GWAS.Results.10 <- read.csv(paste(mydataPath.Results.10,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE)

169 ep=""), head = TRUE) Effect.Estimates.4 <- read.csv(paste(mydataPath.Results.4,"GAPIT..",name[i],".Allelic_Effect_Estimates.csv",s ep=""), head = TRUE) Effect.Estimates.5 <- read.csv(paste(mydataPath.Results.5,"GAPIT..",name[i],".Allelic_Effect_Estimates.csv",s ep=""), head = TRUE) Effect.Estimates.6 <- read.csv(paste(mydataPath.Results.6,"GAPIT..",name[i],".Allelic_Effect_Estimates.csv",s ep=""), head = TRUE) Effect.Estimates.7 <- read.csv(paste(mydataPath.Results.7,"GAPIT..",name[i],".Allelic_Effect_Estimates.csv",s ep=""), head = TRUE)

170

Effect.Estimates.8 <- read.csv(paste(mydataPath.Results.8,"GAPIT..",name[i],".Allelic_Effect_Estimates.csv",s ep=""), head = TRUE) Effect.Estimates.9 <- read.csv(paste(mydataPath.Results.9,"GAPIT..",name[i],".Allelic_Effect_Estimates.csv",s ep=""), head = TRUE) Effect.Estimates.10 <- read.csv(paste(mydataPath.Results.10,"GAPIT..",name[i],".Allelic_Effect_Estimates.csv", sep=""), head = TRUE)

#Append the the GWAS results and alleleic effect estimates onto one folder GWAS.Results <- rbind(GWAS.Results.1, GWAS.Results.2, GWAS.Results.3, GWAS.Results.4, GWAS.Results.5, GWAS.Results.6, GWAS.Results.7, GWAS.Results.8, GWAS.Results.9, GWAS.Results.10) Effect.Estimates <- rbind(Effect.Estimates.1, Effect.Estimates.2, Effect.Estimates.3, Effect.Estimates.4, Effect.Estimates.5, Effect.Estimates.6, Effect.Estimates.7, Effect.Estimates.8, Effect.Estimates.9, Effect.Estimates.10) #Remove the last column, which is the FDR adjusted P-values GWAS.Results <- GWAS.Results[,-ncol(GWAS.Results)] #Run the B-H procedure on the combined data, and append the FDR-adjusted P-values to the GWAS.Results Conduct.FDR <- GAPIT.Perform.BH.FDR.Multiple.Correction.Procedure(PWI = GWAS.Results, FDR.Rate = 0.05, FDR.Procedure = "BH")

170 GWAS.Results.with.FDR <- Conduct.FDR$PWIP #Make QQ-plots GAPIT.QQ(P.values = Conduct.FDR$PWIP[,4], name.of.trait = name[i],DPP=50000) #Make new Manhattan plots with the combined results GAPIT.Manhattan(GI.MP = GWAS.Results.with.FDR[,2:4], name.of.trait = name[i], DPP=50000, plot.type = "Genomewise",cutOff=0.00) GAPIT.Manhattan(GI.MP = GWAS.Results.with.FDR[,2:4], name.of.trait = name[i], DPP=50000, plot.type = "Chromosomewise",cutOff=0.00) #Export the combined GWAS results write.table(GWAS.Results.with.FDR, paste("GAPIT.", name[i], ".GWAS.Results.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE) #Export the combined Alleleic effect estiamtes

171 write.table(Effect.Estimates, paste("GAPIT.", name[i], ".Allelic_Effect_Estimates.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE) rm(GWAS.Results.1) rm(GWAS.Results.2) rm(GWAS.Results.3) rm(GWAS.Results.4) rm(GWAS.Results.5) rm(GWAS.Results.6) rm(GWAS.Results.7) rm(GWAS.Results.8) rm(GWAS.Results.9) rm(GWAS.Results.10) rm(GWAS.Results) rm(GWAS.Results.with.FDR) rm(Effect.Estimates.1) rm(Effect.Estimates.2) rm(Effect.Estimates.3) rm(Effect.Estimates.4) rm(Effect.Estimates.5) rm(Effect.Estimates.6) rm(Effect.Estimates.7) rm(Effect.Estimates.8)

171 rm(Effect.Estimates.9) rm(Effect.Estimates.10) rm(Effect.Estimates) rm(Conduct.FDR) } #End for(i in 1:length(name))

172

Appendix C Maize Leaf N Remobilization ANOVA Outputs

C-1 Trait VTL ANOVA

Sum of Source DF Squares Mean Square F Value Pr > F Model 2079 525845.5 252.9319 5.17 <.0001 Error 2089 102239 48.9416 Corrected Total 4168 628084.4

R -Square Coeff Var Root MSE VTL Mean 0.837221 14.09448 6.995826 49.63523

Source DF Type I SS Mean Square F Value Pr > F GROUPID 2032 516074 253.9734 5.19 <.0001 Year 1 5832.663 5832.663 119.18 <.0001 Range(Year) 46 3938.855 85.6273 1.75 0.0015

Source DF Type III SS Mean Square F Value Pr > F GROUPID 2032 506843.1 249.4307 5.1 <.0001 Year 1 5767.279 5767.279 117.84 <.0001 Range(Year) 46 3938.855 85.6273 1.75 0.0015

172

173

C-2 Trait VTH ANOVA

Sum of Source DF Squares Mean Square F Value Pr > F Model 2079 410576.07 197.49 4.43 <.0001 Error 2089 93055.99 44.55 Corrected Total 4168 503632.1

R -Square Coeff Var Root MSE VTH Mean 0.815230 15.21279 6.674257 43.87268

Source DF Type I SS Mean Square F Value Pr > F GROUPID 2032 395923.9064 194.8444 4.37 <.0001 Year 1 9116.5149 9116.5149 204.66 <.0001 Range(Year) 46 5535.6533 120.3403 2.70 <.0001

Source DF Type III SS Mean Square F Value Pr > F GROUPID 2032 388366.0248 191.1250 4.29 <.0001 Year 1 8998.8712 8998.8712 202.01 <.0001 Range(Year) 46 5535.6533 120.3403 2.70 <.0001

173

174

C-3 Trait R2L ANOVA

Sum of Source DF Squares Mean Square F Value Pr > F Model 2013 676110.2509 335.8720 4.09 <.0001 Error 1959 161046.7435 82.2086 Corrected Total 3972 837156.9944

R -Square Coeff Var Root MSE R2L Mean 0.807627 22.99971 9.066899 39.42179

Source DF Type I SS Mean Square F Value Pr > F GROUPID 1966 663011.1127 337.2386 4.10 <.0001 Year 1 5844.7443 5844.7443 71.10 <.0001 Range(Year) 46 7254.3940 157.7042 1.92 0.0002

Source DF Type III SS Mean Square F Value Pr > F GROUPID 1966 647766.2730 329.4844 4.01 <.0001 Year 1 5957.0427 5957.0427 72.46 <.0001 Range(Year) 46 7254.3940 157.7042 1.92 0.0002

174

175

C-4 Trait R2H ANOVA

Sum of Source DF Squares Mean Square F Value Pr > F Model 2013 626111.4 311.034 4.25 <.0001 Error 1960 143310 73.1174

Corrected Total 3973 769421.4

R -Square Coeff Var Root MSE VTL Mean 0.813743 21.60525 8.55087 39.57774

Source DF Type I SS Mean Square F Value Pr > F GROUPID 1966 603906 307.175 4.2 <.0001 Year 1 15503.76 15503.76 212.04 <.0001 Range(Year) 46 6701.669 145.6884 1.99 <.0001

Source DF Type III SS Mean Square F Value Pr > F GROUPID 1966 590036 300.1201 4.1 <.0001 Year 1 15539.15 15539.15 212.52 <.0001 Range(Year) 46 6701.669 145.6884 1.99 <.0001

175

176

C-5 Trait R4L ANOVA

Sum of Source DF Squares Mean Square F Value Pr > F Model 1843 685387.2 371.8867 3.17 <.0001 Error 1636 191986.1 117.3509

Corrected Total 3479 877373.3

R -Square Coeff Var Root MSE VTL Mean 0.781181 46.23069 10.83286 23.43219

Source DF Type I SS Mean Square F Value Pr > F GROUPID 1796 566580.4 315.4679 2.69 <.0001 Year 1 109394.5 109394.5 932.2 <.0001 Range(Year) 46 9412.246 204.614 1.74 0.0016

Source DF Type III SS Mean Square F Value Pr > F GROUPID 1796 552829.7 307.8116 2.62 <.0001 Year 1 110036.2 110036.2 937.67 <.0001 Range(Year) 46 9412.246 204.614 1.74 0.0016

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177

C-6 Trait R4H ANOVA

Sum of Source DF Squares Mean Square F Value Pr > F Model 1843 619285.5 336.0203 3.33 <.0001 Error 1636 165121.2 100.9298

Corrected Total 3479 784406.7

R -Square Coeff Var Root MSE VTL Mean 0.789495 39.47333 10.04638 25.45107

Source DF Type I SS Mean Square F Value Pr > F GROUPID 1796 466980.9 260.0116 2.58 <.0001 Year 1 147077.1 147077.1 1457.22 <.0001 Range(Year) 46 5227.472 113.6407 1.13 0.2619

Source DF Type III SS Mean Square F Value Pr > F GROUPID 1796 446505.7 248.6112 2.46 <.0001 Year 1 147278 147278 1459.21 <.0001 Range(Year) 46 5227.472 113.6407 1.13 0.2619

177

178

Appendix D Maize Leaf N Remobilization Candidate Genes

D-1 Trait R2HL Candidate Genes

R2 of R2 of Model Model FDR w/o w/ Adjusted Genes within 10Kb SNP Chr Position P.value maf Nobs SNP SNP P-values of SNP Annotation S7_152063911 7 152063911 1.39E-07 0.36 1717 0.14 0.16 0.038 GRMZM2G134545 (TMO6): TARGET OF

MONOPTEROS 6 S8_132877319 8 132877319 1.97E-07 0.18 1717 0.14 0.16 0.038 GRMZM2G056014 (ATECA4,ECA4): endomembrane-type CA-

ATPase 4 S8_132877319 8 132877319 1.97E-07 0.18 1717 0.14 0.16 0.038 GRMZM2G355742 splicing factor PWI domain-

containing protein S8_132877343 8 132877343 4.09E-07 0.17 1717 0.14 0.16 0.044 GRMZM2G056014 (ATECA4,ECA4): endomembrane-type CA-

ATPase 4 S8_132877343 8 132877343 4.09E-07 0.17 1717 0.14 0.16 0.044 GRMZM2G355742 splicing factor PWI domain-

containing protein S8_132879659 8 132879659 4.51E-07 0.31 1717 0.14 0.16 0.044 GRMZM2G056014 (ATECA4,ECA4): endomembrane-type CA-

ATPase 4 S8_132879659 8 132879659 4.51E-07 0.31 1717 0.14 0.16 0.044 GRMZM2G355742 splicing factor PWI domain-

containing protein

178

179

D-2 Trait VTR2 Candidate Genes

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kb SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values of SNP Annotation S2_212641128 2 212641128 3.33E-07 0.43 1675 0.16 0.17 0.032 GRMZM2G064630 (AtMYB124,FLP,MYB124): Duplicated homeodomain-

like superfamily protein

S2_212641128 2 212641128 3.33E-07 0.43 1675 0.16 0.17 0.032 GRMZM2G064640 Ribosomal protein S4 S2_212641128 2 212641128 3.33E-07 0.43 1675 0.16 0.17 0.032 GRMZM2G064941 (ATPIN4,PIN4): Auxin efflux

carrier family protein S4_178040254 4 178040254 1.15E-06 0.19 1675 0.16 0.17 0.049 GRMZM2G158811 (CPR5,HYS1): CPR5 protein,

putative S4_178040254 4 178040254 1.15E-06 0.19 1675 0.16 0.17 0.049 GRMZM2G158839 (CLB19,PDE247): Tetratricopeptide repeat (TPR)-like superfamily

protein S4_228666825 4 228666825 5.40E-07 0.07 1675 0.16 0.17 0.036 GRMZM2G121790 (ATSK21,BIN2,DWF12,SK21, UCU1): Protein kinase

superfamily protein S4_23529175 4 23529175 8.66E-07 0.17 1675 0.16 0.17 0.048 GRMZM2G378580 (ARF1-BP,ARF2,HSS,ORE14):

auxin response factor 2 S4_23529213 4 23529213 5.54E-07 0.17 1675 0.16 0.17 0.036 GRMZM2G378580 (ARF1-BP,ARF2,HSS,ORE14):

auxin response factor 2 S4_23529228 4 23529228 1.15E-06 0.17 1675 0.16 0.17 0.049 GRMZM2G378580 (ARF1-BP,ARF2,HSS,ORE14):

auxin response factor 2 S7_140712419 7 140712419 2.63E-07 0.45 1675 0.16 0.17 0.032 GRMZM2G043636 Molecular chaperone

Hsp40/DnaJ family protein S7_140712419 7 140712419 2.63E-07 0.45 1675 0.16 0.17 0.032 GRMZM2G043600 Basic-leucine zipper (bZIP) transcription factor family

protein

S7_140712419 7 140712419 2.63E-07 0.45 1675 0.16 0.17 0.032 GRMZM2G345081 (ZPR2): protein binding S8_136134655 8 136134655 1.99E-07 0.37 1675 0.16 0.17 0.032 GRMZM2G100146 (ATHD2A,HD2A,HDA3,HDT1) 179

: histone deacetylase 3

180

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kb SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values of SNP Annotation

S8_136134655 8 136134655 1.99E-07 0.37 1675 0.16 0.17 0.032 GRMZM2G100229 (IQD31): IQ-domain 31 S8_136134655 8 136134655 1.99E-07 0.37 1675 0.16 0.17 0.032 GRMZM2G463983 S-adenosyl-L-methionine- dependent methyltransferases

superfamily protein

180

181

D-3 Trait VTR2H Candidate Genes

R2 of R2 of Model FDR Model w/ Adjusted Genes within 10 Kb SNP Chr Position P.value maf N obs w/o SNP SNP P-values of SNP Annotation S1_51400080 1 51400080 4.54E-06 0.07 1675 0.19 0.20 0.037 GRMZM2G070849 (AtMYB112,MYB112): myb

domain protein 112 S1_248676101 1 248676101 3.39E-06 0.09 1675 0.19 0.20 0.033 GRMZM2G335814 GRAS family transcription

factor S1_248676119 1 248676119 3.39E-06 0.09 1675 0.19 0.20 0.033 GRMZM2G335814 GRAS family transcription

factor S2_21908969 2 21908969 2.19E-06 0.16 1675 0.19 0.20 0.030 GRMZM2G132055 GDSL-like Lipase/Acylhydrolase

superfamily protein S2_21908969 2 21908969 2.19E-06 0.16 1675 0.19 0.20 0.030 GRMZM2G131982 (STH2): salt tolerance

homolog2

S2_60879882 2 60879882 2.36E-06 0.31 1675 0.19 0.20 0.030 GRMZM2G068590 zinc ion binding S2_173776029 2 173776029 7.71E-06 0.09 1675 0.19 0.20 0.049 GRMZM2G033694 (ASHH3,SDG7): histone- lysine N-methyltransferase

ASHH3 S2_212641128 2 212641128 1.89E-06 0.43 1675 0.19 0.20 0.030 GRMZM2G064630 (AtMYB124,FLP,MYB124): Duplicated homeodomain-

like superfamily protein S2_212641128 2 212641128 1.89E-06 0.43 1675 0.19 0.20 0.030 GRMZM2G064941 (ATPIN4,PIN4): Auxin efflux

carrier family protein

S2_212641128 2 212641128 1.89E-06 0.43 1675 0.19 0.20 0.030 GRMZM2G064640 Ribosomal protein S4 S2_212641128 2 212641128 1.89E-06 0.43 1675 0.19 0.20 0.030 GRMZM2G064938 helix-loop-helix DNA- binding domain containing

protein, expressed S3_227937830 3 227937830 2.13E-06 0.07 1675 0.19 0.20 0.030 GRMZM2G022841 (ATGSL07,atgsl7,gsl07):

glucan synthase-like 7

181

182

R2 of R2 of Model FDR Model w/ Adjusted Genes within 10 Kb SNP Chr Position P.value maf N obs w/o SNP SNP P-values of SNP Annotation S4_23529175 4 23529175 1.81E-06 0.17 1675 0.19 0.20 0.030 GRMZM2G378580 (ARF1- BP,ARF2,HSS,ORE14): auxin

response factor 2 S4_23529213 4 23529213 1.27E-06 0.17 1675 0.19 0.20 0.030 GRMZM2G378580 (ARF1- BP,ARF2,HSS,ORE14): auxin

response factor 2 S4_23529228 4 23529228 2.22E-06 0.17 1675 0.19 0.20 0.030 GRMZM2G378580 (ARF1- BP,ARF2,HSS,ORE14): auxin

response factor 2 S4_228661301 4 228661301 4.32E-06 0.09 1675 0.19 0.20 0.037 GRMZM2G121790 (ATSK21,BIN2,DWF12,SK21 ,UCU1): Protein kinase

superfamily protein S4_228666825 4 228666825 8.88E-08 0.07 1675 0.19 0.20 0.011 GRMZM2G121790 (ATSK21,BIN2,DWF12,SK21 ,UCU1): Protein kinase

superfamily protein S5_19441400 5 19441400 2.45E-06 0.30 1675 0.19 0.20 0.030 GRMZM2G087233 (RPL10C,SAG24): senescence associated

gene 24 S5_19441400 5 19441400 2.45E-06 0.30 1675 0.19 0.20 0.030 GRMZM2G386714 (ATKRS-1): lysyl-tRNA

synthetase 1

S5_19441400 5 19441400 2.45E-06 0.30 1675 0.19 0.20 0.030 GRMZM2G088005 DNA binding S5_19441400 5 19441400 2.45E-06 0.30 1675 0.19 0.20 0.030 GRMZM2G087165 (RPS19): ribosomal protein

S19 S5_19441434 5 19441434 2.27E-06 0.27 1675 0.19 0.20 0.030 GRMZM2G087233 (RPL10C,SAG24): senescence associated

gene 24 S5_19441434 5 19441434 2.27E-06 0.27 1675 0.19 0.20 0.030 GRMZM2G386714 (ATKRS-1): lysyl-tRNA

synthetase 1

S5_19441434 5 19441434 2.27E-06 0.27 1675 0.19 0.20 0.030 GRMZM2G088005 DNA binding 182

183

R2 of R2 of Model FDR Model w/ Adjusted Genes within 10 Kb SNP Chr Position P.value maf N obs w/o SNP SNP P-values of SNP Annotation S5_19441434 5 19441434 2.27E-06 0.27 1675 0.19 0.20 0.030 GRMZM2G087165 (RPS19): ribosomal protein

S19 S5_19441435 5 19441435 2.15E-06 0.27 1675 0.19 0.20 0.030 GRMZM2G087233 (RPL10C,SAG24): senescence associated

gene 24 S5_19441435 5 19441435 2.15E-06 0.27 1675 0.19 0.20 0.030 GRMZM2G386714 (ATKRS-1): lysyl-tRNA

synthetase 1

S5_19441435 5 19441435 2.15E-06 0.27 1675 0.19 0.20 0.030 GRMZM2G088005 DNA binding S5_19441435 5 19441435 2.15E-06 0.27 1675 0.19 0.20 0.030 GRMZM2G087165 (RPS19): ribosomal protein

S19 S5_19441469 5 19441469 4.50E-07 0.25 1675 0.19 0.20 0.017 GRMZM2G087233 (RPL10C,SAG24): senescence associated

gene 24 S5_19441469 5 19441469 4.50E-07 0.25 1675 0.19 0.20 0.017 GRMZM2G386714 (ATKRS-1): lysyl-tRNA

synthetase 1

S5_19441469 5 19441469 4.50E-07 0.25 1675 0.19 0.20 0.017 GRMZM2G088005 DNA binding S5_19441469 5 19441469 4.50E-07 0.25 1675 0.19 0.20 0.017 GRMZM2G087165 (RPS19): ribosomal protein

S19 S5_19448689 5 19448689 2.59E-06 0.31 1675 0.19 0.20 0.030 GRMZM2G087233 (RPL10C,SAG24): senescence associated

gene 24 S5_19448689 5 19448689 2.59E-06 0.31 1675 0.19 0.20 0.030 GRMZM2G086904 (NRPB6B,NRPE6B): RNA

polymerase Rpb6 S5_19448689 5 19448689 2.59E-06 0.31 1675 0.19 0.20 0.030 GRMZM2G386714 (ATKRS-1): lysyl-tRNA

synthetase 1 S5_19448689 5 19448689 2.59E-06 0.31 1675 0.19 0.20 0.030 GRMZM2G087165 (RPS19): ribosomal protein

S19 S6_122102021 6 122102021 7.85E-06 0.15 1675 0.19 0.20 0.050 GRMZM2G342588 Tesmin/TSO1-like CXC

183 domain-containing protein

184

R2 of R2 of Model FDR Model w/ Adjusted Genes within 10 Kb SNP Chr Position P.value maf N obs w/o SNP SNP P-values of SNP Annotation S6_129661157 6 129661157 5.85E-06 0.31 1675 0.19 0.20 0.042 GRMZM2G141776 Actin-like ATPase

superfamily protein S6_129661157 6 129661157 5.85E-06 0.31 1675 0.19 0.20 0.042 GRMZM2G141810 (TAR2): tryptophan

aminotransferase related 2 S6_156395467 6 156395467 6.12E-06 0.10 1675 0.19 0.20 0.042 GRMZM2G020016 (ATERF12,ERF12): ERF

domain protein 12 S6_156395467 6 156395467 6.12E-06 0.10 1675 0.19 0.20 0.042 GRMZM2G020150 (ATERF- 4,ATERF4,ERF4,RAP2.5): ethylene responsive

element binding factor 4 S6_162153293 6 162153293 4.22E-06 0.19 1675 0.19 0.20 0.037 GRMZM2G476477 (MAPKKK17): mitogen- activated protein kinase

kinase kinase 17 S6_162153293 6 162153293 4.22E-06 0.19 1675 0.19 0.20 0.037 AC204050.4_FG006 (MAPKKK16): mitogen- activated protein kinase

kinase kinase 16 S7_138372020 7 138372020 6.60E-06 0.48 1675 0.19 0.20 0.044 GRMZM2G108133 (BGLU11): beta glucosidase

11 S7_138372020 7 138372020 6.60E-06 0.48 1675 0.19 0.20 0.044 AC186800.3_FG005 retrotransposon protein, putative, unclassified,

expressed S7_138377302 7 138377302 1.84E-06 0.50 1675 0.19 0.20 0.030 GRMZM2G108133 (BGLU11): beta glucosidase

11 S7_138377302 7 138377302 1.84E-06 0.50 1675 0.19 0.20 0.030 AC186800.3_FG005 retrotransposon protein, putative, unclassified,

expressed S7_158754466 7 158754466 6.07E-06 0.26 1675 0.19 0.20 0.042 GRMZM2G333980 (ATPGIP1,PGIP1): polygalacturonase

inhibiting protein 1

184 S7_158754466 7 158754466 6.07E-06 0.26 1675 0.19 0.20 0.042 GRMZM2G028086 (CPK7): calmodulin-domain

protein kinase 7

185

R2 of R2 of Model FDR Model w/ Adjusted Genes within 10 Kb SNP Chr Position P.value maf N obs w/o SNP SNP P-values of SNP Annotation S8_26103587 8 26103587 3.95E-06 0.12 1675 0.19 0.20 0.036 GRMZM2G154221 plant-specific domain TIGR01589 family protein,

putative, expressed S8_123473596 8 123473596 6.03E-06 0.13 1675 0.19 0.20 0.042 GRMZM2G073044 (LBD41): LOB domain-

containing protein 41 S8_131904755 8 131904755 2.50E-06 0.46 1675 0.19 0.20 0.030 AC214648.3_FG001 Tudor/PWWP/MBT

superfamily protein S8_131904775 8 131904775 1.32E-06 0.46 1675 0.19 0.20 0.030 AC214648.3_FG001 Tudor/PWWP/MBT

superfamily protein S8_131904780 8 131904780 1.64E-06 0.46 1675 0.19 0.20 0.030 AC214648.3_FG001 Tudor/PWWP/MBT

superfamily protein S8_131904787 8 131904787 1.64E-06 0.46 1675 0.19 0.20 0.030 AC214648.3_FG001 Tudor/PWWP/MBT

superfamily protein S8_131904985 8 131904985 4.03E-06 0.47 1675 0.19 0.20 0.036 AC214648.3_FG001 Tudor/PWWP/MBT

superfamily protein S8_131905016 8 131905016 5.47E-06 0.48 1675 0.19 0.20 0.042 AC214648.3_FG001 Tudor/PWWP/MBT

superfamily protein S8_131905032 8 131905032 2.46E-06 0.48 1675 0.19 0.20 0.030 AC214648.3_FG001 Tudor/PWWP/MBT

superfamily protein S8_135059199 8 135059199 6.52E-06 0.32 1675 0.19 0.20 0.044 GRMZM2G098153 (AteIF3f,EIF2,eIF3F): eukaryotic translation

initiation factor 2 S8_135059199 8 135059199 6.52E-06 0.32 1675 0.19 0.20 0.044 GRMZM2G098031 (MMT): methionine S-

methyltransferase S8_135059199 8 135059199 6.52E-06 0.32 1675 0.19 0.20 0.044 GRMZM2G098039 (MMT): methionine S-

methyltransferase

S8_136134655 8 136134655 1.06E-06 0.37 1675 0.19 0.20 0.030 GRMZM2G100229 (IQD31): IQ-domain 31

185

186

R2 of R2 of Model FDR Model w/ Adjusted Genes within 10 Kb SNP Chr Position P.value maf N obs w/o SNP SNP P-values of SNP Annotation S8_136134655 8 136134655 1.06E-06 0.37 1675 0.19 0.20 0.030 GRMZM2G463983 S-adenosyl-L-methionine- dependent methyltransferases

superfamily protein S8_136134655 8 136134655 1.06E-06 0.37 1675 0.19 0.20 0.030 GRMZM2G100146 (ATHD2A,HD2A,HDA3,HDT

1): histone deacetylase 3 S9_127304468 9 127304468 3.60E-07 0.25 1675 0.19 0.20 0.017 GRMZM2G148969 (CYP709B2): cytochrome P450, family 709, subfamily

B, polypeptide 2 S9_127304468 9 127304468 3.60E-07 0.25 1675 0.19 0.20 0.017 GRMZM2G020761 (CYP709B2): cytochrome P450, family 709, subfamily

B, polypeptide 2 S9_127304471 9 127304471 3.60E-07 0.25 1675 0.19 0.20 0.017 GRMZM2G148969 (CYP709B2): cytochrome P450, family 709, subfamily

B, polypeptide 2 S9_127304471 9 127304471 3.60E-07 0.25 1675 0.19 0.20 0.017 GRMZM2G020761 (CYP709B2): cytochrome P450, family 709, subfamily

B, polypeptide 2 S9_127304477 9 127304477 3.60E-07 0.25 1675 0.19 0.20 0.017 GRMZM2G148969 (CYP709B2): cytochrome P450, family 709, subfamily

B, polypeptide 2 S9_127304477 9 127304477 3.60E-07 0.25 1675 0.19 0.20 0.017 GRMZM2G020761 (CYP709B2): cytochrome P450, family 709, subfamily

B, polypeptide 2 S9_143037388 9 143037388 2.02E-06 0.05 1675 0.19 0.20 0.030 GRMZM2G149809 T1G20030.2: Pathogenesis- related thaumatin

superfamily protein S9_153831925 9 153831925 6.54E-07 0.25 1675 0.19 0.20 0.023 GRMZM2G171365 (AGL20,ATSOC1,SOC1):

AGAMOUS-like 20

186

187

R2 of R2 of Model FDR Model w/ Adjusted Genes within 10 Kb SNP Chr Position P.value maf N obs w/o SNP SNP P-values of SNP Annotation S9_153831925 9 153831925 6.54E-07 0.25 1675 0.19 0.20 0.023 GRMZM2G171440 MBOAT (membrane bound O-acyl transferase) family

protein S9_153831925 9 153831925 6.54E-07 0.25 1675 0.19 0.20 0.023 GRMZM2G171450 DEA(D/H)-box RNA helicase

family protein S9_153831954 9 153831954 2.95E-06 0.25 1675 0.19 0.20 0.032 GRMZM2G171365 (AGL20,ATSOC1,SOC1):

AGAMOUS-like 20 S9_153831954 9 153831954 2.95E-06 0.25 1675 0.19 0.20 0.032 GRMZM2G171440 MBOAT (membrane bound O-acyl transferase) family

protein S9_153831954 9 153831954 2.95E-06 0.25 1675 0.19 0.20 0.032 GRMZM2G171450 DEA(D/H)-box RNA helicase

family protein

187

188

D-4 Trait VTR2L Candidate Genes

R2 of R2 of Model FDR Model w/ Adjusted Genes within 10 Kb SNP Chr Position P.value maf N obs w/o.SNP SNP P-values of SNP Annotations S1_33448191 1 33448191 1.64E-07 0.40 1674 0.13 0.14 0.039 GRMZM2G149646 retrotransposon protein, putative, unclassified,

expressed

S2_136562876 2 137000000 5.70E-07 0.28 1674 0.13 0.14 0.039 GRMZM2G003234 C2H2-like zinc finger protein

S2_212641128 2 213000000 1.16E-06 0.43 1674 0.13 0.14 0.043 GRMZM2G064630 (AtMYB124,FLP,MYB124): Duplicated homeodomain-

like superfamily protein S2_212641128 2 213000000 1.16E-06 0.43 1674 0.13 0.14 0.043 GRMZM2G064941 (ATPIN4,PIN4): Auxin efflux

carrier family protein

S2_212641128 2 213000000 1.16E-06 0.43 1674 0.13 0.14 0.043 GRMZM2G064640 Ribosomal protein S4

S2_212641128 2 213000000 1.16E-06 0.43 1674 0.13 0.14 0.043 GRMZM2G064938 helix-loop-helix DNA-binding domain containing protein,

expressed S4_32604866 4 32604866 1.14E-06 0.42 1674 0.13 0.14 0.043 GRMZM2G128504 UDP-Glycosyltransferase

superfamily protein S4_33428926 4 33428926 4.73E-07 0.20 1674 0.13 0.14 0.039 GRMZM2G092535 Small nuclear ribonucleoprotein family

protein S4_33428926 4 33428926 4.73E-07 0.20 1674 0.13 0.14 0.039 GRMZM2G092451 (TOP1,TOP1BETA): DNA

topoisomerase 1 beta S4_33428938 4 33428938 6.13E-07 0.20 1674 0.13 0.14 0.039 GRMZM2G092451 (TOP1,TOP1BETA): DNA

topoisomerase 1 beta S4_33428938 4 33428938 6.13E-07 0.20 1674 0.13 0.14 0.039 GRMZM2G092535 Small nuclear ribonucleoprotein family

188 protein

189

R2 of R2 of Model FDR Model w/ Adjusted Genes within 10 Kb SNP Chr Position P.value maf N obs w/o.SNP SNP P-values of SNP Annotations S4_178040254 4 178000000 6.01E-07 0.19 1674 0.13 0.14 0.039 GRMZM2G158839 (CLB19,PDE247): Tetratricopeptide repeat (TPR)-like superfamily

protein S4_178040254 4 178000000 6.01E-07 0.19 1674 0.13 0.14 0.039 GRMZM2G158811 (CPR5,HYS1): CPR5 protein,

putative S5_212614190 5 213000000 2.26E-07 0.06 1674 0.13 0.14 0.039 GRMZM5G852886 CAP (Cysteine-rich secretory proteins, Antigen 5, and Pathogenesis-related 1

protein) superfamily protein S5_212614190 5 213000000 2.26E-07 0.06 1674 0.13 0.14 0.039 GRMZM2G008367 CAP (Cysteine-rich secretory proteins, Antigen 5, and Pathogenesis-related 1

protein) superfamily protein S5_212614190 5 213000000 2.26E-07 0.06 1674 0.13 0.14 0.039 GRMZM2G008406 CAP (Cysteine-rich secretory proteins, Antigen 5, and Pathogenesis-related 1

protein) superfamily protein S5_214336719 5 214000000 1.09E-06 0.15 1674 0.13 0.14 0.043 GRMZM2G027282 (ATS6A.2,RPT5A): regulatory

particle triple-A ATPase 5A S5_214336719 5 214000000 1.09E-06 0.15 1674 0.13 0.14 0.043 GRMZM2G027019 (ATVAMP713,VAMP713): vesicle-associated

membrane protein 713 S7_140712419 7 141000000 1.14E-06 0.45 1674 0.13 0.14 0.043 GRMZM2G043600 Basic-leucine zipper (bZIP) transcription factor family

protein S7_140712419 7 141000000 1.14E-06 0.45 1674 0.13 0.14 0.043 GRMZM2G043636 Molecular chaperone

Hsp40/DnaJ family protein

189

190

D-5 Trait VTR4 Candidate Genes

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_7080149 1 7080149 4.60E-05 0.09 1391 0.20 0.21 0.049 GRMZM2G109566 Protein kinase

superfamily protein S1_7080149 1 7080149 4.60E-05 0.09 1391 0.20 0.21 0.049 GRMZM2G109509 Plant regulator RWP-RK family

protein S1_7080149 1 7080149 4.60E-05 0.09 1391 0.20 0.21 0.049 GRMZM2G409997 Tetratricopeptide repeat (TPR)-like

superfamily protein S1_7080149 1 7080149 4.60E-05 0.09 1391 0.20 0.21 0.049 GRMZM2G409976 Protein kinase

superfamily protein S1_18977637 1 18977637 3.22E-05 0.05 1391 0.20 0.21 0.044 GRMZM2G148706 RING/U-box

superfamily protein S1_18977637 1 18977637 3.22E-05 0.05 1391 0.20 0.21 0.044 GRMZM2G031177 MATE efflux family

protein S1_19263143 1 19263143 4.52E-05 0.29 1391 0.20 0.21 0.049 GRMZM2G132367 (ATHB6,HB6):

homeobox protein 6 S1_23414805 1 23414805 4.45E-05 0.07 1391 0.20 0.21 0.049 GRMZM2G121706 (ATOFP7,OFP7): ovate family protein

S1_23578479 1 23578479 1.42E-05 0.05 1391 0.20 0.21 0.036 AC205725.3_FG010 (RBL): Noc2p family

S1_23578481 1 23578481 1.42E-05 0.05 1391 0.20 0.21 0.036 AC205725.3_FG010 (RBL): Noc2p family S1_24743247 1 24743247 1.54E-05 0.07 1391 0.20 0.21 0.036 GRMZM2G331652 Aminotransferase- like, plant mobile domain family

protein 190

191

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_24743247 1 24743247 1.54E-05 0.07 1391 0.20 0.21 0.036 GRMZM2G331638 Auxin-responsive

family protein S1_25154097 1 25154097 7.15E-06 0.06 1391 0.20 0.21 0.029 GRMZM2G376074 (ATUBP26,SUP32,UB P26): ubiquitin-

specific protease 26 S1_27109194 1 27109194 4.07E-05 0.05 1391 0.20 0.21 0.048 GRMZM2G163129 (PSL5,RSW3): Glycosyl hydrolases

family 31 protein S1_27109194 1 27109194 4.07E-05 0.05 1391 0.20 0.21 0.048 GRMZM2G163154 MATE efflux family

protein

S1_27109194 1 27109194 4.07E-05 0.05 1391 0.20 0.21 0.048 AC208897.3_FG003 myosin-related S1_28424547 1 28424547 1.35E-05 0.28 1391 0.20 0.21 0.036 GRMZM2G099797 (ARR2,RR2): response regulator

2 S1_28424547 1 28424547 1.35E-05 0.28 1391 0.20 0.21 0.036 GRMZM2G397754 Major facilitator

superfamily protein S1_28424548 1 28424548 1.35E-05 0.28 1391 0.20 0.21 0.036 GRMZM2G099797 (ARR2,RR2): response regulator

2 S1_28424548 1 28424548 1.35E-05 0.28 1391 0.20 0.21 0.036 GRMZM2G397754 Major facilitator

superfamily protein S1_31869243 1 31869243 1.67E-05 0.10 1391 0.20 0.21 0.036 GRMZM2G100714 (MAP65-7): microtubule- associated protein

65-7 S1_32871037 1 32871037 4.12E-05 0.44 1391 0.20 0.21 0.048 GRMZM2G077942 (ADF5,ATADF5): actin depolymerizing

factor 5

191

192

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_39895751 1 39895751 5.95E-06 0.17 1391 0.20 0.21 0.028 GRMZM2G078164 (DVL11,RTFL8): ROTUNDIFOLIA like

8 S1_41437359 1 41437359 4.18E-06 0.08 1391 0.20 0.22 0.027 GRMZM2G043857 Ankyrin repeat

family protein S1_41437359 1 41437359 4.18E-06 0.08 1391 0.20 0.22 0.027 GRMZM2G043878 receptor-like protein kinase- related family

protein S1_41539340 1 41539340 2.23E-05 0.08 1391 0.20 0.21 0.039 GRMZM2G157329 RNA-binding (RRM/RBD/RNP motifs) family

protein S1_42012957 1 42012957 7.43E-06 0.06 1391 0.20 0.21 0.030 GRMZM2G150729 basic helix-loop- helix (bHLH) DNA- binding superfamily

protein S1_42520440 1 42520440 1.12E-05 0.17 1391 0.20 0.21 0.034 GRMZM2G042107 Ankyrin repeat

family protein S1_42520440 1 42520440 1.12E-05 0.17 1391 0.20 0.21 0.034 GRMZM2G338333 (ITN1): Ankyrin repeat family

protein S1_42520476 1 42520476 1.12E-05 0.17 1391 0.20 0.21 0.034 GRMZM2G042107 Ankyrin repeat

family protein S1_42520476 1 42520476 1.12E-05 0.17 1391 0.20 0.21 0.034 GRMZM2G338333 (ITN1): Ankyrin repeat family

protein S1_42520536 1 42520536 2.70E-05 0.18 1391 0.20 0.21 0.041 GRMZM2G042107 Ankyrin repeat

family protein S1_42520536 1 42520536 2.70E-05 0.18 1391 0.20 0.21 0.041 GRMZM2G338333 (ITN1): Ankyrin

192 repeat family

protein

193

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_46842397 1 46842397 1.40E-07 0.12 1391 0.20 0.22 0.010 GRMZM2G010545 PLAC8 family

protein S1_46842397 1 46842397 1.40E-07 0.12 1391 0.20 0.22 0.010 GRMZM2G010328 (AGD2): Pyridoxal phosphate (PLP)- dependent transferases

superfamily protein S1_46842398 1 46842398 1.40E-07 0.12 1391 0.20 0.22 0.010 GRMZM2G010545 PLAC8 family

protein S1_46842398 1 46842398 1.40E-07 0.12 1391 0.20 0.22 0.010 GRMZM2G010328 (AGD2): Pyridoxal phosphate (PLP)- dependent transferases

superfamily protein S1_48890554 1 48890554 1.52E-05 0.06 1391 0.20 0.21 0.036 GRMZM2G383790 (ATXT1,XT1,XXT1):

xylosyltransferase 1 S1_72112945 1 72112945 4.64E-05 0.05 1391 0.20 0.21 0.049 GRMZM2G179521 (G6PD2): glucose-6- phosphate

dehydrogenase 2 S1_80952700 1 80952700 3.60E-06 0.06 1391 0.20 0.22 0.027 GRMZM2G434500 Glucose-methanol- choline (GMC) oxidoreductase

family protein

S1_80952700 1 80952700 3.60E-06 0.06 1391 0.20 0.22 0.027 GRMZM2G133968 DNA binding S1_80952700 1 80952700 3.60E-06 0.06 1391 0.20 0.22 0.027 GRMZM2G434514 peptidoglycan- binding LysM domain-containing

protein

193

194

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_81776120 1 81776120 2.71E-05 0.07 1391 0.20 0.21 0.041 GRMZM2G044383 (ATGSTU17,ERD9,GS T30,GST30B): Glutathione S- transferase family

protein S1_162464005 1 162464005 6.30E-06 0.34 1391 0.20 0.21 0.029 GRMZM2G476637 (NPY2): Phototropic- responsive NPH3

family protein S1_170476235 1 170476235 3.41E-05 0.09 1391 0.20 0.21 0.044 GRMZM2G100121 (FBL17): RNI-like

superfamily protein S1_172875668 1 172875668 1.95E-05 0.19 1391 0.20 0.21 0.038 GRMZM5G865967 (PIF4,SRL2): phytochrome

interacting factor 4 S1_172875668 1 172875668 1.95E-05 0.19 1391 0.20 0.21 0.038 GRMZM2G087608 OsFBX436 - F-box domain containing

protein, expressed S1_172903996 1 172903996 9.40E-06 0.25 1391 0.20 0.21 0.034 GRMZM5G852177 Protein kinase

superfamily protein S1_172903996 1 172903996 9.40E-06 0.25 1391 0.20 0.21 0.034 GRMZM2G035444 membrane associated DUF588 domain containing protein, putative,

expressed S1_174284218 1 174284218 1.01E-05 0.46 1391 0.20 0.21 0.034 GRMZM2G118646 (DEG5,DEGP5,HHOA

): DEGP protease 5 S1_174284253 1 174284253 1.20E-05 0.05 1391 0.20 0.21 0.035 GRMZM2G118646 (DEG5,DEGP5,HHOA

): DEGP protease 5 S1_179980108 1 179980108 1.32E-05 0.23 1391 0.20 0.21 0.036 GRMZM2G392791 alpha/beta- Hydrolases

superfamily protein

194

195

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_179980108 1 179980108 1.32E-05 0.23 1391 0.20 0.21 0.036 GRMZM2G093809 Leucine-rich repeat transmembrane protein kinase

family protein S1_179980158 1 179980158 1.49E-05 0.23 1391 0.20 0.21 0.036 GRMZM2G392791 alpha/beta- Hydrolases

superfamily protein S1_179980158 1 179980158 1.49E-05 0.23 1391 0.20 0.21 0.036 GRMZM2G093809 Leucine-rich repeat transmembrane protein kinase

family protein S1_179980698 1 179980698 1.57E-05 0.23 1391 0.20 0.21 0.036 GRMZM2G392791 alpha/beta- Hydrolases

superfamily protein S1_179980698 1 179980698 1.57E-05 0.23 1391 0.20 0.21 0.036 GRMZM2G093809 Leucine-rich repeat transmembrane protein kinase

family protein S1_180817523 1 180817523 4.16E-05 0.14 1391 0.20 0.21 0.048 GRMZM2G151236 Protein kinase

superfamily protein S1_180817523 1 180817523 4.16E-05 0.14 1391 0.20 0.21 0.048 AC195785.3_FG004 S-locus lectin protein kinase

family protein S1_191604990 1 191604990 9.73E-06 0.13 1391 0.20 0.21 0.034 GRMZM2G040509 (ATBPM1,BPM1): BTB-POZ and MATH

domain 1 S1_196204573 1 196204573 2.82E-05 0.05 1391 0.20 0.21 0.042 GRMZM2G053027 (RFI2): RING/U-box

superfamily protein S1_196204573 1 196204573 2.82E-05 0.05 1391 0.20 0.21 0.042 GRMZM2G353483 (ATEXO70F1,EXO70 F1): exocyst subunit

195 exo70 family

protein F1

196

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_196972895 1 196972895 2.14E-05 0.20 1391 0.20 0.21 0.039 GRMZM2G077320 Tetratricopeptide repeat (TPR)-like

superfamily protein S1_199754817 1 199754817 3.19E-05 0.06 1391 0.20 0.21 0.044 GRMZM5G881887 NAD(P)-binding Rossmann-fold

superfamily protein S1_204869927 1 204869927 1.72E-05 0.09 1391 0.20 0.21 0.036 GRMZM2G320689 P-loop containing nucleoside triphosphate hydrolases

superfamily protein S1_204869927 1 204869927 1.72E-05 0.09 1391 0.20 0.21 0.036 GRMZM2G320708 Late embryogenesis abundant (LEA) hydroxyproline-rich

glycoprotein family S1_204869927 1 204869927 1.72E-05 0.09 1391 0.20 0.21 0.036 GRMZM2G022866 Thioredoxin family

protein S1_204871830 1 204871830 4.97E-06 0.10 1391 0.20 0.22 0.027 GRMZM2G320689 P-loop containing nucleoside triphosphate hydrolases

superfamily protein S1_204871830 1 204871830 4.97E-06 0.10 1391 0.20 0.22 0.027 GRMZM2G320708 Late embryogenesis abundant (LEA) hydroxyproline-rich

glycoprotein family S1_204871830 1 204871830 4.97E-06 0.10 1391 0.20 0.22 0.027 GRMZM2G022866 Thioredoxin family

protein

196

197

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_204871832 1 204871832 4.97E-06 0.10 1391 0.20 0.22 0.027 GRMZM2G320689 P-loop containing nucleoside triphosphate hydrolases

superfamily protein S1_204871832 1 204871832 4.97E-06 0.10 1391 0.20 0.22 0.027 GRMZM2G320708 Late embryogenesis abundant (LEA) hydroxyproline-rich

glycoprotein family S1_204871832 1 204871832 4.97E-06 0.10 1391 0.20 0.22 0.027 GRMZM2G022866 Thioredoxin family

protein S1_206903638 1 206903638 4.38E-05 0.15 1391 0.20 0.21 0.049 GRMZM2G063883 (SDG22,SET22,SUVH 9): SU(VAR)3-9

homolog 9 S1_213156463 1 213156463 3.24E-06 0.21 1391 0.20 0.22 0.027 GRMZM2G108600 (ATCSLA09,ATCSLA9 ,CSLA09,CSLA9,RAT4 ): Nucleotide- diphospho-sugar transferases

superfamily protein S1_245697841 1 245697841 1.80E-05 0.20 1391 0.20 0.21 0.038 GRMZM2G455817 (ATHAK5,HAK5): high affinity K+

transporter 5 S1_261218999 1 261218999 4.62E-05 0.05 1391 0.20 0.21 0.049 GRMZM2G412150 Tetratricopeptide repeat (TPR)-like

superfamily protein S1_261218999 1 261218999 4.62E-05 0.05 1391 0.20 0.21 0.049 GRMZM2G412137 hAT dimerisation domain-containing protein /

transposase-related

197

198

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_275086596 1 275086596 2.46E-05 0.07 1391 0.20 0.21 0.041 GRMZM2G149952 (APS3): Pseudouridine synthase/archaeosi ne transglycosylase-

like family protein S1_275086596 1 275086596 2.46E-05 0.07 1391 0.20 0.21 0.041 GRMZM2G149775 (HTA11): histone

H2A 11 S1_275086596 1 275086596 2.46E-05 0.07 1391 0.20 0.21 0.041 GRMZM2G149923 (ACAM- 1,CAM1,TCH1):

calmodulin 1 S1_280686695 1 280686695 4.74E-05 0.05 1391 0.20 0.21 0.050 GRMZM2G164580 Pyridoxal phosphate (PLP)-dependent transferases

superfamily protein S1_280686705 1 280686705 4.74E-05 0.05 1391 0.20 0.21 0.050 GRMZM2G164580 Pyridoxal phosphate (PLP)-dependent transferases

superfamily protein S1_285926857 1 285926857 4.11E-05 0.07 1391 0.20 0.21 0.048 GRMZM2G434533 MD-2-related lipid recognition domain- containing protein / ML domain-

containing protein S1_285926857 1 285926857 4.11E-05 0.07 1391 0.20 0.21 0.048 GRMZM2G135011 RING/U-box

superfamily protein S1_285926857 1 285926857 4.11E-05 0.07 1391 0.20 0.21 0.048 GRMZM2G134917 (ATJ2,J2): DNAJ

homologue 2 S1_290957276 1 290957276 3.03E-05 0.18 1391 0.20 0.21 0.043 GRMZM2G077181 (AtSIP2,SIP2): seed

imbibition 2

198

199

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_290957276 1 290957276 3.03E-05 0.18 1391 0.20 0.21 0.043 GRMZM2G077079 N2,N2- dimethylguanosine tRNA

methyltransferase S1_295724522 1 295724522 2.00E-05 0.06 1391 0.20 0.21 0.038 GRMZM2G369432 Plant invertase/pectin methylesterase inhibitor

superfamily protein S2_2539903 2 2539903 1.72E-05 0.31 1391 0.20 0.21 0.036 GRMZM2G010257 60S acidic ribosomal

protein family S2_2539903 2 2539903 1.72E-05 0.31 1391 0.20 0.21 0.036 GRMZM2G010435 Granulin repeat cysteine protease

family protein S2_2539903 2 2539903 1.72E-05 0.31 1391 0.20 0.21 0.036 GRMZM2G107187 SEC-C motif- containing protein / OTU-like cysteine protease family

protein S2_9018813 2 9018813 1.74E-05 0.06 1391 0.20 0.21 0.037 GRMZM2G000039 SIT4 phosphatase- associated family

protein S2_9018813 2 9018813 1.74E-05 0.06 1391 0.20 0.21 0.037 GRMZM2G000047 (ATHAK5,HAK5): high affinity K+

transporter 5 S2_9018813 2 9018813 1.74E-05 0.06 1391 0.20 0.21 0.037 GRMZM2G000044 RPM1-interacting protein 4 (RIN4)

family protein S2_14891766 2 14891766 2.60E-05 0.45 1391 0.20 0.21 0.041 GRMZM2G129386 SIT4 phosphatase- associated family

199

protein

200

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S2_14891766 2 14891766 2.60E-05 0.45 1391 0.20 0.21 0.041 GRMZM2G129399 Heavy metal transport/detoxifica tion superfamily

protein S2_27955863 2 27955863 3.69E-05 0.25 1391 0.20 0.21 0.045 GRMZM2G079683 Protein of unknown

function, DUF584 S2_27955919 2 27955919 3.85E-05 0.25 1391 0.20 0.21 0.046 GRMZM2G079683 Protein of unknown

function, DUF584 S2_41247680 2 41247680 1.95E-05 0.07 1391 0.20 0.21 0.038 GRMZM2G394321 (RKL1): receptor-like

kinase 1 S2_168550067 2 168550067 1.69E-05 0.07 1391 0.20 0.21 0.036 GRMZM2G092125 (PIP2;2,PIP2B): plasma membrane

intrinsic protein 2 S2_184267183 2 184267183 1.31E-05 0.47 1391 0.20 0.21 0.036 GRMZM2G125482 (CYP75B1,D501,TT7) : Cytochrome P450

superfamily protein S2_187448381 2 187448381 4.56E-05 0.05 1391 0.20 0.21 0.049 GRMZM2G178229 (CYCD4;1): CYCLIN

D4;1 S2_188366566 2 188366566 4.62E-05 0.05 1391 0.20 0.21 0.049 GRMZM2G137532 (AtbZIP3,bZIP3): basic leucine-zipper

3 S2_188366566 2 188366566 4.62E-05 0.05 1391 0.20 0.21 0.049 GRMZM2G137477 retrotransposon protein, putative, unclassified,

expressed S2_192433107 2 192433107 7.05E-06 0.12 1391 0.20 0.21 0.029 GRMZM2G179031 (DRB2): dsRNA-

binding protein 2 S2_192433107 2 192433107 7.05E-06 0.12 1391 0.20 0.21 0.029 GRMZM2G179002 DHHC-type zinc

finger family protein

200

201

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S2_193881769 2 193881769 5.94E-06 0.05 1391 0.20 0.21 0.028 GRMZM2G107560 (ATMYC2,JAI1,JIN1, MYC2,RD22BP1,ZBF 1): Basic helix-loop- helix (bHLH) DNA- binding family

protein

S2_193881792 2 193881792 5.94E-06 0.05 1391 0.20 0.21 0.028 GRMZM2G107560 (ATMYC2,JAI1,JIN1, MYC2,RD22BP1,ZBF 1): Basic helix-loop- helix (bHLH) DNA- binding family protein S2_193881799 2 193881799 5.94E-06 0.05 1391 0.20 0.21 0.028 GRMZM2G107560 (ATMYC2,JAI1,JIN1, MYC2,RD22BP1,ZBF 1): Basic helix-loop- helix (bHLH) DNA- binding family

protein S2_193881814 2 193881814 5.94E-06 0.05 1391 0.20 0.21 0.028 GRMZM2G107560 (ATMYC2,JAI1,JIN1, MYC2,RD22BP1,ZBF 1): Basic helix-loop- helix (bHLH) DNA- binding family

protein S2_194113696 2 194113696 4.52E-06 0.07 1391 0.20 0.22 0.027 GRMZM2G037910 Basic-leucine zipper (bZIP) transcription

factor family protein S2_195036748 2 195036748 9.82E-06 0.05 1391 0.20 0.21 0.034 GRMZM2G034260 Mediator complex,

subunit Med10 201

202

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S2_195036748 2 195036748 9.82E-06 0.05 1391 0.20 0.21 0.034 GRMZM2G034471 (CYP78A6): cytochrome P450, family 78, subfamily

A, polypeptide 6 S2_197227802 2 197227802 1.62E-05 0.06 1391 0.20 0.21 0.036 GRMZM2G140116 Ribosomal protein

L14 S2_197227802 2 197227802 1.62E-05 0.06 1391 0.20 0.21 0.036 GRMZM2G049613 Protein of unknown function (DUF630

and DUF632) S2_206219806 2 206219806 8.57E-06 0.22 1391 0.20 0.21 0.031 GRMZM2G087479 Major facilitator

superfamily protein S2_206219806 2 206219806 8.57E-06 0.22 1391 0.20 0.21 0.031 GRMZM2G087462 GDSL-like Lipase/Acylhydrolas e superfamily

protein S2_206219856 2 206219856 8.57E-06 0.22 1391 0.20 0.21 0.031 GRMZM2G087479 Major facilitator

superfamily protein S2_206219856 2 206219856 8.57E-06 0.22 1391 0.20 0.21 0.031 GRMZM2G087462 GDSL-like Lipase/Acylhydrolas e superfamily

protein S2_206219945 2 206219945 1.13E-05 0.21 1391 0.20 0.21 0.034 GRMZM2G087479 Major facilitator

superfamily protein S2_206219945 2 206219945 1.13E-05 0.21 1391 0.20 0.21 0.034 GRMZM2G087462 GDSL-like Lipase/Acylhydrolas e superfamily

protein S2_213998470 2 213998470 2.24E-06 0.20 1391 0.20 0.22 0.024 GRMZM2G367777 (NSL1): MAC/Perforin domain-containing

02 protein

203

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S2_213998470 2 213998470 2.24E-06 0.20 1391 0.20 0.22 0.024 GRMZM2G322618 Glycoprotein membrane precursor GPI-

anchored S2_213998470 2 213998470 2.24E-06 0.20 1391 0.20 0.22 0.024 GRMZM2G022947 (CYP72A8): cytochrome P450, family 72, subfamily

A, polypeptide 8 S2_233749766 2 233749766 1.90E-05 0.17 1391 0.20 0.21 0.038 GRMZM2G037923 Protein kinase family protein S2_233749766 2 233749766 1.90E-05 0.17 1391 0.20 0.21 0.038 GRMZM2G037614 (DIN4): Transketolase family

protein S2_233749766 2 233749766 1.90E-05 0.17 1391 0.20 0.21 0.038 GRMZM2G340130 (ECT2): evolutionarily conserved C-

terminal region 2 S2_233749766 2 233749766 1.90E-05 0.17 1391 0.20 0.21 0.038 GRMZM2G021051 (AT2353,ATGA20OX 2,GA20OX2): gibberellin 20

oxidase 2 S2_233749766 2 233749766 1.90E-05 0.17 1391 0.20 0.21 0.038 GRMZM5G878490 (AGL62):

AGAMOUS-like 62 S2_233749766 2 233749766 1.90E-05 0.17 1391 0.20 0.21 0.038 AC209768.3_FG005 Polynucleotidyl transferase, ribonuclease H-like

superfamily protein S2_233749780 2 233749780 3.43E-05 0.17 1391 0.20 0.21 0.044 GRMZM2G037923 Protein kinase

family protein S2_233749780 2 233749780 3.43E-05 0.17 1391 0.20 0.21 0.044 GRMZM2G037614 (DIN4):

203 Transketolase family

protein

204

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S2_233749780 2 233749780 3.43E-05 0.17 1391 0.20 0.21 0.044 GRMZM2G340130 (ECT2): evolutionarily conserved C-

terminal region 2 S2_233749780 2 233749780 3.43E-05 0.17 1391 0.20 0.21 0.044 GRMZM2G021051 (AT2353,ATGA20OX 2,GA20OX2): gibberellin 20

oxidase 2 S2_233749780 2 233749780 3.43E-05 0.17 1391 0.20 0.21 0.044 GRMZM5G878490 (AGL62):

AGAMOUS-like 62 S2_233749780 2 233749780 3.43E-05 0.17 1391 0.20 0.21 0.044 AC209768.3_FG005 Polynucleotidyl transferase, ribonuclease H-like

superfamily protein S3_306174 3 306174 2.83E-07 0.24 1391 0.20 0.22 0.014 GRMZM2G035482 Coatomer epsilon

subunit S3_1467296 3 1467296 8.42E-07 0.11 1391 0.20 0.22 0.023 GRMZM2G087804 (ATGLK1,GLK1,GPRI 1): GBF\'s pro-rich region-interacting

factor 1 S3_1467296 3 1467296 8.42E-07 0.11 1391 0.20 0.22 0.023 GRMZM2G087714 (NFD6): nuclear

fusion defective 6 S3_1467297 3 1467297 5.50E-07 0.11 1391 0.20 0.22 0.020 GRMZM2G087804 (ATGLK1,GLK1,GPRI 1): GBF\'s pro-rich region-interacting

factor 1 S3_1467297 3 1467297 5.50E-07 0.11 1391 0.20 0.22 0.020 GRMZM2G087714 (NFD6): nuclear

fusion defective 6 S3_1468707 3 1468707 3.47E-05 0.45 1391 0.20 0.21 0.044 GRMZM2G087804 (ATGLK1,GLK1,GPRI 1): GBF\'s pro-rich

204 region-interacting

factor 1

205

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S3_1468707 3 1468707 3.47E-05 0.45 1391 0.20 0.21 0.044 GRMZM2G087714 (NFD6): nuclear

fusion defective 6 S3_1468710 3 1468710 4.44E-05 0.46 1391 0.20 0.21 0.049 GRMZM2G087804 (ATGLK1,GLK1,GPRI 1): GBF\'s pro-rich region-interacting

factor 1 S3_1468710 3 1468710 4.44E-05 0.46 1391 0.20 0.21 0.049 GRMZM2G087714 (NFD6): nuclear

fusion defective 6 S3_1468711 3 1468711 3.47E-05 0.45 1391 0.20 0.21 0.044 GRMZM2G087804 (ATGLK1,GLK1,GPRI 1): GBF\'s pro-rich region-interacting factor 1 S3_1468711 3 1468711 3.47E-05 0.45 1391 0.20 0.21 0.044 GRMZM2G087714 (NFD6): nuclear

fusion defective 6 S3_1468712 3 1468712 3.47E-05 0.45 1391 0.20 0.21 0.044 GRMZM2G087804 (ATGLK1,GLK1,GPRI 1): GBF\'s pro-rich region-interacting

factor 1 S3_1468712 3 1468712 3.47E-05 0.45 1391 0.20 0.21 0.044 GRMZM2G087714 (NFD6): nuclear

fusion defective 6 S3_1468713 3 1468713 3.47E-05 0.45 1391 0.20 0.21 0.044 GRMZM2G087804 (ATGLK1,GLK1,GPRI 1): GBF\'s pro-rich region-interacting

factor 1 S3_1468713 3 1468713 3.47E-05 0.45 1391 0.20 0.21 0.044 GRMZM2G087714 (NFD6): nuclear

fusion defective 6 S3_1468716 3 1468716 3.47E-05 0.45 1391 0.20 0.21 0.044 GRMZM2G087804 (ATGLK1,GLK1,GPRI 1): GBF\'s pro-rich region-interacting

factor 1

205 S3_1468716 3 1468716 3.47E-05 0.45 1391 0.20 0.21 0.044 GRMZM2G087714 (NFD6): nuclear

fusion defective 6

206

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S3_5850435 3 5850435 3.07E-07 0.09 1391 0.20 0.22 0.014 GRMZM2G470914 Protein kinase

superfamily protein S3_10517929 3 10517929 3.38E-05 0.14 1391 0.20 0.21 0.044 GRMZM5G868061 (BES1,BZR2): Brassinosteroid signalling positive regulator (BZR1)

family protein S3_10517929 3 10517929 3.38E-05 0.14 1391 0.20 0.21 0.044 GRMZM2G348238 Homeodomain-like

superfamily protein S3_17584320 3 17584320 1.65E-05 0.47 1391 0.20 0.21 0.036 GRMZM2G467242 (ATTSC13,CER10,EC R,TSC13): 3-oxo-5- alpha-steroid 4- dehydrogenase

family protein S3_19967649 3 19967649 3.42E-05 0.20 1391 0.20 0.21 0.044 GRMZM2G467671 Protein kinase

superfamily protein S3_26309300 3 26309300 3.78E-05 0.05 1391 0.20 0.21 0.045 GRMZM2G104829 Glycosyltransferase

family 61 protein S3_48493746 3 48493746 2.23E-05 0.26 1391 0.20 0.21 0.039 GRMZM2G017520 (ATMYB61,MYB61): myb domain protein

61 S3_48493947 3 48493947 4.68E-05 0.38 1391 0.20 0.21 0.050 GRMZM2G017520 (ATMYB61,MYB61): myb domain protein

61 S3_141572234 3 141572234 2.16E-05 0.08 1391 0.20 0.21 0.039 GRMZM2G115812 SAP domain containing protein,

expressed S3_166793983 3 166793983 2.52E-05 0.37 1391 0.20 0.21 0.041 GRMZM2G141632 POEI32 - Pollen Ole e I allergen and extensin family

206 protein precursor,

expressed

207

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S3_166793983 3 166793983 2.52E-05 0.37 1391 0.20 0.21 0.041 GRMZM2G141638 (PLT2): Integrase- type DNA-binding

superfamily protein S3_166796168 3 166796168 3.46E-05 0.14 1391 0.20 0.21 0.044 GRMZM2G141632 POEI32 - Pollen Ole e I allergen and extensin family protein precursor,

expressed S3_166796168 3 166796168 3.46E-05 0.14 1391 0.20 0.21 0.044 GRMZM2G141638 (PLT2): Integrase- type DNA-binding

superfamily protein S3_167009322 3 167009322 1.06E-05 0.33 1391 0.20 0.21 0.034 GRMZM2G346132 Protein kinase

superfamily protein S3_167009322 3 167009322 1.06E-05 0.33 1391 0.20 0.21 0.034 GRMZM2G047572 Family of unknown

function (DUF566) S3_167009322 3 167009322 1.06E-05 0.33 1391 0.20 0.21 0.034 GRMZM2G346138 S-adenosyl-L- methionine- dependent methyltransferases

superfamily protein S3_167009322 3 167009322 1.06E-05 0.33 1391 0.20 0.21 0.034 GRMZM2G438045 Ribosomal RNA processing Brix

domain protein S3_167069918 3 167069918 3.74E-05 0.37 1391 0.20 0.21 0.045 GRMZM2G137174 (PLA IIA,PLA2A,PLP2):

phospholipase A 2A S3_167478960 3 167478960 3.02E-05 0.06 1391 0.20 0.21 0.043 GRMZM2G044584 Ribosomal protein

L13 family protein S3_167478960 3 167478960 3.02E-05 0.06 1391 0.20 0.21 0.043 GRMZM2G118362 Tetratricopeptide repeat (TPR)-like

207

superfamily protein

208

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S3_184948734 3 184948734 1.41E-07 0.16 1391 0.20 0.22 0.010 GRMZM2G065290 (ATWRKY46,WRKY4 6): WRKY DNA-

binding protein 46 S3_191777687 3 191777687 4.98E-07 0.39 1391 0.20 0.22 0.020 GRMZM2G093239 Transducin/WD40 repeat-like

superfamily protein S3_191777687 3 191777687 4.98E-07 0.39 1391 0.20 0.22 0.020 GRMZM2G093101 (ATPAP10,PAP10): purple acid

phosphatase 10 S3_195964307 3 195964307 2.23E-05 0.29 1391 0.20 0.21 0.039 GRMZM2G105863 (RIP2): ROP

interactive partner 2 S3_209904642 3 209904642 1.11E-05 0.44 1391 0.20 0.21 0.034 GRMZM2G346639 Nucleotidyltransfera

se family protein S3_209904679 3 209904679 1.11E-05 0.44 1391 0.20 0.21 0.034 GRMZM2G346639 Nucleotidyltransfera

se family protein S3_209904786 3 209904786 1.43E-05 0.48 1391 0.20 0.21 0.036 GRMZM2G346639 Nucleotidyltransfera

se family protein S3_224467850 3 224467850 2.84E-05 0.42 1391 0.20 0.21 0.042 GRMZM5G874955 (ABCG40,ATABCG40 ,ATPDR12,PDR12): pleiotropic drug

resistance 12 S3_224467850 3 224467850 2.84E-05 0.42 1391 0.20 0.21 0.042 GRMZM2G143234 ATP synthase epsilon chain,

mitochondrial S3_225206118 3 225206118 5.28E-06 0.26 1391 0.20 0.22 0.028 GRMZM2G001296 (MEE18): maternal effect embryo arrest

18 S3_225206145 3 225206145 3.00E-06 0.26 1391 0.20 0.22 0.027 GRMZM2G001296 (MEE18): maternal effect embryo arrest

208

209

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S3_228983258 3 228983258 4.11E-05 0.38 1391 0.20 0.21 0.048 GRMZM2G344924 Nucleoporin

autopeptidase S3_228983258 3 228983258 4.11E-05 0.38 1391 0.20 0.21 0.048 GRMZM2G344903 (CYP89A9): cytochrome P450, family 87, subfamily

A, polypeptide 9 S4_18581278 4 18581278 3.14E-05 0.25 1391 0.20 0.21 0.044 GRMZM2G139894 (ATMCM2,MCM2): minichromosome maintenance (MCM2/3/5) family

protein S4_18581278 4 18581278 3.14E-05 0.25 1391 0.20 0.21 0.044 GRMZM2G139880 (THY-1): thymidylate

synthase 1 S4_18581278 4 18581278 3.14E-05 0.25 1391 0.20 0.21 0.044 GRMZM2G440221 Oligosaccharyltransf erase complex/magnesiu m transporter

family protein S4_18581278 4 18581278 3.14E-05 0.25 1391 0.20 0.21 0.044 GRMZM2G440208 6-phosphogluconate dehydrogenase

family protein S4_185864906 4 185864906 3.59E-05 0.06 1391 0.20 0.21 0.045 GRMZM2G071378 Nucleotide-sugar transporter family

protein S4_185864906 4 185864906 3.59E-05 0.06 1391 0.20 0.21 0.045 GRMZM2G071288 Peroxisomal membrane 22 kDa (Mpv17/PMP22)

family protein

209

210

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S4_208396741 4 208396741 4.46E-06 0.21 1391 0.20 0.22 0.027 GRMZM2G413253 (EMB2778,FKP1,HM GS,MVA1): hydroxymethylgluta ryl-CoA synthase / HMG-CoA synthase / 3-hydroxy-3- methylglutaryl coenzyme A

synthase S4_208396741 4 208396741 4.46E-06 0.21 1391 0.20 0.22 0.027 GRMZM2G115245 (EMB2780): DNA binding;nucleotide binding;nucleic acid binding;DNA- directed DNA polymerases;DNA-

directed DNA S4_238297872 4 238297872 1.58E-05 0.26 1391 0.20 0.21 0.036 GRMZM2G061023 (ATRAD1,RAD1,UVH 1): Restriction endonuclease, type II-like superfamily protein S5_938415 5 938415 1.87E-05 0.48 1391 0.20 0.21 0.038 GRMZM2G033117 DCD (Development and Cell Death)

domain protein S5_938415 5 938415 1.87E-05 0.48 1391 0.20 0.21 0.038 GRMZM2G082976 (DER2.2): DERLIN-

2.2 S5_938415 5 938415 1.87E-05 0.48 1391 0.20 0.21 0.038 GRMZM2G030858 transducin family protein / WD-40 repeat family

protein

210 S5_938415 5 938415 1.87E-05 0.48 1391 0.20 0.21 0.038 GRMZM2G028955 (HTA6): histone H2A

211

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_938415 5 938415 1.87E-05 0.48 1391 0.20 0.21 0.038 GRMZM2G028889 hydroxyproline-rich glycoprotein family

protein S5_2796695 5 2796695 4.01E-06 0.06 1391 0.20 0.22 0.027 GRMZM2G108716 (TFIIS): transcript

elongation factor IIS S5_2796695 5 2796695 4.01E-06 0.06 1391 0.20 0.22 0.027 GRMZM2G108677 RNA-binding KH domain-containing

protein S5_2796695 5 2796695 4.01E-06 0.06 1391 0.20 0.22 0.027 GRMZM5G899149 Ribosomal protein

S26e family protein S5_2796695 5 2796695 4.01E-06 0.06 1391 0.20 0.22 0.027 GRMZM2G108694 (CKI1): Signal transduction

histidine kinase S5_2814158 5 2814158 2.25E-05 0.07 1391 0.20 0.21 0.039 GRMZM2G108677 RNA-binding KH domain-containing

protein S5_2814158 5 2814158 2.25E-05 0.07 1391 0.20 0.21 0.039 GRMZM2G108694 (CKI1): Signal transduction

histidine kinase S5_2814158 5 2814158 2.25E-05 0.07 1391 0.20 0.21 0.039 GRMZM2G108643 Ribosomal protein

L17 family protein S5_8006530 5 8006530 1.35E-05 0.17 1391 0.20 0.21 0.036 GRMZM2G023858 Vps51/Vps67 family (components of vesicular transport)

protein S5_11883125 5 11883125 1.99E-05 0.19 1391 0.20 0.21 0.038 GRMZM2G090435 Protein of unknown

function (DUF3049) S5_19681313 5 19681313 4.36E-05 0.33 1391 0.20 0.21 0.049 GRMZM2G124918 (SC3): secretory

carrier 3 S5_19681313 5 19681313 4.36E-05 0.33 1391 0.20 0.21 0.049 GRMZM2G124863 transferases;folic

211

acid binding

212

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_21343857 5 21343857 3.32E-05 0.09 1391 0.20 0.21 0.044 GRMZM5G851862 (CYP76C2): cytochrome P450, family 76, subfamily

C, polypeptide 2 S5_21343857 5 21343857 3.32E-05 0.09 1391 0.20 0.21 0.044 GRMZM5G823318 (AK,AK-LYS1,AK1):

aspartate kinase 1 S5_171964045 5 171964045 3.16E-05 0.05 1391 0.20 0.21 0.044 GRMZM5G839969 (AGL80,FEM111):

AGAMOUS-like 80 S5_179844272 5 179844272 3.66E-05 0.33 1391 0.20 0.21 0.045 GRMZM2G390560 UDP- Glycosyltransferase

superfamily protein S5_179844272 5 179844272 3.66E-05 0.33 1391 0.20 0.21 0.045 GRMZM2G057184 ARM- repeat/Tetratricope ptide repeat (TPR)-

like protein S5_179844272 5 179844272 3.66E-05 0.33 1391 0.20 0.21 0.045 GRMZM2G056988 Protein of unknown

function (DUF581) S5_188388368 5 188388368 3.52E-05 0.07 1391 0.20 0.21 0.044 AC198169.4_FG004 (EMB1586,ISE1): P- loop containing nucleoside triphosphate hydrolases

superfamily protein S5_188388368 5 188388368 3.52E-05 0.07 1391 0.20 0.21 0.044 GRMZM2G172239 BolA-like family

protein S5_188393532 5 188393532 1.06E-05 0.11 1391 0.20 0.21 0.034 AC198169.4_FG004 (EMB1586,ISE1): P- loop containing nucleoside triphosphate hydrolases

212

superfamily protein

213

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_188393532 5 188393532 1.06E-05 0.11 1391 0.20 0.21 0.034 GRMZM2G172239 BolA-like family

protein S5_209524297 5 209524297 2.74E-05 0.09 1391 0.20 0.21 0.041 GRMZM2G046885 (AGL22,SVP): K-box region and MADS- box transcription factor family

protein S5_210874222 5 210874222 8.17E-06 0.06 1391 0.20 0.21 0.031 GRMZM2G046894 Cyclophilin-like peptidyl-prolyl cis- trans isomerase

family protein S5_210874222 5 210874222 8.17E-06 0.06 1391 0.20 0.21 0.031 GRMZM2G046459 O-Glycosyl hydrolases family 17

protein

S5_211720418 5 211720418 1.71E-05 0.09 1391 0.20 0.21 0.036 GRMZM2G049194 (TRFL6): TRF-like 6 S5_211720418 5 211720418 1.71E-05 0.09 1391 0.20 0.21 0.036 GRMZM5G893117 (AtGRF5,GRF5): growth-regulating

factor 5 S5_211720418 5 211720418 1.71E-05 0.09 1391 0.20 0.21 0.036 GRMZM5G842517 (APG12,APG12B): Ubiquitin-like

superfamily protein S6_58561008 6 58561008 2.97E-05 0.20 1391 0.20 0.21 0.043 GRMZM2G095252 (CPN60B,LEN1):

chaperonin 60 beta S6_58561008 6 58561008 2.97E-05 0.20 1391 0.20 0.21 0.043 GRMZM2G133698 TCP-1/cpn60 chaperonin family

protein S6_74595954 6 74595954 3.51E-05 0.06 1391 0.20 0.21 0.044 GRMZM2G393272 (MAX2,ORE9,PPS): RNI-like superfamily

protein

213

214

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S6_74595954 6 74595954 3.51E-05 0.06 1391 0.20 0.21 0.044 GRMZM2G002100 (ATMAPK6,ATMPK6, MAPK6,MPK6): MAP

kinase 6 S6_75619996 6 75619996 2.58E-05 0.06 1391 0.20 0.21 0.041 GRMZM2G351047 Major facilitator

superfamily protein S6_75619996 6 75619996 2.58E-05 0.06 1391 0.20 0.21 0.041 GRMZM5G835276 GDSL-like Lipase/Acylhydrolas e superfamily

protein S6_75619996 6 75619996 2.58E-05 0.06 1391 0.20 0.21 0.041 GRMZM5G829897 SGNH hydrolase- type esterase

superfamily protein S6_88569038 6 88569038 1.39E-05 0.06 1391 0.20 0.21 0.036 GRMZM2G100955 DTW domain-

containing protein S6_88569038 6 88569038 1.39E-05 0.06 1391 0.20 0.21 0.036 GRMZM2G100976 (ATCNFU3,NFU3): NFU domain protein

3 S6_88983465 6 88983465 3.83E-06 0.38 1391 0.20 0.22 0.027 GRMZM2G139657 O- fucosyltransferase

family protein S6_130841169 6 130841169 4.93E-06 0.09 1391 0.20 0.22 0.027 GRMZM2G066341 Protein of unknown

function (DUF581) S6_135656038 6 135656038 7.08E-06 0.08 1391 0.20 0.21 0.029 GRMZM2G358491 (MED33A,RFR1):

REF4-related 1 S6_149678163 6 149678163 3.12E-05 0.44 1391 0.20 0.21 0.044 GRMZM2G000816 Eukaryotic protein of unknown

function (DUF914) S6_153229824 6 153229824 2.87E-05 0.47 1391 0.20 0.21 0.043 AC209257.4_FG006 Integrase-type DNA- binding superfamily

protein

214 S6_153229824 6 153229824 2.87E-05 0.47 1391 0.20 0.21 0.043 AC212394.4_FG010 (CDKB2;1): cyclin-

dependent kinase

215

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation

B2;1

S6_153229824 6 153229824 2.87E-05 0.47 1391 0.20 0.21 0.043 GRMZM5G869403 (ATEXO70B1,EXO70 B1): exocyst subunit exo70 family

protein B1 S6_153229824 6 153229824 2.87E-05 0.47 1391 0.20 0.21 0.043 AC209257.4_FG003 Glutaredoxin family

protein S6_153229824 6 153229824 2.87E-05 0.47 1391 0.20 0.21 0.043 AC209257.4_FG004 DEFL4 - Defensin and Defensin-like DEFL family, expressed S6_157755865 6 157755865 4.49E-05 0.29 1391 0.20 0.21 0.049 GRMZM2G368448 TRAF-like

superfamily protein S6_157818681 6 157818681 2.36E-05 0.15 1391 0.20 0.21 0.040 GRMZM2G060324 Signal recognition particle, SRP54

subunit protein S6_157818681 6 157818681 2.36E-05 0.15 1391 0.20 0.21 0.040 GRMZM2G097040 NADH-ubiquinone oxidoreductase 24 kDa subunit,

putative S6_157818681 6 157818681 2.36E-05 0.15 1391 0.20 0.21 0.040 GRMZM2G060170 tesmin/TSO1-like CXC domain containing protein,

expressed S6_157820015 6 157820015 3.66E-05 0.19 1391 0.20 0.21 0.045 GRMZM2G060324 Signal recognition particle, SRP54

subunit protein

215

216

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S6_157820015 6 157820015 3.66E-05 0.19 1391 0.20 0.21 0.045 GRMZM2G097040 NADH-ubiquinone oxidoreductase 24 kDa subunit,

putative S6_157820015 6 157820015 3.66E-05 0.19 1391 0.20 0.21 0.045 GRMZM2G060170 tesmin/TSO1-like CXC domain containing protein,

expressed S6_162127329 6 162127329 1.50E-05 0.07 1391 0.20 0.21 0.036 GRMZM2G174971 (APC10): anaphase promoting complex

10 S6_162127329 6 162127329 1.50E-05 0.07 1391 0.20 0.21 0.036 GRMZM2G174990 Sec14p-like phosphatidylinositol transfer family

protein S6_162127329 6 162127329 1.50E-05 0.07 1391 0.20 0.21 0.036 GRMZM2G174949 Regulator of chromosome condensation (RCC1) family protein S6_165135369 6 165135369 8.03E-06 0.10 1391 0.20 0.21 0.031 GRMZM2G160460 Major facilitator

superfamily protein S6_165135369 6 165135369 8.03E-06 0.10 1391 0.20 0.21 0.031 GRMZM2G160504 Major facilitator

superfamily protein S6_166890758 6 166890758 1.82E-05 0.43 1391 0.20 0.21 0.038 GRMZM2G159016 (scpl50): serine carboxypeptidase-

like 50 S6_166890758 6 166890758 1.82E-05 0.43 1391 0.20 0.21 0.038 GRMZM2G158998 Phox-associated domain;Phox- like;Sorting nexin, C-

216

terminal

217

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S6_166890758 6 166890758 1.82E-05 0.43 1391 0.20 0.21 0.038 GRMZM2G458538 O-acetyltransferase

family protein S6_166890758 6 166890758 1.82E-05 0.43 1391 0.20 0.21 0.038 GRMZM2G458448 Late embryogenesis abundant (LEA) hydroxyproline-rich

glycoprotein family S6_166890758 6 166890758 1.82E-05 0.43 1391 0.20 0.21 0.038 GRMZM2G159028 RNA-binding (RRM/RBD/RNP motifs) family

protein S7_922357 7 922357 2.61E-05 0.08 1391 0.20 0.21 0.041 GRMZM2G020104 (ATGLR3.4,GLR3.4,G LUR3): glutamate

receptor 3.4 S7_922495 7 922495 1.66E-06 0.07 1391 0.20 0.22 0.024 GRMZM2G020104 (ATGLR3.4,GLR3.4,G LUR3): glutamate

receptor 3.4 S7_1317269 7 1317269 5.93E-06 0.45 1391 0.20 0.21 0.028 GRMZM2G120563 Calcium-dependent lipid-binding (CaLB domain) family

protein S7_1317269 7 1317269 5.93E-06 0.45 1391 0.20 0.21 0.028 GRMZM2G555108 Transducin/WD40 repeat-like

superfamily protein S7_2747413 7 2747413 4.62E-06 0.14 1391 0.20 0.22 0.027 GRMZM5G810231 OsFBL33 - F-box domain and LRR containing protein,

expressed S7_2747427 7 2747427 4.62E-06 0.14 1391 0.20 0.22 0.027 GRMZM5G810231 OsFBL33 - F-box domain and LRR containing protein,

217

expressed

218

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S7_4583854 7 4583854 1.48E-05 0.07 1391 0.20 0.21 0.036 GRMZM2G479980 (anac042,NAC042): NAC domain containing protein

42 S7_4965889 7 4965889 1.81E-05 0.43 1391 0.20 0.21 0.038 GRMZM2G040090 D-isomer specific 2- hydroxyacid dehydrogenase

family protein S7_4965889 7 4965889 1.81E-05 0.43 1391 0.20 0.21 0.038 GRMZM2G039922 (HERK2): hercules

receptor kinase 2 S7_4965890 7 4965890 2.72E-05 0.42 1391 0.20 0.21 0.041 GRMZM2G040090 D-isomer specific 2- hydroxyacid dehydrogenase

family protein S7_4965890 7 4965890 2.72E-05 0.42 1391 0.20 0.21 0.041 GRMZM2G039922 (HERK2): hercules

receptor kinase 2 S7_46304649 7 46304649 6.37E-06 0.09 1391 0.20 0.21 0.029 GRMZM5G803610 Trimeric LpxA-like enzymes

superfamily protein S7_46304649 7 46304649 6.37E-06 0.09 1391 0.20 0.21 0.029 GRMZM2G078424 (PNT1): mannosyltransferas

e family protein S7_46333507 7 46333507 5.69E-06 0.09 1391 0.20 0.22 0.028 GRMZM5G868168 (ATNAP11,NAP11,T GD3): non-intrinsic

ABC protein 11 S7_105364725 7 105364725 1.57E-05 0.44 1391 0.20 0.21 0.036 GRMZM2G476685 (ATCYCD1;1,CYCD1;

1): CYCLIN D1;1 S7_105364741 7 105364741 1.57E-05 0.44 1391 0.20 0.21 0.036 GRMZM2G476685 (ATCYCD1;1,CYCD1;

1): CYCLIN D1;1 S7_106078370 7 106078370 2.26E-05 0.26 1391 0.20 0.21 0.039 GRMZM2G046600 alpha/beta-

218 Hydrolases

superfamily protein

219

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation

S7_118306535 7 118306535 1.94E-05 0.28 1391 0.20 0.21 0.038 GRMZM2G041175 (TET8): tetraspanin8 S7_118306535 7 118306535 1.94E-05 0.28 1391 0.20 0.21 0.038 GRMZM2G040945 HAD-superfamily hydrolase, subfamily

IG, 5\'-nucleotidase S7_118306535 7 118306535 1.94E-05 0.28 1391 0.20 0.21 0.038 GRMZM2G339728 retrotransposon protein, putative, unclassified,

expressed

S7_118306577 7 118306577 2.10E-05 0.29 1391 0.20 0.21 0.039 GRMZM2G041175 (TET8): tetraspanin8 S7_118306577 7 118306577 2.10E-05 0.29 1391 0.20 0.21 0.039 GRMZM2G040945 HAD-superfamily hydrolase, subfamily

IG, 5\'-nucleotidase S7_118306577 7 118306577 2.10E-05 0.29 1391 0.20 0.21 0.039 GRMZM2G339728 retrotransposon protein, putative, unclassified,

expressed

S7_118307964 7 118307964 1.51E-06 0.16 1391 0.20 0.22 0.024 GRMZM2G041175 (TET8): tetraspanin8 S7_118307964 7 118307964 1.51E-06 0.16 1391 0.20 0.22 0.024 GRMZM2G040945 HAD-superfamily hydrolase, subfamily

IG, 5\'-nucleotidase S7_118307964 7 118307964 1.51E-06 0.16 1391 0.20 0.22 0.024 GRMZM2G339728 retrotransposon protein, putative, unclassified,

expressed

S7_118307966 7 118307966 1.51E-06 0.16 1391 0.20 0.22 0.024 GRMZM2G041175 (TET8): tetraspanin8 S7_118307966 7 118307966 1.51E-06 0.16 1391 0.20 0.22 0.024 GRMZM2G040945 HAD-superfamily hydrolase, subfamily

IG, 5\'-nucleotidase

219

220

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S7_118307966 7 118307966 1.51E-06 0.16 1391 0.20 0.22 0.024 GRMZM2G339728 retrotransposon protein, putative, unclassified,

expressed S7_119974729 7 119974729 1.98E-05 0.37 1391 0.20 0.21 0.038 GRMZM2G137676 Plant invertase/pectin methylesterase inhibitor

superfamily S7_119975995 7 119975995 2.18E-05 0.37 1391 0.20 0.21 0.039 GRMZM2G137676 Plant invertase/pectin methylesterase inhibitor

superfamily S7_120201871 7 120201871 2.49E-05 0.18 1391 0.20 0.21 0.041 GRMZM2G138976 ARID/BRIGHT DNA- binding domain-

containing protein S7_120201871 7 120201871 2.49E-05 0.18 1391 0.20 0.21 0.041 GRMZM2G138727 PROLM23 - Prolamin precursor,

expressed S7_120201889 7 120201889 2.16E-05 0.16 1391 0.20 0.21 0.039 GRMZM2G138976 ARID/BRIGHT DNA- binding domain-

containing protein S7_120201889 7 120201889 2.16E-05 0.16 1391 0.20 0.21 0.039 GRMZM2G138727 PROLM23 - Prolamin precursor,

expressed S7_121191933 7 121191933 4.08E-05 0.32 1391 0.20 0.21 0.048 GRMZM2G168020 major ampullate spidroin 2, putative,

expressed S7_121191933 7 121191933 4.08E-05 0.32 1391 0.20 0.21 0.048 GRMZM2G469409 (emb1187): Protein

220 kinase superfamily

protein

221

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S7_122073695 7 122073695 6.48E-07 0.31 1391 0.20 0.22 0.021 GRMZM2G050172 (AT- RSH3,ATRSH3,RSH3) : RELA/SPOT

homolog 3 S7_122073695 7 122073695 6.48E-07 0.31 1391 0.20 0.22 0.021 GRMZM2G086714 (AT- RSH3,ATRSH3,RSH3) : RELA/SPOT

homolog 3 S7_122073695 7 122073695 6.48E-07 0.31 1391 0.20 0.22 0.021 GRMZM2G388045 (ATGEX1,GEX1): gamete expressed

protein 1 S7_124568038 7 124568038 9.53E-06 0.41 1391 0.20 0.21 0.034 GRMZM2G421463 (LYM1): lysm domain GPI- anchored protein 1

precursor S7_154278263 7 154278263 2.75E-05 0.47 1391 0.20 0.21 0.041 GRMZM5G835323 Translation initiation factor SUI1

family protein S7_154278263 7 154278263 2.75E-05 0.47 1391 0.20 0.21 0.041 GRMZM2G080174 (TDP1): tyrosyl-DNA phosphodiesterase-

related S7_162068990 7 162068990 7.38E-06 0.11 1391 0.20 0.21 0.030 GRMZM2G357734 (PDE226,PDS,PDS3): phytoene

desaturase 3 S7_162068990 7 162068990 7.38E-06 0.11 1391 0.20 0.21 0.030 GRMZM2G057247 (ATFH6,FH6): formin

homolog 6 S7_162710260 7 162710260 3.44E-06 0.32 1391 0.20 0.22 0.027 GRMZM2G008712 (ZFP7): zinc finger

protein 7 S7_162710260 7 162710260 3.44E-06 0.32 1391 0.20 0.22 0.027 GRMZM2G309970 (WPP2): WPP

domain protein 2

221

222

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S7_162710260 7 162710260 3.44E-06 0.32 1391 0.20 0.22 0.027 GRMZM2G008468 Got1/Sft2-like vescicle transport

protein family S7_162711840 7 162711840 4.48E-05 0.40 1391 0.20 0.21 0.049 GRMZM2G008712 (ZFP7): zinc finger

protein 7 S7_162711840 7 162711840 4.48E-05 0.40 1391 0.20 0.21 0.049 GRMZM2G309970 (WPP2): WPP

domain protein 2 S7_162711840 7 162711840 4.48E-05 0.40 1391 0.20 0.21 0.049 GRMZM2G008468 Got1/Sft2-like vescicle transport

protein family S7_162801789 7 162801789 2.78E-07 0.37 1391 0.20 0.22 0.014 GRMZM2G119740 Prefoldin chaperone subunit family

protein S7_162801789 7 162801789 2.78E-07 0.37 1391 0.20 0.22 0.014 GRMZM2G119705 ribosome inactivating protein,

putative, expressed S7_176480402 7 176480402 2.26E-05 0.21 1391 0.20 0.21 0.039 AC197544.3_FG002 (ULP1B): UB-like

protease 1B S8_17889029 8 17889029 2.42E-06 0.27 1391 0.20 0.22 0.024 GRMZM2G080521 alpha/beta- Hydrolases

superfamily protein S8_17889039 8 17889039 1.28E-06 0.24 1391 0.20 0.22 0.023 GRMZM2G080521 alpha/beta- Hydrolases

superfamily protein S8_18215458 8 18215458 6.48E-06 0.23 1391 0.20 0.21 0.029 GRMZM2G107696 (ATUBP14,PER1,TTN 6,UBP14): ubiquitin-

specific protease 14 S8_18215760 8 18215760 8.56E-06 0.31 1391 0.20 0.21 0.031 GRMZM2G107696 (ATUBP14,PER1,TTN 6,UBP14): ubiquitin-

specific protease 14

222

223

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S8_18349921 8 18349921 2.33E-05 0.10 1391 0.20 0.21 0.040 GRMZM2G144464 Eukaryotic aspartyl protease family

protein S8_18349921 8 18349921 2.33E-05 0.10 1391 0.20 0.21 0.040 GRMZM2G570006 (RUXF): small nuclear

ribonucleoprotein F S8_18967101 8 18967101 2.15E-05 0.07 1391 0.20 0.21 0.039 GRMZM2G047949 (HEN2): RNA helicase, ATP- dependent,

SK12/DOB1 protein S8_18967107 8 18967107 2.15E-05 0.07 1391 0.20 0.21 0.039 GRMZM2G047949 (HEN2): RNA helicase, ATP- dependent,

SK12/DOB1 protein S8_19122007 8 19122007 4.51E-05 0.05 1391 0.20 0.21 0.049 GRMZM2G125020 DUF581 domain containing protein,

expressed S8_19968068 8 19968068 1.27E-05 0.06 1391 0.20 0.21 0.036 GRMZM2G095280 (UGT74E2): Uridine diphosphate glycosyltransferase

74E2 S8_19968068 8 19968068 1.27E-05 0.06 1391 0.20 0.21 0.036 GRMZM2G095255 RING/U-box

superfamily protein S8_19968068 8 19968068 1.27E-05 0.06 1391 0.20 0.21 0.036 GRMZM2G095265 (SAG12): senescence-

associated gene 12 S8_20091529 8 20091529 2.58E-05 0.22 1391 0.20 0.21 0.041 GRMZM2G395749 (ALY3,ATALY3): DNA

binding

S8_22510436 8 22510436 1.23E-06 0.05 1391 0.20 0.22 0.023 GRMZM2G309568 zinc ion binding

223

224

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S8_22510436 8 22510436 1.23E-06 0.05 1391 0.20 0.22 0.023 GRMZM2G009475 avr9/Cf-9 rapidly elicited protein 146,

putative, expressed S8_26870236 8 26870236 1.87E-05 0.08 1391 0.20 0.21 0.038 GRMZM2G429057 Pyridoxal phosphate (PLP)-dependent transferases

superfamily protein S8_26870236 8 26870236 1.87E-05 0.08 1391 0.20 0.21 0.038 GRMZM2G127650 S-locus lectin protein kinase

family protein S8_26870236 8 26870236 1.87E-05 0.08 1391 0.20 0.21 0.038 GRMZM2G127687 Leucine-rich repeat protein kinase

family protein S8_66288692 8 66288692 2.94E-05 0.24 1391 0.20 0.21 0.043 GRMZM2G477340 phosphatidyl serine synthase family

protein S8_76982738 8 76982738 1.36E-05 0.07 1391 0.20 0.21 0.036 AC233854.1_FG002 (BCS1): cytochrome

BC1 synthesis S8_76982738 8 76982738 1.36E-05 0.07 1391 0.20 0.21 0.036 GRMZM5G884544 Homeodomain-like

superfamily protein S8_104463909 8 104463909 4.54E-06 0.06 1391 0.20 0.22 0.027 GRMZM2G047152 LRR and NB-ARC domains-containing disease resistance

protein S8_104463909 8 104463909 4.54E-06 0.06 1391 0.20 0.22 0.027 GRMZM2G347471 xylose isomerase

family protein S8_104463909 8 104463909 4.54E-06 0.06 1391 0.20 0.22 0.027 AC203955.3_FG005 DUF1517 domain containing protein,

putative, expressed S8_113504730 8 113504730 1.04E-05 0.07 1391 0.20 0.21 0.034 GRMZM2G170552 (CIPK10,PKS2,SIP1,S

224 NRK3.8): SOS3-

interacting protein 1

225

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S8_121895690 8 121895690 3.11E-05 0.48 1391 0.20 0.21 0.044 GRMZM2G384755 (ARK3,RK3):

receptor kinase 3 S8_121895690 8 121895690 3.11E-05 0.48 1391 0.20 0.21 0.044 GRMZM2G082792 (FQR1): flavodoxin- like quinone

reductase 1 S8_124464545 8 124464545 6.67E-06 0.05 1391 0.20 0.21 0.029 GRMZM2G173700 P-loop nucleoside triphosphate hydrolases superfamily protein with CH (Calponin

Homology) domain S8_124490717 8 124490717 1.62E-05 0.05 1391 0.20 0.21 0.036 GRMZM2G173710 (AHP4): HPT phosphotransmitter

4 S8_132204020 8 132204020 1.03E-06 0.10 1391 0.20 0.22 0.023 GRMZM2G474726 (ATTERC,PDE149): integral membrane

TerC family protein S8_132204020 8 132204020 1.03E-06 0.10 1391 0.20 0.22 0.023 GRMZM2G173763 nuclear factor related to kappa-B- binding protein, related, putative,

expressed S8_137974581 8 137974581 4.80E-06 0.06 1391 0.20 0.22 0.027 GRMZM2G081653 rossmann fold nucleotide-binding protein involved in DNA uptake,

putative, expressed S8_140699649 8 140699649 1.84E-05 0.14 1391 0.20 0.21 0.038 GRMZM2G407949 (ALDH1A,ALDH2C4, REF1): aldehyde

dehydrogenase 2C4

225 S8_141928387 8 141928387 3.25E-05 0.47 1391 0.20 0.21 0.044 GRMZM2G044343 C3HC zinc finger-

226

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S8_145846703 8 145846703 2.64E-05 0.13 1391 0.20 0.21 0.041 GRMZM2G131315 (scpl50): serine carboxypeptidase-

like 50 S8_145846703 8 145846703 2.64E-05 0.13 1391 0.20 0.21 0.041 GRMZM2G131334 (ATMPK20,MPK20):

MAP kinase 20 S8_148898590 8 148898590 6.82E-06 0.10 1391 0.20 0.21 0.029 GRMZM2G002297 Magnesium transporter CorA-

like family protein S8_148905557 8 148905557 3.18E-05 0.19 1391 0.20 0.21 0.044 GRMZM2G002297 Magnesium transporter CorA-

like family protein S8_148905809 8 148905809 3.04E-05 0.18 1391 0.20 0.21 0.043 GRMZM2G002297 Magnesium transporter CorA-

like family protein S8_149078078 8 149078078 2.93E-05 0.14 1391 0.20 0.21 0.043 GRMZM5G812272 (ATWRKY71,WRKY7 1): WRKY DNA-

binding protein 71 S8_151270836 8 151270836 7.68E-06 0.22 1391 0.20 0.21 0.030 GRMZM2G017305 (AAA1,ATKTN1,BOT 1,ERH3,FRA2,FRC2,F TR,KTN1,LUE1): P- loop containing nucleoside triphosphate hydrolases

superfamily protein

226

227

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S8_154054055 8 154054055 1.04E-05 0.08 1391 0.20 0.21 0.034 GRMZM2G017305 (AAA1,ATKTN1,BOT 1,ERH3,FRA2,FRC2,F TR,KTN1,LUE1): P- loop containing nucleoside triphosphate hydrolases superfamily protein S8_155968563 8 155968563 3.05E-05 0.33 1391 0.20 0.21 0.043 GRMZM2G144716 NADH:ubiquinone oxidoreductase intermediate- associated protein 30 S8_155968563 8 155968563 3.05E-05 0.33 1391 0.20 0.21 0.043 GRMZM2G144707 (HVA22F): HVA22- like protein F S8_155968563 8 155968563 3.05E-05 0.33 1391 0.20 0.21 0.043 GRMZM2G444819 DUF584 domain containing protein, putative, expressed S8_155968602 8 155968602 5.31E-06 0.35 1391 0.20 0.22 0.028 GRMZM2G144716 NADH:ubiquinone oxidoreductase intermediate- associated protein 30 S8_155968602 8 155968602 5.31E-06 0.35 1391 0.20 0.22 0.028 GRMZM2G144707 (HVA22F): HVA22-

like protein F S8_155968602 8 155968602 5.31E-06 0.35 1391 0.20 0.22 0.028 GRMZM2G444819 DUF584 domain containing protein,

putative, expressed

227

228

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S8_155975151 8 155975151 9.81E-06 0.05 1391 0.20 0.21 0.034 GRMZM2G144716 NADH:ubiquinone oxidoreductase intermediate- associated protein

30 S8_155975151 8 155975151 9.81E-06 0.05 1391 0.20 0.21 0.034 GRMZM2G144707 (HVA22F): HVA22-

like protein F

S8_155975151 8 155975151 9.81E-06 0.05 1391 0.20 0.21 0.034 GRMZM2G444819 (AtS40-3): AtS40-3 S8_155975151 8 155975151 9.81E-06 0.05 1391 0.20 0.21 0.034 GRMZM2G144701 HVA22, putative, expressed S8_157964577 8 157964577 7.70E-06 0.05 1391 0.20 0.21 0.030 GRMZM2G016827 MEMO1, putative, expressed S8_157964577 8 157964577 7.70E-06 0.05 1391 0.20 0.21 0.030 GRMZM2G319187 (ARR9,ATRR4): response regulator

9 S8_159901017 8 159901017 2.42E-06 0.44 1391 0.20 0.22 0.024 GRMZM2G302074 (CYP89A6): cytochrome P450, family 87, subfamily

A, polypeptide 6 S8_159901017 8 159901017 2.42E-06 0.44 1391 0.20 0.22 0.024 GRMZM2G002315 (AAO3,AOdelta,At- AO3,AtAAO3): abscisic aldehyde

oxidase 3 S8_159901017 8 159901017 2.42E-06 0.44 1391 0.20 0.22 0.024 GRMZM2G002147 ARM repeat

superfamily protein S8_159901017 8 159901017 2.42E-06 0.44 1391 0.20 0.22 0.024 GRMZM2G002304 NAD(P)-binding Rossmann-fold

superfamily protein

228

229

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S8_159901017 8 159901017 2.42E-06 0.44 1391 0.20 0.22 0.024 GRMZM2G302045 heparan-alpha- glucosaminide N- acetyltransferase,

putative, expressed

S8_171407343 8 171407343 1.19E-06 0.09 1391 0.20 0.22 0.023 GRMZM2G310115 plectin-related S8_171407343 8 171407343 1.19E-06 0.09 1391 0.20 0.22 0.023 GRMZM2G012160 (ATCYS6,ATCYSB,CY

SB): cystatin B S8_174324099 8 174324099 3.36E-05 0.07 1391 0.20 0.21 0.044 GRMZM2G470499 (ATPERK1,PERK1): proline extensin-like

receptor kinase 1 S9_4651750 9 4651750 4.58E-06 0.07 1391 0.20 0.22 0.027 AC209664.3_FG002 (GAUT8,QUA1): Nucleotide- diphospho-sugar transferases

superfamily protein S9_4651768 9 4651768 2.30E-05 0.07 1391 0.20 0.21 0.040 AC209664.3_FG002 (GAUT8,QUA1): Nucleotide- diphospho-sugar transferases

superfamily protein S9_6066603 9 6066603 1.09E-05 0.25 1391 0.20 0.21 0.034 GRMZM2G019291 TLD-domain containing nucleolar

protein S9_6066607 9 6066607 1.09E-05 0.25 1391 0.20 0.21 0.034 GRMZM2G019291 TLD-domain containing nucleolar

protein S9_18880032 9 18880032 3.40E-05 0.06 1391 0.20 0.21 0.044 GRMZM2G405203 (MAX2,ORE9,PPS): RNI-like superfamily

protein

229

230

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_18880032 9 18880032 3.40E-05 0.06 1391 0.20 0.21 0.044 GRMZM2G405178 (ATHOL3,HOL3): S- adenosyl-L- methionine- dependent methyltransferases

superfamily protein S9_18880032 9 18880032 3.40E-05 0.06 1391 0.20 0.21 0.044 GRMZM2G103137 Hydrolase-like

protein family S9_18880032 9 18880032 3.40E-05 0.06 1391 0.20 0.21 0.044 GRMZM2G020216 (ATMAPK6,ATMPK6, MAPK6,MPK6): MAP

kinase 6 S9_19287636 9 19287636 2.66E-05 0.05 1391 0.20 0.21 0.041 GRMZM2G005522 HXXXD-type acyltransferase family

protein S9_19287636 9 19287636 2.66E-05 0.05 1391 0.20 0.21 0.041 GRMZM2G005339 SNARE-like

superfamily protein

S9_19287636 9 19287636 2.66E-05 0.05 1391 0.20 0.21 0.041 GRMZM2G005461 (UBQ9): ubiquitin 9 S9_20461787 9 20461787 6.84E-06 0.05 1391 0.20 0.21 0.029 GRMZM2G173641 (DXPS3): 1-deoxy-D- xylulose 5- phosphate synthase

3 S9_20461787 9 20461787 6.84E-06 0.05 1391 0.20 0.21 0.029 GRMZM2G173628 (FSD3): Fe superoxide

dismutase 3 S9_20461787 9 20461787 6.84E-06 0.05 1391 0.20 0.21 0.029 GRMZM2G173693 (ATSRL1): PRP38

family protein S9_24366897 9 24366897 2.23E-09 0.22 1391 0.20 0.22 0.001 GRMZM2G069008 (ATNUDT14,ATNUD X14,NUDX14): nudix hydrolase homolog

14 230

231

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_88796128 9 88796128 2.17E-06 0.06 1391 0.20 0.22 0.024 GRMZM2G019872 Zinc-binding dehydrogenase

family protein S9_103176004 9 103176004 1.95E-05 0.09 1391 0.20 0.21 0.038 GRMZM2G135300 (TAF5): TBP-

associated factor 5 S9_103176004 9 103176004 1.95E-05 0.09 1391 0.20 0.21 0.038 AC210199.4_FG003 (TAF5): TBP-

associated factor 5 S9_103176741 9 103176741 2.68E-05 0.11 1391 0.20 0.21 0.041 AC210199.4_FG003 (TAF5): TBP-

associated factor 5 S9_103176741 9 103176741 2.68E-05 0.11 1391 0.20 0.21 0.041 GRMZM2G135300 (TAF5): TBP-

associated factor 5 S9_103176766 9 103176766 2.68E-05 0.11 1391 0.20 0.21 0.041 AC210199.4_FG003 (TAF5): TBP-

associated factor 5 S9_103176766 9 103176766 2.68E-05 0.11 1391 0.20 0.21 0.041 GRMZM2G135300 (TAF5): TBP-

associated factor 5 S9_126935906 9 126935906 1.65E-05 0.31 1391 0.20 0.21 0.036 GRMZM5G806784 SNARE associated

Golgi protein family S9_126935906 9 126935906 1.65E-05 0.31 1391 0.20 0.21 0.036 GRMZM5G880028 calmodulin-binding

family protein S9_126936056 9 126936056 4.49E-05 0.06 1391 0.20 0.21 0.049 GRMZM5G806784 SNARE associated

Golgi protein family S9_126936056 9 126936056 4.49E-05 0.06 1391 0.20 0.21 0.049 GRMZM5G880028 calmodulin-binding

family protein S9_145060462 9 145060462 3.44E-05 0.09 1391 0.20 0.21 0.044 GRMZM2G152919 ARM repeat

superfamily protein S9_146069298 9 146069298 1.09E-06 0.07 1391 0.20 0.22 0.023 GRMZM2G152919 ARM repeat

superfamily protein S10_2032257 10 2032257 5.78E-06 0.10 1391 0.20 0.22 0.028 GRMZM2G180155 glutamine-fructose- 6-phosphate transaminase

231 (isomerizing)s;sugar

bindingtransaminass

232

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S10_2032257 10 2032257 5.78E-06 0.10 1391 0.20 0.22 0.028 GRMZM2G180150 (GRL,NAP1,NAPP): transcription

activators S10_2032257 10 2032257 5.78E-06 0.10 1391 0.20 0.22 0.028 GRMZM2G180205 Transducin/WD40 repeat-like

superfamily protein S10_2032257 10 2032257 5.78E-06 0.10 1391 0.20 0.22 0.028 GRMZM2G180166 Ubiquitin carboxyl- terminal hydrolase

family protein S10_2039204 10 2039204 2.22E-06 0.15 1391 0.20 0.22 0.024 GRMZM2G180244 LRR and NB-ARC domains-containing disease resistance

protein S10_2039204 10 2039204 2.22E-06 0.15 1391 0.20 0.22 0.024 GRMZM2G180150 (GRL,NAP1,NAPP): transcription

activators S10_2039204 10 2039204 2.22E-06 0.15 1391 0.20 0.22 0.024 GRMZM2G180155 glutamine-fructose- 6-phosphate transaminase (isomerizing)s;sugar binding;transaminas

es S10_2039204 10 2039204 2.22E-06 0.15 1391 0.20 0.22 0.024 GRMZM2G180205 Transducin/WD40 repeat-like

superfamily protein S10_2039204 10 2039204 2.22E-06 0.15 1391 0.20 0.22 0.024 GRMZM2G180166 Ubiquitin carboxyl- terminal hydrolase

family protein S10_2466445 10 2466445 3.95E-05 0.09 1391 0.20 0.21 0.047 AC197146.3_FG002 ATMYB30,MYB30): myb domain protein

232

233

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S10_2466445 10 2466445 3.95E-05 0.09 1391 0.20 0.21 0.047 GRMZM5G832378 UDP-N- acetylglucosamine transferase subunit ALG14, putative,

expressed S10_4021401 10 4021401 1.92E-05 0.07 1391 0.20 0.21 0.038 GRMZM2G473138 (ATXR7,SDG25): SET

domain protein 25 S10_4021401 10 4021401 1.92E-05 0.07 1391 0.20 0.21 0.038 GRMZM2G441029 zinc finger (C3HC4- type RING finger)

family protein S10_4021432 10 4021432 1.92E-05 0.07 1391 0.20 0.21 0.038 GRMZM2G473138 (ATXR7,SDG25): SET

domain protein 25 S10_4021432 10 4021432 1.92E-05 0.07 1391 0.20 0.21 0.038 GRMZM2G441029 zinc finger (C3HC4- type RING finger)

family protein S10_4021458 10 4021458 1.92E-05 0.07 1391 0.20 0.21 0.038 GRMZM2G473138 (ATXR7,SDG25): SET

domain protein 25 S10_4021458 10 4021458 1.92E-05 0.07 1391 0.20 0.21 0.038 GRMZM2G441029 zinc finger (C3HC4- type RING finger)

family protein S10_10829311 10 10829311 1.84E-05 0.47 1391 0.20 0.21 0.038 GRMZM5G803992 (NRPB10,NRPD10,N RPE10): RNA polymerases N / 8

kDa subunit S10_10829311 10 10829311 1.84E-05 0.47 1391 0.20 0.21 0.038 GRMZM2G418432 Protein kinase protein with adenine nucleotide alpha hydrolases-

like domain S10_14910839 10 14910839 2.93E-05 0.09 1391 0.20 0.21 0.043 GRMZM2G027522 (TPD1): tapetum

233

determinant 1

234

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S10_65738413 10 65738413 2.21E-05 0.05 1391 0.20 0.21 0.039 GRMZM2G404426 (EMB1135): RING/FYVE/PHD zinc finger superfamily

protein S10_74902428 10 74902428 1.53E-05 0.05 1391 0.20 0.21 0.036 GRMZM2G165757 (ABCG14): ATP-

binding cassette 14 S10_74902428 10 74902428 1.53E-05 0.05 1391 0.20 0.21 0.036 GRMZM2G165775 transposon protein, putative, Pong sub-

class, expressed S10_74902436 10 74902436 4.03E-05 0.07 1391 0.20 0.21 0.048 GRMZM2G165757 (ABCG14): ATP-

binding cassette 14 S10_74902436 10 74902436 4.03E-05 0.07 1391 0.20 0.21 0.048 GRMZM2G165775 transposon protein, putative, Pong sub-

class, expressed S10_75666498 10 75666498 2.08E-05 0.09 1391 0.20 0.21 0.039 GRMZM2G369260 (POLD4):

polymerase delta 4 S10_75666498 10 75666498 2.08E-05 0.09 1391 0.20 0.21 0.039 GRMZM2G055125 Mob1/phocein

family protein S10_75810235 10 75810235 5.96E-06 0.07 1391 0.20 0.21 0.028 GRMZM2G068808 (ABC33,ATCPS1,CPS, CPS1,GA1): Terpenoid cyclases/Protein prenyltransferases

superfamily protein S10_117565741 10 117565741 3.30E-05 0.09 1391 0.20 0.21 0.044 GRMZM2G072513 Protein of unknown function (DUF668) S10_117565741 10 117565741 3.30E-05 0.09 1391 0.20 0.21 0.044 GRMZM2G072337 Methylthiotransfera

234

235

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S10_117565741 10 117565741 3.30E-05 0.09 1391 0.20 0.21 0.044 GRMZM2G072322 late embryogenesis abundant domain- containing protein / LEA domain-

containing protein S10_117565741 10 117565741 3.30E-05 0.09 1391 0.20 0.21 0.044 GRMZM2G072174 Photosystem II reaction center PsbP

family protein S10_121747137 10 121747137 1.62E-05 0.09 1391 0.20 0.21 0.036 GRMZM5G870959 (ATSERK1,SERK1): somatic embryogenesis receptor-like kinase

1 S10_121747137 10 121747137 1.62E-05 0.09 1391 0.20 0.21 0.036 GRMZM5G889705 (LIP1): lipoic acid

synthase 1 S10_122268779 10 122268779 3.76E-05 0.12 1391 0.20 0.21 0.045 GRMZM2G125424 (ABCB19,ATABCB19, ATMDR1,ATMDR11, ATPGP19,MDR1,MD R11,PGP19): ATP binding cassette

subfamily B19 S10_133420139 10 133420139 1.48E-05 0.08 1391 0.20 0.21 0.036 GRMZM2G065176 SH3 domain-

containing protein S10_133420141 10 133420141 1.48E-05 0.08 1391 0.20 0.21 0.036 GRMZM2G065176 SH3 domain-

containing protein S10_134498587 10 134498587 1.48E-06 0.06 1391 0.20 0.22 0.024 GRMZM2G063972 DNAJ heat shock N- terminal domain-

containing protein S10_135056584 10 135056584 1.22E-05 0.06 1391 0.20 0.21 0.035 AC233979.1_FG006 DUF581 domain containing protein,

235

expressed

236

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S10_136834080 10 136834080 2.85E-05 0.07 1391 0.20 0.21 0.042 GRMZM2G702529 (CYP87A2): cytochrome P450, family 87, subfamily

A, polypeptide 2 S10_136834081 10 136834081 2.42E-06 0.06 1391 0.20 0.22 0.024 GRMZM2G702529 1(CYP87A2): cytochrome P450, family 87, subfamily

A, polypeptide 2 S10_136834102 10 136834102 3.27E-06 0.06 1391 0.20 0.22 0.027 GRMZM2G702529 (CYP87A2): cytochrome P450, family 87, subfamily

A, polypeptide 2 S10_136876614 10 136876614 7.64E-06 0.44 1391 0.20 0.21 0.030 GRMZM5G845601 (IQD22): IQ-domain

22 S10_147212427 10 147212427 3.61E-05 0.05 1391 0.20 0.21 0.045 GRMZM2G033375 (UCH3): ubiquitin C-

terminal hydrolase 3 S10_147212427 10 147212427 3.61E-05 0.05 1391 0.20 0.21 0.045 GRMZM2G125083 Phospholipid/glycer ol acyltransferase

family protein S10_147212427 10 147212427 3.61E-05 0.05 1391 0.20 0.21 0.045 GRMZM5G814035 Phospholipid/glycer ol acyltransferase

family protein S10_147212427 10 147212427 3.61E-05 0.05 1391 0.20 0.21 0.045 GRMZM2G033388 Ribosomal protein L7Ae/L30e/S12e/Ga

dd45 family protein S10_147212427 10 147212427 3.61E-05 0.05 1391 0.20 0.21 0.045 GRMZM2G423861 (KCBP,PKCBP,ZWI): kinesin-like calmodulin-binding

protein (ZWICHEL) S10_147212429 10 147212429 3.61E-05 0.05 1391 0.20 0.21 0.045 GRMZM2G033375 (UCH3): ubiquitin C-

236

terminal hydrolase 3

237

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S10_147212429 10 147212429 3.61E-05 0.05 1391 0.20 0.21 0.045 GRMZM2G125083 Phospholipid/glycer ol acyltransferase

family protein S10_147212429 10 147212429 3.61E-05 0.05 1391 0.20 0.21 0.045 GRMZM5G814035 Phospholipid/glycer ol acyltransferase

family protein S10_147212429 10 147212429 3.61E-05 0.05 1391 0.20 0.21 0.045 GRMZM2G033388 Ribosomal protein L7Ae/L30e/S12e/Ga

dd45 family protein S10_147212429 10 147212429 3.61E-05 0.05 1391 0.20 0.21 0.045 GRMZM2G423861 (KCBP,PKCBP,ZWI): kinesin-like calmodulin-binding

protein (ZWICHEL) S10_147401517 10 147401517 2.43E-05 0.05 1391 0.20 0.21 0.041 GRMZM2G464137 (ATMTK,MTK): S- methyl-5-thioribose

kinase S10_147401517 10 147401517 2.43E-05 0.05 1391 0.20 0.21 0.041 GRMZM2G164563 Pentatricopeptide repeat (PPR)

superfamily protein S10_147401517 10 147401517 2.43E-05 0.05 1391 0.20 0.21 0.041 GRMZM2G565856 (GAUT1,LGT1): galacturonosyltransf

erase 1 S10_147401517 10 147401517 2.43E-05 0.05 1391 0.20 0.21 0.041 GRMZM2G464157 (SOBER1):

carboxylesterases S10_147401519 10 147401519 2.43E-05 0.05 1391 0.20 0.21 0.041 GRMZM2G464137 (ATMTK,MTK): S- methyl-5-thioribose

kinase S10_147401519 10 147401519 2.43E-05 0.05 1391 0.20 0.21 0.041 GRMZM2G164563 Pentatricopeptide repeat (PPR)

superfamily protein

237

238

R2 of R2of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S10_147401519 10 147401519 2.43E-05 0.05 1391 0.20 0.21 0.041 GRMZM2G565856 (GAUT1,LGT1): galacturonosyltransf

erase 1 S10_147401519 10 147401519 2.43E-05 0.05 1391 0.20 0.21 0.041 GRMZM2G464157 (SOBER1):

carboxylesterases

238

239

D-6 Trait VTR4H Candidate Genes

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S1_5246908 1 5246908 1.12E-05 0.10 1391 0.09 0.10 0.026 GRMZM2G165422 Protein kinase superfamily

protein S1_6199066 1 6199066 1.90E-05 0.12 1391 0.09 0.10 0.029 GRMZM2G032852 (ATCDPK3,ATCPK6,CPK6): Calcium-dependent protein

kinase family protein S1_6201133 1 6201133 8.26E-05 0.09 1391 0.09 0.10 0.046 GRMZM2G032852 (ATCDPK3,ATCPK6,CPK6): Calcium-dependent protein

kinase family protein S1_6201134 1 6201134 1.85E-05 0.09 1391 0.09 0.10 0.029 GRMZM2G032852 (ATCDPK3,ATCPK6,CPK6): Calcium-dependent protein

kinase family protein S1_6201158 1 6201158 4.50E-05 0.10 1391 0.09 0.10 0.037 GRMZM2G032852 (ATCDPK3,ATCPK6,CPK6): Calcium-dependent protein

kinase family protein S1_7080149 1 7080149 4.16E-05 0.09 1391 0.09 0.10 0.036 GRMZM2G109566 Protein kinase superfamily

protein S1_7080149 1 7080149 4.16E-05 0.09 1391 0.09 0.10 0.036 GRMZM2G109509 Plant regulator RWP-RK

family protein S1_7080149 1 7080149 4.16E-05 0.09 1391 0.09 0.10 0.036 GRMZM2G409997 Tetratricopeptide repeat (TPR)-like superfamily

protein S1_7080149 1 7080149 4.16E-05 0.09 1391 0.09 0.10 0.036 GRMZM2G409976 Protein kinase superfamily

protein S1_7091354 1 7091354 3.15E-05 0.14 1391 0.09 0.10 0.033 GRMZM2G109509 Plant regulator RWP-RK

family protein S1_7091354 1 7091354 3.15E-05 0.14 1391 0.09 0.10 0.033 GRMZM2G409976 Protein kinase superfamily

239 protein

240

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S1_11991432 1 11991432 8.99E-05 0.39 1391 0.09 0.10 0.048 GRMZM2G027821 (MCA1): PLAC8 family

protein S1_11991432 1 11991432 8.99E-05 0.39 1391 0.09 0.10 0.048 GRMZM5G813886 ABC-2 type transporter

family protein S1_12165394 1 12165394 8.89E-06 0.43 1391 0.09 0.10 0.024 GRMZM2G076062 (ECT2): evolutionarily conserved C-terminal

region 2 S1_12165405 1 12165405 3.32E-05 0.42 1391 0.09 0.10 0.034 GRMZM2G076062 (ECT2): evolutionarily conserved C-terminal

region 2 S1_16356432 1 16356432 4.03E-05 0.06 1391 0.09 0.10 0.035 GRMZM2G064732 (ATGPA1,GP ALPHA 1,GPA1): G protein alpha

subunit 1 S1_16356432 1 16356432 4.03E-05 0.06 1391 0.09 0.10 0.035 GRMZM2G064663 (ATYLMG2,YLMG2): YGGT

family protein S1_24743247 1 24743247 4.28E-05 0.07 1391 0.09 0.10 0.037 GRMZM2G331652 Aminotransferase-like, plant mobile domain family

protein S1_24743247 1 24743247 4.28E-05 0.07 1391 0.09 0.10 0.037 GRMZM2G331638 Auxin-responsive family

protein

S1_28641355 1 28641355 1.15E-05 0.27 1391 0.09 0.10 0.026 GRMZM2G344416 (SDS): Cyclin family protein S1_28641355 1 28641355 1.15E-05 0.27 1391 0.09 0.10 0.026 GRMZM2G040828 Tetratricopeptide repeat (TPR)-like superfamily

protein

S1_28641394 1 28641394 2.31E-05 0.24 1391 0.09 0.10 0.032 GRMZM2G344416 (SDS): Cyclin family protein S1_28641394 1 28641394 2.31E-05 0.24 1391 0.09 0.10 0.032 GRMZM2G040828 Tetratricopeptide repeat (TPR)-like superfamily

protein

240

241

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S1_28796566 1 28796566 6.61E-05 0.45 1391 0.09 0.10 0.043 GRMZM2G103579 conserved oligomeric complex COG6 family

protein, expressed S1_28798077 1 28798077 2.91E-05 0.46 1391 0.09 0.10 0.033 GRMZM2G103579 conserved oligomeric complex COG6 family

protein, expressed S1_29403083 1 29403083 1.44E-05 0.13 1391 0.09 0.10 0.028 GRMZM2G091456 (SQE1,XF1): FAD/NAD(P)- binding oxidoreductase

family protein S1_42520440 1 42520440 1.54E-05 0.17 1391 0.09 0.10 0.028 GRMZM2G042107 Ankyrin repeat family

protein S1_42520440 1 42520440 1.54E-05 0.17 1391 0.09 0.10 0.028 GRMZM2G338333 (ITN1): Ankyrin repeat

family protein S1_42520476 1 42520476 1.54E-05 0.17 1391 0.09 0.10 0.028 GRMZM2G042107 Ankyrin repeat family

protein S1_42520476 1 42520476 1.54E-05 0.17 1391 0.09 0.10 0.028 GRMZM2G338333 (ITN1): Ankyrin repeat

family protein S1_42520536 1 42520536 6.28E-05 0.18 1391 0.09 0.10 0.042 GRMZM2G042107 Ankyrin repeat family

protein S1_42520536 1 42520536 6.28E-05 0.18 1391 0.09 0.10 0.042 GRMZM2G338333 AT3G12360.1(ITN1): Ankyrin repeat family

protein S1_45513765 1 45513765 6.38E-05 0.30 1391 0.09 0.10 0.042 GRMZM2G087186 Thiamine pyrophosphate dependent pyruvate decarboxylase family

protein

S1_45513765 1 45513765 6.38E-05 0.30 1391 0.09 0.10 0.042 GRMZM2G087161 (APTX): APRATAXIN-like S1_74276118 1 74276118 8.35E-05 0.18 1391 0.09 0.10 0.047 GRMZM2G036543 (APG10,HISN3): Aldolase-

type TIM barrel family 241

protein

242

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S1_75145014 1 75145014 1.86E-05 0.19 1391 0.09 0.10 0.029 GRMZM2G043141 Protein of unknown

function (DUF1336) S1_75145015 1 75145015 1.86E-05 0.19 1391 0.09 0.10 0.029 GRMZM2G043141 Protein of unknown

function (DUF1336) S1_77033323 1 77033323 6.25E-05 0.32 1391 0.09 0.10 0.042 AC190695.3_FG00 retrotransposon protein, 3 putative, Ty3-gypsy

subclass, expressed

S1_77564107 1 77564107 5.47E-05 0.36 1391 0.09 0.10 0.040 GRMZM2G028914 (MSL2): MSCS-like 2

S1_80952759 1 80952759 5.31E-05 0.08 1391 0.09 0.10 0.039 GRMZM2G133968 DNA binding S1_80952759 1 80952759 5.31E-05 0.08 1391 0.09 0.10 0.039 GRMZM2G434514 peptidoglycan-binding LysM

domain-containing protein S1_162463291 1 162463291 2.69E-05 0.47 1391 0.09 0.10 0.033 GRMZM2G476637 (NPY2): Phototropic- responsive NPH3 family

protein S1_174284218 1 174284218 5.68E-05 0.46 1391 0.09 0.10 0.040 GRMZM2G118646 (DEG5,DEGP5,HHOA): DEGP

protease 5

S1_180398780 1 180398780 1.19E-06 0.38 1391 0.09 0.10 0.010 GRMZM2G085474 Thiolase family protein S1_180398780 1 180398780 1.19E-06 0.38 1391 0.09 0.10 0.010 GRMZM2G085411 Major facilitator

superfamily protein S1_180607582 1 180607582 1.37E-05 0.21 1391 0.09 0.10 0.027 GRMZM2G108135 Thioesterase superfamily

protein

S1_180607582 1 180607582 1.37E-05 0.21 1391 0.09 0.10 0.027 GRMZM5G893912 (AATP1): AAA-ATPase 1 S1_180608940 1 180608940 1.28E-05 0.18 1391 0.09 0.10 0.027 GRMZM2G108135 Thioesterase superfamily

protein

S1_180608940 1 180608940 1.28E-05 0.18 1391 0.09 0.10 0.027 GRMZM5G893912 (AATP1): AAA-ATPase 1 S1_180608961 1 180608961 1.28E-05 0.18 1391 0.09 0.10 0.027 GRMZM2G108135 Thioesterase superfamily

protein

S1_180608961 1 180608961 1.28E-05 0.18 1391 0.09 0.10 0.027 GRMZM5G893912 (AATP1): AAA-ATPase 1 242

243

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S1_180610086 1 180610086 4.46E-06 0.22 1391 0.09 0.10 0.016 GRMZM2G108135 Thioesterase superfamily

protein

S1_180610086 1 180610086 4.46E-06 0.22 1391 0.09 0.10 0.016 GRMZM5G893912 (AATP1): AAA-ATPase 1 S1_195560594 1 195560594 2.75E-05 0.26 1391 0.09 0.10 0.033 GRMZM2G159996 B-box type zinc finger

protein with CCT domain S1_196212859 1 196212859 1.83E-05 0.23 1391 0.09 0.10 0.029 GRMZM2G053117 (ATPSAT1,PSAT1): phospholipid sterol acyl

transferase 1 S1_196212859 1 196212859 1.83E-05 0.23 1391 0.09 0.10 0.029 GRMZM2G053231 (SPDS1): spermidine

synthase 1 S1_196212859 1 196212859 1.83E-05 0.23 1391 0.09 0.10 0.029 GRMZM2G053027 (RFI2): RING/U-box

superfamily protein S1_197269767 1 197269767 7.07E-05 0.31 1391 0.09 0.10 0.044 GRMZM2G175423 GroES-like zinc-binding alcohol dehydrogenase

family protein S1_197269767 1 197269767 7.07E-05 0.31 1391 0.09 0.10 0.044 GRMZM2G175856 (CBF4,DREB1D): C-repeat-

binding factor 4 S1_202298027 1 202298027 8.61E-05 0.21 1391 0.09 0.10 0.047 GRMZM2G315375 (ABCB1,ATPGP1,PGP1): ATP binding cassette subfamily

B1 S1_202298027 1 202298027 8.61E-05 0.21 1391 0.09 0.10 0.047 GRMZM2G491632 zinc finger (C2H2 type)

family protein S1_206903638 1 206903638 7.59E-05 0.15 1391 0.09 0.10 0.046 GRMZM2G063883 (SDG22,SET22,SUVH9):

SU(VAR)3-9 homolog 9 S1_215898320 1 215898320 1.34E-05 0.22 1391 0.09 0.10 0.027 GRMZM2G101000 DNAse I-like superfamily

protein S1_216581239 1 216581239 1.95E-05 0.16 1391 0.09 0.10 0.030 GRMZM2G325026 (ATCB5LP,B5 #5,CB5LP):

cytochrome B5-like protein

243

244

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S1_216581239 1 216581239 1.95E-05 0.16 1391 0.09 0.10 0.030 GRMZM2G324999 (AtWRKY41,WRKY41): WRKY family transcription

factor

S1_225871338 1 225871338 3.29E-05 0.34 1391 0.09 0.10 0.034 GRMZM2G129135 (TET10): tetraspanin10 S1_225871338 1 225871338 3.29E-05 0.34 1391 0.09 0.10 0.034 GRMZM2G129007 (ATRH8,RH8): RNAhelicase-

like 8 S1_225871338 1 225871338 3.29E-05 0.34 1391 0.09 0.10 0.034 GRMZM2G129266 HXXXD-type acyl-

transferase family protein S1_245032439 1 245032439 6.99E-07 0.14 1391 0.09 0.10 0.010 GRMZM2G174549 (ATPAP18,PAP18): purple

acid phosphatase 18 S1_245032439 1 245032439 6.99E-07 0.14 1391 0.09 0.10 0.010 GRMZM2G472403 histone-lysine N-

methyltransferases S1_245032439 1 245032439 6.99E-07 0.14 1391 0.09 0.10 0.010 GRMZM2G174574 AMP-dependent synthetase

and ligase family protein S1_245697841 1 245697841 6.97E-08 0.20 1391 0.09 0.11 0.002 GRMZM2G455817 (ATHAK5,HAK5): high

affinity K+ transporter 5 S1_245697867 1 245697867 8.91E-06 0.18 1391 0.09 0.10 0.024 GRMZM2G455817 (ATHAK5,HAK5): high

affinity K+ transporter 5 S1_267867095 1 267867095 5.61E-05 0.32 1391 0.09 0.10 0.040 GRMZM2G022859 (MMZ1,UEV1A): MMS ZWEI

homologue 1

S1_267867095 1 267867095 5.61E-05 0.32 1391 0.09 0.10 0.040 GRMZM2G023110 (RKL1): receptor-like kinase S1_271902568 1 271902568 4.40E-05 0.15 1391 0.09 0.10 0.037 GRMZM2G141472 OsFBX109 - F-box domain containing protein,

expressed S1_271902570 1 271902570 2.94E-05 0.15 1391 0.09 0.10 0.033 GRMZM2G141472 OsFBX109 - F-box domain containing protein,

expressed S1_271902572 1 271902572 4.40E-05 0.15 1391 0.09 0.10 0.037 GRMZM2G141472 OsFBX109 - F-box domain

containing protein, 244

expressed

245

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S1_271902573 1 271902573 4.40E-05 0.15 1391 0.09 0.10 0.037 GRMZM2G141472 OsFBX109 - F-box domain containing protein,

expressed S1_271902574 1 271902574 2.02E-05 0.15 1391 0.09 0.10 0.030 GRMZM2G141472 OsFBX109 - F-box domain containing protein,

expressed S1_271902576 1 271902576 4.40E-05 0.15 1391 0.09 0.10 0.037 GRMZM2G141472 OsFBX109 - F-box domain containing protein,

expressed S1_271902577 1 271902577 4.83E-05 0.15 1391 0.09 0.10 0.038 GRMZM2G141472 OsFBX109 - F-box domain containing protein,

expressed S1_271902578 1 271902578 4.40E-05 0.15 1391 0.09 0.10 0.037 GRMZM2G141472 OsFBX109 - F-box domain containing protein,

expressed S1_271902579 1 271902579 2.94E-05 0.15 1391 0.09 0.10 0.033 GRMZM2G141472 OsFBX109 - F-box domain containing protein,

expressed S1_271902580 1 271902580 4.40E-05 0.15 1391 0.09 0.10 0.037 GRMZM2G141472 OsFBX109 - F-box domain containing protein,

expressed S1_272275112 1 272275112 1.99E-05 0.14 1391 0.09 0.10 0.030 GRMZM2G137891 Thioredoxin superfamily

protein S1_272275112 1 272275112 1.99E-05 0.14 1391 0.09 0.10 0.030 GRMZM2G137891 Thioredoxin superfamily

protein S1_272341227 1 272341227 1.62E-05 0.18 1391 0.09 0.10 0.028 GRMZM2G178261 (AtGRF1,GRF1): growth-

regulating factor 1 S1_272452285 1 272452285 6.97E-05 0.14 1391 0.09 0.10 0.044 GRMZM2G089102 (ACR3): ACT domain repeat

245 S1_281334197 1 281334197 2.66E-05 0.12 1391 0.09 0.10 0.033 GRMZM2G177046 (AtbZIP58,bZIP58): basic

leucine-zipper 58

246

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S1_289270921 1 289270921 3.26E-05 0.45 1391 0.09 0.10 0.033 GRMZM2G049906 Protein kinase superfamily

protein S1_289270921 1 289270921 3.26E-05 0.45 1391 0.09 0.10 0.033 GRMZM2G049888 Tetratricopeptide repeat (TPR)-like superfamily

protein S1_289270921 1 289270921 3.26E-05 0.45 1391 0.09 0.10 0.033 GRMZM2G049790 OsFBDUF18 - F-box and DUF domain containing protein,

expressed S1_289566288 1 289566288 8.08E-05 0.29 1391 0.09 0.10 0.046 GRMZM2G176630 Galactosyltransferase family

protein S1_289566288 1 289566288 8.08E-05 0.29 1391 0.09 0.10 0.046 GRMZM2G176662 Ribosomal protein L4/L1

family S1_289566288 1 289566288 8.08E-05 0.29 1391 0.09 0.10 0.046 GRMZM2G474798 (NOV): Histidine kinase-, DNA gyrase B-, and HSP90-

like ATPase family protein S1_289572136 1 289572136 2.90E-05 0.20 1391 0.09 0.10 0.033 GRMZM2G176630 Galactosyltransferase family

protein S1_289572136 1 289572136 2.90E-05 0.20 1391 0.09 0.10 0.033 GRMZM2G176662 Ribosomal protein L4/L1

family S1_289572136 1 289572136 2.90E-05 0.20 1391 0.09 0.10 0.033 GRMZM2G474798 (NOV): Histidine kinase-, DNA gyrase B-, and HSP90-

like ATPase family protein S1_293163491 1 293163491 4.44E-05 0.23 1391 0.09 0.10 0.037 GRMZM2G361210 C2H2-type zinc finger family

protein S1_293163491 1 293163491 4.44E-05 0.23 1391 0.09 0.10 0.037 GRMZM2G061626 (RHL41,ZAT12): C2H2-type

zinc finger family protein S1_293163491 1 293163491 4.44E-05 0.23 1391 0.09 0.10 0.037 GRMZM2G060702 (ADF4,ATADF4): actin

depolymerizing factor 4 S1_294168120 1 294168120 4.24E-06 0.48 1391 0.09 0.10 0.016 GRMZM2G043235 (PTAC2): plastid

246

transcriptionally active 2

247

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S1_294168120 1 294168120 4.24E-06 0.48 1391 0.09 0.10 0.016 GRMZM2G343741 (PTAC2): plastid

transcriptionally active 2 S1_294168120 1 294168120 4.24E-06 0.48 1391 0.09 0.10 0.016 GRMZM2G405185 (ATGIP1,GIP1): AtGCP3

interacting protein 1 S1_296770795 1 296770795 1.75E-05 0.42 1391 0.09 0.10 0.029 GRMZM2G470422 (STOP1): C2H2 and C2HC zinc fingers superfamily

protein S1_296770795 1 296770795 1.75E-05 0.42 1391 0.09 0.10 0.029 GRMZM2G170137 Mitochondrial transcription termination factor family

protein S1_296770795 1 296770795 1.75E-05 0.42 1391 0.09 0.10 0.029 GRMZM2G470382 Ribosomal protein S8e

family protein S1_296849274 1 296849274 8.35E-06 0.22 1391 0.09 0.10 0.023 GRMZM2G114992 hydroxyproline-rich

glycoprotein family protein S1_296849274 1 296849274 8.35E-06 0.22 1391 0.09 0.10 0.023 GRMZM2G114899 Protein kinase protein with adenine nucleotide alpha

hydrolases-like domain S1_296849361 1 296849361 7.37E-05 0.24 1391 0.09 0.10 0.046 GRMZM2G114992 hydroxyproline-rich

glycoprotein family protein S1_296849361 1 296849361 7.37E-05 0.24 1391 0.09 0.10 0.046 GRMZM2G114899 Protein kinase protein with adenine nucleotide alpha

hydrolases-like domain S1_296849363 1 296849363 5.80E-05 0.24 1391 0.09 0.10 0.041 GRMZM2G114992 hydroxyproline-rich

glycoprotein family protein S1_296849363 1 296849363 5.80E-05 0.24 1391 0.09 0.10 0.041 GRMZM2G114899 Protein kinase protein with adenine nucleotide alpha

hydrolases-like domain S1_296894613 1 296894613 3.36E-05 0.35 1391 0.09 0.10 0.034 AC217358.3_FG00 (ATPHB2,PHB2): prohibitin

5 2

247 S1_296894613 1 296894613 3.36E-05 0.35 1391 0.09 0.10 0.034 GRMZM2G704150 Domain of unknown

function (DUF543)

248

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S1_296894613 1 296894613 3.36E-05 0.35 1391 0.09 0.10 0.034 GRMZM5G891724 (ATVPS9A,VPS9,VPS9A): Vacuolar sorting protein 9

(VPS9) domain S1_296894613 1 296894613 3.36E-05 0.35 1391 0.09 0.10 0.034 AC217358.3_FG00 diphthamide synthesis

3 DPH2 family protein S1_296894613 1 296894613 3.36E-05 0.35 1391 0.09 0.10 0.034 GRMZM5G881369 FAD binding protein,

putative, expressed S1_297768134 1 297768134 6.93E-05 0.13 1391 0.09 0.10 0.044 GRMZM2G016738 nuclear antigen, putative,

expressed S1_297798468 1 297798468 5.86E-05 0.41 1391 0.09 0.10 0.041 GRMZM2G016892 Protein prenylyltransferase

superfamily protein S1_297798468 1 297798468 5.86E-05 0.41 1391 0.09 0.10 0.041 GRMZM2G016774 (AAE16): AMP-dependent synthetase and ligase family

protein S1_298432473 1 298432473 3.35E-05 0.35 1391 0.09 0.10 0.034 GRMZM2G021742 (U2A\'): U2 small nuclear

ribonucleoprotein A S1_298432473 1 298432473 3.35E-05 0.35 1391 0.09 0.10 0.034 GRMZM2G021642 (FLA,FRI): FRIGIDA-like

protein S1_298433594 1 298433594 7.08E-05 0.34 1391 0.09 0.10 0.044 GRMZM2G021742 (U2A\'): U2 small nuclear

ribonucleoprotein A S1_298433594 1 298433594 7.08E-05 0.34 1391 0.09 0.10 0.044 GRMZM2G021642 (FLA,FRI): FRIGIDA-like

protein S1_300739896 1 300739896 5.49E-05 0.45 1391 0.09 0.10 0.040 GRMZM2G115190 (ZIP10): zinc transporter 10

precursor S1_300739896 1 300739896 5.49E-05 0.45 1391 0.09 0.10 0.040 GRMZM2G415077 Homeodomain-like

superfamily protein S1_300739896 1 300739896 5.49E-05 0.45 1391 0.09 0.10 0.040 GRMZM2G115162 (ATNPR3,NPR3): NPR1-like

protein 3

248

249

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S2_1918175 2 1918175 2.61E-05 0.41 1391 0.09 0.10 0.033 GRMZM2G105319 (ABAR,CCH,CCH1,CHLH,GU N5): magnesium-chelatase subunit chlH, chloroplast, putative / Mg- protoporphyrin IX

chelatase, putative (CHLH) S2_1918175 2 1918175 2.61E-05 0.41 1391 0.09 0.10 0.033 GRMZM2G105330 (AAE5): acyl activating

enzyme 5 S2_1918175 2 1918175 2.61E-05 0.41 1391 0.09 0.10 0.033 GRMZM2G407347 Cytokine-induced anti- apoptosis inhibitor 1, Fe-S

biogenesis S2_1918192 2 1918192 4.33E-05 0.43 1391 0.09 0.10 0.037 GRMZM2G105319 (ABAR,CCH,CCH1,CHLH,GU N5): magnesium-chelatase subunit chlH, chloroplast, putative / Mg- protoporphyrin IX

chelatase, putative (CHLH) S2_1918192 2 1918192 4.33E-05 0.43 1391 0.09 0.10 0.037 GRMZM2G105330 (AAE5): acyl activating

enzyme 5 S2_1918192 2 1918192 4.33E-05 0.43 1391 0.09 0.10 0.037 GRMZM2G407347 Cytokine-induced anti- apoptosis inhibitor 1, Fe-S

biogenesis S2_2539903 2 2539903 5.88E-06 0.31 1391 0.09 0.10 0.020 GRMZM2G010257 60S acidic ribosomal protein

family S2_2539903 2 2539903 5.88E-06 0.31 1391 0.09 0.10 0.020 GRMZM2G010435 Granulin repeat cysteine

protease family protein S2_2539903 2 2539903 5.88E-06 0.31 1391 0.09 0.10 0.020 GRMZM2G107187 SEC-C motif-containing protein / OTU-like cysteine

protease family protein

249

250

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S2_5929569 2 5929569 9.21E-05 0.13 1391 0.09 0.10 0.049 GRMZM2G372074 Bifunctional inhibitor/lipid- transfer protein/seed storage 2S albumin

superfamily protein S2_5929569 2 5929569 9.21E-05 0.13 1391 0.09 0.10 0.049 GRMZM2G070881 ubiquitin-associated (UBA)/TS-N domain-

containing protein S2_5929569 2 5929569 9.21E-05 0.13 1391 0.09 0.10 0.049 GRMZM2G372102 (AZI1): azelaic acid induced

1 S2_15989267 2 15989267 4.76E-05 0.11 1391 0.09 0.10 0.037 GRMZM2G114220 (UFD1): ubiquitin fusion

degradation 1 S2_15989267 2 15989267 4.76E-05 0.11 1391 0.09 0.10 0.037 GRMZM2G114192 Rho GTPase activating protein with PAK-box/P21-

Rho-binding domain S2_15989267 2 15989267 4.76E-05 0.11 1391 0.09 0.10 0.037 GRMZM2G114276 Leucine-rich receptor-like protein kinase family

protein S2_15989296 2 15989296 4.76E-05 0.11 1391 0.09 0.10 0.037 GRMZM2G114220 (UFD1): ubiquitin fusion

degradation 1 S2_15989296 2 15989296 4.76E-05 0.11 1391 0.09 0.10 0.037 GRMZM2G114192 Rho GTPase activating protein with PAK-box/P21-

Rho-binding domain S2_15989296 2 15989296 4.76E-05 0.11 1391 0.09 0.10 0.037 GRMZM2G114276 Leucine-rich receptor-like protein kinase family

protein S2_15993429 2 15993429 8.18E-05 0.12 1391 0.09 0.10 0.046 GRMZM2G114220 (UFD1): ubiquitin fusion

degradation 1 S2_15993429 2 15993429 8.18E-05 0.12 1391 0.09 0.10 0.046 GRMZM2G114276 Leucine-rich receptor-like protein kinase family

250

protein

251

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S2_20123366 2 20123366 3.64E-05 0.14 1391 0.09 0.10 0.035 GRMZM2G105137 (DUO1): myb-like HTH transcriptional regulator

family protein S2_20123371 2 20123371 8.10E-05 0.14 1391 0.09 0.10 0.046 GRMZM2G105137 (DUO1): myb-like HTH transcriptional regulator

family protein S2_26772022 2 26772022 3.42E-05 0.07 1391 0.09 0.10 0.034 GRMZM2G474575 Kunitz family trypsin and

protease inhibitor protein S2_26772022 2 26772022 3.42E-05 0.07 1391 0.09 0.10 0.034 GRMZM2G171410 S-adenosyl-L-methionine- dependent methyltransferases

superfamily protein S2_184267183 2 184267183 8.16E-05 0.47 1391 0.09 0.10 0.046 GRMZM2G125482 (CYP75B1,D501,TT7): Cytochrome P450

superfamily protein S2_188775125 2 188775125 6.22E-05 0.10 1391 0.09 0.10 0.042 AC198353.5_FG00 NOL1/NOP2/sun family 4 protein / antitermination NusB domain-containing

protein S2_188817050 2 188817050 1.05E-05 0.15 1391 0.09 0.10 0.025 GRMZM2G703293 (scpl28): serine

carboxypeptidase-like 28 S2_188817052 2 188817052 1.05E-05 0.15 1391 0.09 0.10 0.025 GRMZM2G703293 (scpl28): serine

carboxypeptidase-like 28 S2_188817054 2 188817054 1.05E-05 0.15 1391 0.09 0.10 0.025 GRMZM2G703293 (scpl28): serine

carboxypeptidase-like 28 S2_188817055 2 188817055 1.05E-05 0.15 1391 0.09 0.10 0.025 GRMZM2G703293 (scpl28): serine

carboxypeptidase-like 28 S2_233749766 2 233749766 4.42E-05 0.17 1391 0.09 0.10 0.037 GRMZM2G037923 Protein kinase family

protein

251 S2_233749766 2 233749766 4.42E-05 0.17 1391 0.09 0.10 0.037 GRMZM2G037614 (DIN4): Transketolase family

protein

252

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S2_233749766 2 233749766 4.42E-05 0.17 1391 0.09 0.10 0.037 GRMZM2G340130 (ECT2): evolutionarily conserved C-terminal

region 2 S2_233749766 2 233749766 4.42E-05 0.17 1391 0.09 0.10 0.037 GRMZM2G021051 (AT2353,ATGA20OX2,GA20 OX2): gibberellin 20 oxidase

S2_233749766 2 233749766 4.42E-05 0.17 1391 0.09 0.10 0.037 GRMZM5G878490 (AGL62): AGAMOUS-like 62 S2_233749766 2 233749766 4.42E-05 0.17 1391 0.09 0.10 0.037 AC209768.3_FG00 Polynucleotidyl 5 transferase, ribonuclease H-

like superfamily protein

S3_306174 3 306174 4.58E-05 0.24 1391 0.09 0.10 0.037 GRMZM2G035482 Coatomer epsilon subunit S3_1467296 3 1467296 2.68E-06 0.11 1391 0.09 0.10 0.013 GRMZM2G087804 (ATGLK1,GLK1,GPRI1): GBF\'s pro-rich region-

interacting factor 1 S3_1467296 3 1467296 2.68E-06 0.11 1391 0.09 0.10 0.013 GRMZM2G087714 (NFD6): nuclear fusion

defective 6 S3_1467297 3 1467297 2.27E-06 0.11 1391 0.09 0.10 0.012 GRMZM2G087804 (ATGLK1,GLK1,GPRI1): GBF\'s pro-rich region-

interacting factor 1 S3_1467297 3 1467297 2.27E-06 0.11 1391 0.09 0.10 0.012 GRMZM2G087714 (NFD6): nuclear fusion

defective 6 S3_2117273 3 2117273 1.83E-05 0.41 1391 0.09 0.10 0.029 GRMZM2G470305 (ATNRPD1B,DMS5,DRD3,NR PD1B,NRPE1): nuclear RNA

polymerase D1B S3_2117273 3 2117273 1.83E-05 0.41 1391 0.09 0.10 0.029 GRMZM2G170047 (CYP71A25): cytochrome P450, family 71, subfamily

A, polypeptide 25 S3_2144579 3 2144579 7.61E-05 0.13 1391 0.09 0.10 0.046 GRMZM2G169973 (ATOFP7,OFP7): ovate

252 family protein 7

253

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S3_2144579 3 2144579 7.61E-05 0.13 1391 0.09 0.10 0.046 GRMZM2G170013 (NYC1): NAD(P)-binding Rossmann-fold superfamily

protein S3_2144579 3 2144579 7.61E-05 0.13 1391 0.09 0.10 0.046 GRMZM2G169951 (SLAH3): SLAC1 homologue

3 S3_2155514 3 2155514 4.54E-05 0.46 1391 0.09 0.10 0.037 GRMZM2G169973 (ATOFP7,OFP7): ovate

family protein 7 S3_2155514 3 2155514 4.54E-05 0.46 1391 0.09 0.10 0.037 GRMZM2G169951 (SLAH3): SLAC1 homologue

3 S3_3464599 3 3464599 8.59E-05 0.39 1391 0.09 0.10 0.047 GRMZM2G400907 (GTE4): global transcription

factor group E4 S3_3464599 3 3464599 8.59E-05 0.39 1391 0.09 0.10 0.047 GRMZM2G102572 SGNH hydrolase-type esterase superfamily

protein S3_4190285 3 4190285 9.61E-05 0.36 1391 0.09 0.10 0.050 GRMZM2G352926 transposable element protein, putative, containing Pfam profile: PF03732, Retrotrans_gag,

expressed S3_4190285 3 4190285 9.61E-05 0.36 1391 0.09 0.10 0.050 GRMZM2G051262 Alg9-like

mannosyltransferase family S3_4340829 3 4340829 7.66E-05 0.27 1391 0.09 0.10 0.046 GRMZM2G045259 Protein kinase family

protein S3_4340829 3 4340829 7.66E-05 0.27 1391 0.09 0.10 0.046 GRMZM2G346457 (ATECI3,ECI3,HCD1): 3- hydroxyacyl-CoA

dehydratase 1 S3_4340829 3 4340829 7.66E-05 0.27 1391 0.09 0.10 0.046 GRMZM2G346466 (MRH1): Leucine-rich repeat protein kinase family

protein

253

254

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S3_4340829 3 4340829 7.66E-05 0.27 1391 0.09 0.10 0.046 GRMZM2G045330 (ATSK21,BIN2,DWF12,SK21, UCU1): Protein kinase

superfamily protein S3_4341536 3 4341536 3.28E-05 0.15 1391 0.09 0.10 0.034 GRMZM2G045259 Protein kinase family

protein S3_4341536 3 4341536 3.28E-05 0.15 1391 0.09 0.10 0.034 GRMZM2G346457 (ATECI3,ECI3,HCD1): 3- hydroxyacyl-CoA

dehydratase 1 S3_4341536 3 4341536 3.28E-05 0.15 1391 0.09 0.10 0.034 GRMZM2G346466 (MRH1): Leucine-rich repeat protein kinase family

protein S3_4341536 3 4341536 3.28E-05 0.15 1391 0.09 0.10 0.034 GRMZM2G045330 (ATSK21,BIN2,DWF12,SK21, UCU1): Protein kinase

superfamily protein S3_4861946 3 4861946 4.78E-05 0.43 1391 0.09 0.10 0.038 GRMZM2G471089 (AG): K-box region and MADS-box transcription

factor family protein S3_4862339 3 4862339 4.95E-05 0.30 1391 0.09 0.10 0.038 GRMZM2G471089 (AG): K-box region and MADS-box transcription

factor family protein S3_5850435 3 5850435 1.56E-05 0.09 1391 0.09 0.10 0.028 GRMZM2G470914 Protein kinase superfamily

protein S3_8881339 3 8881339 2.18E-05 0.09 1391 0.09 0.10 0.031 GRMZM2G083797 disease resistance family

protein / LRR family protein S3_8881339 3 8881339 2.18E-05 0.09 1391 0.09 0.10 0.031 GRMZM2G083763 Pre-mRNA cleavage

complex II protein family S3_8881339 3 8881339 2.18E-05 0.09 1391 0.09 0.10 0.031 GRMZM2G083810 (HSP17.6II): 17.6 kDa class II

heat shock protein S3_8881647 3 8881647 8.22E-05 0.08 1391 0.09 0.10 0.046 GRMZM2G083797 disease resistance family

254

protein / LRR family protein

255

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S3_8881647 3 8881647 8.22E-05 0.08 1391 0.09 0.10 0.046 GRMZM2G083763 Pre-mRNA cleavage

complex II protein family S3_8881647 3 8881647 8.22E-05 0.08 1391 0.09 0.10 0.046 GRMZM2G083810 (HSP17.6II): 17.6 kDa class II

heat shock protein S3_10516591 3 10516591 3.86E-05 0.31 1391 0.09 0.10 0.035 GRMZM5G868061 (BES1,BZR2): Brassinosteroid signalling positive regulator (BZR1)

family protein S3_10516591 3 10516591 3.86E-05 0.31 1391 0.09 0.10 0.035 GRMZM2G348238 Homeodomain-like

superfamily protein S3_10516593 3 10516593 3.86E-05 0.31 1391 0.09 0.10 0.035 GRMZM5G868061 (BES1,BZR2): Brassinosteroid signalling positive regulator (BZR1)

family protein S3_10516593 3 10516593 3.86E-05 0.31 1391 0.09 0.10 0.035 GRMZM2G348238 Homeodomain-like

superfamily protein S3_13872412 3 13872412 7.98E-05 0.18 1391 0.09 0.10 0.046 GRMZM2G102714 (CAN): Ca-2+ dependent

nuclease S3_13872412 3 13872412 7.98E-05 0.18 1391 0.09 0.10 0.046 GRMZM2G102664 (TAF4,TAF4B): TBP-

associated factor 4 S3_13872429 3 13872429 7.98E-05 0.18 1391 0.09 0.10 0.046 GRMZM2G102714 (CAN): Ca-2+ dependent

nuclease S3_13872429 3 13872429 7.98E-05 0.18 1391 0.09 0.10 0.046 GRMZM2G102664 (TAF4,TAF4B): TBP-

associated factor 4 S3_48493746 3 48493746 3.52E-05 0.26 1391 0.09 0.10 0.034 GRMZM2G017520 (ATMYB61,MYB61): myb

domain protein 61 S3_175692005 3 175692005 5.89E-06 0.35 1391 0.09 0.10 0.020 GRMZM5G866954 (AtTLP5,TLP5): tubby like

protein 5 S3_175692005 3 175692005 5.89E-06 0.35 1391 0.09 0.10 0.020 AC155610.2_FG00 Small nuclear

255 9 ribonucleoprotein family

protein

256

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S3_175692005 3 175692005 5.89E-06 0.35 1391 0.09 0.10 0.020 AC155610.2_FG00 HXXXD-type acyl-

7 transferase family protein S3_176039717 3 176039717 5.00E-05 0.22 1391 0.09 0.10 0.038 GRMZM2G061289 UDP-Glycosyltransferase

superfamily protein S3_176039717 3 176039717 5.00E-05 0.22 1391 0.09 0.10 0.038 GRMZM2G061321 UDP-Glycosyltransferase

superfamily protein S3_176039721 3 176039721 5.00E-05 0.22 1391 0.09 0.10 0.038 GRMZM2G061289 UDP-Glycosyltransferase

superfamily protein S3_176039721 3 176039721 5.00E-05 0.22 1391 0.09 0.10 0.038 GRMZM2G061321 UDP-Glycosyltransferase

superfamily protein

S3_181007577 3 181007577 5.51E-05 0.13 1391 0.09 0.10 0.040 GRMZM2G463415 ENTH/VHS family protein

S3_181007585 3 181007585 5.51E-05 0.13 1391 0.09 0.10 0.040 GRMZM2G463415 ENTH/VHS family protein S3_181751306 3 181751306 6.82E-05 0.34 1391 0.09 0.10 0.044 GRMZM2G126083 alpha/beta-Hydrolases

superfamily protein S3_181751306 3 181751306 6.82E-05 0.34 1391 0.09 0.10 0.044 GRMZM2G123977 (ITN1): Ankyrin repeat

family protein S3_181751306 3 181751306 6.82E-05 0.34 1391 0.09 0.10 0.044 GRMZM2G126077 Pectin lyase-like

superfamily protein S3_183381586 3 183381586 2.42E-05 0.32 1391 0.09 0.10 0.032 GRMZM2G006229 thioredoxin, putative,

expressed S3_183385606 3 183385606 3.08E-05 0.35 1391 0.09 0.10 0.033 GRMZM2G006229 thioredoxin, putative,

expressed S3_183385627 3 183385627 3.08E-05 0.35 1391 0.09 0.10 0.033 GRMZM2G006229 thioredoxin, putative,

expressed S3_184948734 3 184948734 2.37E-07 0.16 1391 0.09 0.10 0.006 GRMZM2G065290 (ATWRKY46,WRKY46): WRKY DNA-binding protein

46 S3_185026390 3 185026390 4.98E-05 0.16 1391 0.09 0.10 0.038 GRMZM2G382350 (ATWRKY64,WRKY64):

WRKY DNA-binding protein 256

257

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S3_185026412 3 185026412 6.73E-05 0.18 1391 0.09 0.10 0.043 GRMZM2G382350 (ATWRKY64,WRKY64): WRKY DNA-binding protein

64 S3_185244417 3 185244417 6.41E-05 0.36 1391 0.09 0.10 0.043 GRMZM2G098042 Protein kinase family protein with ARM repeat

domain S3_185244417 3 185244417 6.41E-05 0.36 1391 0.09 0.10 0.043 GRMZM2G098078 Protein kinase family protein with ARM repeat

domain S3_187719236 3 187719236 3.87E-06 0.25 1391 0.09 0.10 0.016 GRMZM2G137942 (ATLFNR2,FNR2): ferredoxin-NADP(+)-

oxidoreductase 2 S3_187719236 3 187719236 3.87E-06 0.25 1391 0.09 0.10 0.016 GRMZM2G138074 (CYP98A3): cytochrome P450, family 98, subfamily

A, polypeptide 3 S3_187719236 3 187719236 3.87E-06 0.25 1391 0.09 0.10 0.016 GRMZM2G438551 (ATCYS6,ATCYSB,CYSB):

cystatin B S3_190782534 3 190782534 1.02E-05 0.17 1391 0.09 0.10 0.025 GRMZM2G062373 Adenine nucleotide alpha hydrolases-like superfamily

protein S3_190782534 3 190782534 1.02E-05 0.17 1391 0.09 0.10 0.025 GRMZM2G062429 (ATDGK5,DGK5):

diacylglycerol kinase 5 S3_191368630 3 191368630 9.61E-05 0.23 1391 0.09 0.10 0.050 AC210529.3_FG00 Regulator of chromosome 4 condensation (RCC1) family

protein S3_191368630 3 191368630 9.61E-05 0.23 1391 0.09 0.10 0.050 GRMZM2G026333 Regulator of chromosome condensation (RCC1) family

protein S3_191777687 3 191777687 7.34E-08 0.39 1391 0.09 0.11 0.002 GRMZM2G093239 Transducin/WD40 repeat-

257

like superfamily protein

258

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S3_191777687 3 191777687 7.34E-08 0.39 1391 0.09 0.11 0.002 GRMZM2G093101 (ATPAP10,PAP10): purple

acid phosphatase 10 S3_199622620 3 199622620 7.75E-05 0.40 1391 0.09 0.10 0.046 GRMZM5G887890 (ATSNF4,SNF4): homolog of yeast sucrose

nonfermenting 4 S3_199622620 3 199622620 7.75E-05 0.40 1391 0.09 0.10 0.046 GRMZM2G005082 O-Glycosyl hydrolases

family 17 protein

S3_199622620 3 199622620 7.75E-05 0.40 1391 0.09 0.10 0.046 GRMZM2G140455 (PRF5): profilin 5 S3_202039340 3 202039340 6.21E-05 0.46 1391 0.09 0.10 0.042 GRMZM2G158013 (AST12,SULTR3;1): sulfate

transporter 3;1 S3_202039340 3 202039340 6.21E-05 0.46 1391 0.09 0.10 0.042 AC197055.3_FG00 retrotransposon protein, 3 putative, Ty3-gypsy

subclass, expressed S3_202069791 3 202069791 7.27E-05 0.38 1391 0.09 0.10 0.045 GRMZM2G150450 Heavy metal transport/detoxification

superfamily protein S3_202183055 3 202183055 1.69E-05 0.24 1391 0.09 0.10 0.028 GRMZM2G015908 (ATPS2,PS2): phosphate

starvation-induced gene 2 S3_202183058 3 202183058 1.69E-05 0.24 1391 0.09 0.10 0.028 GRMZM2G015908 (ATPS2,PS2): phosphate

starvation-induced gene 2 S3_205242872 3 205242872 9.48E-05 0.14 1391 0.09 0.10 0.050 GRMZM2G386113 RING/U-box superfamily

protein S3_205242878 3 205242878 8.77E-06 0.20 1391 0.09 0.10 0.024 GRMZM2G386113 RING/U-box superfamily

protein S3_205364922 3 205364922 3.76E-05 0.13 1391 0.09 0.10 0.035 GRMZM2G041774 (MAPKKK16): mitogen- activated protein kinase

kinase kinase 16 S3_205364922 3 205364922 3.76E-05 0.13 1391 0.09 0.10 0.035 GRMZM2G165099 (MAPKKK16): mitogen-

activated protein kinase 258

kinase kinase 16

259

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S3_205364933 3 205364933 3.76E-05 0.13 1391 0.09 0.10 0.035 GRMZM2G041774 (MAPKKK16): mitogen- activated protein kinase

kinase kinase 16 S3_205364933 3 205364933 3.76E-05 0.13 1391 0.09 0.10 0.035 GRMZM2G165099 (MAPKKK16): mitogen- activated protein kinase

kinase kinase 16 S3_205364934 3 205364934 3.76E-05 0.13 1391 0.09 0.10 0.035 GRMZM2G041774 (MAPKKK16): mitogen- activated protein kinase

kinase kinase 16 S3_205364934 3 205364934 3.76E-05 0.13 1391 0.09 0.10 0.035 GRMZM2G165099 (MAPKKK16): mitogen- activated protein kinase

kinase kinase 16 S3_205364946 3 205364946 3.76E-05 0.13 1391 0.09 0.10 0.035 GRMZM2G041774 (MAPKKK16): mitogen- activated protein kinase

kinase kinase 16 S3_205364946 3 205364946 3.76E-05 0.13 1391 0.09 0.10 0.035 GRMZM2G165099 (MAPKKK16): mitogen- activated protein kinase

kinase kinase 16 S3_205474471 3 205474471 4.22E-05 0.07 1391 0.09 0.10 0.037 GRMZM2G420334 SWAP (Suppressor-of- White-APricot)/surp

domain-containing protein S3_205474506 3 205474506 2.78E-05 0.07 1391 0.09 0.10 0.033 GRMZM2G420334 SWAP (Suppressor-of- White-APricot)/surp

domain-containing protein S3_205474509 3 205474509 2.78E-05 0.07 1391 0.09 0.10 0.033 GRMZM2G420334 SWAP (Suppressor-of- White-APricot)/surp

domain-containing protein S3_205816848 3 205816848 4.24E-05 0.07 1391 0.09 0.10 0.037 AC233882.1_FG00 (ATKCO2,ATTPK2,KCO2): 5 Ca2+ activated outward

259

rectifying K+ channel 2

260

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S3_205816882 3 205816882 1.18E-05 0.06 1391 0.09 0.10 0.027 AC233882.1_FG00 (ATKCO2,ATTPK2,KCO2): 5 Ca2+ activated outward

rectifying K+ channel 2 S3_208618536 3 208618536 8.22E-05 0.11 1391 0.09 0.10 0.046 GRMZM2G022052 (TAF11): TBP-associated

factor 11 S3_208618542 3 208618542 8.22E-05 0.11 1391 0.09 0.10 0.046 GRMZM2G022052 (TAF11): TBP-associated

factor 11 S3_209854372 3 209854372 1.80E-05 0.21 1391 0.09 0.10 0.029 GRMZM5G862131 (UBC13B,UBC36): ubiquitin-

conjugating enzyme 36 S3_209854372 3 209854372 1.80E-05 0.21 1391 0.09 0.10 0.029 GRMZM2G034526 Protein of unknown

function (DUF1421) S3_209854395 3 209854395 2.97E-05 0.22 1391 0.09 0.10 0.033 GRMZM5G862131 (UBC13B,UBC36): ubiquitin-

conjugating enzyme 36 S3_209854395 3 209854395 2.97E-05 0.22 1391 0.09 0.10 0.033 GRMZM2G034526 Protein of unknown

function (DUF1421) S3_209904642 3 209904642 1.23E-05 0.44 1391 0.09 0.10 0.027 GRMZM2G346639 Nucleotidyltransferase

family protein S3_209904679 3 209904679 1.23E-05 0.44 1391 0.09 0.10 0.027 GRMZM2G346639 Nucleotidyltransferase

family protein S3_209904786 3 209904786 9.31E-05 0.48 1391 0.09 0.10 0.049 GRMZM2G346639 Nucleotidyltransferase

family protein S3_211231422 3 211231422 3.79E-06 0.14 1391 0.09 0.10 0.016 GRMZM2G346639 Nucleotidyltransferase

family protein S3_212154979 3 212154979 7.40E-05 0.16 1391 0.09 0.10 0.046 GRMZM2G070360 (VHA-E3): vacuolar H+-

ATPase subunit E isoform 3 S3_212154980 3 212154980 7.40E-05 0.16 1391 0.09 0.10 0.046 GRMZM2G070360 (VHA-E3): vacuolar H+-

ATPase subunit E isoform 3 S3_212154981 3 212154981 7.40E-05 0.16 1391 0.09 0.10 0.046 GRMZM2G070360 (VHA-E3): vacuolar H+-

ATPase subunit E isoform 3

260 S3_217895070 3 217895070 2.42E-05 0.25 1391 0.09 0.10 0.032 GRMZM2G148555 extra-large G-protein-

related, putative, expressed

261

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S3_217939392 3 217939392 3.99E-05 0.26 1391 0.09 0.10 0.035 GRMZM2G057733 Transmembrane amino acid

transporter family protein S3_217939393 3 217939393 3.99E-05 0.26 1391 0.09 0.10 0.035 GRMZM2G057733 Transmembrane amino acid

transporter family protein S3_218004766 3 218004766 9.48E-06 0.20 1391 0.09 0.10 0.024 GRMZM2G057853 (SEH1H): Transducin/WD40 repeat-like superfamily

protein S3_218010952 3 218010952 2.38E-05 0.50 1391 0.09 0.10 0.032 GRMZM2G057853 (SEH1H): Transducin/WD40 repeat-like superfamily

protein S3_218010952 3 218010952 2.38E-05 0.50 1391 0.09 0.10 0.032 GRMZM2G057955 (CPL3,ETC3): CAPRICE-like

MYB3 S3_218013695 3 218013695 9.27E-05 0.48 1391 0.09 0.10 0.049 GRMZM2G057853 (SEH1H): Transducin/WD40 repeat-like superfamily

protein S3_218013695 3 218013695 9.27E-05 0.48 1391 0.09 0.10 0.049 GRMZM2G057955 (CPL3,ETC3): CAPRICE-like

MYB3 S3_218014024 3 218014024 8.47E-05 0.47 1391 0.09 0.10 0.047 GRMZM2G057853 (SEH1H): Transducin/WD40 repeat-like superfamily

protein S3_218014024 3 218014024 8.47E-05 0.47 1391 0.09 0.10 0.047 GRMZM2G057955 (CPL3,ETC3): CAPRICE-like

MYB3 S3_218015637 3 218015637 2.41E-05 0.49 1391 0.09 0.10 0.032 GRMZM2G057853 (SEH1H): Transducin/WD40 repeat-like superfamily

protein S3_218015637 3 218015637 2.41E-05 0.49 1391 0.09 0.10 0.032 GRMZM2G057955 (CPL3,ETC3): CAPRICE-like

MYB3 S3_218018302 3 218018302 7.83E-06 0.21 1391 0.09 0.10 0.023 GRMZM2G057853 (SEH1H): Transducin/WD40 repeat-like superfamily

261

protein

262

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S3_218018302 3 218018302 7.83E-06 0.21 1391 0.09 0.10 0.023 GRMZM2G057955 (CPL3,ETC3): CAPRICE-like

MYB3 S3_218018303 3 218018303 2.66E-06 0.21 1391 0.09 0.10 0.013 GRMZM2G057853 (SEH1H): Transducin/WD40 repeat-like superfamily

protein S3_218018303 3 218018303 2.66E-06 0.21 1391 0.09 0.10 0.013 GRMZM2G057955 (CPL3,ETC3): CAPRICE-like

MYB3 S3_218116595 3 218116595 9.35E-05 0.21 1391 0.09 0.10 0.049 GRMZM2G073460 (EMB2758): Tetratricopeptide repeat (TPR)-like superfamily

protein S3_218184961 3 218184961 3.18E-05 0.46 1391 0.09 0.10 0.033 GRMZM2G156126 alpha/beta-Hydrolases

superfamily protein S3_218184961 3 218184961 3.18E-05 0.46 1391 0.09 0.10 0.033 GRMZM2G156158 P-loop containing nucleoside triphosphate hydrolases superfamily

protein

S3_218184961 3 218184961 3.18E-05 0.46 1391 0.09 0.10 0.033 GRMZM2G156069 (FTSH11): FTSH protease 11 S3_218184997 3 218184997 3.08E-05 0.46 1391 0.09 0.10 0.033 GRMZM2G156126 alpha/beta-Hydrolases

superfamily protein S3_218184997 3 218184997 3.08E-05 0.46 1391 0.09 0.10 0.033 GRMZM2G156158 P-loop containing nucleoside triphosphate hydrolases superfamily

protein

S3_218184997 3 218184997 3.08E-05 0.46 1391 0.09 0.10 0.033 GRMZM2G156069 (FTSH11): FTSH protease 11 S3_219787109 3 219787109 2.80E-05 0.14 1391 0.09 0.10 0.033 GRMZM5G838579 (RHD3): Root hair defective 3 GTP-binding protein

(RHD3)

262

263

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S3_219787109 3 219787109 2.80E-05 0.14 1391 0.09 0.10 0.033 GRMZM5G873287 (RHD3): Root hair defective 3 GTP-binding protein

(RHD3) S3_219787126 3 219787126 2.80E-05 0.14 1391 0.09 0.10 0.033 GRMZM5G838579 (RHD3): Root hair defective 3 GTP-binding protein

(RHD3) S3_219787126 3 219787126 2.80E-05 0.14 1391 0.09 0.10 0.033 GRMZM5G873287 (RHD3): Root hair defective 3 GTP-binding protein

(RHD3) S3_220686816 3 220686816 1.56E-05 0.19 1391 0.09 0.10 0.028 GRMZM2G371606 (CHUP1): Hydroxyproline- rich glycoprotein family

protein S3_220686816 3 220686816 1.56E-05 0.19 1391 0.09 0.10 0.028 GRMZM2G371628 (ULP1B): UB-like protease

1B S3_220686816 3 220686816 1.56E-05 0.19 1391 0.09 0.10 0.028 AC184699.3_FG00 (LUT2): Lycopene

5 beta/epsilon cyclase protein S3_223174336 3 223174336 2.75E-05 0.24 1391 0.09 0.10 0.033 GRMZM2G142334 (ATB BETA): Protein phosphatase 2A, regulatory

subunit PR55 S3_223174337 3 223174337 2.75E-05 0.24 1391 0.09 0.10 0.033 GRMZM2G142334 (ATB BETA): Protein phosphatase 2A, regulatory

subunit PR55 S3_223353988 3 223353988 3.60E-05 0.23 1391 0.09 0.10 0.035 GRMZM2G120619 (LHB1B2,LHCB1.5): photosystem II light harvesting complex gene

B1B2 S3_223691724 3 223691724 3.43E-05 0.09 1391 0.09 0.10 0.034 GRMZM2G072052 EF hand calcium-binding

protein family S3_223691724 3 223691724 3.43E-05 0.09 1391 0.09 0.10 0.034 GRMZM2G071977 myb-like transcription

263

factor family protein

264

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S3_225831095 3 225831095 7.39E-07 0.33 1391 0.09 0.10 0.010 GRMZM2G093098 Pentatricopeptide repeat

(PPR) superfamily protein S3_225831095 3 225831095 7.39E-07 0.33 1391 0.09 0.10 0.010 GRMZM2G093032 (GAMMA- VPE,GAMMAVPE): gamma

vacuolar processing enzyme S3_225898255 3 225898255 2.63E-05 0.37 1391 0.09 0.10 0.033 GRMZM2G392649 Insulinase (Peptidase family

M16) protein S3_225898255 3 225898255 2.63E-05 0.37 1391 0.09 0.10 0.033 GRMZM2G090647 thioredoxin, putative,

expressed S3_225898385 3 225898385 4.74E-05 0.38 1391 0.09 0.10 0.037 GRMZM2G392649 Insulinase (Peptidase family

M16) protein S3_225898385 3 225898385 4.74E-05 0.38 1391 0.09 0.10 0.037 GRMZM2G090647 thioredoxin, putative,

expressed S3_225898464 3 225898464 5.24E-05 0.36 1391 0.09 0.10 0.039 GRMZM2G392649 Insulinase (Peptidase family

M16) protein S3_225898464 3 225898464 5.24E-05 0.36 1391 0.09 0.10 0.039 GRMZM2G090647 thioredoxin, putative,

expressed S3_226807153 3 226807153 6.90E-05 0.45 1391 0.09 0.10 0.044 GRMZM2G369703 Ribonuclease P protein

subunit P38-related S4_6609226 4 6609226 6.02E-05 0.29 1391 0.09 0.10 0.042 GRMZM2G133675 (PYE): basic helix-loop-helix (bHLH) DNA-binding

superfamily protein S4_6609226 4 6609226 6.02E-05 0.29 1391 0.09 0.10 0.042 GRMZM2G133756 SNARE associated Golgi

protein family

S4_11410371 4 11410371 8.96E-05 0.13 1391 0.09 0.10 0.048 GRMZM2G008259 (AL7): alfin-like 7 S4_12782501 4 12782501 6.05E-06 0.17 1391 0.09 0.10 0.020 GRMZM2G139533 NagB/RpiA/CoA transferase-like superfamily

protein

264

265

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S4_18117145 4 18117145 8.70E-06 0.41 1391 0.09 0.10 0.024 AC204611.4_FG00 Pyridoxal phosphate (PLP)- 1 dependent transferases

superfamily protein S4_18581278 4 18581278 1.82E-05 0.25 1391 0.09 0.10 0.029 GRMZM2G139894 (ATMCM2,MCM2): minichromosome maintenance (MCM2/3/5)

family protein S4_18581278 4 18581278 1.82E-05 0.25 1391 0.09 0.10 0.029 GRMZM2G139880 (THY-1): thymidylate

synthase 1 S4_18581278 4 18581278 1.82E-05 0.25 1391 0.09 0.10 0.029 GRMZM2G440221 Oligosaccharyltransferase complex/magnesium

transporter family protein S4_18581278 4 18581278 1.82E-05 0.25 1391 0.09 0.10 0.029 GRMZM2G440208 6-phosphogluconate dehydrogenase family

protein S4_18581648 4 18581648 3.25E-05 0.25 1391 0.09 0.10 0.033 GRMZM2G139894 (ATMCM2,MCM2): minichromosome maintenance (MCM2/3/5)

family protein S4_18581648 4 18581648 3.25E-05 0.25 1391 0.09 0.10 0.033 GRMZM2G139880 (THY-1): thymidylate

synthase 1 S4_18581648 4 18581648 3.25E-05 0.25 1391 0.09 0.10 0.033 GRMZM2G440221 Oligosaccharyltransferase complex/magnesium

transporter family protein S4_18581648 4 18581648 3.25E-05 0.25 1391 0.09 0.10 0.033 GRMZM2G440208 6-phosphogluconate dehydrogenase family

protein S4_187412483 4 187412483 4.69E-05 0.14 1391 0.09 0.10 0.037 GRMZM5G832805 (IAGLU): indole-3-acetate

beta-D-glucosyltransferase

265 S4_187412483 4 187412483 4.69E-05 0.14 1391 0.09 0.10 0.037 GRMZM5G896260 (IAGLU): indole-3-acetate

beta-D-glucosyltransferase

266

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S4_228553735 4 228553735 8.08E-05 0.30 1391 0.09 0.10 0.046 GRMZM2G307241 (BZR1): Brassinosteroid signalling positive regulator

(BZR1) family protein S4_233203671 4 233203671 3.49E-05 0.22 1391 0.09 0.10 0.034 GRMZM2G155822 Calcium-binding EF-hand

family protein S4_233203671 4 233203671 3.49E-05 0.22 1391 0.09 0.10 0.034 GRMZM2G030542 Regulator of chromosome condensation (RCC1) family

protein S4_237517637 4 237517637 5.74E-06 0.14 1391 0.09 0.10 0.020 GRMZM2G165917 Translation initiation factor

IF2/IF5 S4_237517637 4 237517637 5.74E-06 0.14 1391 0.09 0.10 0.020 GRMZM2G166032 (ATEXO70G1,EXO70G1): exocyst subunit exo70

family protein G1 S4_237517637 4 237517637 5.74E-06 0.14 1391 0.09 0.10 0.020 GRMZM2G166035 (WIN2): HOPW1-1-

interacting 2 S4_238056221 4 238056221 5.83E-07 0.33 1391 0.09 0.10 0.010 AC233922.1_FG00 Amino acid dehydrogenase

5 family protein S4_238056221 4 238056221 5.83E-07 0.33 1391 0.09 0.10 0.010 GRMZM5G846811 (ARAC3,ATROP6,RAC3,RHO

1PS,ROP6): RAC-like 3 S4_238056221 4 238056221 5.83E-07 0.33 1391 0.09 0.10 0.010 AC233922.1_FG00 (ATERS,ERS,OVA3):

4 glutamate tRNA synthetase S4_238057665 4 238057665 1.48E-05 0.18 1391 0.09 0.10 0.028 AC233922.1_FG00 Amino acid dehydrogenase

5 family protein S4_238057665 4 238057665 1.48E-05 0.18 1391 0.09 0.10 0.028 GRMZM5G846811 (ARAC3,ATROP6,RAC3,RHO

1PS,ROP6): RAC-like 3 S4_238057665 4 238057665 1.48E-05 0.18 1391 0.09 0.10 0.028 AC233922.1_FG00 (ATERS,ERS,OVA3):

4 glutamate tRNA synthetase S4_238057919 4 238057919 2.01E-05 0.44 1391 0.09 0.10 0.030 AC233922.1_FG00 Amino acid dehydrogenase

5 family protein

266 S4_238057919 4 238057919 2.01E-05 0.44 1391 0.09 0.10 0.030 GRMZM5G846811 (ARAC3,ATROP6,RAC3,RHO

1PS,ROP6): RAC-like 3

267

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S4_238057919 4 238057919 2.01E-05 0.44 1391 0.09 0.10 0.030 AC233922.1_FG00 (ATERS,ERS,OVA3):

4 glutamate tRNA synthetase S4_238122679 4 238122679 6.16E-05 0.17 1391 0.09 0.10 0.042 GRMZM2G389768 (CSDP1): cold shock domain

protein 1 S4_238356952 4 238356952 6.33E-05 0.23 1391 0.09 0.10 0.042 GRMZM2G423129 Calcium-binding EF-hand

family protein S4_238356952 4 238356952 6.33E-05 0.23 1391 0.09 0.10 0.042 GRMZM2G121269 (AT- SRP40,ATRSP35,ATRSP40,RS P35): arginine/serine-rich

splicing factor 35 S4_238356952 4 238356952 6.33E-05 0.23 1391 0.09 0.10 0.042 GRMZM2G362021 (FDH): formate

dehydrogenase S4_238356972 4 238356972 9.48E-06 0.23 1391 0.09 0.10 0.024 GRMZM2G423129 Calcium-binding EF-hand

family protein S4_238356972 4 238356972 9.48E-06 0.23 1391 0.09 0.10 0.024 GRMZM2G121269 (AT- SRP40,ATRSP35,ATRSP40,RS P35): arginine/serine-rich

splicing factor 35 S4_238356972 4 238356972 9.48E-06 0.23 1391 0.09 0.10 0.024 GRMZM2G362021 (FDH): formate

dehydrogenase S4_238356976 4 238356976 1.23E-05 0.23 1391 0.09 0.10 0.027 GRMZM2G423129 Calcium-binding EF-hand

family protein S4_238356976 4 238356976 1.23E-05 0.23 1391 0.09 0.10 0.027 GRMZM2G121269 (AT- SRP40,ATRSP35,ATRSP40,RS P35): arginine/serine-rich

splicing factor 35 S4_238356976 4 238356976 1.23E-05 0.23 1391 0.09 0.10 0.027 GRMZM2G362021 (FDH): formate

dehydrogenase S4_238759421 4 238759421 4.01E-05 0.41 1391 0.09 0.10 0.035 GRMZM2G027209 basal transcription factor

267

complex subunit-related

268

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S4_238759421 4 238759421 4.01E-05 0.41 1391 0.09 0.10 0.035 GRMZM2G027043 (CDS4): cytidinediphosphate

diacylglycerol synthase 4 S4_238759421 4 238759421 4.01E-05 0.41 1391 0.09 0.10 0.035 GRMZM2G027187 (ATMAP65-3,MAP65-3,PLE): Microtubule associated protein (MAP65/ASE1)

family protein S4_238952009 4 238952009 8.20E-05 0.41 1391 0.09 0.10 0.046 AC214641.2_FG00 Tetratricopeptide repeat 2 (TPR)-like superfamily

protein S4_238952009 4 238952009 8.20E-05 0.41 1391 0.09 0.10 0.046 GRMZM2G019597 tRNA (guanine-N-7)

methyltransferase S4_238952009 4 238952009 8.20E-05 0.41 1391 0.09 0.10 0.046 GRMZM2G019838 (EMB139,EMB506): Ankyrin

repeat family protein S4_238952013 4 238952013 8.20E-05 0.41 1391 0.09 0.10 0.046 AC214641.2_FG00 Tetratricopeptide repeat 2 (TPR)-like superfamily

protein S4_238952013 4 238952013 8.20E-05 0.41 1391 0.09 0.10 0.046 GRMZM2G019597 tRNA (guanine-N-7)

methyltransferase S4_238952013 4 238952013 8.20E-05 0.41 1391 0.09 0.10 0.046 GRMZM2G019838 (EMB139,EMB506): Ankyrin

repeat family protein S4_238952014 4 238952014 8.20E-05 0.41 1391 0.09 0.10 0.046 AC214641.2_FG00 Tetratricopeptide repeat 2 (TPR)-like superfamily

protein S4_238952014 4 238952014 8.20E-05 0.41 1391 0.09 0.10 0.046 GRMZM2G019597 tRNA (guanine-N-7)

methyltransferase S4_238952014 4 238952014 8.20E-05 0.41 1391 0.09 0.10 0.046 GRMZM2G019838 (EMB139,EMB506): Ankyrin

repeat family protein S4_238952016 4 238952016 8.20E-05 0.41 1391 0.09 0.10 0.046 AC214641.2_FG00 Tetratricopeptide repeat 2 (TPR)-like superfamily

268

protein

269

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S4_238952016 4 238952016 8.20E-05 0.41 1391 0.09 0.10 0.046 GRMZM2G019597 tRNA (guanine-N-7)

methyltransferase S4_238952016 4 238952016 8.20E-05 0.41 1391 0.09 0.10 0.046 GRMZM2G019838 (EMB139,EMB506): Ankyrin

repeat family protein S4_239160184 4 239160184 6.99E-05 0.16 1391 0.09 0.10 0.044 GRMZM2G324285 anthranilate phosphoribosyltransferase,

putative S4_239160184 4 239160184 6.99E-05 0.16 1391 0.09 0.10 0.044 GRMZM2G024310 (MGP1): copper ion binding;cobalt ion

binding;zinc ion binding S4_239370342 4 239370342 6.84E-05 0.20 1391 0.09 0.10 0.044 GRMZM2G382581 (AtMC6,MC6): metacaspase

6 S4_239436102 4 239436102 4.88E-05 0.14 1391 0.09 0.10 0.038 GRMZM5G878541 (ATWEE1,WEE1): WEE1

kinase homolog

S4_239436102 4 239436102 4.88E-05 0.14 1391 0.09 0.10 0.038 GRMZM2G374088 (MPK9): MAP kinase 9 S4_239436102 4 239436102 4.88E-05 0.14 1391 0.09 0.10 0.038 GRMZM2G374084 retrotransposon protein, putative, unclassified,

expressed S5_2537530 5 2537530 8.87E-05 0.11 1391 0.09 0.10 0.048 GRMZM2G160046 Transducin/WD40 repeat-

like superfamily protein S5_2537530 5 2537530 8.87E-05 0.11 1391 0.09 0.10 0.048 GRMZM2G458266 Transducin/WD40 repeat-

like superfamily protein S5_2537530 5 2537530 8.87E-05 0.11 1391 0.09 0.10 0.048 GRMZM2G160027 glycine-rich protein A3,

putative, expressed

S5_3048977 5 3048977 4.15E-05 0.47 1391 0.09 0.10 0.036 GRMZM2G095865 (GYRA): DNA GYRASE A S5_3048977 5 3048977 4.15E-05 0.47 1391 0.09 0.10 0.036 GRMZM2G395844 (ARFA1B,ATARFA1B): ADP-

ribosylation factor A1B

S5_3048977 5 3048977 4.15E-05 0.47 1391 0.09 0.10 0.036 GRMZM2G096165 Ribosomal protein L36 269

270

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S5_6985197 5 6985197 5.28E-05 0.17 1391 0.09 0.10 0.039 GRMZM2G553379 (AGL7,AP1): K-box region and MADS-box transcription

factor family protein S5_8006530 5 8006530 8.98E-06 0.17 1391 0.09 0.10 0.024 GRMZM2G023858 Vps51/Vps67 family (components of vesicular

transport) protein S5_8006549 5 8006549 5.69E-05 0.15 1391 0.09 0.10 0.040 GRMZM2G023858 Vps51/Vps67 family (components of vesicular

transport) protein S5_11883125 5 11883125 1.39E-05 0.19 1391 0.09 0.10 0.027 GRMZM2G090435 Protein of unknown

function (DUF3049) S5_15516150 5 15516150 3.37E-06 0.16 1391 0.09 0.10 0.015 GRMZM2G037146 HSP20-like chaperones

superfamily protein S5_91356835 5 91356835 1.21E-06 0.32 1391 0.09 0.10 0.010 GRMZM5G832138 RNA recognition motif

(RRM)-containing protein S5_91356835 5 91356835 1.21E-06 0.32 1391 0.09 0.10 0.010 GRMZM2G133308 RNA recognition motif

(RRM)-containing protein S5_91813307 5 91813307 9.42E-05 0.12 1391 0.09 0.10 0.050 GRMZM2G059363 Uncharacterised BCR, YbaB

family COG0718 S5_91813307 5 91813307 9.42E-05 0.12 1391 0.09 0.10 0.050 GRMZM2G360455 Protein phosphatase 2C

family protein S5_92354079 5 92354079 5.42E-05 0.25 1391 0.09 0.10 0.040 GRMZM2G057328 (ATCCR1,CCR1,IRX4):

cinnamoyl coa reductase 1 S5_92354081 5 92354081 5.42E-05 0.25 1391 0.09 0.10 0.040 GRMZM2G057328 (ATCCR1,CCR1,IRX4):

cinnamoyl coa reductase 1 S5_92354212 5 92354212 6.17E-05 0.25 1391 0.09 0.10 0.042 GRMZM2G057328 (ATCCR1,CCR1,IRX4):

cinnamoyl coa reductase 1 S5_92354246 5 92354246 4.51E-05 0.25 1391 0.09 0.10 0.037 GRMZM2G057328 (ATCCR1,CCR1,IRX4):

cinnamoyl coa reductase 1

270

271

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S5_92802848 5 92802848 1.02E-05 0.31 1391 0.09 0.10 0.025 GRMZM2G120320 (ATWRKY40,WRKY40): WRKY DNA-binding protein

40 S5_106088856 5 106088856 7.29E-06 0.18 1391 0.09 0.10 0.022 GRMZM2G102189 Galactose oxidase/kelch

repeat superfamily protein S5_106129890 5 106129890 3.26E-05 0.19 1391 0.09 0.10 0.033 GRMZM2G102189 Galactose oxidase/kelch

repeat superfamily protein S5_106634957 5 106634957 1.37E-05 0.18 1391 0.09 0.10 0.027 GRMZM2G014577 Apoptosis inhibitory

protein 5 (API5) S5_108641312 5 108641312 2.22E-05 0.16 1391 0.09 0.10 0.031 GRMZM2G072407 Eukaryotic protein of

unknown function (DUF914) S5_117930520 5 117930520 6.09E-06 0.12 1391 0.09 0.10 0.020 GRMZM2G117700 Ribosomal protein L12/ ATP-dependent Clp protease adaptor protein

ClpS family protein S5_166517075 5 166517075 6.71E-05 0.07 1391 0.09 0.10 0.043 GRMZM2G047999 Integrase-type DNA-binding

superfamily protein S5_171964045 5 171964045 1.76E-06 0.05 1391 0.09 0.10 0.011 GRMZM5G839969 (AGL80,FEM111):

AGAMOUS-like 80 S5_172100820 5 172100820 8.66E-05 0.08 1391 0.09 0.10 0.047 GRMZM2G165631 (AtTMN1,TMN1):

transmembrane nine 1 S5_172100820 5 172100820 8.66E-05 0.08 1391 0.09 0.10 0.047 GRMZM2G114241 (OTP81): Tetratricopeptide repeat (TPR)-like

superfamily protein S5_175687414 5 175687414 6.54E-05 0.11 1391 0.09 0.10 0.043 GRMZM2G023988 (STOP1): C2H2 and C2HC zinc fingers superfamily

protein S5_179790765 5 179790765 2.03E-05 0.37 1391 0.09 0.10 0.030 GRMZM2G390560 UDP-Glycosyltransferase

superfamily protein

271

272

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S5_179790765 5 179790765 2.03E-05 0.37 1391 0.09 0.10 0.030 GRMZM2G091160 CRP12 - Cysteine-rich family protein precursor,

expressed S5_179790765 5 179790765 2.03E-05 0.37 1391 0.09 0.10 0.030 GRMZM2G091176 (UGT73B5): UDP-glucosyl

transferase 73B5 S5_179844272 5 179844272 1.64E-05 0.33 1391 0.09 0.10 0.028 GRMZM2G390560 UDP-Glycosyltransferase

superfamily protein S5_179844272 5 179844272 1.64E-05 0.33 1391 0.09 0.10 0.028 GRMZM2G057184 ARM- repeat/Tetratricopeptide

repeat (TPR)-like protein S5_179844272 5 179844272 1.64E-05 0.33 1391 0.09 0.10 0.028 GRMZM2G056988 Protein of unknown

function (DUF581) S5_179844274 5 179844274 2.44E-05 0.33 1391 0.09 0.10 0.032 GRMZM2G390560 UDP-Glycosyltransferase

superfamily protein S5_179844274 5 179844274 2.44E-05 0.33 1391 0.09 0.10 0.032 GRMZM2G057184 ARM- repeat/Tetratricopeptide

repeat (TPR)-like protein S5_179844274 5 179844274 2.44E-05 0.33 1391 0.09 0.10 0.032 GRMZM2G056988 Protein of unknown

function (DUF581) S5_180370661 5 180370661 3.40E-05 0.20 1391 0.09 0.10 0.034 GRMZM2G038073 (ANAC008,SOG1): NAC (No Apical Meristem) domain transcriptional regulator

superfamily protein S5_186725178 5 186725178 7.46E-05 0.30 1391 0.09 0.10 0.046 GRMZM2G029048 (ATPAL1,PAL1): PHE

ammonia lyase 1 S5_186725178 5 186725178 7.46E-05 0.30 1391 0.09 0.10 0.046 GRMZM2G334660 (ATPAL1,PAL1): PHE

ammonia lyase 1 S5_188195099 5 188195099 4.09E-06 0.44 1391 0.09 0.10 0.016 GRMZM2G393673 (SCPL34): serine

carboxypeptidase-like 34

272 S5_188195101 5 188195101 4.09E-06 0.44 1391 0.09 0.10 0.016 GRMZM2G393673 (SCPL34): serine

carboxypeptidase-like 34

273

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S5_188195102 5 188195102 4.09E-06 0.44 1391 0.09 0.10 0.016 GRMZM2G393673 (SCPL34): serine

carboxypeptidase-like 34 S5_188195131 5 188195131 1.29E-06 0.45 1391 0.09 0.10 0.010 GRMZM2G393673 (SCPL34): serine

carboxypeptidase-like 34 S5_188393532 5 188393532 3.11E-05 0.11 1391 0.09 0.10 0.033 AC198169.4_FG00 (EMB1586,ISE1): P-loop 4 containing nucleoside triphosphate hydrolases

superfamily protein

S5_188393532 5 188393532 3.11E-05 0.11 1391 0.09 0.10 0.033 GRMZM2G172239 BolA-like family protein

S5_188467607 5 188467607 4.48E-05 0.14 1391 0.09 0.10 0.037 GRMZM2G178517 (AtNIT4,NIT4): nitrilase 4 S5_188467607 5 188467607 4.48E-05 0.14 1391 0.09 0.10 0.037 GRMZM2G178603 TCP family transcription

factor S5_188467607 5 188467607 4.48E-05 0.14 1391 0.09 0.10 0.037 GRMZM2G178509 GRAM domain-containing protein / ABA-responsive

protein-related S5_188467607 5 188467607 4.48E-05 0.14 1391 0.09 0.10 0.037 GRMZM2G178595 e2f-associated phosphoprotein, putative,

expressed

S5_188467634 5 188467634 4.48E-05 0.14 1391 0.09 0.10 0.037 GRMZM2G178517 (AtNIT4,NIT4): nitrilase 4 S5_188467634 5 188467634 4.48E-05 0.14 1391 0.09 0.10 0.037 GRMZM2G178603 TCP family transcription

factor S5_188467634 5 188467634 4.48E-05 0.14 1391 0.09 0.10 0.037 GRMZM2G178509 GRAM domain-containing protein / ABA-responsive

protein-related S5_188467634 5 188467634 4.48E-05 0.14 1391 0.09 0.10 0.037 GRMZM2G178595 e2f-associated phosphoprotein, putative,

expressed S5_199209615 5 199209615 3.39E-05 0.09 1391 0.09 0.10 0.034 GRMZM2G060837 (XTH30,XTR4): xyloglucan endotransglucosylase/hydr 273

olase 30

274

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S5_204866676 5 204866676 2.95E-06 0.14 1391 0.09 0.10 0.014 GRMZM2G175875 Ribosomal protein L17

family protein S5_212818816 5 212818816 1.22E-05 0.43 1391 0.09 0.10 0.027 GRMZM2G040890 Double Clp-N motif- containing P-loop nucleoside triphosphate hydrolases superfamily

protein S5_212819001 5 212819001 6.12E-05 0.17 1391 0.09 0.10 0.042 GRMZM2G040890 Double Clp-N motif- containing P-loop nucleoside triphosphate hydrolases superfamily

protein S5_213077900 5 213077900 6.06E-05 0.14 1391 0.09 0.10 0.042 GRMZM2G122284 (MEE16): RING/U-box

superfamily protein S5_214404494 5 214404494 8.51E-05 0.09 1391 0.09 0.10 0.047 GRMZM2G092632 (CLPP6,NCLPP1,NCLPP6): CLP protease proteolytic

subunit 6 S5_214404494 5 214404494 8.51E-05 0.09 1391 0.09 0.10 0.047 GRMZM2G030465 (IAA13): auxin-induced

protein 13 S5_214952422 5 214952422 2.63E-05 0.34 1391 0.09 0.10 0.033 GRMZM5G857701 (anac074,NAC074): NAC domain containing protein

74 S6_58561008 6 58561008 8.30E-05 0.20 1391 0.09 0.10 0.047 GRMZM2G095252 (CPN60B,LEN1): chaperonin

60 beta S6_58561008 6 58561008 8.30E-05 0.20 1391 0.09 0.10 0.047 GRMZM2G133698 TCP-1/cpn60 chaperonin

family protein S6_85412122 6 85412122 6.49E-06 0.26 1391 0.09 0.10 0.020 GRMZM2G048430 Plant invertase/pectin methylesterase inhibitor

superfamily protein

274 S6_85412122 6 85412122 6.49E-06 0.26 1391 0.09 0.10 0.020 GRMZM2G048561 calcineurin B subunit-

275

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S6_85412122 6 85412122 6.49E-06 0.26 1391 0.09 0.10 0.020 GRMZM2G048644 Protein of unknown

function (DUF544) S6_85412330 6 85412330 1.60E-05 0.26 1391 0.09 0.10 0.028 GRMZM2G048430 Plant invertase/pectin methylesterase inhibitor

superfamily protein S6_85412330 6 85412330 1.60E-05 0.26 1391 0.09 0.10 0.028 GRMZM2G048561 calcineurin B subunit-

related S6_85412330 6 85412330 1.60E-05 0.26 1391 0.09 0.10 0.028 GRMZM2G048644 Protein of unknown

function (DUF544) S6_85414004 6 85414004 8.82E-05 0.25 1391 0.09 0.10 0.048 GRMZM2G048430 Plant invertase/pectin methylesterase inhibitor

superfamily protein S6_85414004 6 85414004 8.82E-05 0.25 1391 0.09 0.10 0.048 GRMZM2G048561 calcineurin B subunit-

related S6_85414004 6 85414004 8.82E-05 0.25 1391 0.09 0.10 0.048 GRMZM2G048644 Protein of unknown

function (DUF544) S6_85798174 6 85798174 4.59E-05 0.27 1391 0.09 0.10 0.037 GRMZM2G365961 prephenate dehydrogenase

family protein S6_85798184 6 85798184 4.94E-05 0.28 1391 0.09 0.10 0.038 GRMZM2G365961 prephenate dehydrogenase

family protein S6_85798187 6 85798187 4.94E-05 0.28 1391 0.09 0.10 0.038 GRMZM2G365961 prephenate dehydrogenase

family protein S6_86627731 6 86627731 1.89E-05 0.19 1391 0.09 0.10 0.029 GRMZM2G181649 (CID11): CTC-interacting

domain 11 S6_86627731 6 86627731 1.89E-05 0.19 1391 0.09 0.10 0.029 GRMZM2G378770 60S acidic ribosomal protein

family S6_90932048 6 90932048 7.59E-05 0.17 1391 0.09 0.10 0.046 GRMZM2G343068 (ATMYB33,MYB33): myb

domain protein 33 S6_96329922 6 96329922 3.61E-05 0.23 1391 0.09 0.10 0.035 AC209050.3_FG00 (ATWRKY40,WRKY40):

275 3 WRKY DNA-binding protein

276

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S6_96329922 6 96329922 3.61E-05 0.23 1391 0.09 0.10 0.035 GRMZM5G848603 alpha/beta-Hydrolases

superfamily protein S6_124025725 6 124025725 8.82E-05 0.47 1391 0.09 0.10 0.048 GRMZM2G126484 kelch repeat-containing

protein, putative, expressed S6_124026042 6 124026042 8.73E-05 0.46 1391 0.09 0.10 0.048 GRMZM2G126484 kelch repeat-containing

protein, putative, expressed S6_124855815 6 124855815 5.88E-05 0.09 1391 0.09 0.10 0.041 GRMZM2G083975 (ATRSZ33,RSZ33): arginine/serine-rich zinc knuckle-containing protein

33 S6_124855815 6 124855815 5.88E-05 0.09 1391 0.09 0.10 0.041 GRMZM2G174621 (FQR1): flavodoxin-like

quinone reductase 1 S6_126371299 6 126371299 8.08E-05 0.19 1391 0.09 0.10 0.046 AC207728.2_FG00 suppressor of Mek,

3 putative, expressed S6_126790864 6 126790864 8.82E-05 0.19 1391 0.09 0.10 0.048 GRMZM2G159369 (ATPDI11,ATPDIL2- 1,MEE30,PDI11,UNE5):

thioredoxin family protein S6_130590950 6 130590950 2.81E-05 0.09 1391 0.09 0.10 0.033 GRMZM2G149201 Leucine-rich repeat (LRR)

family protein S6_130759105 6 130759105 2.84E-05 0.07 1391 0.09 0.10 0.033 GRMZM2G106233 (MFP1): MAR binding

filament-like protein 1 S6_130841169 6 130841169 1.27E-06 0.09 1391 0.09 0.10 0.010 GRMZM2G066341 Protein of unknown

function (DUF581) S6_134148722 6 134148722 8.64E-05 0.09 1391 0.09 0.10 0.047 GRMZM2G044301 Transcription factor jumonji (jmj) family protein / zinc finger (C5HC2 type) family

protein S6_134565969 6 134565969 2.41E-05 0.32 1391 0.09 0.10 0.032 GRMZM2G100067 RAD3-like DNA-binding

helicase protein

276 S6_134565969 6 134565969 2.41E-05 0.32 1391 0.09 0.10 0.032 GRMZM5G870381 RAD3-like DNA-binding

helicase protein

277

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S6_134565969 6 134565969 2.41E-05 0.32 1391 0.09 0.10 0.032 GRMZM2G100133 (ATOFP7,OFP7): ovate

family protein 7 S6_134650360 6 134650360 1.66E-06 0.45 1391 0.09 0.10 0.011 GRMZM2G061469 (SLAH3): SLAC1 homologue

3 S6_144784636 6 144784636 4.00E-05 0.15 1391 0.09 0.10 0.035 GRMZM2G087758 Chaperone DnaJ-domain

superfamily protein S6_147880140 6 147880140 1.76E-05 0.29 1391 0.09 0.10 0.029 GRMZM2G180328 (ANAC002,ATAF1): NAC (No Apical Meristem) domain transcriptional regulator

superfamily protein S6_147880140 6 147880140 1.76E-05 0.29 1391 0.09 0.10 0.029 GRMZM2G018971 DUF803 domain containing,

putative, expressed S6_147880140 6 147880140 1.76E-05 0.29 1391 0.09 0.10 0.029 GRMZM2G456512 DUF630/DUF632 domains containing protein,

putative, expressed S6_147887743 6 147887743 5.13E-05 0.14 1391 0.09 0.10 0.039 GRMZM2G456512 Protein of unknown function (DUF630 and

DUF632) S6_147887743 6 147887743 5.13E-05 0.14 1391 0.09 0.10 0.039 GRMZM2G018971 Protein of unknown

function (DUF803) S6_149678160 6 149678160 8.06E-05 0.45 1391 0.09 0.10 0.046 GRMZM2G000816 Eukaryotic protein of

unknown function (DUF914) S6_149678163 6 149678163 4.54E-05 0.44 1391 0.09 0.10 0.037 GRMZM2G000816 Eukaryotic protein of

unknown function (DUF914) S6_149719096 6 149719096 2.85E-05 0.18 1391 0.09 0.10 0.033 GRMZM2G171139 (CYP94C1): cytochrome P450, family 94, subfamily

C, polypeptide 1 S6_149836032 6 149836032 1.81E-05 0.36 1391 0.09 0.10 0.029 GRMZM2G131756 (DML1,ROS1): demeter-like

277 S6_150512702 6 150512702 7.91E-05 0.09 1391 0.09 0.10 0.046 GRMZM2G011169 alpha/beta-Hydrolases

superfamily protein

278

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S6_150512702 6 150512702 7.91E-05 0.09 1391 0.09 0.10 0.046 GRMZM2G118037 Proteinase inhibitor,

propeptide

S6_150689387 6 150689387 1.89E-05 0.10 1391 0.09 0.10 0.029 GRMZM2G077662 GTP-binding family protein S6_150689387 6 150689387 1.89E-05 0.10 1391 0.09 0.10 0.029 GRMZM2G077789 (ATMYB4,MYB4): myb

domain protein 4 S6_150695207 6 150695207 4.39E-05 0.10 1391 0.09 0.10 0.037 GRMZM2G077621 Protein of unknown

function (DUF668)

S6_150695207 6 150695207 4.39E-05 0.10 1391 0.09 0.10 0.037 GRMZM2G077662 GTP-binding family protein S6_150695207 6 150695207 4.39E-05 0.10 1391 0.09 0.10 0.037 GRMZM2G077789 (ATMYB4,MYB4): myb

domain protein 4 S6_150736439 6 150736439 2.15E-05 0.16 1391 0.09 0.10 0.031 GRMZM2G066153 C2 calcium/lipid-binding plant phosphoribosyltransferase

family protein

S6_150736439 6 150736439 2.15E-05 0.16 1391 0.09 0.10 0.031 AC194828.3_FG00 PAR1 protein 4 S6_150736657 6 150736657 8.03E-05 0.17 1391 0.09 0.10 0.046 GRMZM2G066153 C2 calcium/lipid-binding plant phosphoribosyltransferase

family protein

S6_150736657 6 150736657 8.03E-05 0.17 1391 0.09 0.10 0.046 AC194828.3_FG00 PAR1 protein 4 S6_150772349 6 150772349 2.10E-05 0.12 1391 0.09 0.10 0.030 GRMZM2G067036 (AtIPCS1): Arabidopsis Inositol phosphorylceramide

synthase 1 S6_150772349 6 150772349 2.10E-05 0.12 1391 0.09 0.10 0.030 GRMZM2G067117 harpin-induced protein 1 domain containing protein,

278 expressed

279

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S6_150886817 6 150886817 3.86E-05 0.16 1391 0.09 0.10 0.035 GRMZM2G093272 Adenine nucleotide alpha hydrolases-like superfamily

protein S6_151543745 6 151543745 3.46E-05 0.13 1391 0.09 0.10 0.034 GRMZM2G146152 (ATLAC17,LAC17): laccase

17 S6_153100632 6 153100632 1.39E-05 0.46 1391 0.09 0.10 0.027 GRMZM2G396076 DNA repair metallo-beta-

lactamase family protein S6_153100632 6 153100632 1.39E-05 0.46 1391 0.09 0.10 0.027 GRMZM2G047762 (ZIP1): zinc transporter 1

precursor S6_153229787 6 153229787 1.02E-05 0.45 1391 0.09 0.10 0.025 AC209257.4_FG00 Integrase-type DNA-binding

6 superfamily protein S6_153229787 6 153229787 1.02E-05 0.45 1391 0.09 0.10 0.025 AC212394.4_FG01 (CDKB2;1): cyclin-

0 dependent kinase B2;1 S6_153229787 6 153229787 1.02E-05 0.45 1391 0.09 0.10 0.025 GRMZM5G869403 (ATEXO70B1,EXO70B1): exocyst subunit exo70

family protein B1

S6_153229787 6 153229787 1.02E-05 0.45 1391 0.09 0.10 0.025 AC209257.4_FG00 Glutaredoxin family protein 3 S6_153229787 6 153229787 1.02E-05 0.45 1391 0.09 0.10 0.025 AC209257.4_FG00 DEFL4 - Defensin and 4 Defensin-like DEFL family,

expressed S6_153229824 6 153229824 1.79E-06 0.47 1391 0.09 0.10 0.011 AC209257.4_FG00 Integrase-type DNA-binding

6 superfamily protein S6_153229824 6 153229824 1.79E-06 0.47 1391 0.09 0.10 0.011 AC212394.4_FG01 (CDKB2;1): cyclin-

0 dependent kinase B2;1 S6_153229824 6 153229824 1.79E-06 0.47 1391 0.09 0.10 0.011 GRMZM5G869403 (ATEXO70B1,EXO70B1): exocyst subunit exo70

family protein B1

S6_153229824 6 153229824 1.79E-06 0.47 1391 0.09 0.10 0.011 AC209257.4_FG00 Glutaredoxin family protein

279 3

280

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S6_153229824 6 153229824 1.79E-06 0.47 1391 0.09 0.10 0.011 AC209257.4_FG00 DEFL4 - Defensin and 4 Defensin-like DEFL family,

expressed S6_153843846 6 153843846 7.05E-05 0.38 1391 0.09 0.10 0.044 GRMZM2G026927 (ATOFP4,OFP4): ovate

family protein 4 S6_162601738 6 162601738 5.96E-05 0.36 1391 0.09 0.10 0.041 GRMZM2G061568 (ATLPP2,ATPAP2,LPP2): lipid

phosphate phosphatase 2 S6_162601738 6 162601738 5.96E-05 0.36 1391 0.09 0.10 0.041 GRMZM2G061663 RING/U-box superfamily

protein S6_162601742 6 162601742 6.39E-05 0.35 1391 0.09 0.10 0.042 GRMZM2G061568 (ATLPP2,ATPAP2,LPP2): lipid

phosphate phosphatase 2 S6_162601742 6 162601742 6.39E-05 0.35 1391 0.09 0.10 0.042 GRMZM2G061663 RING/U-box superfamily

protein S6_162604684 6 162604684 9.43E-07 0.15 1391 0.09 0.10 0.010 GRMZM2G061663 RING/U-box superfamily

protein S6_162604684 6 162604684 9.43E-07 0.15 1391 0.09 0.10 0.010 GRMZM2G061568 (ATLPP2,ATPAP2,LPP2): lipid

phosphate phosphatase 2 S6_163014254 6 163014254 1.68E-05 0.31 1391 0.09 0.10 0.028 GRMZM2G057388 Ribosomal protein L7/L12, oligomerisation;Ribosomal protein L7/L12, C- terminal/adaptor protein

ClpS- S6_163014254 6 163014254 1.68E-05 0.31 1391 0.09 0.10 0.028 GRMZM2G057251 (ATSYP71,SYP71): syntaxin

of plants 71 S6_163014254 6 163014254 1.68E-05 0.31 1391 0.09 0.10 0.028 GRMZM2G057369 (ASF1B,SGA01,SGA1): anti-

silencing function 1b S6_163014254 6 163014254 1.68E-05 0.31 1391 0.09 0.10 0.028 GRMZM2G057508 Rab5-interacting family

protein S6_163179226 6 163179226 2.88E-06 0.06 1391 0.09 0.10 0.013 GRMZM2G481261 2Fe-2S ferredoxin-like

280

superfamily protein

281

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S6_163179226 6 163179226 2.88E-06 0.06 1391 0.09 0.10 0.013 GRMZM2G181104 Protein phosphatase 2A regulatory B subunit family

protein S6_163854039 6 163854039 3.95E-05 0.38 1391 0.09 0.10 0.035 GRMZM2G381709 (ATUBC24,PHO2,UBC24):

phosphate 2 S6_163854039 6 163854039 3.95E-05 0.38 1391 0.09 0.10 0.035 GRMZM2G085641 alpha/beta-Hydrolases

superfamily protein S6_163854039 6 163854039 3.95E-05 0.38 1391 0.09 0.10 0.035 GRMZM2G085675 (NFD1): Ribosomal protein

L21 S6_166170826 6 166170826 7.42E-05 0.14 1391 0.09 0.10 0.046 GRMZM2G114592 DNA glycosylase

superfamily protein S6_166170826 6 166170826 7.42E-05 0.14 1391 0.09 0.10 0.046 GRMZM2G114578 AMP-dependent synthetase

and ligase family protein S6_166170826 6 166170826 7.42E-05 0.14 1391 0.09 0.10 0.046 GRMZM2G414844 (ATHB22,HB22,MEE68):

homeobox protein 22 S7_922357 7 922357 1.46E-05 0.08 1391 0.09 0.10 0.028 GRMZM2G020104 (ATGLR3.4,GLR3.4,GLUR3):

glutamate receptor 3.4 S7_922495 7 922495 1.45E-06 0.07 1391 0.09 0.10 0.011 GRMZM2G020104 (ATGLR3.4,GLR3.4,GLUR3):

glutamate receptor 3.4 S7_1317269 7 1317269 1.19E-06 0.45 1391 0.09 0.10 0.010 GRMZM2G120563 Calcium-dependent lipid- binding (CaLB domain)

family protein S7_1317269 7 1317269 1.19E-06 0.45 1391 0.09 0.10 0.010 GRMZM2G555108 Transducin/WD40 repeat-

like superfamily protein S7_2615969 7 2615969 7.22E-05 0.23 1391 0.09 0.10 0.045 GRMZM2G015654 (ATFT1,ATFUT1,FT1,MUR2):

fucosyltransferase 1 S7_2747413 7 2747413 1.40E-05 0.14 1391 0.09 0.10 0.027 GRMZM5G810231 OsFBL33 - F-box domain and LRR containing protein,

expressed

281

282

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S7_2747427 7 2747427 1.40E-05 0.14 1391 0.09 0.10 0.027 GRMZM5G810231 OsFBL33 - F-box domain and LRR containing protein,

expressed S7_3892074 7 3892074 8.16E-05 0.17 1391 0.09 0.10 0.046 GRMZM2G148831 stress-induced protein,

putative, expressed

S7_8701577 7 8701577 6.23E-06 0.44 1391 0.09 0.10 0.020 GRMZM2G011742 FRIGIDA-like protein

S7_8702036 7 8702036 2.61E-06 0.43 1391 0.09 0.10 0.013 GRMZM2G011742 FRIGIDA-like protein S7_13176585 7 13176585 2.77E-05 0.48 1391 0.09 0.10 0.033 GRMZM2G144653 (ATTRX H1,ATTRX1,TRX1):

thioredoxin H-type 1 S7_13398348 7 13398348 8.42E-05 0.42 1391 0.09 0.10 0.047 GRMZM2G117369 FAD-linked oxidases family

protein S7_13615721 7 13615721 4.41E-05 0.29 1391 0.09 0.10 0.037 GRMZM2G458494 Major facilitator

superfamily protein S7_13615721 7 13615721 4.41E-05 0.29 1391 0.09 0.10 0.037 GRMZM2G158489 (PHF1): phosphate transporter traffic

facilitator1 S7_13615721 7 13615721 4.41E-05 0.29 1391 0.09 0.10 0.037 GRMZM2G022616 Leucine Rich Repeat family

protein, expressed S7_14459910 7 14459910 5.23E-05 0.34 1391 0.09 0.10 0.039 GRMZM2G104325 (AHA11,HA11): H(+)-ATPase

11 S7_46304649 7 46304649 8.58E-05 0.09 1391 0.09 0.10 0.047 GRMZM5G803610 Trimeric LpxA-like enzymes

superfamily protein S7_46304649 7 46304649 8.58E-05 0.09 1391 0.09 0.10 0.047 GRMZM2G078424 (PNT1): mannosyltransferase family

protein S7_46333507 7 46333507 1.84E-05 0.09 1391 0.09 0.10 0.029 GRMZM5G868168 (ATNAP11,NAP11,TGD3):

non-intrinsic ABC protein 11 S7_46481332 7 46481332 3.07E-05 0.31 1391 0.09 0.10 0.033 GRMZM2G011129 (ATRBP31,ATRBP33,CP31,R

BP31): 31-kDa RNA binding 282

protein

283

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S7_46481332 7 46481332 3.07E-05 0.31 1391 0.09 0.10 0.033 GRMZM2G308441 isochorismatase family

protein, putative, expressed S7_93389680 7 93389680 2.28E-05 0.06 1391 0.09 0.10 0.031 GRMZM2G115670 (CYCT1;4): Cyclin family

protein S7_94857069 7 94857069 6.60E-05 0.35 1391 0.09 0.10 0.043 GRMZM5G843174 retrotransposon protein, putative, unclassified,

expressed S7_97337344 7 97337344 1.92E-05 0.49 1391 0.09 0.10 0.029 GRMZM2G132184 Protein kinase superfamily

protein

S7_100523905 7 100523905 3.74E-05 0.20 1391 0.09 0.10 0.035 GRMZM2G126413 VQ motif-containing protein

S7_100524600 7 100524600 5.86E-05 0.27 1391 0.09 0.10 0.041 GRMZM2G126413 VQ motif-containing protein

S7_100524634 7 100524634 2.84E-05 0.28 1391 0.09 0.10 0.033 GRMZM2G126413 VQ motif-containing protein S7_100804760 7 100804760 1.12E-06 0.43 1391 0.09 0.10 0.010 GRMZM2G176759 Major facilitator

superfamily protein S7_100804760 7 100804760 1.12E-06 0.43 1391 0.09 0.10 0.010 GRMZM2G176780 (UNE2): Major facilitator

superfamily protein S7_100804760 7 100804760 1.12E-06 0.43 1391 0.09 0.10 0.010 GRMZM2G176721 Major facilitator

superfamily protein S7_100804832 7 100804832 1.31E-05 0.47 1391 0.09 0.10 0.027 GRMZM2G176759 Major facilitator

superfamily protein S7_100804832 7 100804832 1.31E-05 0.47 1391 0.09 0.10 0.027 GRMZM2G176780 (UNE2): Major facilitator

superfamily protein S7_100804832 7 100804832 1.31E-05 0.47 1391 0.09 0.10 0.027 GRMZM2G176721 Major facilitator

superfamily protein S7_100805646 7 100805646 7.12E-07 0.44 1391 0.09 0.10 0.010 GRMZM2G176759 Major facilitator

superfamily protein S7_100805646 7 100805646 7.12E-07 0.44 1391 0.09 0.10 0.010 GRMZM2G176780 (UNE2): Major facilitator

superfamily protein S7_100805646 7 100805646 7.12E-07 0.44 1391 0.09 0.10 0.010 GRMZM2G176721 Major facilitator 283

superfamily protein

284

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S7_103297819 7 103297819 7.26E-05 0.49 1391 0.09 0.10 0.045 GRMZM2G172065 RING/U-box superfamily

protein S7_103305137 7 103305137 5.25E-05 0.46 1391 0.09 0.10 0.039 GRMZM2G172065 RING/U-box superfamily

protein S7_103947088 7 103947088 7.87E-05 0.30 1391 0.09 0.10 0.046 GRMZM2G175910 UDP-Glycosyltransferase

superfamily protein S7_105362359 7 105362359 3.67E-05 0.41 1391 0.09 0.10 0.035 GRMZM2G476685 (ATCYCD1;1,CYCD1;1):

CYCLIN D1;1 S7_105362741 7 105362741 2.28E-06 0.48 1391 0.09 0.10 0.012 GRMZM2G476685 (ATCYCD1;1,CYCD1;1):

CYCLIN D1;1 S7_105364711 7 105364711 2.62E-07 0.50 1391 0.09 0.10 0.006 GRMZM2G476685 (ATCYCD1;1,CYCD1;1):

CYCLIN D1;1 S7_105364725 7 105364725 1.71E-08 0.44 1391 0.09 0.11 0.001 GRMZM2G476685 (ATCYCD1;1,CYCD1;1):

CYCLIN D1;1 S7_105364741 7 105364741 1.71E-08 0.44 1391 0.09 0.11 0.001 GRMZM2G476685 (ATCYCD1;1,CYCD1;1):

CYCLIN D1;1 S7_105364743 7 105364743 3.49E-07 0.50 1391 0.09 0.10 0.007 GRMZM2G476685 (ATCYCD1;1,CYCD1;1):

CYCLIN D1;1 S7_105628618 7 105628618 7.70E-06 0.40 1391 0.09 0.10 0.023 GRMZM2G100090 RING/U-box superfamily protein with ARM repeat

domain S7_105628645 7 105628645 8.39E-06 0.40 1391 0.09 0.10 0.023 GRMZM2G100090 RING/U-box superfamily protein with ARM repeat

domain S7_105629529 7 105629529 4.41E-05 0.23 1391 0.09 0.10 0.037 GRMZM2G100090 RING/U-box superfamily protein with ARM repeat

domain S7_105629541 7 105629541 2.17E-05 0.22 1391 0.09 0.10 0.031 GRMZM2G100090 RING/U-box superfamily protein with ARM repeat

284

domain

285

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S7_106078238 7 106078238 3.30E-05 0.25 1391 0.09 0.10 0.034 GRMZM2G046600 alpha/beta-Hydrolases

superfamily protein S7_106078370 7 106078370 1.45E-06 0.26 1391 0.09 0.10 0.011 GRMZM2G046600 alpha/beta-Hydrolases

superfamily protein S7_106467784 7 106467784 7.32E-06 0.32 1391 0.09 0.10 0.022 GRMZM2G372961 retrotransposon protein, putative, unclassified,

expressed S7_106784548 7 106784548 3.80E-05 0.19 1391 0.09 0.10 0.035 GRMZM2G151921 DNAse I-like superfamily

protein S7_106784563 7 106784563 3.80E-05 0.19 1391 0.09 0.10 0.035 GRMZM2G151921 DNAse I-like superfamily

protein S7_106784566 7 106784566 3.80E-05 0.19 1391 0.09 0.10 0.035 GRMZM2G151921 DNAse I-like superfamily

protein S7_106784642 7 106784642 8.64E-05 0.13 1391 0.09 0.10 0.047 GRMZM2G151921 DNAse I-like superfamily

protein S7_108843811 7 108843811 2.85E-05 0.09 1391 0.09 0.10 0.033 GRMZM2G126507 (JAZ1,TIFY10A): jasmonate-

zim-domain protein 1 S7_115182294 7 115182294 8.02E-06 0.13 1391 0.09 0.10 0.023 GRMZM2G171408 ARM repeat superfamily

protein S7_115310293 7 115310293 5.53E-05 0.11 1391 0.09 0.10 0.040 GRMZM2G125653 (ATWRKY40,WRKY40): WRKY DNA-binding protein

40 S7_117975644 7 117975644 4.80E-06 0.49 1391 0.09 0.10 0.017 GRMZM2G009091 queuine tRNA- ribosyltransferase, putative,

expressed S7_118289896 7 118289896 7.61E-05 0.32 1391 0.09 0.10 0.046 GRMZM2G040945 HAD-superfamily hydrolase, subfamily IG, 5\'-

nucleotidase

S7_118306535 7 118306535 4.36E-05 0.28 1391 0.09 0.10 0.037 GRMZM2G041175 (TET8): tetraspanin8

285

286

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S7_118306535 7 118306535 4.36E-05 0.28 1391 0.09 0.10 0.037 GRMZM2G040945 HAD-superfamily hydrolase, subfamily IG, 5\'-

nucleotidase S7_118306535 7 118306535 4.36E-05 0.28 1391 0.09 0.10 0.037 GRMZM2G339728 retrotransposon protein, putative, unclassified,

expressed

S7_118306577 7 118306577 2.89E-05 0.29 1391 0.09 0.10 0.033 GRMZM2G041175 (TET8): tetraspanin8 S7_118306577 7 118306577 2.89E-05 0.29 1391 0.09 0.10 0.033 GRMZM2G040945 HAD-superfamily hydrolase, subfamily IG, 5\'-

nucleotidase S7_118306577 7 118306577 2.89E-05 0.29 1391 0.09 0.10 0.033 GRMZM2G339728 retrotransposon protein, putative, unclassified,

expressed

S7_118307964 7 118307964 2.00E-06 0.16 1391 0.09 0.10 0.011 GRMZM2G041175 (TET8): tetraspanin8 S7_118307964 7 118307964 2.00E-06 0.16 1391 0.09 0.10 0.011 GRMZM2G040945 HAD-superfamily hydrolase, subfamily IG, 5\'-

nucleotidase S7_118307964 7 118307964 2.00E-06 0.16 1391 0.09 0.10 0.011 GRMZM2G339728 retrotransposon protein, putative, unclassified,

expressed

S7_118307966 7 118307966 2.00E-06 0.16 1391 0.09 0.10 0.011 GRMZM2G041175 (TET8): tetraspanin8 S7_118307966 7 118307966 2.00E-06 0.16 1391 0.09 0.10 0.011 GRMZM2G040945 HAD-superfamily hydrolase, subfamily IG, 5\'-

nucleotidase S7_118307966 7 118307966 2.00E-06 0.16 1391 0.09 0.10 0.011 GRMZM2G339728 retrotransposon protein, putative, unclassified,

expressed

286

287

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S7_119130885 7 119130885 4.25E-05 0.22 1391 0.09 0.10 0.037 GRMZM2G158636 pentatricopeptide (PPR) repeat-containing protein / CBS domain-containing

protein S7_120201871 7 120201871 7.08E-05 0.18 1391 0.09 0.10 0.044 GRMZM2G138976 ARID/BRIGHT DNA-binding

domain-containing protein S7_120201871 7 120201871 7.08E-05 0.18 1391 0.09 0.10 0.044 GRMZM2G138727 PROLM23 - Prolamin

precursor, expressed S7_120201889 7 120201889 7.68E-05 0.16 1391 0.09 0.10 0.046 GRMZM2G138976 ARID/BRIGHT DNA-binding

domain-containing protein S7_120201889 7 120201889 7.68E-05 0.16 1391 0.09 0.10 0.046 GRMZM2G138727 PROLM23 - Prolamin

precursor, expressed S7_121191933 7 121191933 1.09E-06 0.32 1391 0.09 0.10 0.010 GRMZM2G168020 major ampullate spidroin 2,

putative, expressed S7_121191933 7 121191933 1.09E-06 0.32 1391 0.09 0.10 0.010 GRMZM2G469409 (emb1187): Protein kinase

superfamily protein S7_121192632 7 121192632 4.21E-05 0.47 1391 0.09 0.10 0.037 GRMZM2G469409 (emb1187): Protein kinase

superfamily protein S7_121192632 7 121192632 4.21E-05 0.47 1391 0.09 0.10 0.037 GRMZM2G168020 major ampullate spidroin 2,

putative, expressed S7_121192685 7 121192685 9.61E-05 0.41 1391 0.09 0.10 0.050 GRMZM2G469409 (emb1187): Protein kinase

superfamily protein S7_121192685 7 121192685 9.61E-05 0.41 1391 0.09 0.10 0.050 GRMZM2G168020 major ampullate spidroin 2,

putative, expressed S7_121676937 7 121676937 4.36E-06 0.41 1391 0.09 0.10 0.016 GRMZM2G172320 keratin-associated protein

5-4, putative, expressed S7_121676978 7 121676978 2.59E-05 0.41 1391 0.09 0.10 0.032 GRMZM2G172320 keratin-associated protein

5-4, putative, expressed S7_121677026 7 121677026 5.23E-06 0.46 1391 0.09 0.10 0.018 GRMZM2G172320 keratin-associated protein

287

5-4, putative, expressed

288

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S7_121677032 7 121677032 1.61E-05 0.47 1391 0.09 0.10 0.028 GRMZM2G172320 keratin-associated protein

5-4, putative, expressed S7_121816050 7 121816050 2.87E-05 0.21 1391 0.09 0.10 0.033 GRMZM2G004207 Protein kinase superfamily

protein S7_121816629 7 121816629 6.16E-05 0.22 1391 0.09 0.10 0.042 GRMZM2G004207 Protein kinase superfamily

protein S7_121816641 7 121816641 5.15E-05 0.22 1391 0.09 0.10 0.039 GRMZM2G004207 Protein kinase superfamily

protein S7_121982515 7 121982515 9.47E-06 0.24 1391 0.09 0.10 0.024 GRMZM2G038636 (AALP,ALP,SAG2): aleurain-

like protease S7_122070868 7 122070868 7.90E-05 0.27 1391 0.09 0.10 0.046 GRMZM2G050172 (AT-RSH3,ATRSH3,RSH3):

RELA/SPOT homolog 3 S7_122070868 7 122070868 7.90E-05 0.27 1391 0.09 0.10 0.046 GRMZM2G086714 AT1G54130.1(AT- RSH3,ATRSH3,RSH3):

RELA/SPOT homolog 3 S7_122070868 7 122070868 7.90E-05 0.27 1391 0.09 0.10 0.046 GRMZM2G388045 (ATGEX1,GEX1): gamete

expressed protein 1 S7_122070869 7 122070869 7.90E-05 0.27 1391 0.09 0.10 0.046 GRMZM2G050172 (AT-RSH3,ATRSH3,RSH3):

RELA/SPOT homolog 3 S7_122070869 7 122070869 7.90E-05 0.27 1391 0.09 0.10 0.046 GRMZM2G086714 (AT-RSH3,ATRSH3,RSH3):

RELA/SPOT homolog 3 S7_122070869 7 122070869 7.90E-05 0.27 1391 0.09 0.10 0.046 GRMZM2G388045 (ATGEX1,GEX1): gamete

expressed protein 1 S7_122073695 7 122073695 3.74E-07 0.31 1391 0.09 0.10 0.007 GRMZM2G050172 (AT-RSH3,ATRSH3,RSH3):

RELA/SPOT homolog 3 S7_122073695 7 122073695 3.74E-07 0.31 1391 0.09 0.10 0.007 GRMZM2G086714 (AT-RSH3,ATRSH3,RSH3):

RELA/SPOT homolog 3 S7_122073695 7 122073695 3.74E-07 0.31 1391 0.09 0.10 0.007 GRMZM2G388045 (ATGEX1,GEX1): gamete

expressed protein 1

288 S7_122073698 7 122073698 2.84E-05 0.28 1391 0.09 0.10 0.033 GRMZM2G050172 (AT-RSH3,ATRSH3,RSH3):

RELA/SPOT homolog 3

289

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S7_122073698 7 122073698 2.84E-05 0.28 1391 0.09 0.10 0.033 GRMZM2G086714 AT1G54130.1(AT- RSH3,ATRSH3,RSH3):

RELA/SPOT homolog 3 S7_122073698 7 122073698 2.84E-05 0.28 1391 0.09 0.10 0.033 GRMZM2G388045 (ATGEX1,GEX1): gamete

expressed protein 1 S7_124382048 7 124382048 7.76E-06 0.19 1391 0.09 0.10 0.023 GRMZM2G389173 (ATPDI10,ATPDIL2- 2,PDI10,PDIL2-2): PDI-like 2-

2 S7_124403369 7 124403369 1.33E-06 0.20 1391 0.09 0.10 0.011 GRMZM2G092409 DNA-binding storekeeper protein-related

transcriptional regulator S7_124403373 7 124403373 1.59E-06 0.20 1391 0.09 0.10 0.011 GRMZM2G092409 DNA-binding storekeeper protein-related

transcriptional regulator S7_137514390 7 137514390 1.09E-05 0.24 1391 0.09 0.10 0.025 GRMZM2G066202 (AIR12): auxin-responsive

family protein S7_137514390 7 137514390 1.09E-05 0.24 1391 0.09 0.10 0.025 GRMZM2G066219 Auxin-responsive family

protein

S7_137514390 7 137514390 1.09E-05 0.24 1391 0.09 0.10 0.025 GRMZM2G065868 Ribosomal protein L32e

S7_140707833 7 140707833 4.18E-06 0.43 1391 0.09 0.10 0.016 GRMZM2G043650 DNA binding S7_140707833 7 140707833 4.18E-06 0.43 1391 0.09 0.10 0.016 GRMZM2G043600 Basic-leucine zipper (bZIP) transcription factor family

protein S7_140707833 7 140707833 4.18E-06 0.43 1391 0.09 0.10 0.016 GRMZM2G043636 Molecular chaperone

Hsp40/DnaJ family protein

S7_140709870 7 140709870 3.07E-05 0.40 1391 0.09 0.10 0.033 GRMZM2G043650 DNA binding S7_140709870 7 140709870 3.07E-05 0.40 1391 0.09 0.10 0.033 GRMZM2G043600 Basic-leucine zipper (bZIP) transcription factor family

289

protein

290

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S7_140709870 7 140709870 3.07E-05 0.40 1391 0.09 0.10 0.033 GRMZM2G043636 Molecular chaperone

Hsp40/DnaJ family protein S7_141546601 7 141546601 3.55E-05 0.27 1391 0.09 0.10 0.034 GRMZM2G089241 (AtUGT85A2,UGT85A2): UDP-glucosyl transferase

85A2 S7_158959978 7 158959978 8.80E-05 0.44 1391 0.09 0.10 0.048 GRMZM2G081782 zinc finger (C2H2 type, AN1-

like) family protein

S7_158959978 7 158959978 8.80E-05 0.44 1391 0.09 0.10 0.048 GRMZM2G081668 TatD related DNase S7_158959978 7 158959978 8.80E-05 0.44 1391 0.09 0.10 0.048 GRMZM2G081803 Chaperonin-like RbcX

protein S7_158960009 7 158960009 8.53E-05 0.48 1391 0.09 0.10 0.047 GRMZM2G081782 zinc finger (C2H2 type, AN1-

like) family protein

S7_158960009 7 158960009 8.53E-05 0.48 1391 0.09 0.10 0.047 GRMZM2G081668 TatD related DNase S7_158960009 7 158960009 8.53E-05 0.48 1391 0.09 0.10 0.047 GRMZM2G081803 Chaperonin-like RbcX

protein S7_161958761 7 161958761 5.25E-05 0.18 1391 0.09 0.10 0.039 GRMZM2G180490 Phototropic-responsive

NPH3 family protein S7_162671654 7 162671654 9.82E-06 0.42 1391 0.09 0.10 0.025 GRMZM2G053338 (AUR3,BRU6,GH3- 2,GH3.2,YDK1): Auxin- responsive GH3 family

protein

S7_162710260 7 162710260 3.75E-06 0.32 1391 0.09 0.10 0.016 GRMZM2G008712 (ZFP7): zinc finger protein 7 S7_162710260 7 162710260 3.75E-06 0.32 1391 0.09 0.10 0.016 GRMZM2G309970 (WPP2): WPP domain

protein 2 S7_162710260 7 162710260 3.75E-06 0.32 1391 0.09 0.10 0.016 GRMZM2G008468 Got1/Sft2-like vescicle

transport protein family

S7_162711752 7 162711752 9.35E-05 0.49 1391 0.09 0.10 0.049 GRMZM2G008712 (ZFP7): zinc finger protein 7 S7_162711752 7 162711752 9.35E-05 0.49 1391 0.09 0.10 0.049 GRMZM2G309970 (WPP2): WPP domain

290

protein 2

291

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S7_162711752 7 162711752 9.35E-05 0.49 1391 0.09 0.10 0.049 GRMZM2G008468 Got1/Sft2-like vescicle

transport protein family

S7_162711840 7 162711840 1.27E-05 0.40 1391 0.09 0.10 0.027 GRMZM2G008712 (ZFP7): zinc finger protein 7 S7_162711840 7 162711840 1.27E-05 0.40 1391 0.09 0.10 0.027 GRMZM2G309970 (WPP2): WPP domain

protein 2 S7_162762970 7 162762970 3.51E-06 0.45 1391 0.09 0.10 0.015 GRMZM2G056075 (ATMSH2,MSH2): MUTS

homolog 2 S7_162762981 7 162762981 4.12E-06 0.45 1391 0.09 0.10 0.016 GRMZM2G056075 (ATMSH2,MSH2): MUTS

homolog 2 S7_162763106 7 162763106 3.01E-06 0.45 1391 0.09 0.10 0.014 GRMZM2G056075 (ATMSH2,MSH2): MUTS

homolog 2 S7_162766528 7 162766528 1.02E-06 0.44 1391 0.09 0.10 0.010 GRMZM2G056075 (ATMSH2,MSH2): MUTS

homolog 2 S7_162766759 7 162766759 2.64E-06 0.43 1391 0.09 0.10 0.013 GRMZM2G056075 (ATMSH2,MSH2): MUTS

homolog 2 S7_162801789 7 162801789 3.38E-08 0.37 1391 0.09 0.11 0.002 GRMZM2G119740 Prefoldin chaperone

subunit family protein S7_162801789 7 162801789 3.38E-08 0.37 1391 0.09 0.11 0.002 GRMZM2G119705 ribosome inactivating

protein, putative, expressed S7_162959549 7 162959549 2.00E-05 0.33 1391 0.09 0.10 0.030 GRMZM2G432738 DHHC-type zinc finger

family protein

S7_162959549 7 162959549 2.00E-05 0.33 1391 0.09 0.10 0.030 GRMZM2G132810 actin binding S7_162962138 7 162962138 1.06E-05 0.26 1391 0.09 0.10 0.025 GRMZM2G432738 DHHC-type zinc finger

family protein

S7_162962138 7 162962138 1.06E-05 0.26 1391 0.09 0.10 0.025 GRMZM2G132810 actin binding S7_166959164 7 166959164 4.27E-05 0.32 1391 0.09 0.10 0.037 GRMZM2G407361 Pentatricopeptide repeat

(PPR) superfamily protein S8_11529072 8 11529072 6.23E-05 0.29 1391 0.09 0.10 0.042 GRMZM2G155709 Protein of unknown function DUF2359, 291

transmembrane

292

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S8_16749187 8 16749187 2.99E-05 0.48 1391 0.09 0.10 0.033 AC211474.3_FG00 O-fucosyltransferase family

6 protein S8_16749187 8 16749187 2.99E-05 0.48 1391 0.09 0.10 0.033 GRMZM2G143211 (ATATG18D,ATG18D): homolog of yeast

autophagy 18 (ATG18) D S8_16749187 8 16749187 2.99E-05 0.48 1391 0.09 0.10 0.033 GRMZM2G143258 alpha/beta-Hydrolases

superfamily protein S8_16756080 8 16756080 2.34E-05 0.35 1391 0.09 0.10 0.032 AC211474.3_FG00 O-fucosyltransferase family

6 protein S8_16756080 8 16756080 2.34E-05 0.35 1391 0.09 0.10 0.032 GRMZM2G143211 (ATATG18D,ATG18D): homolog of yeast

autophagy 18 (ATG18) D S8_16756080 8 16756080 2.34E-05 0.35 1391 0.09 0.10 0.032 GRMZM2G143258 alpha/beta-Hydrolases

superfamily protein S8_17889029 8 17889029 1.53E-05 0.27 1391 0.09 0.10 0.028 GRMZM2G080521 alpha/beta-Hydrolases

superfamily protein S8_17889039 8 17889039 1.78E-06 0.24 1391 0.09 0.10 0.011 GRMZM2G080521 alpha/beta-Hydrolases

superfamily protein S8_18215458 8 18215458 2.81E-07 0.23 1391 0.09 0.10 0.006 GRMZM2G107696 (ATUBP14,PER1,TTN6,UBP1 4): ubiquitin-specific

protease 14 S8_18215497 8 18215497 8.67E-05 0.43 1391 0.09 0.10 0.047 GRMZM2G107696 (ATUBP14,PER1,TTN6,UBP1 4): ubiquitin-specific

protease 14 S8_18215760 8 18215760 1.09E-06 0.31 1391 0.09 0.10 0.010 GRMZM2G107696 (ATUBP14,PER1,TTN6,UBP1 4): ubiquitin-specific

protease 14 S8_18224564 8 18224564 9.72E-07 0.43 1391 0.09 0.10 0.010 GRMZM2G107639 Pyridoxal phosphate (PLP)- dependent transferases

292

superfamily protein

293

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S8_18224564 8 18224564 9.72E-07 0.43 1391 0.09 0.10 0.010 GRMZM2G107696 (ATUBP14,PER1,TTN6,UBP1 4): ubiquitin-specific

protease 14 S8_18349921 8 18349921 5.03E-05 0.10 1391 0.09 0.10 0.038 GRMZM2G144464 Eukaryotic aspartyl

protease family protein S8_18349921 8 18349921 5.03E-05 0.10 1391 0.09 0.10 0.038 GRMZM2G570006 (RUXF): small nuclear

ribonucleoprotein F S8_18349964 8 18349964 1.31E-05 0.06 1391 0.09 0.10 0.027 GRMZM2G144464 Eukaryotic aspartyl

protease family protein S8_18349964 8 18349964 1.31E-05 0.06 1391 0.09 0.10 0.027 GRMZM2G570006 (RUXF): small nuclear

ribonucleoprotein F S8_18782460 8 18782460 2.81E-05 0.13 1391 0.09 0.10 0.033 GRMZM2G365983 Enhancer of polycomb-like

transcription factor protein S8_18894973 8 18894973 2.38E-05 0.10 1391 0.09 0.10 0.032 GRMZM2G088356 Serinc-domain containing serine and sphingolipid

biosynthesis protein S8_18895000 8 18895000 2.38E-05 0.10 1391 0.09 0.10 0.032 GRMZM2G088356 Serinc-domain containing serine and sphingolipid

biosynthesis protein S8_116858220 8 116858220 1.47E-05 0.22 1391 0.09 0.10 0.028 GRMZM5G883149 SNARE-like superfamily

protein S8_116858220 8 116858220 1.47E-05 0.22 1391 0.09 0.10 0.028 GRMZM2G336908 DHBP synthase RibB-like alpha/beta domain;GTP

cyclohydrolase II S8_116858220 8 116858220 1.47E-05 0.22 1391 0.09 0.10 0.028 GRMZM2G035202 Protein-tyrosine

phosphatase-like, PTPLA S8_117071209 8 117071209 7.59E-05 0.30 1391 0.09 0.10 0.046 GRMZM2G178803 harpin-induced protein 1 domain containing protein,

expressed

293

294

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S8_117074103 8 117074103 2.00E-05 0.30 1391 0.09 0.10 0.030 GRMZM2G178803 harpin-induced protein 1 domain containing protein,

expressed S8_117162784 8 117162784 3.37E-05 0.27 1391 0.09 0.10 0.034 GRMZM2G390400 SAC3/GANP/Nin1/mts3/eIF-

3 p25 family S8_117298330 8 117298330 1.14E-05 0.48 1391 0.09 0.10 0.026 GRMZM2G095905 Tudor/PWWP/MBT

superfamily protein S8_117433926 8 117433926 1.41E-05 0.34 1391 0.09 0.10 0.027 GRMZM2G422641 Kinase interacting (KIP1-

like) family protein S8_117433926 8 117433926 1.41E-05 0.34 1391 0.09 0.10 0.027 AC206698.2_FG00 zinc knuckle family protein,

2 expressed S8_117433929 8 117433929 1.41E-05 0.34 1391 0.09 0.10 0.027 GRMZM2G422641 Kinase interacting (KIP1-

like) family protein S8_117433929 8 117433929 1.41E-05 0.34 1391 0.09 0.10 0.027 AC206698.2_FG00 zinc knuckle family protein,

2 expressed S8_117433935 8 117433935 1.41E-05 0.34 1391 0.09 0.10 0.027 GRMZM2G422641 Kinase interacting (KIP1-

like) family protein S8_117433935 8 117433935 1.41E-05 0.34 1391 0.09 0.10 0.027 AC206698.2_FG00 zinc knuckle family protein,

2 expressed S8_118009048 8 118009048 8.26E-05 0.30 1391 0.09 0.10 0.046 GRMZM2G179728 GDSL-like Lipase/Acylhydrolase

superfamily protein S8_118009048 8 118009048 8.26E-05 0.30 1391 0.09 0.10 0.046 GRMZM2G173874 (SELT): SELT-like protein

precursor S8_120146282 8 120146282 6.04E-05 0.30 1391 0.09 0.10 0.042 GRMZM2G080731 (BZIP45,TGA6): TGACG

motif-binding factor 6 S8_120146282 8 120146282 6.04E-05 0.30 1391 0.09 0.10 0.042 GRMZM2G036980 VQ domain containing

protein, putative, expressed S8_120146298 8 120146298 7.03E-05 0.31 1391 0.09 0.10 0.044 GRMZM2G080731 (BZIP45,TGA6): TGACG

294

motif-binding factor 6

295

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S8_120146298 8 120146298 7.03E-05 0.31 1391 0.09 0.10 0.044 GRMZM2G036980 VQ domain containing

protein, putative, expressed S8_120149919 8 120149919 9.46E-05 0.36 1391 0.09 0.10 0.050 GRMZM2G036980 VQ domain containing

protein, putative, expressed S8_120218638 8 120218638 2.08E-05 0.33 1391 0.09 0.10 0.030 GRMZM2G025459 (AKINBETA1): 5\'-AMP- activated protein kinase

beta-2 subunit protein S8_121895690 8 121895690 3.97E-06 0.48 1391 0.09 0.10 0.016 GRMZM2G384755 (ARK3,RK3): receptor kinase

3 S8_121895690 8 121895690 3.97E-06 0.48 1391 0.09 0.10 0.016 GRMZM2G082792 (FQR1): flavodoxin-like

quinone reductase 1 S8_121895915 8 121895915 2.94E-05 0.40 1391 0.09 0.10 0.033 GRMZM2G384755 (ARK3,RK3): receptor kinase

3 S8_121895915 8 121895915 2.94E-05 0.40 1391 0.09 0.10 0.033 GRMZM2G082792 (FQR1): flavodoxin-like

quinone reductase 1 S8_122031304 8 122031304 3.81E-05 0.34 1391 0.09 0.10 0.035 GRMZM2G402137 (ATNAF1,NAF1): nuclear

assembly factor 1

S8_122031304 8 122031304 3.81E-05 0.34 1391 0.09 0.10 0.035 GRMZM2G100809 (SC3): secretory carrier 3 S8_124464545 8 124464545 1.78E-05 0.05 1391 0.09 0.10 0.029 GRMZM2G173700 P-loop nucleoside triphosphate hydrolases superfamily protein with CH (Calponin Homology)

domain S8_131779375 8 131779375 1.07E-05 0.17 1391 0.09 0.10 0.025 AC214648.3_FG00 (LBD11): LOB domain-

5 containing protein 11

S8_131779375 8 131779375 1.07E-05 0.17 1391 0.09 0.10 0.025 GRMZM2G700662 GTP binding S8_131782523 8 131782523 5.48E-05 0.19 1391 0.09 0.10 0.040 AC214648.3_FG00 (LBD11): LOB domain-

5 containing protein 11

295 S8_131782523 8 131782523 5.48E-05 0.19 1391 0.09 0.10 0.040 GRMZM2G700662 GTP binding

296

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S8_131782839 8 131782839 2.75E-06 0.18 1391 0.09 0.10 0.013 AC214648.3_FG00 (LBD11): LOB domain-

5 containing protein 11

S8_131782839 8 131782839 2.75E-06 0.18 1391 0.09 0.10 0.013 GRMZM2G700662 GTP binding S8_135455561 8 135455561 2.22E-05 0.29 1391 0.09 0.10 0.031 GRMZM2G363429 (CYP722A1): cytochrome P450, family 722, subfamily

A, polypeptide 1 S8_135455561 8 135455561 2.22E-05 0.29 1391 0.09 0.10 0.031 GRMZM2G363460 (ATPEX14,PED2,PEX14):

peroxin 14 S8_136092219 8 136092219 1.82E-05 0.28 1391 0.09 0.10 0.029 GRMZM2G088132 (ATVDAC1,VDAC1): voltage

dependent anion channel 1 S8_137974581 8 137974581 8.99E-05 0.06 1391 0.09 0.10 0.048 GRMZM2G081653 rossmann fold nucleotide- binding protein involved in DNA uptake, putative,

expressed S8_140007509 8 140007509 9.56E-05 0.39 1391 0.09 0.10 0.050 GRMZM5G852378 (QKY): C2 calcium/lipid- binding plant phosphoribosyltransferase

family protein S8_141909884 8 141909884 4.26E-05 0.21 1391 0.09 0.10 0.037 GRMZM2G065829 myb-like transcription

factor family protein S8_141909905 8 141909905 4.26E-05 0.21 1391 0.09 0.10 0.037 GRMZM2G065829 myb-like transcription

factor family protein

S8_141928387 8 141928387 8.59E-05 0.47 1391 0.09 0.10 0.047 GRMZM2G044343 C3HC zinc finger-like S8_144538753 8 144538753 4.89E-05 0.14 1391 0.09 0.10 0.038 GRMZM2G052844 Pectin lyase-like

superfamily protein S8_145601959 8 145601959 6.83E-05 0.16 1391 0.09 0.10 0.044 GRMZM2G102318 (CYP72A9): cytochrome P450, family 72, subfamily

A, polypeptide 9

296

297

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S8_145607484 8 145607484 2.77E-05 0.09 1391 0.09 0.10 0.033 GRMZM2G102318 (CYP72A9): cytochrome P450, family 72, subfamily

A, polypeptide 9 S8_145607484 8 145607484 2.77E-05 0.09 1391 0.09 0.10 0.033 GRMZM2G056247 (CYP72A15): cytochrome P450, family 72, subfamily

A, polypeptide 15 S8_145684083 8 145684083 7.74E-05 0.21 1391 0.09 0.10 0.046 GRMZM2G021436 (CYP72A15): cytochrome P450, family 72, subfamily

A, polypeptide 15 S8_145684083 8 145684083 7.74E-05 0.21 1391 0.09 0.10 0.046 AC199439.4_FG00 (BIP1): heat shock protein

5 70 (Hsp 70) family protein S8_145846703 8 145846703 1.73E-05 0.13 1391 0.09 0.10 0.029 GRMZM2G131315 (scpl50): serine

carboxypeptidase-like 50 S8_145846703 8 145846703 1.73E-05 0.13 1391 0.09 0.10 0.029 GRMZM2G131334 (ATMPK20,MPK20): MAP

kinase 20 S8_146038333 8 146038333 1.06E-05 0.44 1391 0.09 0.10 0.025 GRMZM2G017386 Protein kinase superfamily

protein S8_146155471 8 146155471 8.88E-05 0.40 1391 0.09 0.10 0.048 GRMZM2G070913 (ATPE11,PE11):

pectinesterase 11 S8_146155471 8 146155471 8.88E-05 0.40 1391 0.09 0.10 0.048 GRMZM2G070837 AMP-dependent synthetase

and ligase family protein S8_148135413 8 148135413 3.08E-05 0.15 1391 0.09 0.10 0.033 GRMZM2G151542 (CRF4): cytokinin response

factor 4

S8_148482585 8 148482585 5.46E-05 0.12 1391 0.09 0.10 0.040 GRMZM2G540589 PNAS-3 related S8_148482585 8 148482585 5.46E-05 0.12 1391 0.09 0.10 0.040 GRMZM2G098973 Phosphoglycerate mutase

family protein

S8_148482647 8 148482647 2.91E-05 0.12 1391 0.09 0.10 0.033 GRMZM2G540589 PNAS-3 related S8_148482647 8 148482647 2.91E-05 0.12 1391 0.09 0.10 0.033 GRMZM2G098973 Phosphoglycerate mutase

297 family protein

S8_148482696 8 148482696 2.21E-05 0.11 1391 0.09 0.10 0.031 GRMZM2G540589 PNAS-3 related

298

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S8_148482696 8 148482696 2.21E-05 0.11 1391 0.09 0.10 0.031 GRMZM2G098973 Phosphoglycerate mutase

family protein

S8_148482717 8 148482717 2.21E-05 0.11 1391 0.09 0.10 0.031 GRMZM2G540589 PNAS-3 related S8_148482717 8 148482717 2.21E-05 0.11 1391 0.09 0.10 0.031 GRMZM2G098973 Phosphoglycerate mutase

family protein

S8_148482731 8 148482731 2.21E-05 0.11 1391 0.09 0.10 0.031 GRMZM2G540589 PNAS-3 related S8_148482731 8 148482731 2.21E-05 0.11 1391 0.09 0.10 0.031 GRMZM2G098973 Phosphoglycerate mutase

family protein S8_148676320 8 148676320 1.25E-05 0.18 1391 0.09 0.10 0.027 GRMZM2G130586 Kinase-related protein of unknown function

(DUF1296) S8_148898590 8 148898590 2.19E-06 0.10 1391 0.09 0.10 0.012 GRMZM2G002297 Magnesium transporter

CorA-like family protein S8_148898667 8 148898667 1.57E-05 0.11 1391 0.09 0.10 0.028 GRMZM2G002297 Magnesium transporter

CorA-like family protein S8_148905557 8 148905557 2.60E-06 0.19 1391 0.09 0.10 0.013 GRMZM2G002297 Magnesium transporter

CorA-like family protein S8_148905809 8 148905809 7.89E-07 0.18 1391 0.09 0.10 0.010 GRMZM2G002297 Magnesium transporter

CorA-like family protein S8_149037561 8 149037561 3.21E-05 0.15 1391 0.09 0.10 0.033 GRMZM2G178346 pfkB-like carbohydrate

kinase family protein S8_149037561 8 149037561 3.21E-05 0.15 1391 0.09 0.10 0.033 GRMZM2G007630 pfkB-like carbohydrate

kinase family protein S8_149037561 8 149037561 3.21E-05 0.15 1391 0.09 0.10 0.033 GRMZM2G007848 (ATMPK20,MPK20): MAP

kinase 20 S8_149039837 8 149039837 6.56E-05 0.17 1391 0.09 0.10 0.043 GRMZM2G178346 pfkB-like carbohydrate

kinase family protein S8_149039837 8 149039837 6.56E-05 0.17 1391 0.09 0.10 0.043 GRMZM2G007630 pfkB-like carbohydrate

298 kinase family protein

299

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S8_149039837 8 149039837 6.56E-05 0.17 1391 0.09 0.10 0.043 GRMZM2G007848 (ATMPK20,MPK20): MAP

kinase 20 S8_149040647 8 149040647 1.39E-05 0.23 1391 0.09 0.10 0.027 GRMZM2G178346 pfkB-like carbohydrate

kinase family protein S8_149040647 8 149040647 1.39E-05 0.23 1391 0.09 0.10 0.027 GRMZM2G007630 pfkB-like carbohydrate

kinase family protein S8_149040647 8 149040647 1.39E-05 0.23 1391 0.09 0.10 0.027 GRMZM2G007848 (ATMPK20,MPK20): MAP

kinase 20 S8_149078078 8 149078078 1.34E-05 0.14 1391 0.09 0.10 0.027 GRMZM5G812272 (ATWRKY71,WRKY71): WRKY DNA-binding protein

71 S8_150011108 8 150011108 6.97E-06 0.50 1391 0.09 0.10 0.021 GRMZM2G115828 (UBC13B,UBC36): ubiquitin-

conjugating enzyme 36 S8_150011108 8 150011108 6.97E-06 0.50 1391 0.09 0.10 0.021 GRMZM2G115766 P-loop containing nucleoside triphosphate hydrolases superfamily

protein S8_150574712 8 150574712 4.19E-06 0.35 1391 0.09 0.10 0.016 GRMZM2G163843 (ANAC009,FEZ): NAC (No Apical Meristem) domain transcriptional regulator

superfamily protein S8_150574712 8 150574712 4.19E-06 0.35 1391 0.09 0.10 0.016 GRMZM2G163848 (IAA8): indoleacetic acid-

induced protein 8 S8_150574712 8 150574712 4.19E-06 0.35 1391 0.09 0.10 0.016 GRMZM2G163841 (ANAC059,ATNAC3,NAC3): NAC domain containing

protein 3 S8_150574713 8 150574713 4.19E-06 0.35 1391 0.09 0.10 0.016 GRMZM2G163843 (ANAC009,FEZ): NAC (No Apical Meristem) domain transcriptional regulator

299

superfamily protein

300

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S8_150574713 8 150574713 4.19E-06 0.35 1391 0.09 0.10 0.016 GRMZM2G163848 (IAA8): indoleacetic acid-

induced protein 8 S8_150574713 8 150574713 4.19E-06 0.35 1391 0.09 0.10 0.016 GRMZM2G163841 (ANAC059,ATNAC3,NAC3): NAC domain containing

protein 3 S8_151221458 8 151221458 6.47E-05 0.20 1391 0.09 0.10 0.043 GRMZM2G077054 (GLT1): NADH-dependent

glutamate synthase 1 S8_151221492 8 151221492 6.47E-05 0.20 1391 0.09 0.10 0.043 GRMZM2G077054 (GLT1): NADH-dependent

glutamate synthase 1 S8_151270836 8 151270836 2.86E-05 0.22 1391 0.09 0.10 0.033 GRMZM2G017305 (AAA1,ATKTN1,BOT1,ERH3, FRA2,FRC2,FTR,KTN1,LUE1): P-loop containing nucleoside triphosphate hydrolases superfamily

protein S8_151339181 8 151339181 6.76E-05 0.17 1391 0.09 0.10 0.044 GRMZM2G006352 (AtMYB36,MYB36): myb

domain protein 36 S8_151345882 8 151345882 1.61E-06 0.42 1391 0.09 0.10 0.011 GRMZM2G006352 (AtMYB36,MYB36): myb

domain protein 36 S8_151345883 8 151345883 1.97E-06 0.42 1391 0.09 0.10 0.011 GRMZM2G006352 (AtMYB36,MYB36): myb

domain protein 36 S8_151593980 8 151593980 1.93E-06 0.21 1391 0.09 0.10 0.011 GRMZM2G393014 (ATIPT1,IPT1):

isopentenyltransferase 1 S8_151594388 8 151594388 1.73E-05 0.21 1391 0.09 0.10 0.029 GRMZM2G393014 (ATIPT1,IPT1):

isopentenyltransferase 1 S8_151594650 8 151594650 8.40E-06 0.20 1391 0.09 0.10 0.023 GRMZM2G393014 (ATIPT1,IPT1):

isopentenyltransferase 1 S8_151596078 8 151596078 5.89E-05 0.24 1391 0.09 0.10 0.041 GRMZM2G393014 (ATIPT1,IPT1):

isopentenyltransferase 1

300 S8_151658081 8 151658081 3.26E-06 0.19 1391 0.09 0.10 0.015 GRMZM2G085438 alpha/beta-Hydrolases

superfamily protein

301

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S8_151658081 8 151658081 3.26E-06 0.19 1391 0.09 0.10 0.015 GRMZM2G085408 Protein of unknown

function (DUF1639) S8_151659682 8 151659682 2.93E-05 0.24 1391 0.09 0.10 0.033 GRMZM2G085438 alpha/beta-Hydrolases

superfamily protein S8_151659682 8 151659682 2.93E-05 0.24 1391 0.09 0.10 0.033 GRMZM2G085408 Protein of unknown

function (DUF1639) S8_151660149 8 151660149 8.29E-08 0.30 1391 0.09 0.11 0.003 GRMZM2G085438 alpha/beta-Hydrolases

superfamily protein S8_151660149 8 151660149 8.29E-08 0.30 1391 0.09 0.11 0.003 GRMZM2G085408 Protein of unknown

function (DUF1639) S8_151660348 8 151660348 1.79E-06 0.25 1391 0.09 0.10 0.011 GRMZM2G085438 alpha/beta-Hydrolases

superfamily protein S8_151660348 8 151660348 1.79E-06 0.25 1391 0.09 0.10 0.011 GRMZM2G085408 Protein of unknown

function (DUF1639) S8_152048312 8 152048312 2.31E-05 0.47 1391 0.09 0.10 0.032 GRMZM2G451147 (SNC4): suppressor of npr1-

1 constitutive 4 S8_152048315 8 152048315 3.93E-05 0.49 1391 0.09 0.10 0.035 GRMZM2G451147 (SNC4): suppressor of npr1-

1 constitutive 4 S8_152048358 8 152048358 3.93E-05 0.49 1391 0.09 0.10 0.035 GRMZM2G451147 (SNC4): suppressor of npr1-

1 constitutive 4 S8_152112282 8 152112282 4.70E-05 0.19 1391 0.09 0.10 0.037 GRMZM2G164640 Protein kinase superfamily

protein S8_152112282 8 152112282 4.70E-05 0.19 1391 0.09 0.10 0.037 GRMZM2G164612 (SNC4): suppressor of npr1-

1 constitutive 4 S8_152112284 8 152112284 4.70E-05 0.19 1391 0.09 0.10 0.037 GRMZM2G164640 Protein kinase superfamily

protein S8_152112284 8 152112284 4.70E-05 0.19 1391 0.09 0.10 0.037 GRMZM2G164612 (SNC4): suppressor of npr1-

1 constitutive 4 S8_152256263 8 152256263 5.70E-05 0.24 1391 0.09 0.10 0.040 GRMZM2G518717 Calcineurin-like metallo-

301 phosphoesterase

superfamily protein

302

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S8_152256263 8 152256263 5.70E-05 0.24 1391 0.09 0.10 0.040 GRMZM5G843389 RING/U-box superfamily

protein S8_152256291 8 152256291 5.76E-05 0.24 1391 0.09 0.10 0.041 GRMZM2G518717 Calcineurin-like metallo- phosphoesterase

superfamily protein S8_152256291 8 152256291 5.76E-05 0.24 1391 0.09 0.10 0.041 GRMZM5G843389 RING/U-box superfamily

protein S8_152256292 8 152256292 4.43E-05 0.24 1391 0.09 0.10 0.037 GRMZM2G518717 Calcineurin-like metallo- phosphoesterase

superfamily protein S8_152256292 8 152256292 4.43E-05 0.24 1391 0.09 0.10 0.037 GRMZM5G843389 RING/U-box superfamily

protein S8_152769998 8 152769998 1.80E-05 0.46 1391 0.09 0.10 0.029 GRMZM2G395672 (ATMYB5,MYB5): myb

domain protein 5 S8_152769998 8 152769998 1.80E-05 0.46 1391 0.09 0.10 0.029 GRMZM2G094879 AGAP000425-PA, putative,

expressed S8_152900382 8 152900382 6.43E-05 0.45 1391 0.09 0.10 0.043 GRMZM2G126691 SWAP (Suppressor-of- White-APricot)/surp

domain-containing protein S8_153018091 8 153018091 8.24E-05 0.25 1391 0.09 0.10 0.046 GRMZM2G173965 (MAPKKK15): mitogen- activated protein kinase

kinase kinase 15 S8_153018099 8 153018099 8.24E-05 0.25 1391 0.09 0.10 0.046 GRMZM2G173965 (MAPKKK15): mitogen- activated protein kinase

kinase kinase 15 S8_154054055 8 154054055 7.71E-06 0.08 1391 0.09 0.10 0.023 GRMZM2G017305 (AAA1,ATKTN1,BOT1,ERH3, FRA2,FRC2,FTR,KTN1,LUE1): P-loop containing nucleoside triphosphate

302 hydrolases superfamily

protein

303

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation

S8_155897660 8 155897660 3.82E-05 0.08 1391 0.09 0.10 0.035 GRMZM2G061602 (SPA4): SPA1-related 4 S8_155897660 8 155897660 3.82E-05 0.08 1391 0.09 0.10 0.035 GRMZM2G061521 Pollen Ole e 1 allergen and

extensin family protein S8_155968563 8 155968563 6.47E-07 0.33 1391 0.09 0.10 0.010 GRMZM2G144716 NADH:ubiquinone oxidoreductase intermediate-associated

protein 30 S8_155968563 8 155968563 6.47E-07 0.33 1391 0.09 0.10 0.010 GRMZM2G144707 (HVA22F): HVA22-like

protein F S8_155968563 8 155968563 6.47E-07 0.33 1391 0.09 0.10 0.010 GRMZM2G444819 DUF584 domain containing

protein, putative, expressed S8_155968602 8 155968602 9.52E-06 0.35 1391 0.09 0.10 0.024 GRMZM2G144716 NADH:ubiquinone oxidoreductase intermediate-associated

protein 30 S8_155968602 8 155968602 9.52E-06 0.35 1391 0.09 0.10 0.024 GRMZM2G144707 (HVA22F): HVA22-like

protein F S8_155968602 8 155968602 9.52E-06 0.35 1391 0.09 0.10 0.024 GRMZM2G444819 DUF584 domain containing

protein, putative, expressed S8_155984115 8 155984115 4.87E-05 0.32 1391 0.09 0.10 0.038 GRMZM2G144716 NADH:ubiquinone oxidoreductase intermediate-associated protein 30 S8_155984115 8 155984115 4.87E-05 0.32 1391 0.09 0.10 0.038 GRMZM2G144707 (HVA22F): HVA22-like

protein F

S8_155984115 8 155984115 4.87E-05 0.32 1391 0.09 0.10 0.038 GRMZM2G444819 (AtS40-3): AtS40-3

S8_155984115 8 155984115 4.87E-05 0.32 1391 0.09 0.10 0.038 GRMZM2G144701 HVA22, putative, expressed S8_159398650 8 159398650 3.05E-05 0.12 1391 0.09 0.10 0.033 GRMZM2G005170 (VAP27-2): vamp/synaptobrevin- 303

associated protein 27-2

304

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S8_159398650 8 159398650 3.05E-05 0.12 1391 0.09 0.10 0.033 GRMZM2G005290 Eukaryotic aspartyl

protease family protein S8_159398650 8 159398650 3.05E-05 0.12 1391 0.09 0.10 0.033 GRMZM2G303587 Tetratricopeptide repeat (TPR)-like superfamily

protein S8_159398650 8 159398650 3.05E-05 0.12 1391 0.09 0.10 0.033 GRMZM2G005433 (PSB28): photosystem II reaction center PSB28

protein S8_159398650 8 159398650 3.05E-05 0.12 1391 0.09 0.10 0.033 AC198923.4_FG00 classical arabinogalactan 2 protein 26 precursor,

putative, expressed S8_159398651 8 159398651 3.05E-05 0.12 1391 0.09 0.10 0.033 GRMZM2G005170 (VAP27-2): vamp/synaptobrevin-

associated protein 27-2 S8_159398651 8 159398651 3.05E-05 0.12 1391 0.09 0.10 0.033 GRMZM2G005290 Eukaryotic aspartyl

protease family protein S8_159398651 8 159398651 3.05E-05 0.12 1391 0.09 0.10 0.033 GRMZM2G303587 Tetratricopeptide repeat (TPR)-like superfamily

protein S8_159398651 8 159398651 3.05E-05 0.12 1391 0.09 0.10 0.033 GRMZM2G005433 (PSB28): photosystem II reaction center PSB28

protein S8_159398651 8 159398651 3.05E-05 0.12 1391 0.09 0.10 0.033 AC198923.4_FG00 classical arabinogalactan 2 protein 26 precursor,

putative, expressed S8_159704241 8 159704241 1.62E-05 0.31 1391 0.09 0.10 0.028 GRMZM2G423959 (ATRALF1,RALF1,RALFL1):

rapid alkalinization factor 1 S8_159704241 8 159704241 1.62E-05 0.31 1391 0.09 0.10 0.028 GRMZM2G423917 Calcium-dependent lipid- binding (CaLB domain)

304

family protein

305

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S8_159704241 8 159704241 1.62E-05 0.31 1391 0.09 0.10 0.028 GRMZM2G122607 (AtATG18a): Transducin/WD40 repeat-

like superfamily protein S8_159704260 8 159704260 1.62E-05 0.31 1391 0.09 0.10 0.028 GRMZM2G423959 (ATRALF1,RALF1,RALFL1):

rapid alkalinization factor 1 S8_159704260 8 159704260 1.62E-05 0.31 1391 0.09 0.10 0.028 GRMZM2G423917 Calcium-dependent lipid- binding (CaLB domain)

family protein S8_159704260 8 159704260 1.62E-05 0.31 1391 0.09 0.10 0.028 GRMZM2G122607 (AtATG18a): Transducin/WD40 repeat-

like superfamily protein S8_159709705 8 159709705 3.85E-05 0.09 1391 0.09 0.10 0.035 GRMZM2G423959 (ATRALF1,RALF1,RALFL1):

rapid alkalinization factor 1 S8_159709705 8 159709705 3.85E-05 0.09 1391 0.09 0.10 0.035 GRMZM2G423917 Calcium-dependent lipid- binding (CaLB domain)

family protein S8_159709705 8 159709705 3.85E-05 0.09 1391 0.09 0.10 0.035 GRMZM2G122607 (AtATG18a): Transducin/WD40 repeat-

like superfamily protein S8_159709798 8 159709798 9.14E-05 0.07 1391 0.09 0.10 0.049 GRMZM2G423959 (ATRALF1,RALF1,RALFL1):

rapid alkalinization factor 1 S8_159709798 8 159709798 9.14E-05 0.07 1391 0.09 0.10 0.049 GRMZM2G423917 Calcium-dependent lipid- binding (CaLB domain)

family protein S8_159709798 8 159709798 9.14E-05 0.07 1391 0.09 0.10 0.049 GRMZM2G122607 (AtATG18a): Transducin/WD40 repeat-

like superfamily protein S8_159801090 8 159801090 5.48E-05 0.06 1391 0.09 0.10 0.040 GRMZM2G395429 (ATRALF1,RALF1,RALFL1):

rapid alkalinization factor 1

305

306

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S8_159801090 8 159801090 5.48E-05 0.06 1391 0.09 0.10 0.040 GRMZM2G095538 Protein of unknown

function (DUF567) S8_159801090 8 159801090 5.48E-05 0.06 1391 0.09 0.10 0.040 GRMZM2G095510 BTB/POZ domain-containing

protein S8_159801090 8 159801090 5.48E-05 0.06 1391 0.09 0.10 0.040 GRMZM2G095541 DUF567 domain containing

protein, putative, expressed S8_159900209 8 159900209 6.56E-05 0.20 1391 0.09 0.10 0.043 GRMZM2G302074 (CYP89A6): cytochrome P450, family 87, subfamily

A, polypeptide 6 S8_159900209 8 159900209 6.56E-05 0.20 1391 0.09 0.10 0.043 GRMZM2G002315 (AAO3,AOdelta,At- AO3,AtAAO3): abscisic

aldehyde oxidase 3 S8_159900209 8 159900209 6.56E-05 0.20 1391 0.09 0.10 0.043 GRMZM2G002147 ARM repeat superfamily

protein S8_159900209 8 159900209 6.56E-05 0.20 1391 0.09 0.10 0.043 GRMZM2G002304 NAD(P)-binding Rossmann-

fold superfamily protein S8_159900209 8 159900209 6.56E-05 0.20 1391 0.09 0.10 0.043 GRMZM2G302045 heparan-alpha- glucosaminide N- acetyltransferase, putative,

expressed S8_159901017 8 159901017 6.05E-09 0.44 1391 0.09 0.11 0.001 GRMZM2G302074 (CYP89A6): cytochrome P450, family 87, subfamily

A, polypeptide 6 S8_159901017 8 159901017 6.05E-09 0.44 1391 0.09 0.11 0.001 GRMZM2G002315 (AAO3,AOdelta,At- AO3,AtAAO3): abscisic

aldehyde oxidase 3 S8_159901017 8 159901017 6.05E-09 0.44 1391 0.09 0.11 0.001 GRMZM2G002147 ARM repeat superfamily

protein S8_159901017 8 159901017 6.05E-09 0.44 1391 0.09 0.11 0.001 GRMZM2G002304 NAD(P)-binding Rossmann-

306

fold superfamily protein

307

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S8_159901017 8 159901017 6.05E-09 0.44 1391 0.09 0.11 0.001 GRMZM2G302045 heparan-alpha- glucosaminide N- acetyltransferase, putative,

expressed S8_159901047 8 159901047 5.23E-06 0.19 1391 0.09 0.10 0.018 GRMZM2G302074 (CYP89A6): cytochrome P450, family 87, subfamily

A, polypeptide 6 S8_159901047 8 159901047 5.23E-06 0.19 1391 0.09 0.10 0.018 GRMZM2G002315 (AAO3,AOdelta,At- AO3,AtAAO3): abscisic

aldehyde oxidase 3 S8_159901047 8 159901047 5.23E-06 0.19 1391 0.09 0.10 0.018 GRMZM2G002147 ARM repeat superfamily

protein S8_159901047 8 159901047 5.23E-06 0.19 1391 0.09 0.10 0.018 GRMZM2G002304 NAD(P)-binding Rossmann-

fold superfamily protein S8_159901047 8 159901047 5.23E-06 0.19 1391 0.09 0.10 0.018 GRMZM2G302045 heparan-alpha- glucosaminide N- acetyltransferase, putative,

expressed S8_161081093 8 161081093 1.54E-05 0.13 1391 0.09 0.10 0.028 GRMZM2G145280 (ATBBC1,BBC1,RSU2):

breast basic conserved 1 S8_161081093 8 161081093 1.54E-05 0.13 1391 0.09 0.10 0.028 GRMZM2G145496 (RPL27): ribosomal protein

large subunit 27 S8_161081098 8 161081098 2.36E-05 0.13 1391 0.09 0.10 0.032 GRMZM2G145280 (ATBBC1,BBC1,RSU2):

breast basic conserved 1 S8_161081098 8 161081098 2.36E-05 0.13 1391 0.09 0.10 0.032 GRMZM2G145496 (RPL27): ribosomal protein

large subunit 27 S8_161106966 8 161106966 4.34E-06 0.29 1391 0.09 0.10 0.016 GRMZM2G064954 Galactose oxidase/kelch

repeat superfamily protein S8_161106966 8 161106966 4.34E-06 0.29 1391 0.09 0.10 0.016 GRMZM2G064933 NOP56-like pre RNA

307 processing

ribonucleoprotein

308

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S8_161109256 8 161109256 2.56E-06 0.27 1391 0.09 0.10 0.013 GRMZM2G064954 Galactose oxidase/kelch

repeat superfamily protein S8_161109256 8 161109256 2.56E-06 0.27 1391 0.09 0.10 0.013 GRMZM2G064933 NOP56-like pre RNA processing

ribonucleoprotein S8_161109334 8 161109334 4.82E-05 0.48 1391 0.09 0.10 0.038 GRMZM2G064954 Galactose oxidase/kelch

repeat superfamily protein S8_161109334 8 161109334 4.82E-05 0.48 1391 0.09 0.10 0.038 GRMZM2G064933 NOP56-like pre RNA processing

ribonucleoprotein S8_161109338 8 161109338 6.37E-05 0.48 1391 0.09 0.10 0.042 GRMZM2G064954 Galactose oxidase/kelch

repeat superfamily protein S8_161109338 8 161109338 6.37E-05 0.48 1391 0.09 0.10 0.042 GRMZM2G064933 NOP56-like pre RNA processing

ribonucleoprotein S8_161109341 8 161109341 6.37E-05 0.48 1391 0.09 0.10 0.042 GRMZM2G064954 Galactose oxidase/kelch

repeat superfamily protein S8_161109341 8 161109341 6.37E-05 0.48 1391 0.09 0.10 0.042 GRMZM2G064933 NOP56-like pre RNA processing

ribonucleoprotein S8_161109388 8 161109388 9.22E-05 0.48 1391 0.09 0.10 0.049 GRMZM2G064954 Galactose oxidase/kelch

repeat superfamily protein S8_161109388 8 161109388 9.22E-05 0.48 1391 0.09 0.10 0.049 GRMZM2G064933 NOP56-like pre RNA processing

ribonucleoprotein S8_161109437 8 161109437 3.36E-05 0.47 1391 0.09 0.10 0.034 GRMZM2G064954 Galactose oxidase/kelch

repeat superfamily protein S8_161109437 8 161109437 3.36E-05 0.47 1391 0.09 0.10 0.034 GRMZM2G064933 NOP56-like pre RNA processing

308

ribonucleoprotein

309

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation

S8_161189906 8 161189906 9.95E-07 0.31 1391 0.09 0.10 0.010 GRMZM2G461793 MAK16 protein-related S8_161189906 8 161189906 9.95E-07 0.31 1391 0.09 0.10 0.010 GRMZM2G160791 Tetratricopeptide repeat (TPR)-like superfamily

protein

S8_161189914 8 161189914 2.80E-07 0.25 1391 0.09 0.10 0.006 GRMZM2G461793 MAK16 protein-related S8_161189914 8 161189914 2.80E-07 0.25 1391 0.09 0.10 0.006 GRMZM2G160791 Tetratricopeptide repeat (TPR)-like superfamily

protein

S8_161189985 8 161189985 2.06E-05 0.46 1391 0.09 0.10 0.030 GRMZM2G461793 MAK16 protein-related S8_161189985 8 161189985 2.06E-05 0.46 1391 0.09 0.10 0.030 GRMZM2G160791 Tetratricopeptide repeat (TPR)-like superfamily

protein

S8_161190126 8 161190126 2.34E-05 0.48 1391 0.09 0.10 0.032 GRMZM2G461793 MAK16 protein-related S8_161190126 8 161190126 2.34E-05 0.48 1391 0.09 0.10 0.032 GRMZM2G160791 Tetratricopeptide repeat (TPR)-like superfamily

protein

S8_161190176 8 161190176 1.73E-05 0.42 1391 0.09 0.10 0.029 GRMZM2G461793 MAK16 protein-related S8_161190176 8 161190176 1.73E-05 0.42 1391 0.09 0.10 0.029 GRMZM2G160791 Tetratricopeptide repeat (TPR)-like superfamily

protein

S8_161190207 8 161190207 6.13E-05 0.48 1391 0.09 0.10 0.042 GRMZM2G461793 MAK16 protein-related S8_161190207 8 161190207 6.13E-05 0.48 1391 0.09 0.10 0.042 GRMZM2G160791 Tetratricopeptide repeat (TPR)-like superfamily

protein

S8_161191820 8 161191820 6.44E-06 0.43 1391 0.09 0.10 0.020 GRMZM2G461793 MAK16 protein-related S8_161191820 8 161191820 6.44E-06 0.43 1391 0.09 0.10 0.020 GRMZM2G160791 Tetratricopeptide repeat (TPR)-like superfamily

309

protein

310

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S8_161725980 8 161725980 4.88E-05 0.42 1391 0.09 0.10 0.038 GRMZM2G481052 Nucleotide-diphospho- sugar transferase family

protein S8_161725980 8 161725980 4.88E-05 0.42 1391 0.09 0.10 0.038 GRMZM2G180330 regulatory protein,

putative, expressed S8_170287066 8 170287066 4.29E-05 0.38 1391 0.09 0.10 0.037 GRMZM2G140822 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase

superfamily protein S8_170287066 8 170287066 4.29E-05 0.38 1391 0.09 0.10 0.037 GRMZM2G140837 Endoplasmic reticulum

vesicle transporter protein S8_170287066 8 170287066 4.29E-05 0.38 1391 0.09 0.10 0.037 GRMZM2G440125 RING/U-box superfamily

protein S8_170287066 8 170287066 4.29E-05 0.38 1391 0.09 0.10 0.037 AC204502.4_FG00 ATOFP3,OFP3): ovate family

6 protein 3 S8_171172962 8 171172962 8.80E-06 0.09 1391 0.09 0.10 0.024 GRMZM2G028054 (ATMYB65,MYB65): myb

domain protein 65 S8_173848889 8 173848889 5.49E-05 0.19 1391 0.09 0.10 0.040 GRMZM2G031607 SGS domain-containing

protein S8_173848889 8 173848889 5.49E-05 0.19 1391 0.09 0.10 0.040 GRMZM2G031724 (ATGA2OX1,GA2OX1): Arabidopsis thaliana

gibberellin 2-oxidase 1

S8_173848889 8 173848889 5.49E-05 0.19 1391 0.09 0.10 0.040 GRMZM2G327427 (PYD2): pyrimidine 2 S9_4651750 9 4651750 4.75E-05 0.07 1391 0.09 0.10 0.037 AC209664.3_FG00 (GAUT8,QUA1): Nucleotide- 2 diphospho-sugar transferases superfamily

protein S9_24366897 9 24366897 6.99E-11 0.22 1391 0.09 0.12 0.000 GRMZM2G069008 (ATNUDT14,ATNUDX14,NU DX14): nudix hydrolase

homolog 14 310

311

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S9_57012019 9 57012019 7.50E-05 0.48 1391 0.09 0.10 0.046 GRMZM2G113203 (ATMRP6,MRP6): multidrug resistance-associated

protein 6 S9_57012525 9 57012525 6.65E-05 0.49 1391 0.09 0.10 0.043 GRMZM2G113203 (ATMRP6,MRP6): multidrug resistance-associated

protein 6 S9_57012530 9 57012530 6.65E-05 0.49 1391 0.09 0.10 0.043 GRMZM2G113203 (ATMRP6,MRP6): multidrug resistance-associated

protein 6 S9_92718497 9 92718497 2.84E-05 0.45 1391 0.09 0.10 0.033 GRMZM5G833760 Protein kinase superfamily

protein S9_126935906 9 126935906 3.75E-05 0.31 1391 0.09 0.10 0.035 GRMZM5G806784 SNARE associated Golgi

protein family S9_126935906 9 126935906 3.75E-05 0.31 1391 0.09 0.10 0.035 GRMZM5G880028 calmodulin-binding family

protein S9_130873209 9 130873209 8.31E-05 0.34 1391 0.09 0.10 0.047 GRMZM2G015280 Peroxidase superfamily

protein S9_130873282 9 130873282 1.84E-05 0.34 1391 0.09 0.10 0.029 GRMZM2G015280 Peroxidase superfamily

protein S9_131523649 9 131523649 8.65E-05 0.12 1391 0.09 0.10 0.047 GRMZM2G027437 PRC-barrel domain protein,

putative, expressed

S9_144614980 9 144614980 4.46E-05 0.24 1391 0.09 0.10 0.037 GRMZM2G177878 (SRO1): similar to RCD one 1 S9_146069298 9 146069298 5.57E-06 0.07 1391 0.09 0.10 0.019 GRMZM2G152919 ARM repeat superfamily

protein S9_149039766 9 149039766 6.88E-05 0.29 1391 0.09 0.10 0.044 GRMZM2G096348 Mitochondrial import inner membrane translocase subunit Tim17/Tim22/Tim23 family

protein 311

312

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S9_149039766 9 149039766 6.88E-05 0.29 1391 0.09 0.10 0.044 GRMZM2G096352 Acyl-CoA N-acyltransferases

(NAT) superfamily protein S9_149039766 9 149039766 6.88E-05 0.29 1391 0.09 0.10 0.044 GRMZM2G057467 Cytochrome b561/ferric reductase transmembrane with DOMON related

domain S9_156413618 9 156413618 7.70E-05 0.47 1391 0.09 0.10 0.046 GRMZM2G168760 (MEE13): myosin heavy

chain-related S10_3182843 10 3182843 2.75E-05 0.17 1391 0.09 0.10 0.033 GRMZM2G058595 (RPT2): Phototropic- responsive NPH3 family

protein S10_3182843 10 3182843 2.75E-05 0.17 1391 0.09 0.10 0.033 GRMZM2G058531 Phototropic-responsive

NPH3 family protein S10_9537289 10 9537289 2.52E-05 0.39 1391 0.09 0.10 0.032 GRMZM2G028432 (AVA-P4): vacuolar H+- pumping ATPase 16 kDa

proteolipid subunit 4 S10_9537289 10 9537289 2.52E-05 0.39 1391 0.09 0.10 0.032 GRMZM2G324131 (GATA12): GATA

transcription factor 12 S10_9598175 10 9598175 1.86E-05 0.12 1391 0.09 0.10 0.029 GRMZM2G142019 Plant protein of unknown

function (DUF869) S10_9598175 10 9598175 1.86E-05 0.12 1391 0.09 0.10 0.029 GRMZM2G443495 (AtFAAH,FAAH): fatty acid

amide hydrolase S10_9598419 10 9598419 1.07E-06 0.39 1391 0.09 0.10 0.010 GRMZM2G142019 Plant protein of unknown

function (DUF869) S10_9598419 10 9598419 1.07E-06 0.39 1391 0.09 0.10 0.010 GRMZM2G443495 (AtFAAH,FAAH): fatty acid

amide hydrolase S10_10668188 10 10668188 6.28E-06 0.46 1391 0.09 0.10 0.020 GRMZM2G319435 Transducin/WD40 repeat-

like superfamily protein S10_10669561 10 10669561 2.72E-06 0.45 1391 0.09 0.10 0.013 GRMZM2G319435 Transducin/WD40 repeat-

312

like superfamily protein

313

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S10_10829311 10 10829311 7.63E-06 0.47 1391 0.09 0.10 0.023 GRMZM5G803992 (NRPB10,NRPD10,NRPE10): RNA polymerases N / 8 kDa

subunit S10_10829311 10 10829311 7.63E-06 0.47 1391 0.09 0.10 0.023 GRMZM2G418432 Protein kinase protein with adenine nucleotide alpha

hydrolases-like domain S10_10829400 10 10829400 2.96E-05 0.28 1391 0.09 0.10 0.033 GRMZM5G803992 (NRPB10,NRPD10,NRPE10): RNA polymerases N / 8 kDa

subunit S10_10829400 10 10829400 2.96E-05 0.28 1391 0.09 0.10 0.033 GRMZM2G418432 Protein kinase protein with adenine nucleotide alpha

hydrolases-like domain S10_11315679 10 11315679 5.56E-05 0.50 1391 0.09 0.10 0.040 GRMZM2G157168 (AAP3,ATAAP3): amino acid

permease 3 S10_14910839 10 14910839 1.62E-05 0.09 1391 0.09 0.10 0.028 GRMZM2G027522 (TPD1): tapetum

determinant 1 S10_77109259 10 77109259 1.31E-05 0.47 1391 0.09 0.10 0.027 GRMZM2G171236 NADH-ubiquinone

oxidoreductase-related S10_77109259 10 77109259 1.31E-05 0.47 1391 0.09 0.10 0.027 GRMZM2G171229 (ATCCT2,CCT2): phosphorylcholine

cytidylyltransferase2 S10_77109259 10 77109259 1.31E-05 0.47 1391 0.09 0.10 0.027 GRMZM2G171187 DNAJ heat shock family

protein S10_77109275 10 77109275 6.78E-05 0.33 1391 0.09 0.10 0.044 GRMZM2G171236 NADH-ubiquinone

oxidoreductase-related S10_77109275 10 77109275 6.78E-05 0.33 1391 0.09 0.10 0.044 GRMZM2G171229 (ATCCT2,CCT2): phosphorylcholine

cytidylyltransferase2 S10_77109275 10 77109275 6.78E-05 0.33 1391 0.09 0.10 0.044 GRMZM2G171187 DNAJ heat shock family

313

protein

314

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 6800 SNP Chr Position P.value maf obs w/o SNP SNP P-values Bp of SNP Annotation S10_146474711 10 146474711 8.06E-05 0.07 1391 0.09 0.10 0.046 GRMZM2G098290 (ATGSL1,GLN2,GS2):

glutamine synthetase 1 S10_147122400 10 147122400 5.14E-05 0.30 1391 0.09 0.10 0.039 GRMZM2G086949 (ARF5,IAA24,MP): Transcriptional factor B3 family protein / auxin- responsive factor AUX/IAA-

related S10_147238446 10 147238446 9.44E-05 0.38 1391 0.09 0.10 0.050 GRMZM2G405662 Heavy metal transport/detoxification

superfamily protein S10_147238446 10 147238446 9.44E-05 0.38 1391 0.09 0.10 0.050 GRMZM2G107620 regulatory protein RecX

family protein S10_147238446 10 147238446 9.44E-05 0.38 1391 0.09 0.10 0.050 GRMZM2G033375 (UCH3): ubiquitin C-

terminal hydrolase 3 S10_147311605 10 147311605 2.10E-05 0.43 1391 0.09 0.10 0.030 GRMZM2G179523 Phosphatidylinositol 3- and

4-kinase family protein S10_147311605 10 147311605 2.10E-05 0.43 1391 0.09 0.10 0.030 GRMZM2G179532 Galactose oxidase/kelch

repeat superfamily protein

S10_148423385 10 148423385 1.00E-05 0.11 1391 0.09 0.10 0.025 GRMZM2G142820 Tetraspanin family protein

S10_148423385 10 148423385 1.00E-05 0.11 1391 0.09 0.10 0.025 GRMZM2G142757 Clathrin light chain protein S10_148423385 10 148423385 1.00E-05 0.11 1391 0.09 0.10 0.025 GRMZM2G142743 N- acetylglucosaminylphospha tidylinositol de-N-acetylase

family protein S10_148423385 10 148423385 1.00E-05 0.11 1391 0.09 0.10 0.025 GRMZM2G142802 Aluminium induced protein

with YGL and LRDR motifs S10_148423385 10 148423385 1.00E-05 0.11 1391 0.09 0.10 0.025 GRMZM2G440259 RING/U-box superfamily

protein

314

315

D-7 Trait VTR4L Candidate Genes

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation

S1_8154097 1 8154097 3.04E-05 0.07 1391 0.23 0.24 0.044 GRMZM2G176397 (ACO3): aconitase 3

S1_8154114 1 8154114 3.04E-05 0.07 1391 0.23 0.24 0.044 GRMZM2G176397 (ACO3): aconitase 3 S1_18977637 1 18977637 2.76E-05 0.05 1391 0.23 0.24 0.042 GRMZM2G148706 RING/U-box superfamily

protein S1_18977637 1 18977637 2.76E-05 0.05 1391 0.23 0.24 0.042 GRMZM2G031177 MATE efflux family

protein

S1_23578479 1 23578479 8.43E-06 0.05 1391 0.23 0.24 0.030 AC205725.3_FG010 (RBL): Noc2p family

S1_23578481 1 23578481 8.43E-06 0.05 1391 0.23 0.24 0.030 AC205725.3_FG010 (RBL): Noc2p family

S1_23579658 1 23579658 1.92E-05 0.18 1391 0.23 0.24 0.037 AC205725.3_FG010 (RBL): Noc2p family

S1_23579660 1 23579660 1.92E-05 0.18 1391 0.23 0.24 0.037 AC205725.3_FG010 (RBL): Noc2p family S1_25154097 1 25154097 2.73E-06 0.06 1391 0.23 0.24 0.028 GRMZM2G376074 (ATUBP26,SUP32,UBP26): ubiquitin-specific protease

26 S1_25164763 1 25164763 3.71E-05 0.05 1391 0.23 0.24 0.047 GRMZM2G077045 (ANAC008,SOG1): NAC (No Apical Meristem) domain transcriptional regulator superfamily

protein S1_25164763 1 25164763 3.71E-05 0.05 1391 0.23 0.24 0.047 GRMZM2G376074 (ATUBP26,SUP32,UBP26): ubiquitin-specific protease

26 S1_27109194 1 27109194 2.92E-05 0.05 1391 0.23 0.24 0.044 GRMZM2G163129 (PSL5,RSW3): Glycosyl hydrolases family 31

protein S1_27109194 1 27109194 2.92E-05 0.05 1391 0.23 0.24 0.044 GRMZM2G163154 MATE efflux family

315

protein

S1_27109194 1 27109194 2.92E-05 0.05 1391 0.23 0.24 0.044 AC208897.3_FG003 myosin-related

316

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S1_28376756 1 28376756 1.76E-05 0.22 1391 0.23 0.24 0.037 GRMZM2G140991 UDP-3-O-acyl N- acetylglycosamine

deacetylase family protein S1_28424547 1 28424547 4.47E-06 0.28 1391 0.23 0.24 0.028 GRMZM2G099797 (ARR2,RR2): response

regulator 2 S1_28424547 1 28424547 4.47E-06 0.28 1391 0.23 0.24 0.028 GRMZM2G397754 Major facilitator

superfamily protein S1_28424548 1 28424548 4.47E-06 0.28 1391 0.23 0.24 0.028 GRMZM2G099797 (ARR2,RR2): response

regulator 2 S1_28424548 1 28424548 4.47E-06 0.28 1391 0.23 0.24 0.028 GRMZM2G397754 Major facilitator

superfamily protein S1_28443725 1 28443725 3.75E-05 0.19 1391 0.23 0.24 0.047 GRMZM2G099860 (ATTPS6,TPS6): UDP- Glycosyltransferase / trehalose-phosphatase

family protein S1_28459164 1 28459164 2.76E-05 0.25 1391 0.23 0.24 0.042 GRMZM2G099860 (ATTPS6,TPS6): UDP- Glycosyltransferase / trehalose-phosphatase

family protein S1_31869243 1 31869243 6.54E-06 0.10 1391 0.23 0.24 0.030 GRMZM2G100714 (MAP65-7): microtubule-

associated protein 65-7 S1_32054015 1 32054015 3.23E-05 0.08 1391 0.23 0.24 0.045 GRMZM2G152477 Calcineurin-like metallo- phosphoesterase

superfamily protein S1_32871017 1 32871017 4.10E-05 0.48 1391 0.23 0.24 0.049 GRMZM2G077942 (ADF5,ATADF5): actin

depolymerizing factor 5 S1_32871037 1 32871037 8.90E-06 0.44 1391 0.23 0.24 0.030 GRMZM2G077942 (ADF5,ATADF5): actin

depolymerizing factor 5 S1_39895751 1 39895751 6.66E-07 0.17 1391 0.23 0.24 0.017 GRMZM2G078164 (DVL11,RTFL8):

316

ROTUNDIFOLIA like 8

317

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S1_39904572 1 39904572 3.76E-05 0.10 1391 0.23 0.24 0.047 GRMZM2G078164 (DVL11,RTFL8):

ROTUNDIFOLIA like 8 S1_41437359 1 41437359 6.88E-06 0.08 1391 0.23 0.24 0.030 GRMZM2G043857 Ankyrin repeat family

protein S1_41437359 1 41437359 6.88E-06 0.08 1391 0.23 0.24 0.030 GRMZM2G043878 receptor-like protein kinase-related family

protein S1_41539340 1 41539340 1.03E-05 0.08 1391 0.23 0.24 0.032 GRMZM2G157329 RNA-binding (RRM/RBD/RNP motifs)

family protein S1_42012957 1 42012957 5.81E-07 0.06 1391 0.23 0.24 0.017 GRMZM2G150729 basic helix-loop-helix (bHLH) DNA-binding

superfamily protein S1_42012968 1 42012968 1.37E-05 0.06 1391 0.23 0.24 0.035 GRMZM2G150729 basic helix-loop-helix (bHLH) DNA-binding

superfamily protein S1_42520440 1 42520440 4.10E-06 0.17 1391 0.23 0.24 0.028 GRMZM2G042107 Ankyrin repeat family

protein S1_42520440 1 42520440 4.10E-06 0.17 1391 0.23 0.24 0.028 GRMZM2G338333 (ITN1): Ankyrin repeat

family protein S1_42520476 1 42520476 4.10E-06 0.17 1391 0.23 0.24 0.028 GRMZM2G042107 Ankyrin repeat family

protein S1_42520476 1 42520476 4.10E-06 0.17 1391 0.23 0.24 0.028 GRMZM2G338333 (ITN1): Ankyrin repeat

family protein S1_42520536 1 42520536 7.71E-06 0.18 1391 0.23 0.24 0.030 GRMZM2G042107 Ankyrin repeat family

protein S1_42520536 1 42520536 7.71E-06 0.18 1391 0.23 0.24 0.030 GRMZM2G338333 (ITN1): Ankyrin repeat

family protein S1_46125691 1 46125691 3.45E-05 0.05 1391 0.23 0.24 0.046 GRMZM2G030016 Ribosomal protein S7e

317

family protein

318

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S1_46125691 1 46125691 3.45E-05 0.05 1391 0.23 0.24 0.046 GRMZM2G032182 Mitochondrial substrate

carrier family protein S1_46125691 1 46125691 3.45E-05 0.05 1391 0.23 0.24 0.046 GRMZM2G029543 catalytics;transferases;[ac yl-carrier-protein] S- malonyltransferases;bindi

ng S1_46125691 1 46125691 3.45E-05 0.05 1391 0.23 0.24 0.046 GRMZM2G032047 DUF538 domain containing protein,

putative, expressed

S1_46842397 1 46842397 5.63E-07 0.12 1391 0.23 0.24 0.017 GRMZM2G010545 PLAC8 family protein S1_46842397 1 46842397 5.63E-07 0.12 1391 0.23 0.24 0.017 GRMZM2G010328 (AGD2): Pyridoxal phosphate (PLP)- dependent transferases

superfamily protein

S1_46842398 1 46842398 5.63E-07 0.12 1391 0.23 0.24 0.017 GRMZM2G010545 PLAC8 family protein S1_46842398 1 46842398 5.63E-07 0.12 1391 0.23 0.24 0.017 GRMZM2G010328 (AGD2): Pyridoxal phosphate (PLP)- dependent transferases

superfamily protein S1_47457464 1 47457464 1.63E-05 0.09 1391 0.23 0.24 0.036 GRMZM2G300692 (GATL7): galacturonosyltransferase

-like 7 S1_48890554 1 48890554 1.39E-05 0.06 1391 0.23 0.24 0.035 GRMZM2G383790 (ATXT1,XT1,XXT1):

xylosyltransferase 1 S1_69541255 1 69541255 4.18E-05 0.06 1391 0.23 0.24 0.049 GRMZM2G111208 (FAB1B): phosphatidylinositol-4- phosphate 5-kinase family

protein

318

319

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S1_77141196 1 77141196 2.45E-05 0.11 1391 0.23 0.24 0.040 GRMZM2G044902 (ASL39,LBD37): LOB domain-containing

protein 37 S1_80952700 1 80952700 1.27E-05 0.06 1391 0.23 0.24 0.034 GRMZM2G434500 Glucose-methanol-choline (GMC) oxidoreductase

family protein

S1_80952700 1 80952700 1.27E-05 0.06 1391 0.23 0.24 0.034 GRMZM2G133968 DNA binding S1_80952700 1 80952700 1.27E-05 0.06 1391 0.23 0.24 0.034 GRMZM2G434514 peptidoglycan-binding LysM domain-containing

protein S1_81776120 1 81776120 2.54E-05 0.07 1391 0.23 0.24 0.040 GRMZM2G044383 (ATGSTU17,ERD9,GST30,G ST30B): Glutathione S-

transferase family protein S1_162464005 1 162464005 3.17E-06 0.34 1391 0.23 0.24 0.028 GRMZM2G476637 (NPY2): Phototropic- responsive NPH3 family

protein S1_170476235 1 170476235 1.52E-05 0.09 1391 0.23 0.24 0.036 GRMZM2G100121 (FBL17): RNI-like

superfamily protein S1_172875668 1 172875668 2.95E-05 0.19 1391 0.23 0.24 0.044 GRMZM5G865967 (PIF4,SRL2): phytochrome

interacting factor 4 S1_172875668 1 172875668 2.95E-05 0.19 1391 0.23 0.24 0.044 GRMZM2G087608 OsFBX436 - F-box domain containing protein,

expressed S1_172903996 1 172903996 1.46E-05 0.25 1391 0.23 0.24 0.035 GRMZM5G852177 Protein kinase superfamily

protein S1_172903996 1 172903996 1.46E-05 0.25 1391 0.23 0.24 0.035 GRMZM2G035444 membrane associated DUF588 domain containing protein,

putative, expressed 319

320

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S1_174284218 1 174284218 8.80E-06 0.46 1391 0.23 0.24 0.030 GRMZM2G118646 (DEG5,DEGP5,HHOA):

DEGP protease 5 S1_174284253 1 174284253 2.55E-05 0.05 1391 0.23 0.24 0.040 GRMZM2G118646 (DEG5,DEGP5,HHOA):

DEGP protease 5 S1_179980108 1 179980108 6.49E-06 0.23 1391 0.23 0.24 0.030 GRMZM2G392791 alpha/beta-Hydrolases

superfamily protein S1_179980108 1 179980108 6.49E-06 0.23 1391 0.23 0.24 0.030 GRMZM2G093809 Leucine-rich repeat transmembrane protein

kinase family protein S1_179980158 1 179980158 5.62E-06 0.23 1391 0.23 0.24 0.030 GRMZM2G392791 alpha/beta-Hydrolases

superfamily protein S1_179980158 1 179980158 5.62E-06 0.23 1391 0.23 0.24 0.030 GRMZM2G093809 Leucine-rich repeat transmembrane protein

kinase family protein S1_179980698 1 179980698 1.27E-05 0.23 1391 0.23 0.24 0.034 GRMZM2G392791 alpha/beta-Hydrolases

superfamily protein S1_179980698 1 179980698 1.27E-05 0.23 1391 0.23 0.24 0.034 GRMZM2G093809 Leucine-rich repeat transmembrane protein

kinase family protein S1_188064698 1 188064698 4.24E-05 0.14 1391 0.23 0.24 0.049 AC234203.1_FG011 (AtEIL3,ATSLIM,EIL3,SLIM 1): ETHYLENE-

INSENSITIVE3-like 3 S1_191604990 1 191604990 3.66E-05 0.13 1391 0.23 0.24 0.047 GRMZM2G040509 (ATBPM1,BPM1): BTB-POZ

and MATH domain 1 S1_195560594 1 195560594 6.68E-06 0.26 1391 0.23 0.24 0.030 GRMZM2G159996 B-box type zinc finger

protein with CCT domain S1_196214395 1 196214395 2.35E-05 0.09 1391 0.23 0.24 0.039 GRMZM2G053027 (RFI2): RING/U-box

superfamily protein S1_196214395 1 196214395 2.35E-05 0.09 1391 0.23 0.24 0.039 GRMZM2G053117 (ATPSAT1,PSAT1):

320 phospholipid sterol acyl

transferase 1

321

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S1_196214395 1 196214395 2.35E-05 0.09 1391 0.23 0.24 0.039 GRMZM2G053231 appr-1-p processing

enzyme family protein S1_196692720 1 196692720 1.55E-05 0.20 1391 0.23 0.24 0.036 GRMZM2G322748 LRR and NB-ARC domains- containing disease

resistance protein S1_196972895 1 196972895 2.83E-06 0.20 1391 0.23 0.24 0.028 GRMZM2G077320 Tetratricopeptide repeat (TPR)-like superfamily

protein S1_200409130 1 200409130 3.46E-05 0.16 1391 0.23 0.24 0.046 GRMZM2G082630 basic helix-loop-helix (bHLH) DNA-binding

superfamily protein S1_200409130 1 200409130 3.46E-05 0.16 1391 0.23 0.24 0.046 GRMZM2G082640 PWWP domain containing

protein, expressed

S1_200412392 1 200412392 2.55E-05 0.18 1391 0.23 0.24 0.040 GRMZM2G082573 transcription regulators S1_200412392 1 200412392 2.55E-05 0.18 1391 0.23 0.24 0.040 GRMZM2G082630 basic helix-loop-helix (bHLH) DNA-binding

superfamily protein S1_200412392 1 200412392 2.55E-05 0.18 1391 0.23 0.24 0.040 GRMZM2G082640 PWWP domain containing

protein, expressed S1_204869927 1 204869927 1.60E-05 0.09 1391 0.23 0.24 0.036 GRMZM2G320689 P-loop containing nucleoside triphosphate hydrolases superfamily

protein S1_204869927 1 204869927 1.60E-05 0.09 1391 0.23 0.24 0.036 GRMZM2G320708 Late embryogenesis abundant (LEA) hydroxyproline-rich

glycoprotein family

S1_204869927 1 204869927 1.60E-05 0.09 1391 0.23 0.24 0.036 GRMZM2G022866 Thioredoxin family protein

321

322

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S1_204871830 1 204871830 6.37E-06 0.10 1391 0.23 0.24 0.030 GRMZM2G320689 P-loop containing nucleoside triphosphate hydrolases superfamily

protein S1_204871830 1 204871830 6.37E-06 0.10 1391 0.23 0.24 0.030 GRMZM2G320708 Late embryogenesis abundant (LEA) hydroxyproline-rich

glycoprotein family

S1_204871830 1 204871830 6.37E-06 0.10 1391 0.23 0.24 0.030 GRMZM2G022866 Thioredoxin family protein S1_204871832 1 204871832 6.37E-06 0.10 1391 0.23 0.24 0.030 GRMZM2G320689 P-loop containing nucleoside triphosphate hydrolases superfamily

protein S1_204871832 1 204871832 6.37E-06 0.10 1391 0.23 0.24 0.030 GRMZM2G320708 Late embryogenesis abundant (LEA) hydroxyproline-rich

glycoprotein family

S1_204871832 1 204871832 6.37E-06 0.10 1391 0.23 0.24 0.030 GRMZM2G022866 Thioredoxin family protein S1_211621970 1 211621970 2.51E-05 0.46 1391 0.23 0.24 0.040 GRMZM2G078569 (FAD6,FADC,SFD4): fatty

acid desaturase 6 S1_213156463 1 213156463 2.90E-06 0.21 1391 0.23 0.24 0.028 GRMZM2G108600 (ATCSLA09,ATCSLA9,CSLA 09,CSLA9,RAT4): Nucleotide-diphospho- sugar transferases

superfamily protein S1_274735370 1 274735370 1.15E-05 0.06 1391 0.23 0.24 0.033 GRMZM2G301089 (BHLH92): basic helix- loop-helix (bHLH) DNA- binding superfamily

322 protein

323

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation

S1_275086548 1 275086548 3.25E-05 0.07 1391 0.23 0.24 0.045 GRMZM2G149775 (HTA11): histone H2A 11 S1_275086548 1 275086548 3.25E-05 0.07 1391 0.23 0.24 0.045 GRMZM2G149952 (APS3): Pseudouridine synthase/archaeosine transglycosylase-like

family protein S1_275086548 1 275086548 3.25E-05 0.07 1391 0.23 0.24 0.045 GRMZM2G149923 (ACAM-1,CAM1,TCH1):

calmodulin 1 S1_275086596 1 275086596 4.76E-06 0.07 1391 0.23 0.24 0.028 GRMZM2G149952 (APS3): Pseudouridine synthase/archaeosine transglycosylase-like

family protein

S1_275086596 1 275086596 4.76E-06 0.07 1391 0.23 0.24 0.028 GRMZM2G149775 (HTA11): histone H2A 11 S1_275086596 1 275086596 4.76E-06 0.07 1391 0.23 0.24 0.028 GRMZM2G149923 (ACAM-1,CAM1,TCH1):

calmodulin 1 S1_285926805 1 285926805 3.88E-05 0.08 1391 0.23 0.24 0.047 GRMZM2G434533 MD-2-related lipid recognition domain- containing protein / ML domain-containing

protein S1_285926805 1 285926805 3.88E-05 0.08 1391 0.23 0.24 0.047 GRMZM2G135011 RING/U-box superfamily

protein S1_285926805 1 285926805 3.88E-05 0.08 1391 0.23 0.24 0.047 GRMZM2G134917 (ATJ2,J2): DNAJ

homologue 2 S1_285926812 1 285926812 3.88E-05 0.08 1391 0.23 0.24 0.047 GRMZM2G434533 MD-2-related lipid recognition domain- containing protein / ML domain-containing

protein

S1_285926812 1 285926812 3.88E-05 0.08 1391 0.23 0.24 0.047 GRMZM2G135011 RING/U-box superfamily 323

protein

324

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S1_285926812 1 285926812 3.88E-05 0.08 1391 0.23 0.24 0.047 GRMZM2G134917 (ATJ2,J2): DNAJ

homologue 2 S1_285926857 1 285926857 3.23E-06 0.07 1391 0.23 0.24 0.028 GRMZM2G434533 MD-2-related lipid recognition domain- containing protein / ML domain-containing

protein S1_285926857 1 285926857 3.23E-06 0.07 1391 0.23 0.24 0.028 GRMZM2G135011 RING/U-box superfamily

protein S1_285926857 1 285926857 3.23E-06 0.07 1391 0.23 0.24 0.028 GRMZM2G134917 (ATJ2,J2): DNAJ

homologue 2 S1_285977854 1 285977854 3.23E-05 0.05 1391 0.23 0.24 0.045 GRMZM2G028926 (ATCPK1,CPK1): calcium dependent protein kinase

1 S1_285977854 1 285977854 3.23E-05 0.05 1391 0.23 0.24 0.045 GRMZM2G329181 (FLA17): FASCICLIN-like arabinogalactan protein

17 precursor S1_295724522 1 295724522 1.21E-05 0.06 1391 0.23 0.24 0.033 GRMZM2G369432 Plant invertase/pectin methylesterase inhibitor

superfamily protein S2_9018813 2 9018813 1.87E-05 0.06 1391 0.23 0.24 0.037 GRMZM2G000039 SIT4 phosphatase-

associated family protein S2_9018813 2 9018813 1.87E-05 0.06 1391 0.23 0.24 0.037 GRMZM2G000047 (ATHAK5,HAK5): high

affinity K+ transporter 5 S2_9018813 2 9018813 1.87E-05 0.06 1391 0.23 0.24 0.037 GRMZM2G000044 RPM1-interacting protein

4 (RIN4) family protein S2_44719146 2 44719146 2.43E-05 0.06 1391 0.23 0.24 0.039 GRMZM2G355906 (GAD2): glutamate

decarboxylase 2 S2_44719146 2 44719146 2.43E-05 0.06 1391 0.23 0.24 0.039 GRMZM2G053985 (ATOFP8,OFP8): ovate

324

family protein 8

325

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S2_168550067 2 168550067 3.10E-05 0.07 1391 0.23 0.24 0.044 GRMZM2G092125 (PIP2;2,PIP2B): plasma membrane intrinsic

protein 2 S2_187131510 2 187131510 2.16E-05 0.06 1391 0.23 0.24 0.039 GRMZM2G085210 Major facilitator

superfamily protein S2_188366566 2 188366566 1.37E-05 0.05 1391 0.23 0.24 0.035 GRMZM2G137532 (AtbZIP3,bZIP3): basic

leucine-zipper 3 S2_188366566 2 188366566 1.37E-05 0.05 1391 0.23 0.24 0.035 GRMZM2G137477 retrotransposon protein, putative, unclassified,

expressed S2_192433107 2 192433107 1.89E-06 0.12 1391 0.23 0.24 0.028 GRMZM2G179031 (DRB2): dsRNA-binding

protein 2 S2_192433107 2 192433107 1.89E-06 0.12 1391 0.23 0.24 0.028 GRMZM2G179002 DHHC-type zinc finger

family protein S2_193881769 2 193881769 3.59E-06 0.05 1391 0.23 0.24 0.028 GRMZM2G107560 (ATMYC2,JAI1,JIN1,MYC2, RD22BP1,ZBF1): Basic helix-loop-helix (bHLH) DNA-binding family

protein S2_193881792 2 193881792 3.59E-06 0.05 1391 0.23 0.24 0.028 GRMZM2G107560 (ATMYC2,JAI1,JIN1,MYC2, RD22BP1,ZBF1): Basic helix-loop-helix (bHLH) DNA-binding family

protein S2_193881799 2 193881799 3.59E-06 0.05 1391 0.23 0.24 0.028 GRMZM2G107560 (ATMYC2,JAI1,JIN1,MYC2, RD22BP1,ZBF1): Basic helix-loop-helix (bHLH) DNA-binding family

protein

325

326

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S2_193881814 2 193881814 3.59E-06 0.05 1391 0.23 0.24 0.028 GRMZM2G107560 (ATMYC2,JAI1,JIN1,MYC2, RD22BP1,ZBF1): Basic helix-loop-helix (bHLH) DNA-binding family

protein S2_194113696 2 194113696 5.85E-06 0.07 1391 0.23 0.24 0.030 GRMZM2G037910 Basic-leucine zipper (bZIP) transcription factor family

protein S2_194937752 2 194937752 2.32E-05 0.05 1391 0.23 0.24 0.039 GRMZM2G368827 (SAG29): senescence-

associated gene 29

S2_197227802 2 197227802 1.57E-05 0.06 1391 0.23 0.24 0.036 GRMZM2G140116 Ribosomal protein L14 S2_197227802 2 197227802 1.57E-05 0.06 1391 0.23 0.24 0.036 GRMZM2G049613 Protein of unknown function (DUF630 and

DUF632) S2_205837144 2 205837144 4.98E-06 0.09 1391 0.23 0.24 0.028 GRMZM2G104516 (ATZFP2,ZFP2): zinc finger

protein 2 S2_206219806 2 206219806 7.58E-06 0.22 1391 0.23 0.24 0.030 GRMZM2G087479 Major facilitator

superfamily protein S2_206219806 2 206219806 7.58E-06 0.22 1391 0.23 0.24 0.030 GRMZM2G087462 GDSL-like Lipase/Acylhydrolase

superfamily protein S2_206219856 2 206219856 7.58E-06 0.22 1391 0.23 0.24 0.030 GRMZM2G087479 Major facilitator

superfamily protein S2_206219856 2 206219856 7.58E-06 0.22 1391 0.23 0.24 0.030 GRMZM2G087462 GDSL-like Lipase/Acylhydrolase

superfamily protein S2_206219945 2 206219945 1.55E-05 0.21 1391 0.23 0.24 0.036 GRMZM2G087479 Major facilitator

superfamily protein

326

327

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S2_206219945 2 206219945 1.55E-05 0.21 1391 0.23 0.24 0.036 GRMZM2G087462 GDSL-like Lipase/Acylhydrolase

superfamily protein S2_213998470 2 213998470 8.93E-07 0.20 1391 0.23 0.24 0.019 GRMZM2G367777 (NSL1): MAC/Perforin domain-containing

protein S2_213998470 2 213998470 8.93E-07 0.20 1391 0.23 0.24 0.019 GRMZM2G322618 Glycoprotein membrane

precursor GPI-anchored S2_213998470 2 213998470 8.93E-07 0.20 1391 0.23 0.24 0.019 GRMZM2G022947 (CYP72A8): cytochrome P450, family 72, subfamily

A, polypeptide 8

S3_306174 3 306174 1.83E-07 0.24 1391 0.23 0.24 0.017 GRMZM2G035482 Coatomer epsilon subunit S3_1467296 3 1467296 1.19E-05 0.11 1391 0.23 0.24 0.033 GRMZM2G087804 (ATGLK1,GLK1,GPRI1): GBF\'s pro-rich region-

interacting factor 1 S3_1467296 3 1467296 1.19E-05 0.11 1391 0.23 0.24 0.033 GRMZM2G087714 (NFD6): nuclear fusion

defective 6 S3_1467297 3 1467297 7.80E-06 0.11 1391 0.23 0.24 0.030 GRMZM2G087804 (ATGLK1,GLK1,GPRI1): GBF\'s pro-rich region-

interacting factor 1 S3_1467297 3 1467297 7.80E-06 0.11 1391 0.23 0.24 0.030 GRMZM2G087714 (NFD6): nuclear fusion

defective 6 S3_1468707 3 1468707 1.91E-05 0.45 1391 0.23 0.24 0.037 GRMZM2G087804 (ATGLK1,GLK1,GPRI1): GBF\'s pro-rich region-

interacting factor 1 S3_1468707 3 1468707 1.91E-05 0.45 1391 0.23 0.24 0.037 GRMZM2G087714 (NFD6): nuclear fusion

defective 6 S3_1468710 3 1468710 2.97E-05 0.46 1391 0.23 0.24 0.044 GRMZM2G087804 (ATGLK1,GLK1,GPRI1):

GBF\'s pro-rich region- 327

interacting factor 1

328

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S3_1468710 3 1468710 2.97E-05 0.46 1391 0.23 0.24 0.044 GRMZM2G087714 (NFD6): nuclear fusion

defective 6 S3_1468711 3 1468711 1.91E-05 0.45 1391 0.23 0.24 0.037 GRMZM2G087804 (ATGLK1,GLK1,GPRI1): GBF\'s pro-rich region-

interacting factor 1 S3_1468711 3 1468711 1.91E-05 0.45 1391 0.23 0.24 0.037 GRMZM2G087714 (NFD6): nuclear fusion

defective 6 S3_1468712 3 1468712 1.91E-05 0.45 1391 0.23 0.24 0.037 GRMZM2G087804 (ATGLK1,GLK1,GPRI1): GBF\'s pro-rich region-

interacting factor 1 S3_1468712 3 1468712 1.91E-05 0.45 1391 0.23 0.24 0.037 GRMZM2G087714 (NFD6): nuclear fusion

defective 6 S3_1468713 3 1468713 1.91E-05 0.45 1391 0.23 0.24 0.037 GRMZM2G087804 (ATGLK1,GLK1,GPRI1): GBF\'s pro-rich region-

interacting factor 1 S3_1468713 3 1468713 1.91E-05 0.45 1391 0.23 0.24 0.037 GRMZM2G087714 (NFD6): nuclear fusion

defective 6 S3_1468716 3 1468716 1.91E-05 0.45 1391 0.23 0.24 0.037 GRMZM2G087804 (ATGLK1,GLK1,GPRI1): GBF\'s pro-rich region-

interacting factor 1 S3_1468716 3 1468716 1.91E-05 0.45 1391 0.23 0.24 0.037 GRMZM2G087714 (NFD6): nuclear fusion

defective 6 S3_5850435 3 5850435 7.95E-08 0.09 1391 0.23 0.24 0.010 GRMZM2G470914 Protein kinase superfamily

protein

S3_6002435 3 6002435 1.70E-05 0.38 1391 0.23 0.24 0.037 GRMZM2G077227 (IQD6): IQ-domain 6 S3_6293807 3 6293807 1.07E-05 0.48 1391 0.23 0.24 0.032 GRMZM2G378490 (ADOF1,DOF1): DOF zinc

finger protein 1 S3_6293807 3 6293807 1.07E-05 0.48 1391 0.23 0.24 0.032 GRMZM2G121452 (RPN12a): regulatory

particle non-ATPase 12A 328

329

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S3_6293807 3 6293807 1.07E-05 0.48 1391 0.23 0.24 0.032 GRMZM2G077981 F-box/RNI-like superfamily

protein S3_10284707 3 10284707 4.04E-05 0.14 1391 0.23 0.24 0.048 GRMZM2G118243 (ATPDR4,PDR4): pleiotropic drug

resistance 4 S3_10449787 3 10449787 2.33E-05 0.14 1391 0.23 0.24 0.039 GRMZM2G036340 (ATGA3OX1,GA3OX1,GA4)

: gibberellin 3-oxidase 1 S3_10449805 3 10449805 2.33E-05 0.14 1391 0.23 0.24 0.039 GRMZM2G036340 (ATGA3OX1,GA3OX1,GA4)

: gibberellin 3-oxidase 1 S3_10517929 3 10517929 2.38E-05 0.14 1391 0.23 0.24 0.039 GRMZM5G868061 (BES1,BZR2): Brassinosteroid signalling positive regulator (BZR1)

family protein S3_10517929 3 10517929 2.38E-05 0.14 1391 0.23 0.24 0.039 GRMZM2G348238 Homeodomain-like

superfamily protein S3_10531056 3 10531056 3.89E-05 0.22 1391 0.23 0.24 0.047 GRMZM2G348238 Homeodomain-like

superfamily protein S3_17584320 3 17584320 6.12E-06 0.47 1391 0.23 0.24 0.030 GRMZM2G467242 (ATTSC13,CER10,ECR,TSC1 3): 3-oxo-5-alpha-steroid 4-dehydrogenase family

protein S3_19967649 3 19967649 2.60E-05 0.20 1391 0.23 0.24 0.041 GRMZM2G467671 Protein kinase superfamily

protein S3_20746930 3 20746930 3.88E-05 0.21 1391 0.23 0.24 0.047 GRMZM2G003794 (ATXYN1,RXF12): glycosyl hydrolase family 10 protein / carbohydrate- binding domain-

containing protein

329

330

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S3_20746933 3 20746933 3.88E-05 0.21 1391 0.23 0.24 0.047 GRMZM2G003794 (ATXYN1,RXF12): glycosyl hydrolase family 10 protein / carbohydrate- binding domain-

containing protein S3_26309300 3 26309300 3.60E-06 0.05 1391 0.23 0.24 0.028 GRMZM2G104829 Glycosyltransferase family

61 protein S3_141572234 3 141572234 3.74E-05 0.08 1391 0.23 0.24 0.047 GRMZM2G115812 SAP domain containing

protein, expressed S3_166796168 3 166796168 2.67E-05 0.14 1391 0.23 0.24 0.041 GRMZM2G141632 POEI32 - Pollen Ole e I allergen and extensin family protein precursor,

expressed S3_166796168 3 166796168 2.67E-05 0.14 1391 0.23 0.24 0.041 GRMZM2G141638 (PLT2): Integrase-type DNA-binding superfamily

protein S3_167009322 3 167009322 3.42E-05 0.33 1391 0.23 0.24 0.046 GRMZM2G346132 Protein kinase superfamily

protein S3_167009322 3 167009322 3.42E-05 0.33 1391 0.23 0.24 0.046 GRMZM2G047572 Family of unknown

function (DUF566) S3_167009322 3 167009322 3.42E-05 0.33 1391 0.23 0.24 0.046 GRMZM2G346138 S-adenosyl-L-methionine- dependent methyltransferases

superfamily protein S3_167009322 3 167009322 3.42E-05 0.33 1391 0.23 0.24 0.046 GRMZM2G438045 Ribosomal RNA processing

Brix domain protein S3_167073581 3 167073581 1.64E-05 0.10 1391 0.23 0.24 0.036 GRMZM2G137174 (PLA IIA,PLA2A,PLP2):

phospholipase A 2A S3_167478960 3 167478960 8.86E-07 0.06 1391 0.23 0.24 0.019 GRMZM2G044584 Ribosomal protein L13

330

family protein

331

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S3_167478960 3 167478960 8.86E-07 0.06 1391 0.23 0.24 0.019 GRMZM2G118362 Tetratricopeptide repeat (TPR)-like superfamily

protein S3_167479036 3 167479036 2.01E-05 0.08 1391 0.23 0.24 0.037 GRMZM2G044584 Ribosomal protein L13

family protein S3_167479036 3 167479036 2.01E-05 0.08 1391 0.23 0.24 0.037 GRMZM2G118362 Tetratricopeptide repeat (TPR)-like superfamily

protein S3_184948734 3 184948734 4.80E-07 0.16 1391 0.23 0.24 0.017 GRMZM2G065290 (ATWRKY46,WRKY46): WRKY DNA-binding

protein 46 S3_191777687 3 191777687 2.65E-06 0.39 1391 0.23 0.24 0.028 GRMZM2G093239 Transducin/WD40 repeat-

like superfamily protein S3_191777687 3 191777687 2.65E-06 0.39 1391 0.23 0.24 0.028 GRMZM2G093101 (ATPAP10,PAP10): purple

acid phosphatase 10 S3_199293203 3 199293203 1.95E-05 0.13 1391 0.23 0.24 0.037 GRMZM5G818186 6-phosphogluconate dehydrogenase family

protein S3_199561708 3 199561708 1.53E-05 0.16 1391 0.23 0.24 0.036 GRMZM2G078210 stress-induced protein,

putative, expressed S3_199561708 3 199561708 1.53E-05 0.16 1391 0.23 0.24 0.036 GRMZM5G815165 Peptidase M28 family

protein S3_209904786 3 209904786 7.40E-06 0.48 1391 0.23 0.24 0.030 GRMZM2G346639 Nucleotidyltransferase

family protein S3_224467850 3 224467850 4.03E-06 0.42 1391 0.23 0.24 0.028 GRMZM5G874955 (ABCG40,ATABCG40,ATPD R12,PDR12): pleiotropic

drug resistance 12 S3_224467850 3 224467850 4.03E-06 0.42 1391 0.23 0.24 0.028 GRMZM2G143234 ATP synthase epsilon

chain, mitochondrial

331 S3_225206118 3 225206118 3.36E-05 0.26 1391 0.23 0.24 0.046 GRMZM2G001296 (MEE18): maternal effect

embryo arrest 18

332

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S3_225206145 3 225206145 2.34E-05 0.26 1391 0.23 0.24 0.039 GRMZM2G001296 (MEE18): maternal effect

embryo arrest 18 S4_185864906 4 185864906 3.78E-05 0.06 1391 0.23 0.24 0.047 GRMZM2G071378 Nucleotide-sugar

transporter family protein S4_185864906 4 185864906 3.78E-05 0.06 1391 0.23 0.24 0.047 GRMZM2G071288 Peroxisomal membrane 22 kDa (Mpv17/PMP22)

family protein S4_206079691 4 206079691 1.86E-05 0.07 1391 0.23 0.24 0.037 GRMZM2G046024 (ABCG25,ATABCG25): ATP-binding casette family

G25 S4_208396741 4 208396741 1.57E-05 0.21 1391 0.23 0.24 0.036 GRMZM2G413253 (EMB2778,FKP1,HMGS,M VA1): hydroxymethylglutaryl- CoA synthase / HMG-CoA synthase / 3-hydroxy-3- methylglutaryl coenzyme

A synthase S4_208396741 4 208396741 1.57E-05 0.21 1391 0.23 0.24 0.036 GRMZM2G115245 (EMB2780): DNA binding;nucleotide binding;nucleic acid binding;DNA-directed DNA polymerases;DNA-

directed DNA S4_238297872 4 238297872 4.22E-06 0.26 1391 0.23 0.24 0.028 GRMZM2G061023 (ATRAD1,RAD1,UVH1): Restriction endonuclease, type II-like superfamily

protein

S4_240106489 4 240106489 3.47E-05 0.21 1391 0.23 0.24 0.046 GRMZM2G079348 (CAT1): catalase 1

S4_240106495 4 240106495 3.27E-05 0.22 1391 0.23 0.24 0.045 GRMZM2G079348 (CAT1): catalase 1 332

S4_240106513 4 240106513 2.59E-05 0.28 1391 0.23 0.24 0.041 GRMZM2G079348 (CAT1): catalase 1

333

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S5_2796695 5 2796695 7.49E-06 0.06 1391 0.23 0.24 0.030 GRMZM2G108716 (TFIIS): transcript

elongation factor IIS S5_2796695 5 2796695 7.49E-06 0.06 1391 0.23 0.24 0.030 GRMZM2G108677 RNA-binding KH domain-

containing protein S5_2796695 5 2796695 7.49E-06 0.06 1391 0.23 0.24 0.030 GRMZM5G899149 Ribosomal protein S26e

family protein S5_2796695 5 2796695 7.49E-06 0.06 1391 0.23 0.24 0.030 GRMZM2G108694 (CKI1): Signal transduction

histidine kinase S5_14023517 5 14023517 1.82E-05 0.12 1391 0.23 0.24 0.037 GRMZM2G166099 gp176, putative,

expressed S5_20199715 5 20199715 1.28E-05 0.28 1391 0.23 0.24 0.034 GRMZM2G070523 (ATM1,ATMYB101,MYB10 1): myb domain protein

101 S5_21343857 5 21343857 1.05E-05 0.09 1391 0.23 0.24 0.032 GRMZM5G851862 (CYP76C2): cytochrome P450, family 76, subfamily

C, polypeptide 2 S5_21343857 5 21343857 1.05E-05 0.09 1391 0.23 0.24 0.032 GRMZM5G823318 (AK,AK-LYS1,AK1):

aspartate kinase 1 S5_58135277 5 58135277 1.07E-05 0.14 1391 0.23 0.24 0.032 GRMZM2G083472 myb-like HTH transcriptional regulator

family protein S5_58135277 5 58135277 1.07E-05 0.14 1391 0.23 0.24 0.032 GRMZM2G083515 (ATRING1A,RING1A): RING

1A S5_58135277 5 58135277 1.07E-05 0.14 1391 0.23 0.24 0.032 GRMZM2G076437 transposon protein, putative, Mariner sub-

class, expressed S5_187201430 5 187201430 1.12E-05 0.12 1391 0.23 0.24 0.033 GRMZM2G098474 (ARR4,ATRR1,IBC7,MEE7):

response regulator 4 S5_187201430 5 187201430 1.12E-05 0.12 1391 0.23 0.24 0.033 GRMZM2G398809 ARM repeat superfamily

333

protein

334

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S5_188393532 5 188393532 2.10E-06 0.11 1391 0.23 0.24 0.028 AC198169.4_FG004 (EMB1586,ISE1): P-loop containing nucleoside triphosphate hydrolases superfamily protein S5_188393532 5 188393532 2.10E-06 0.11 1391 0.23 0.24 0.028 GRMZM2G172239 BolA-like family protein S5_189042095 5 189042095 4.07E-05 0.07 1391 0.23 0.24 0.049 GRMZM2G066885 (ACYB-2): Cytochrome b561/ferric reductase transmembrane protein

family

S5_189042095 5 189042095 4.07E-05 0.07 1391 0.23 0.24 0.049 GRMZM2G066997 Remorin family protein S5_211516081 5 211516081 1.71E-05 0.07 1391 0.23 0.24 0.037 GRMZM2G385925 P-loop containing nucleoside triphosphate hydrolases superfamily

protein S5_211731565 5 211731565 1.61E-05 0.36 1391 0.23 0.24 0.036 GRMZM5G893117 (AtGRF5,GRF5): growth-

regulating factor 5 S6_62445041 6 62445041 2.13E-05 0.36 1391 0.23 0.24 0.038 GRMZM2G444845 (ATBAG3,BAG3): BCL-2-

associated athanogene 3 S6_73331053 6 73331053 5.10E-06 0.06 1391 0.23 0.24 0.028 GRMZM5G811212 Lactate/malate dehydrogenase family

protein S6_75619996 6 75619996 2.95E-05 0.06 1391 0.23 0.24 0.044 GRMZM2G351047 Major facilitator

superfamily protein S6_75619996 6 75619996 2.95E-05 0.06 1391 0.23 0.24 0.044 GRMZM5G835276 GDSL-like Lipase/Acylhydrolase

superfamily protein S6_75619996 6 75619996 2.95E-05 0.06 1391 0.23 0.24 0.044 GRMZM5G829897 SGNH hydrolase-type esterase superfamily

334 protein

335

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S6_88983465 6 88983465 4.30E-06 0.38 1391 0.23 0.24 0.028 GRMZM2G139657 O-fucosyltransferase

family protein S6_89067954 6 89067954 2.68E-05 0.10 1391 0.23 0.24 0.041 GRMZM2G089400 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily

protein S6_131141133 6 131141133 3.05E-05 0.07 1391 0.23 0.24 0.044 GRMZM2G051474 (UGT72B3): UDP-glucosyl

transferase 72B3 S6_132888711 6 132888711 3.47E-05 0.06 1391 0.23 0.24 0.046 GRMZM2G030123 basic helix-loop-helix (bHLH) DNA-binding

superfamily protein S6_164689232 6 164689232 2.41E-05 0.05 1391 0.23 0.24 0.039 GRMZM2G022453 Ribosomal protein L18ae

family S6_164689232 6 164689232 2.41E-05 0.05 1391 0.23 0.24 0.039 GRMZM2G023190 F-box/RNI-like superfamily

protein S6_164689232 6 164689232 2.41E-05 0.05 1391 0.23 0.24 0.039 GRMZM2G022619 Ribosomal protein

L18ae/LX family protein S6_164689232 6 164689232 2.41E-05 0.05 1391 0.23 0.24 0.039 GRMZM2G023133 Cytochrome b561/ferric reductase transmembrane

protein family S6_165135369 6 165135369 1.17E-05 0.10 1391 0.23 0.24 0.033 GRMZM2G160460 Major facilitator

superfamily protein S6_165135369 6 165135369 1.17E-05 0.10 1391 0.23 0.24 0.033 GRMZM2G160504 Major facilitator

superfamily protein S6_165151862 6 165151862 9.12E-06 0.05 1391 0.23 0.24 0.030 GRMZM2G160430 Major facilitator

superfamily protein S6_166890758 6 166890758 2.96E-06 0.43 1391 0.23 0.24 0.028 GRMZM2G159016 (scpl50): serine

carboxypeptidase-like 50

335

336

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S6_166890758 6 166890758 2.96E-06 0.43 1391 0.23 0.24 0.028 GRMZM2G158998 Phox-associated domain;Phox-like;Sorting

nexin, C-terminal S6_166890758 6 166890758 2.96E-06 0.43 1391 0.23 0.24 0.028 GRMZM2G458538 O-acetyltransferase family

protein S6_166890758 6 166890758 2.96E-06 0.43 1391 0.23 0.24 0.028 GRMZM2G458448 Late embryogenesis abundant (LEA) hydroxyproline-rich

glycoprotein family S6_166890758 6 166890758 2.96E-06 0.43 1391 0.23 0.24 0.028 GRMZM2G159028 RNA-binding (RRM/RBD/RNP motifs)

family protein S7_922201 7 922201 3.70E-05 0.08 1391 0.23 0.24 0.047 GRMZM2G020104 (ATGLR3.4,GLR3.4,GLUR3)

: glutamate receptor 3.4 S7_922495 7 922495 6.22E-06 0.07 1391 0.23 0.24 0.030 GRMZM2G020104 (ATGLR3.4,GLR3.4,GLUR3)

: glutamate receptor 3.4 S7_1317269 7 1317269 1.94E-05 0.45 1391 0.23 0.24 0.037 GRMZM2G120563 Calcium-dependent lipid- binding (CaLB domain)

family protein S7_1317269 7 1317269 1.94E-05 0.45 1391 0.23 0.24 0.037 GRMZM2G555108 Transducin/WD40 repeat-

like superfamily protein S7_2747413 7 2747413 1.05E-05 0.14 1391 0.23 0.24 0.032 GRMZM5G810231 OsFBL33 - F-box domain and LRR containing

protein, expressed S7_2747427 7 2747427 1.05E-05 0.14 1391 0.23 0.24 0.032 GRMZM5G810231 OsFBL33 - F-box domain and LRR containing

protein, expressed S7_4965889 7 4965889 2.23E-05 0.43 1391 0.23 0.24 0.039 GRMZM2G040090 D-isomer specific 2- hydroxyacid

336 dehydrogenase family

protein

337

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S7_4965889 7 4965889 2.23E-05 0.43 1391 0.23 0.24 0.039 GRMZM2G039922 (HERK2): hercules

receptor kinase 2 S7_8048336 7 8048336 2.96E-05 0.32 1391 0.23 0.24 0.044 GRMZM2G074479 (ATUBC2,UBC2): ubiquiting-conjugating

enzyme 2 S7_8048336 7 8048336 2.96E-05 0.32 1391 0.23 0.24 0.044 GRMZM5G860810 Leucine-rich repeat protein kinase family

protein

S7_118306535 7 118306535 5.84E-06 0.28 1391 0.23 0.24 0.030 GRMZM2G041175 (TET8): tetraspanin8 S7_118306535 7 118306535 5.84E-06 0.28 1391 0.23 0.24 0.030 GRMZM2G040945 HAD-superfamily hydrolase, subfamily IG,

5\'-nucleotidase S7_118306535 7 118306535 5.84E-06 0.28 1391 0.23 0.24 0.030 GRMZM2G339728 retrotransposon protein, putative, unclassified,

expressed

S7_118306577 7 118306577 8.30E-06 0.29 1391 0.23 0.24 0.030 GRMZM2G041175 (TET8): tetraspanin8 S7_118306577 7 118306577 8.30E-06 0.29 1391 0.23 0.24 0.030 GRMZM2G040945 HAD-superfamily hydrolase, subfamily IG,

5\'-nucleotidase S7_118306577 7 118306577 8.30E-06 0.29 1391 0.23 0.24 0.030 GRMZM2G339728 retrotransposon protein, putative, unclassified,

expressed

S7_118307964 7 118307964 1.05E-06 0.16 1391 0.23 0.24 0.020 GRMZM2G041175 (TET8): tetraspanin8 S7_118307964 7 118307964 1.05E-06 0.16 1391 0.23 0.24 0.020 GRMZM2G040945 HAD-superfamily hydrolase, subfamily IG,

5\'-nucleotidase S7_118307964 7 118307964 1.05E-06 0.16 1391 0.23 0.24 0.020 GRMZM2G339728 retrotransposon protein, putative, unclassified,

337

expressed

S7_118307966 7 118307966 1.05E-06 0.16 1391 0.23 0.24 0.020 GRMZM2G041175 (TET8): tetraspanin8

338

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S7_118307966 7 118307966 1.05E-06 0.16 1391 0.23 0.24 0.020 GRMZM2G040945 HAD-superfamily hydrolase, subfamily IG,

5\'-nucleotidase S7_118307966 7 118307966 1.05E-06 0.16 1391 0.23 0.24 0.020 GRMZM2G339728 retrotransposon protein, putative, unclassified,

expressed S7_118508768 7 118508768 3.08E-05 0.13 1391 0.23 0.24 0.044 GRMZM2G114751 nodulin MtN21 /EamA- like transporter family

protein S7_118508768 7 118508768 3.08E-05 0.13 1391 0.23 0.24 0.044 GRMZM2G114642 (CER3,FLP1,WAX2,YRE): Fatty acid hydroxylase

superfamily S7_119974729 7 119974729 6.35E-06 0.37 1391 0.23 0.24 0.030 GRMZM2G137676 Plant invertase/pectin methylesterase inhibitor

superfamily S7_119975995 7 119975995 2.62E-06 0.37 1391 0.23 0.24 0.028 GRMZM2G137676 Plant invertase/pectin methylesterase inhibitor

superfamily S7_120201871 7 120201871 2.50E-05 0.18 1391 0.23 0.24 0.040 GRMZM2G138976 ARID/BRIGHT DNA- binding domain-

containing protein S7_120201871 7 120201871 2.50E-05 0.18 1391 0.23 0.24 0.040 GRMZM2G138727 PROLM23 - Prolamin

precursor, expressed S7_120201889 7 120201889 1.30E-05 0.16 1391 0.23 0.24 0.035 GRMZM2G138976 ARID/BRIGHT DNA- binding domain-

containing protein S7_120201889 7 120201889 1.30E-05 0.16 1391 0.23 0.24 0.035 GRMZM2G138727 PROLM23 - Prolamin

precursor, expressed S7_122073695 7 122073695 2.40E-06 0.31 1391 0.23 0.24 0.028 GRMZM2G050172 (AT-RSH3,ATRSH3,RSH3):

338

RELA/SPOT homolog 3

339

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S7_122073695 7 122073695 2.40E-06 0.31 1391 0.23 0.24 0.028 GRMZM2G086714 (AT-RSH3,ATRSH3,RSH3):

RELA/SPOT homolog 3 S7_122073695 7 122073695 2.40E-06 0.31 1391 0.23 0.24 0.028 GRMZM2G388045 (ATGEX1,GEX1): gamete

expressed protein 1 S7_124568038 7 124568038 3.56E-06 0.41 1391 0.23 0.24 0.028 GRMZM2G421463 (LYM1): lysm domain GPI- anchored protein 1

precursor S7_144303950 7 144303950 3.69E-05 0.24 1391 0.23 0.24 0.047 GRMZM2G095839 SAUR-like auxin-

responsive protein family S7_161684220 7 161684220 1.17E-05 0.08 1391 0.23 0.24 0.033 GRMZM2G396397 (FRO1): NADH-ubiquinone

oxidoreductase-related S7_162068990 7 162068990 1.10E-06 0.11 1391 0.23 0.24 0.020 GRMZM2G357734 (PDE226,PDS,PDS3):

phytoene desaturase 3 S7_162068990 7 162068990 1.10E-06 0.11 1391 0.23 0.24 0.020 GRMZM2G057247 (ATFH6,FH6): formin

homolog 6 S7_162710260 7 162710260 2.29E-06 0.32 1391 0.23 0.24 0.028 GRMZM2G008712 (ZFP7): zinc finger protein

7 S7_162710260 7 162710260 2.29E-06 0.32 1391 0.23 0.24 0.028 GRMZM2G309970 (WPP2): WPP domain

protein 2 S7_162710260 7 162710260 2.29E-06 0.32 1391 0.23 0.24 0.028 GRMZM2G008468 Got1/Sft2-like vescicle

transport protein family S7_162801789 7 162801789 1.86E-06 0.37 1391 0.23 0.24 0.028 GRMZM2G119740 Prefoldin chaperone

subunit family protein S7_162801789 7 162801789 1.86E-06 0.37 1391 0.23 0.24 0.028 GRMZM2G119705 ribosome inactivating protein, putative,

expressed S7_176480402 7 176480402 2.05E-05 0.21 1391 0.23 0.24 0.037 AC197544.3_FG002 (ULP1B): UB-like protease

339

340

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S8_18967101 8 18967101 7.02E-06 0.07 1391 0.23 0.24 0.030 GRMZM2G047949 (HEN2): RNA helicase, ATP-dependent,

SK12/DOB1 protein S8_18967107 8 18967107 7.02E-06 0.07 1391 0.23 0.24 0.030 GRMZM2G047949 (HEN2): RNA helicase, ATP-dependent,

SK12/DOB1 protein S8_19122007 8 19122007 4.35E-06 0.05 1391 0.23 0.24 0.028 GRMZM2G125020 DUF581 domain containing protein,

expressed S8_19961897 8 19961897 1.44E-05 0.11 1391 0.23 0.24 0.035 GRMZM2G095280 (UGT74E2): Uridine diphosphate

glycosyltransferase 74E2 S8_19961897 8 19961897 1.44E-05 0.11 1391 0.23 0.24 0.035 GRMZM2G095265 (SAG12): senescence-

associated gene 12 S8_19968068 8 19968068 7.45E-06 0.06 1391 0.23 0.24 0.030 GRMZM2G095280 (UGT74E2): Uridine diphosphate

glycosyltransferase 74E2 S8_19968068 8 19968068 7.45E-06 0.06 1391 0.23 0.24 0.030 GRMZM2G095255 RING/U-box superfamily

protein S8_19968068 8 19968068 7.45E-06 0.06 1391 0.23 0.24 0.030 GRMZM2G095265 (SAG12): senescence-

associated gene 12 S8_20091529 8 20091529 4.14E-05 0.22 1391 0.23 0.24 0.049 GRMZM2G395749 (ALY3,ATALY3): DNA

binding S8_21615429 8 21615429 8.95E-06 0.07 1391 0.23 0.24 0.030 GRMZM2G034157 (HSP17.6II): 17.6 kDa class

II heat shock protein S8_21830626 8 21830626 8.55E-06 0.06 1391 0.23 0.24 0.030 GRMZM2G032049 (OVA9): glutamine-tRNA ligase, putative / glutaminyl-tRNA synthetase, putative /

340

GlnRS, putative

341

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S8_21830626 8 21830626 8.55E-06 0.06 1391 0.23 0.24 0.030 GRMZM2G032252 (ATHMG,HMG,NFD,SSRP1

): high mobility group

S8_22510436 8 22510436 8.18E-06 0.05 1391 0.23 0.24 0.030 GRMZM2G309568 zinc ion binding S8_22510436 8 22510436 8.18E-06 0.05 1391 0.23 0.24 0.030 GRMZM2G009475 avr9/Cf-9 rapidly elicited protein 146, putative,

expressed S8_66288692 8 66288692 1.88E-05 0.24 1391 0.23 0.24 0.037 GRMZM2G477340 phosphatidyl serine

synthase family protein S8_104463909 8 104463909 1.37E-05 0.06 1391 0.23 0.24 0.035 GRMZM2G047152 LRR and NB-ARC domains- containing disease

resistance protein S8_104463909 8 104463909 1.37E-05 0.06 1391 0.23 0.24 0.035 GRMZM2G347471 xylose isomerase family

protein S8_104463909 8 104463909 1.37E-05 0.06 1391 0.23 0.24 0.035 AC203955.3_FG005 DUF1517 domain containing protein,

putative, expressed S8_113504730 8 113504730 1.34E-05 0.07 1391 0.23 0.24 0.035 GRMZM2G170552 (CIPK10,PKS2,SIP1,SNRK3. 8): SOS3-interacting

protein 1 S8_124490717 8 124490717 4.02E-05 0.05 1391 0.23 0.24 0.048 GRMZM2G173710 (AHP4): HPT

phosphotransmitter 4 S8_132204020 8 132204020 8.88E-07 0.10 1391 0.23 0.24 0.019 GRMZM2G474726 (ATTERC,PDE149): integral membrane TerC family

protein S8_132204020 8 132204020 8.88E-07 0.10 1391 0.23 0.24 0.019 GRMZM2G173763 nuclear factor related to kappa-B-binding protein, related, putative,

expressed

341

342

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S8_137974581 8 137974581 1.86E-05 0.06 1391 0.23 0.24 0.037 GRMZM2G081653 rossmann fold nucleotide- binding protein involved in DNA uptake, putative,

expressed

S8_141928387 8 141928387 3.64E-05 0.47 1391 0.23 0.24 0.047 GRMZM2G044343 C3HC zinc finger-like S8_151270836 8 151270836 7.89E-06 0.22 1391 0.23 0.24 0.030 GRMZM2G017305 (AAA1,ATKTN1,BOT1,ERH 3,FRA2,FRC2,FTR,KTN1,LU E1): P-loop containing nucleoside triphosphate hydrolases superfamily

protein S8_155975151 8 155975151 1.19E-05 0.05 1391 0.23 0.24 0.033 GRMZM2G144716 NADH:ubiquinone oxidoreductase intermediate-associated

protein 30 S8_155975151 8 155975151 1.19E-05 0.05 1391 0.23 0.24 0.033 GRMZM2G144707 (HVA22F): HVA22-like

protein F

S8_155975151 8 155975151 1.19E-05 0.05 1391 0.23 0.24 0.033 GRMZM2G444819 (AtS40-3): AtS40-3 S8_155975151 8 155975151 1.19E-05 0.05 1391 0.23 0.24 0.033 GRMZM2G144701 HVA22, putative,

expressed S8_157964577 8 157964577 8.83E-06 0.05 1391 0.23 0.24 0.030 GRMZM2G016827 MEMO1, putative,

expressed S8_157964577 8 157964577 8.83E-06 0.05 1391 0.23 0.24 0.030 GRMZM2G319187 (ARR9,ATRR4): response

regulator 9 S8_158576441 8 158576441 3.08E-05 0.05 1391 0.23 0.24 0.044 GRMZM2G101053 Essential protein Yae1, N-

terminal S8_158576441 8 158576441 3.08E-05 0.05 1391 0.23 0.24 0.044 GRMZM2G101080 Plant calmodulin-binding

protein-related

342

343

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S8_158576441 8 158576441 3.08E-05 0.05 1391 0.23 0.24 0.044 GRMZM2G402708 Early-responsive to dehydration stress protein

(ERD4) S8_158576443 8 158576443 3.08E-05 0.05 1391 0.23 0.24 0.044 GRMZM2G101053 Essential protein Yae1, N-

terminal S8_158576443 8 158576443 3.08E-05 0.05 1391 0.23 0.24 0.044 GRMZM2G101080 Plant calmodulin-binding

protein-related S8_158576443 8 158576443 3.08E-05 0.05 1391 0.23 0.24 0.044 GRMZM2G402708 Early-responsive to dehydration stress protein

(ERD4) S8_158576448 8 158576448 3.90E-05 0.05 1391 0.23 0.24 0.047 GRMZM2G101080 Plant calmodulin-binding

protein-related S8_158576448 8 158576448 3.90E-05 0.05 1391 0.23 0.24 0.047 GRMZM2G101053 Essential protein Yae1, N-

terminal S8_158576448 8 158576448 3.90E-05 0.05 1391 0.23 0.24 0.047 GRMZM2G402708 Early-responsive to dehydration stress protein

(ERD4) S8_161081093 8 161081093 1.42E-05 0.13 1391 0.23 0.24 0.035 GRMZM2G145280 (ATBBC1,BBC1,RSU2):

breast basic conserved 1 S8_161081093 8 161081093 1.42E-05 0.13 1391 0.23 0.24 0.035 GRMZM2G145496 (RPL27): ribosomal

protein large subunit 27 S8_161081098 8 161081098 1.88E-05 0.13 1391 0.23 0.24 0.037 GRMZM2G145280 (ATBBC1,BBC1,RSU2):

breast basic conserved 1 S8_161081098 8 161081098 1.88E-05 0.13 1391 0.23 0.24 0.037 GRMZM2G145496 (RPL27): ribosomal

protein large subunit 27

S8_170060763 8 170060763 2.03E-05 0.18 1391 0.23 0.24 0.037 GRMZM2G043498 (SNX2b): sorting nexin 2B

S8_171407343 8 171407343 4.03E-07 0.09 1391 0.23 0.24 0.017 GRMZM2G310115 plectin-related S8_171407343 8 171407343 4.03E-07 0.09 1391 0.23 0.24 0.017 GRMZM2G012160 (ATCYS6,ATCYSB,CYSB):

343 cystatin B

S8_171407349 8 171407349 3.31E-05 0.09 1391 0.23 0.24 0.045 GRMZM2G310115 plectin-related

344

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S8_171407349 8 171407349 3.31E-05 0.09 1391 0.23 0.24 0.045 GRMZM2G012160 (ATCYS6,ATCYSB,CYSB):

cystatin B S9_3895906 9 3895906 3.79E-05 0.13 1391 0.23 0.24 0.047 GRMZM2G048243 protein tyrosine kinase

family protein S9_6066603 9 6066603 9.42E-06 0.25 1391 0.23 0.24 0.031 GRMZM2G019291 TLD-domain containing

nucleolar protein S9_6066607 9 6066607 9.42E-06 0.25 1391 0.23 0.24 0.031 GRMZM2G019291 TLD-domain containing

nucleolar protein S9_18880032 9 18880032 3.23E-05 0.06 1391 0.23 0.24 0.045 GRMZM2G405203 (MAX2,ORE9,PPS): RNI-

like superfamily protein S9_18880032 9 18880032 3.23E-05 0.06 1391 0.23 0.24 0.045 GRMZM2G405178 (ATHOL3,HOL3): S- adenosyl-L-methionine- dependent methyltransferases

superfamily protein S9_18880032 9 18880032 3.23E-05 0.06 1391 0.23 0.24 0.045 GRMZM2G103137 Hydrolase-like protein

family S9_18880032 9 18880032 3.23E-05 0.06 1391 0.23 0.24 0.045 GRMZM2G020216 (ATMAPK6,ATMPK6,MAPK

6,MPK6): MAP kinase 6 S9_20461787 9 20461787 2.66E-06 0.05 1391 0.23 0.24 0.028 GRMZM2G173641 (DXPS3): 1-deoxy-D- xylulose 5-phosphate

synthase 3 S9_20461787 9 20461787 2.66E-06 0.05 1391 0.23 0.24 0.028 GRMZM2G173628 (FSD3): Fe superoxide

dismutase 3 S9_20461787 9 20461787 2.66E-06 0.05 1391 0.23 0.24 0.028 GRMZM2G173693 (ATSRL1): PRP38 family

protein S9_24366897 9 24366897 1.94E-08 0.22 1391 0.23 0.24 0.004 GRMZM2G069008 (ATNUDT14,ATNUDX14,N UDX14): nudix hydrolase

homolog 14

344

345

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S9_88298335 9 88298335 2.94E-05 0.05 1391 0.23 0.24 0.044 GRMZM2G337594 RALFL28 - Rapid ALkalinization Factor RALF family protein precursor,

expressed S9_88298362 9 88298362 2.94E-05 0.05 1391 0.23 0.24 0.044 GRMZM2G337594 RALFL28 - Rapid ALkalinization Factor RALF family protein precursor,

expressed S9_88796128 9 88796128 6.15E-07 0.06 1391 0.23 0.24 0.017 GRMZM2G019872 Zinc-binding dehydrogenase family

protein S9_101204234 9 101204234 3.06E-05 0.06 1391 0.23 0.24 0.044 GRMZM2G378653 basic helix-loop-helix (bHLH) DNA-binding

superfamily protein

S9_113813946 9 113813946 6.13E-06 0.09 1391 0.23 0.24 0.030 GRMZM2G103236 GroES-like family protein S9_113813946 9 113813946 6.13E-06 0.09 1391 0.23 0.24 0.030 GRMZM2G103169 Peroxidase superfamily

protein S9_126935906 9 126935906 2.37E-05 0.31 1391 0.23 0.24 0.039 GRMZM5G806784 SNARE associated Golgi

protein family S9_126935906 9 126935906 2.37E-05 0.31 1391 0.23 0.24 0.039 GRMZM5G880028 calmodulin-binding family

protein S9_134998591 9 134998591 1.53E-05 0.06 1391 0.23 0.24 0.036 GRMZM2G092174 (HY3,OOP1,PHYB):

phytochrome B S9_135275877 9 135275877 1.18E-05 0.06 1391 0.23 0.24 0.033 GRMZM5G875502 (CLF,ICU1,SDG1,SET1): SET domain-containing

protein S9_135275877 9 135275877 1.18E-05 0.06 1391 0.23 0.24 0.033 AC233955.1_FG008 Calcium-dependent phosphotriesterase

superfamily protein 345

346

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S9_135275877 9 135275877 1.18E-05 0.06 1391 0.23 0.24 0.033 AC233955.1_FG009 (TBL6): TRICHOME

BIREFRINGENCE-LIKE 6 S9_146069298 9 146069298 7.79E-06 0.07 1391 0.23 0.24 0.030 GRMZM2G152919 ARM repeat superfamily

protein S9_149247063 9 149247063 2.49E-05 0.11 1391 0.23 0.24 0.040 GRMZM2G004377 Protein phosphatase 2C

family protein S9_149247063 9 149247063 2.49E-05 0.11 1391 0.23 0.24 0.040 GRMZM2G004528 (ATIPS1,ATMIPS1,MI-1-P SYNTHASE,MIPS1): myo- inositol-1-phosphate

synthase 1 S9_149247063 9 149247063 2.49E-05 0.11 1391 0.23 0.24 0.040 GRMZM2G004466 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily

protein S9_150243350 9 150243350 3.35E-05 0.06 1391 0.23 0.24 0.046 GRMZM2G036349 ZIM domain containing protein, putative,

expressed S9_150243350 9 150243350 3.35E-05 0.06 1391 0.23 0.24 0.046 GRMZM2G036351 (JAZ2,TIFY10B): TIFY domain/Divergent CCT

motif family protein S9_150243350 9 150243350 3.35E-05 0.06 1391 0.23 0.24 0.046 GRMZM2G036411 (FDH,KCS10): 3-ketoacyl-

CoA synthase 10 S9_151246748 9 151246748 1.90E-05 0.07 1391 0.23 0.24 0.037 GRMZM2G087901 (ATSUC3,ATSUT2,SUC3,SU

T2): sucrose transporter 2 S9_151289456 9 151289456 4.14E-05 0.05 1391 0.23 0.24 0.049 GRMZM2G178859 (COX10): cytochrome c

oxidase 10

346

347

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S9_151289456 9 151289456 4.14E-05 0.05 1391 0.23 0.24 0.049 GRMZM2G178880 (ATCSLA09,ATCSLA9,CSLA 09,CSLA9,RAT4): Nucleotide-diphospho- sugar transferases

superfamily protein S9_151289456 9 151289456 4.14E-05 0.05 1391 0.23 0.24 0.049 GRMZM2G178826 3-dehydroquinate synthase, putative,

expressed S9_151490165 9 151490165 1.90E-05 0.46 1391 0.23 0.24 0.037 GRMZM2G120975 Calcium-binding EF hand

family protein S9_151490165 9 151490165 1.90E-05 0.46 1391 0.23 0.24 0.037 GRMZM2G420926 (PP2A-3): protein

phosphatase 2A-3 S9_151490165 9 151490165 1.90E-05 0.46 1391 0.23 0.24 0.037 GRMZM2G120987 (FAR2,MS2): Jojoba acyl CoA reductase-related

male sterility protein S9_151498902 9 151498902 2.23E-06 0.47 1391 0.23 0.24 0.028 GRMZM2G120975 Calcium-binding EF hand

family protein S9_151820305 9 151820305 2.18E-05 0.11 1391 0.23 0.24 0.039 GRMZM2G010017 Protein phosphatase 2C

family protein S9_154780055 9 154780055 4.12E-06 0.10 1391 0.23 0.24 0.028 GRMZM2G113267 DEA(D/H)-box RNA

helicase family protein

S9_154780055 9 154780055 4.12E-06 0.10 1391 0.23 0.24 0.028 GRMZM2G113245 (F8H): FRA8 homolog S9_154780058 9 154780058 4.12E-06 0.10 1391 0.23 0.24 0.028 GRMZM2G113267 DEA(D/H)-box RNA

helicase family protein

S9_154780058 9 154780058 4.12E-06 0.10 1391 0.23 0.24 0.028 GRMZM2G113245 (F8H): FRA8 homolog S10_2032257 10 2032257 1.96E-05 0.10 1391 0.23 0.24 0.037 GRMZM2G180155 glutamine-fructose-6- phosphate transaminase (isomerizing)s;sugar

347 binding;transaminases

348

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S10_2032257 10 2032257 1.96E-05 0.10 1391 0.23 0.24 0.037 GRMZM2G180150 (GRL,NAP1,NAPP):

transcription activators S10_2032257 10 2032257 1.96E-05 0.10 1391 0.23 0.24 0.037 GRMZM2G180205 Transducin/WD40 repeat-

like superfamily protein S10_2032257 10 2032257 1.96E-05 0.10 1391 0.23 0.24 0.037 GRMZM2G180166 Ubiquitin carboxyl- terminal hydrolase family

protein S10_2039204 10 2039204 1.06E-05 0.15 1391 0.23 0.24 0.032 GRMZM2G180244 LRR and NB-ARC domains- containing disease

resistance protein S10_2039204 10 2039204 1.06E-05 0.15 1391 0.23 0.24 0.032 GRMZM2G180150 (GRL,NAP1,NAPP):

transcription activators S10_2039204 10 2039204 1.06E-05 0.15 1391 0.23 0.24 0.032 GRMZM2G180155 glutamine-fructose-6- phosphate transaminase (isomerizing)s;sugar

binding;transaminases S10_2039204 10 2039204 1.06E-05 0.15 1391 0.23 0.24 0.032 GRMZM2G180205 Transducin/WD40 repeat-

like superfamily protein S10_2039204 10 2039204 1.06E-05 0.15 1391 0.23 0.24 0.032 GRMZM2G180166 Ubiquitin carboxyl- terminal hydrolase family

protein S10_4675692 10 4675692 1.20E-05 0.07 1391 0.23 0.24 0.033 GRMZM2G003750 CAAX amino terminal

protease family protein S10_4675692 10 4675692 1.20E-05 0.07 1391 0.23 0.24 0.033 GRMZM2G004414 (ATCAX11,CAX11): cation

exchanger 11 S10_4675692 10 4675692 1.20E-05 0.07 1391 0.23 0.24 0.033 GRMZM2G003762 (AILP1,ATAILP1): Aluminium induced protein with YGL and

LRDR motifs

348

349

R2 of R2 of Model FDR N Model w/ Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP SNP P-values of SNP Annotation S10_65738413 10 65738413 2.63E-05 0.05 1391 0.23 0.24 0.041 GRMZM2G404426 (EMB1135): RING/FYVE/PHD zinc

finger superfamily protein S10_122268779 10 122268779 2.22E-05 0.12 1391 0.23 0.24 0.039 GRMZM2G125424 (ABCB19,ATABCB19,ATM DR1,ATMDR11,ATPGP19, MDR1,MDR11,PGP19): ATP binding cassette

subfamily B19 S10_134498587 10 134498587 4.80E-06 0.06 1391 0.23 0.24 0.028 GRMZM2G063972 DNAJ heat shock N- terminal domain-

containing protein S10_135056584 10 135056584 3.31E-06 0.06 1391 0.23 0.24 0.028 AC233979.1_FG006 DUF581 domain containing protein,

expressed S10_135577386 10 135577386 3.76E-05 0.08 1391 0.23 0.24 0.047 GRMZM2G086553 AT hook motif DNA-

binding family protein S10_136834081 10 136834081 2.34E-05 0.06 1391 0.23 0.24 0.039 GRMZM2G702529 (CYP87A2): cytochrome P450, family 87, subfamily

A, polypeptide 2

S10_136876614 10 136876614 1.54E-05 0.44 1391 0.23 0.24 0.036 GRMZM5G845601 (IQD22): IQ-domain 22 S10_142782318 10 142782318 5.51E-06 0.08 1391 0.23 0.24 0.030 GRMZM2G029039 Galactose oxidase/kelch repeat superfamily

protein

349

350

Appendix E Maize Kernel Composition NIR Calibration Correlations

Calibration Report

Corn - Whole Grain

Last Updated: March 7, 2008

NOTES Moisture Basis: As Is Sample Preparation: None Large Sample Presentation: Dish Temperature Variation: None 5nm filtered, both High Data Format: and Low Gain Slovania, Sample Origin: Germany, US Number of Instruments: 8

350 Crude

Moisture Protein Oil Starch Density Fiber Ash Min 7.38 4.86 2.16 48.29 1.146 1.10 1.01 Max 37.60 15.27 13.50 67.92 1.353 2.40 1.31 R2 0.994 0.947 0.937 0.938 0.863 0.110 0.155 SECV 0.39 0.33 0.42 0.678 0.012 0.29 0.068 Spectra 2897 1787 1761 814 931 79 80

351

Appendix F Maize Kernel Composition SAS Code for BLUP Analysis

Below is BLUP SAS code for the trait Protein, all other traits use similar code for BLUP calculations

/****** For Combined analysis of 2012 and 2013 for PROTEIN*/ data AMES12; infile 'U:\Research Projects\Kernel Composition\Perten Runs\Compiled Final File AMES 2012.csv' dsd firstobs=2 missover; input Plot Range Row GROUPID$ MaturityGroup ITEM$ ACCESSION$ Moisture Protein Oil Starch Density Fiber Ash treatn$ new; Year = '1'; if GroupID= 'C1' then GroupID= '3000'; if GroupID= 'C2' then GroupID= '4000'; Data AMES12AVG; set AMES12; keep Plot Range Row GROUPID MaturityGroup ITEM ACCESSION Moisture Protein Oil Starch Density Fiber Ash treatn new year; proc sort; by maturitygroup plot; run; Data AMES12AVG1; set AMES12; keep Range GROUPID MaturityGroup ITEM ACCESSION treatn new PROTEIN; rename range =range12; rename PROTEIN = PROTEIN12; proc sort; by GroupID ; run; data AMES13; infile 'U:\Research Projects\Kernel Composition\Perten

351 Runs\Compiled Final File AMES 2013.csv' dsd firstobs=2 missover;

input Plot Range Row GROUPID$ MaturityGroup ITEM$ ACCESSION$ Moisture Protein Oil Starch Density Fiber Ash treatn$ new; Year = '2'; if GroupID= 'C1' then GroupID= '3000'; if GroupID= 'C2' then GroupID= '4000'; Data AMES13AVG; set AMES13; keep Plot Range Row GROUPID MaturityGroup ITEM ACCESSION Moisture Protein Oil Starch Density Fiber Ash treatn new year; proc sort; by maturitygroup plot; run; Data AMES13AVG1; set AMES13; keep Range GROUPID MaturityGroup ITEM ACCESSION treatn new PROTEIN; rename range =range13; rename PROTEIN = PROTEIN13;

352 proc sort; by GroupID ; run; Data AmesComb; set AMES12AVG AMES13AVG; run; proc sort; by maturitygroup plot; run; Data AmesComb1; merge AMES12AVG1 AMES13AVG1; by GroupID; keep range12 range13 MaturityGroup GroupID ITEM ACCESSION treatn new PROTEIN12 PROTEIN13; run; proc sort; by maturitygroup; run;

/* To run an ANOVA on protein*/ proc glm data=AMESComb; class GroupID year range; model protein=groupid year range(year); random year range(year); run;

/*To calculate BLUP*/ proc mixed data=AMESComb; by MaturityGroup; class year range GroupID treatn; model PROTEIN = treatn /solution; random year range(year) GroupID*New/ solution; lsmeans treatn; ods listing exclude solutionr; ods output solutionr=sr LSMeans=lsm;

run; 352 proc sort data = sr; by effect maturityGroup year;

/* Attempt to combine the Estimates for the different traits with the original data to compute BLUPs*/ Data LS; set lsm; rename Estimate=PROTEINuMean; proc sort Data=LS; By MaturityGroup treatn; run; proc sort data=AMESComb1; By MaturityGroup treatn; run; Data PROTEINREP; merge LS AMESComb1; By MaturityGroup treatn;

353

keep range12 range13 treatn GROUPID MaturityGroup ITEM ACCESSION PROTEINuMean PROTEIN12 PROTEIN13; Data PROTEINRan; set sr; if Effect= 'Year' then delete; if GroupID= " " then PROTEINRan=Estimate; else delete; Data PROTEINEST; set sr; if GroupID= '' then delete; keep MaturityGroup GroupID Estimate; rename Estimate=PROTEINEst; run; Data PROTEINRan12; set PROTEINRan; if Year=1 then PROTEINRan12=PROTEINRan; else delete; keep MaturityGroup Effect Range PROTEINRan12; rename Range=Range12; Proc sort data=PROTEINRan12; by MaturityGroup Range12; run; Data PROTEINRan13; set PROTEINRan; if year=2 then PROTEINRan13=PROTEINRan; else delete; keep MaturityGroup Effect Range PROTEINRan13; rename Range=Range13; Proc Sort data=PROTEINRan13; by MaturityGroup Range13; run; proc sort data=AmesComb1; by MaturityGroup Range12; run; data PROTEINRan12Comb;

merge AmesComb1 PROTEINRan12; 353 by MaturityGroup Range12; keep range12 range13 treatn GroupID MaturityGroup Item Accession PROTEINRan12 PROTEIN12 PROTEIN13; proc sort data=AmesComb1; by MaturityGroup Range13; run; data PROTEINRan13Comb; merge AmesComb1 PROTEINRan13; by MaturityGroup Range13; keep range12 range13 treatn GROUPID MaturityGroup ITEM ACCESSION PROTEINRan13 PROTEIN12 PROTEIN13; proc sort data=PROTEINRan12Comb; by MaturityGroup GroupID; run; proc sort data=PROTEINRan13Comb; by MaturityGroup GroupID; run; data PROTEINRanComb;

354

merge PROTEINRan12Comb PROTEINRan13Comb; by MaturityGroup GroupID; keep range12 range13 treatn GroupID MaturityGroup Item Accession PROTEINRan12 PROTEINRan13 PROTEIN12 PROTEIN13; data combranrep; merge PROTEINRanComb PROTEINRep; by MaturityGroup; run; proc sort data=combranrep; by MaturityGroup GroupID; run; proc sort data=PROTEINEst; by MaturityGroup GroupID; run; Data CombinedPROTEIN; merge CombRanRep PROTEINEST; by MaturityGroup GroupID; PROTEINBLUP= (PROTEINEST + PROTEINRan12 + PROTEINRan13 + PROTEINuMean); if PROTEIN12='.' then PROTEINBLUP='.'; if PROTEIN13='.' then PROTEINBLUP='.'; keep Range12 Range13 treatn GROUPID MaturityGroup ITEM ACCESSION PROTEIN12 PROTEIN13 PROTEINEST PROTEINRan12 PROTEINRan13 PROTEINuMean PROTEINBLUP; run;

/*To check for normality of the BLUP data*/ proc univariate data = combinedprotein; qqplot proteinblup; histogram proteinBLUP; run;

/* To Check to see if transformations necessary*/ proc transreg data= combinedprotein; model Box (proteinBLUP / lambda = 0 to 1 by 0.5)= class(GroupID);

run; 354

/*To Compute the transformed BLUP value based on the BOXCOX suggestions*/ Data proteinfinal; set combinedprotein; proteinBLUP= (log(proteinBLUP)); keep plot range row groupid maturitygroup item accession protein proteinblup; run;

/*NO TRANSFORMATION NECESSARY*/ proc print data=CombinedPROTEIN;run; proc export DATA= CombinedPROTEIN outfile="U:\Research Projects\Kernel Composition\Perten Runs\BLUPs Calculated\CombinedPROTEIN.csv" dbms=CSV ;run;

355

Appendix G Maize Kernel Composition R Code for GWAS Analysis

Below is R GWAS code for the trait protein, all other traits use similar code for GWAS analysis rm(biocLite) source("http://www.bioconductor.org/biocLite.R") biocLite("multtest") install.packages("gplots") install.packages("LDheatmap") install.packages("genetics") library("multtest") library("gplots") library("LDheatmap") library("genetics") library("compiler") #this library is already installed in R source("http://www.maizegenetics.net/images/stories/bioinformatics/GAPIT/gapit_fun ctions.txt") source("http://www.maizegenetics.net/images/stories/bioinformatics/GAPIT/emma.txt ")

setwd("U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN") 355 myY <- read.table("PROTEIN.txt",sep="", head = TRUE)

head(myY) setwd("U:/Research Projects/GAPIT/diagrid") myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c1.hmp.txt ",sep= "", head = FALSE) head(myG)[,1:20] setwd("U:/Research Projects/Leaf N Movement/2013/GAPIT RUNS/") myKI <- read.table("Ames_50%SNPs_Comprehensive_K_JanuaryGBS_Names.txt", sep = "", head = FALSE) head(myKI)[,1:20] is.numeric(myKI[,2])

356 myCV <- read.table("GAPIT.PCA_Ames2012_JanuaryGBS_names_50%SNP_estimated_short.txt", sep = "", head = TRUE) head(myCV)

#moving to dir to dump GAPIT results #setwd("/results") setwd("U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr1")

#Step 2: Run GAPIT for Chromosome 1 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV, group.from = 1300, group.to = 1500, group.by=10, #group.by = c(seq(1,1817,by=200),1817), G=myG, Model.selection=TRUE )

356 setwd("U:/Research Projects/GAPIT/diagrid") myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c2.hmp.txt ",sep= "", head = FALSE) setwd("U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr2")

#Step 2: Run GAPIT for Chromosome 2 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV,

357

group.from = 1440, group.to = 1440, G=myG, Model.selection=TRUE ) setwd("U:/Research Projects/GAPIT/diagrid") myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c3.hmp.txt ",sep= "", head = FALSE) setwd("U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr3")

#Step 2: Run GAPIT for Chromosome 3 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV, group.from = 1440, group.to = 1440, G=myG, Model.selection=TRUE )

357 setwd("U:/Research Projects/GAPIT/diagrid") myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c4.hmp.txt ",sep= "", head = FALSE) setwd("U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr4")

#Step 2: Run GAPIT for Chromosome 4 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV, group.from = 1440,

358

group.to = 1440, G=myG, Model.selection=TRUE ) setwd("U:/Research Projects/GAPIT/diagrid") myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c5.hmp.txt ",sep= "", head = FALSE) setwd("U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr5")

#Step 2: Run GAPIT for Chromosome 5 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV, group.from = 1440, group.to = 1440, G=myG, Model.selection=TRUE ) setwd("U:/Research Projects/GAPIT/diagrid")

358 myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c6.hmp.txt ",sep= "", head = FALSE) setwd("U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr6")

#Step 2: Run GAPIT for Chromosome 6 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV, group.from = 1440, group.to = 1440,

359

G=myG, Model.selection=TRUE ) setwd("U:/Research Projects/GAPIT/diagrid") myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c7.hmp.txt ",sep= "", head = FALSE) setwd("U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr7")

#Step 2: Run GAPIT for Chromosome 7 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV, group.from = 1440, group.to = 1440, G=myG, Model.selection=TRUE ) setwd("U:/Research Projects/GAPIT/diagrid") myG <-

359 read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c8.hmp.txt ",sep= "", head = FALSE) setwd("U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr8")

#Step 2: Run GAPIT for Chromosome 8 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV, group.from = 1440, group.to = 1440, G=myG,

360

Model.selection=TRUE ) setwd("U:/Research Projects/GAPIT/diagrid") myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c9.hmp.txt ",sep= "", head = FALSE) setwd("U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr9")

#Step 2: Run GAPIT for Chromosome 9 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV, group.from = 1440, group.to = 1440, G=myG, Model.selection=TRUE ) setwd("U:/Research Projects/GAPIT/diagrid") myG <- read.delim("One_taxa_Ames20120110_scv10mF8maf002_mgs_E1pLD5kpUn.c10.hmp.t

360 xt",sep= "", head = FALSE) setwd("U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr10")

#Step 2: Run GAPIT for Chromosome 10 myGAPIT <- GAPIT( Y=myY, KI=myKI, CV=myCV, group.from = 1440, group.to = 1440, G=myG, Model.selection=TRUE)

361

##################################################################### To Combine all the runs into 1 analysis #Step 0: In your working directory, create three folders, and name them "Results_1", #"Results_2", and "Results_Combined". Put all of the GAPIT output files from one set up SNPs in # "Results_1", and all of the GAPIT output files from the second set of SNPs in "Results_2". # Finally, suppose that two traits named "trait1" and "trait2" are being analyzed ######################################################################## ############### library('MASS') library(multtest) library(gplots) setwd("U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN") #Import the source code source("http://www.maizegenetics.net/images/stories/bioinformatics/GAPIT/emma.txt ") source("http://www.maizegenetics.net/images/stories/bioinformatics/GAPIT/gapit_fun ctions.txt") #Step 1: Set data directory and import files ######################################################################## ############### mydataPath.Results.1="U:/Research Projects/Kernel Composition/Perten Runs/GAPIT

361 RUNS/Combined_Traits/PROTEIN/Chr1/" mydataPath.Results.2="U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr2/" mydataPath.Results.3="U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr3/" mydataPath.Results.4="U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr4/" mydataPath.Results.5="U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr5/" mydataPath.Results.6="U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr6/" mydataPath.Results.7="U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr7/"

362 mydataPath.Results.8="U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr8/" mydataPath.Results.9="U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr9/" mydataPath.Results.10="U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Chr10/" name <- c("Protein") #Step 2: Set the result directory to where the combined data will go ######################################################################## ############### setwd("U:/Research Projects/Kernel Composition/Perten Runs/GAPIT RUNS/Combined_Traits/PROTEIN/Results_Combined") for(i in 1:length(name)){ #Read in the GWAS and Allelic effect estimates GWAS.Results.1 <- read.csv(paste(mydataPath.Results.1,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE) GWAS.Results.2 <- read.csv(paste(mydataPath.Results.2,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE) GWAS.Results.3 <- read.csv(paste(mydataPath.Results.3,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE)

362 GWAS.Results.4 <- read.csv(paste(mydataPath.Results.4,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE) GWAS.Results.5 <- read.csv(paste(mydataPath.Results.5,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE) GWAS.Results.6 <- read.csv(paste(mydataPath.Results.6,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE) GWAS.Results.7 <- read.csv(paste(mydataPath.Results.7,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE)

363

GWAS.Results.8 <- read.csv(paste(mydataPath.Results.8,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE) GWAS.Results.9 <- read.csv(paste(mydataPath.Results.9,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE) GWAS.Results.10 <- read.csv(paste(mydataPath.Results.10,"GAPIT..",name[i],".GWAS.Results.csv",sep=""), head = TRUE)

Effect.Estimates.1 <- read.csv(paste(mydataPath.Results.1,"GAPIT..",name[i],".Allelic_Effect_Estimates.csv",s ep=""), head = TRUE) Effect.Estimates.2 <- read.csv(paste(mydataPath.Results.2,"GAPIT..",name[i],".Allelic_Effect_Estimates.csv",s ep=""), head = TRUE) Effect.Estimates.3 <- read.csv(paste(mydataPath.Results.3,"GAPIT..",name[i],".Allelic_Effect_Estimates.csv",s ep=""), head = TRUE) Effect.Estimates.4 <- read.csv(paste(mydataPath.Results.4,"GAPIT..",name[i],".Allelic_Effect_Estimates.csv",s ep=""), head = TRUE) Effect.Estimates.5 <- read.csv(paste(mydataPath.Results.5,"GAPIT..",name[i],".Allelic_Effect_Estimates.csv",s

363 ep=""), head = TRUE) Effect.Estimates.6 <- read.csv(paste(mydataPath.Results.6,"GAPIT..",name[i],".Allelic_Effect_Estimates.csv",s ep=""), head = TRUE) Effect.Estimates.7 <- read.csv(paste(mydataPath.Results.7,"GAPIT..",name[i],".Allelic_Effect_Estimates.csv",s ep=""), head = TRUE) Effect.Estimates.8 <- read.csv(paste(mydataPath.Results.8,"GAPIT..",name[i],".Allelic_Effect_Estimates.csv",s ep=""), head = TRUE) Effect.Estimates.9 <- read.csv(paste(mydataPath.Results.9,"GAPIT..",name[i],".Allelic_Effect_Estimates.csv",s ep=""), head = TRUE)

364

Effect.Estimates.10 <- read.csv(paste(mydataPath.Results.10,"GAPIT..",name[i],".Allelic_Effect_Estimates.csv", sep=""), head = TRUE)

364 GAPIT.Manhattan(GI.MP = GWAS.Results.with.FDR[,2:4], name.of.trait = name[i], DPP=50000, plot.type = "Chromosomewise",cutOff=0.00) #Export the combined GWAS results write.table(GWAS.Results.with.FDR, paste("GAPIT.", name[i], ".GWAS.Results.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE) #Export the combined Alleleic effect estiamtes write.table(Effect.Estimates, paste("GAPIT.", name[i], ".Allelic_Effect_Estimates.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE) rm(GWAS.Results.1) rm(GWAS.Results.2)

365 rm(GWAS.Results.3) rm(GWAS.Results.4) rm(GWAS.Results.5) rm(GWAS.Results.6) rm(GWAS.Results.7) rm(GWAS.Results.8) rm(GWAS.Results.9) rm(GWAS.Results.10) rm(GWAS.Results) rm(GWAS.Results.with.FDR) rm(Effect.Estimates.1) rm(Effect.Estimates.2) rm(Effect.Estimates.3) rm(Effect.Estimates.4) rm(Effect.Estimates.5) rm(Effect.Estimates.6) rm(Effect.Estimates.7) rm(Effect.Estimates.8) rm(Effect.Estimates.9) rm(Effect.Estimates.10) rm(Effect.Estimates) rm(Conduct.FDR) } #End for(i in 1:length(name))

365

366

Appendix H Maize Kernel Composition ANOVA Outputs

H-1 Maize Kernel Ash ANOVA

Sum of Source DF Squares Mean Square F Value Pr > F Model 1293 11.02841 0.008529 1.57 <.0001 Error 866 4.706103 0.005434 Corrected Total 2159 15.73452

R -Square C oeff Var Root MSE VTL Mean 0.700906 6.615222 0.073718 1.114365

Source DF Type I SS Mean Square F Value Pr > F GROUPID 1246 10.72171 0.008605 1.58 <.0001 Year 1 0.00723 0.00723 1.33 0.2491 Range(Year) 46 0.29947 0.00651 1.2 0.1761

Source DF Type III SS Mean Square F Value Pr > F GROUPID 1246 10.32428 0.008286 1.52 <.0001 Year 1 0.005263 0.005263 0.97 0.3253 Range(Year) 46 0.29947 0.00651 1.2 0.1761

366

367

H-2 Maize Kernel Density ANOVA

Sum of Source DF Squares Mean Square F Value Pr > F Model 2317 20.06118 0.008658 6.38 <.0001 Error 2585 3.50816 0.001357

Corrected Total 4902 23.56934

R -Square Coeff Var Root MSE VTL Mean 0.851156 2.51998 0.036839 1.461882

Source DF Type I SS Mean Square F Value Pr > F GROUPID 2270 11.59369 0.005107 3.76 <.0001 Year 1 8.289517 8.289517 6108.16 <.0001 Range(Year) 46 0.17798 0.003869 2.85 <.0001

Source DF Type III SS Mean Square F Value Pr > F GROUPID 2270 10.58113 0.004661 3.43 <.0001 Year 1 8.199349 8.199349 6041.72 <.0001 Range(Year) 46 0.17798 0.003869 2.85 <.0001

367

368

H-3 Maize Kernel Fiber ANOVA

Sum of Source DF Squares Mean Square F Value Pr > F Model 1527 824.3044 0.53982 1.45 <.0001 Error 1083 403.6136 0.372681 Corrected Total 2610 1227.918

R -Square Coeff Var Root MSE VTL Mean 0.671303 31.84907 0.610476 1.916778

Source DF Type I SS Mean Square F Value Pr > F GROUPID 1480 762.1229 0.514948 1.38 <.0001 Year 1 47.63191 47.63191 127.81 <.0001 Range(Year) 46 14.54965 0.316297 0.85 0.7534

Source DF Type III SS Mean Square F Value Pr > F GROUPID 1480 774.3981 0.523242 1.4 <.0001 Year 1 46.17841 46.17841 123.91 <.0001 Range(Year) 46 14.54965 0.316297 0.85 0.7534

368

369

H-4 Maize Kernel Oil ANOVA

Sum of Source DF Squares Mean Square F Value Pr > F Model 2312 4879.709 2.110601 2.49 <.0001 Error 2571 2178.776 0.847443 Corrected Total 4883 7058.485

R -Square Coeff Var Root MSE VTL Mean 0.691325 19.86472 0.920567 4.634178

Source DF Type I SS Mean Square F Value Pr > F GROUPID 2265 4525.302 1.997926 2.36 <.0001 Year 1 329.7161 329.7161 389.07 <.0001 Range(Year) 46 24.69102 0.536761 0.63 0.9745

Source DF Type III SS Mean Square F Value Pr > F GROUPID 2265 4466.954 1.972165 2.33 <.0001 Year 1 329.5309 329.5309 388.85 <.0001 Range(Year) 46 24.69102 0.536761 0.63 0.9745

369

370

H-5 Maize Kernel Protein ANOVA

Sum of Source DF Squares Mean Square F Value Pr > F Model 2317 15138.29 6.53357 3.77 <.0001 Error 2586 4486.684 1.73499 Corrected Total 4903 19624.98

R -Square Coeff Var Root MSE VTL Mean 0.771379 8.83031 1.31719 14.91669

Source DF Type I SS Mean Square F Value Pr > F GROUPID 2270 13833.56 6.09408 3.51 <.0001 Year 1 1138.737 1138.737 656.34 <.0001 Range(Year) 46 165.9975 3.60864 2.08 <.0001

Source DF Type III SS Mean Square F Value Pr > F GROUPID 2270 13751.12 6.05776 3.49 <.0001 Year 1 1125.814 1125.814 648.89 <.0001 Range(Year) 46 165.9975 3.60864 2.08 <.0001

370

371

H-6 Maize Kernel Starch ANOVA

Sum of Source DF Squares Mean Square F Value Pr > F Model 2274 80010.67 35.185 3.16 <.0001 Error 2429 27030.47 11.1282 Corrected Total 4703 107041.1

R -Square Coeff Var Root MSE VTL Mean 0.747476 5.613049 3.3359 59.43115

Source DF Type I SS Mean Square F Value Pr > F GROUPID 2227 57255.53 25.70971 2.31 <.0001 Year 1 20946.42 20946.42 1882.28 <.0001 Range(Year) 46 1808.721 39.32002 3.53 <.0001

Source DF Type III SS Mean Square F Value Pr > F GROUPID 2227 55556 24.94657 2.24 <.0001 Year 1 20698.63 20698.63 1860.01 <.0001 Range(Year) 46 1808.721 39.32002 3.53 <.0001

371

372

Appendix I Maize Kernel Composition Candidate Genes

I-1 Maize Kernel Density Candidate Genes

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P value maf obs w/o SNP w/ SNP P-values of SNP Annotation S1_79702201 1 79702201 4.10E-07 0.27 1759 0.25 0.26 0.007 GRMZM2G044481 (ABC33,ATCPS1,CPS,CPS 1,GA1): Terpenoid cyclases/Protein prenyltransferases

superfamily protein S1_79702201 1 79702201 4.10E-07 0.27 1759 0.25 0.26 0.007 GRMZM2G343688 UBX domain-containing

protein S1_87162133 1 87162133 1.06E-05 0.16 1759 0.25 0.26 0.042 GRMZM2G177391 ATEXPB2,ATHEXP BETA

1.4,EXPB2): expansin B2 S1_87162133 1 87162133 1.06E-05 0.16 1759 0.25 0.26 0.042 GRMZM2G177400 LYR family of Fe/S cluster biogenesis

protein S1_87301407 1 87301407 6.42E-06 0.31 1759 0.25 0.26 0.037 GRMZM2G046848 U-box domain- containing protein

kinase family protein S1_87301407 1 87301407 6.42E-06 0.31 1759 0.25 0.26 0.037 U-box domain- containing protein kinase family protein S1_89236435 1 89236435 6.91E-07 0.24 1759 0.25 0.26 0.010 GRMZM2G114906 Plant protein of unknown function

(DUF863) S1_89236435 1 89236435 6.91E-07 0.24 1759 0.25 0.26 0.010 GRMZM2G114893 zinc finger family protein, putative,

expressed

372

373

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P value maf obs w/o SNP w/ SNP P-values of SNP Annotation S1_89236468 1 89236468 1.89E-06 0.24 1759 0.25 0.26 0.018 GRMZM2G114893 : zinc finger family protein, putative,

expressed S1_89236468 1 89236468 1.89E-06 0.24 1759 0.25 0.26 0.018 GRMZM2G114906 Plant protein of unknown function

(DUF863) S1_90222083 1 90222083 1.45E-06 0.36 1759 0.25 0.26 0.015 GRMZM2G154580 CCT motif family

protein, expressed S1_90222083 1 90222083 1.45E-06 0.36 1759 0.25 0.26 0.015 GRMZM2G154487 Ribosomal L18p/L5e

family protein

S1_182103887 1 182103887 2.54E-06 0.06 1759 0.25 0.26 0.021 GRMZM2G023847 (UCC1): uclacyanin 1

S1_182103887 1 182103887 2.54E-06 0.06 1759 0.25 0.26 0.021 GRMZM2G023906 LETM1-like protein S1_182103887 1 182103887 2.54E-06 0.06 1759 0.25 0.26 0.021 GRMZM2G023591 RNA-binding (RRM/RBD/RNP motifs) family protein S2_9000281 2 9000281 1.08E-05 0.19 1759 0.25 0.26 0.042 GRMZM2G000047 (ATHAK5,HAK5): high

affinity K+ transporter 5 S2_9000281 2 9000281 1.08E-05 0.19 1759 0.25 0.26 0.042 GRMZM2G000052 (ATPAO2,PAO2):

polyamine oxidase 2 S2_9000281 2 9000281 1.08E-05 0.19 1759 0.25 0.26 0.042 GRMZM2G300500 (GTE7): global transcription factor

group E7 S2_9000281 2 9000281 1.08E-05 0.19 1759 0.25 0.26 0.042 GRMZM2G300497 Disease resistance protein (TIR-NBS-LRR

class) family S2_10337822 2 10337822 4.29E-06 0.35 1759 0.25 0.26 0.030 GRMZM2G005310 (CMT3):

chromomethylase 3 S2_29227142 2 29227142 1.55E-06 0.41 1759 0.25 0.26 0.016 GRMZM2G147241 DUF640 domain containing protein,

373 putative, expressed

374

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P value maf obs w/o SNP w/ SNP P-values of SNP Annotation S2_29227143 2 29227143 4.46E-06 0.41 1759 0.25 0.26 0.030 GRMZM2G147241 DUF640 domain containing protein,

putative, expressed S2_45989688 2 45989688 2.01E-07 0.06 1759 0.25 0.26 0.005 GRMZM2G028258 (SKOR): STELAR K+

outward rectifier S2_45989688 2 45989688 2.01E-07 0.06 1759 0.25 0.26 0.005 GRMZM2G028139 Translation initiation factor 2, small GTP-

binding protein S2_45989726 2 45989726 6.20E-06 0.06 1759 0.25 0.26 0.036 GRMZM2G028258 (SKOR): STELAR K+

outward rectifier S2_45989726 2 45989726 6.20E-06 0.06 1759 0.25 0.26 0.036 GRMZM2G028139 Translation initiation factor 2, small GTP-

binding protein S2_45989738 2 45989738 6.20E-06 0.06 1759 0.25 0.26 0.036 GRMZM2G028258 (SKOR): STELAR K+

outward rectifier S2_45989738 2 45989738 6.20E-06 0.06 1759 0.25 0.26 0.036 GRMZM2G028139 Translation initiation factor 2, small GTP-

binding protein S2_45989741 2 45989741 6.20E-06 0.06 1759 0.25 0.26 0.036 GRMZM2G028258 (SKOR): STELAR K+

outward rectifier S2_45989741 2 45989741 6.20E-06 0.06 1759 0.25 0.26 0.036 GRMZM2G028139 Translation initiation factor 2, small GTP-

binding protein S2_172249005 2 172249005 7.89E-06 0.28 1759 0.25 0.26 0.039 GRMZM2G014106 Enhancer of polycomb- like transcription factor

protein S2_172249030 2 172249030 7.89E-06 0.28 1759 0.25 0.26 0.039 GRMZM2G014106 Enhancer of polycomb- like transcription factor

protein S2_172249055 2 172249055 7.89E-06 0.28 1759 0.25 0.26 0.039 GRMZM2G014106 Enhancer of polycomb-

374 like transcription factor

protein

375

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P value maf obs w/o SNP w/ SNP P-values of SNP Annotation S2_172252535 2 172252535 1.10E-06 0.29 1759 0.25 0.26 0.013 GRMZM2G014106 Enhancer of polycomb- like transcription factor

protein S2_206891194 2 206891194 1.07E-05 0.38 1759 0.25 0.26 0.042 GRMZM2G113396 (CIN4,COP10,EMB144,F US9): Ubiquitin- conjugating enzyme

family protein S2_206891194 2 206891194 1.07E-05 0.38 1759 0.25 0.26 0.042 GRMZM2G113420 O-Glycosyl hydrolases

family 17 protein S2_206902729 2 206902729 1.04E-06 0.46 1759 0.25 0.26 0.012 GRMZM2G113396 (CIN4,COP10,EMB144,F US9): Ubiquitin- conjugating enzyme

family protein S2_206902729 2 206902729 1.04E-06 0.46 1759 0.25 0.26 0.012 GRMZM2G113420 O-Glycosyl hydrolases

family 17 protein S2_206902863 2 206902863 2.28E-06 0.45 1759 0.25 0.26 0.021 GRMZM2G113396 (CIN4,COP10,EMB144,F US9): Ubiquitin- conjugating enzyme

family protein S2_206902863 2 206902863 2.28E-06 0.45 1759 0.25 0.26 0.021 GRMZM2G113420 O-Glycosyl hydrolases

family 17 protein S2_206902934 2 206902934 1.37E-05 0.45 1759 0.25 0.26 0.046 GRMZM2G113396 (CIN4,COP10,EMB144,F US9): Ubiquitin- conjugating enzyme

family protein S2_206902934 2 206902934 1.37E-05 0.45 1759 0.25 0.26 0.046 GRMZM2G113420 O-Glycosyl hydrolases

family 17 protein S2_206902935 2 206902935 1.37E-05 0.45 1759 0.25 0.26 0.046 GRMZM2G113396 (CIN4,COP10,EMB144,F US9): Ubiquitin- conjugating enzyme

375

family protein

376

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P value maf obs w/o SNP w/ SNP P-values of SNP Annotation S2_206902935 2 206902935 1.37E-05 0.45 1759 0.25 0.26 0.046 GRMZM2G113420 O-Glycosyl hydrolases

family 17 protein S2_206902936 2 206902936 1.37E-05 0.45 1759 0.25 0.26 0.046 GRMZM2G113396 (CIN4,COP10,EMB144,F US9): Ubiquitin- conjugating enzyme

family protein S2_206902936 2 206902936 1.37E-05 0.45 1759 0.25 0.26 0.046 GRMZM2G113420 O-Glycosyl hydrolases

family 17 protein S3_13528961 3 13528961 1.04E-05 0.14 1759 0.25 0.26 0.042 GRMZM5G832229 (PSBX): photosystem II

subunit X S3_13528961 3 13528961 1.04E-05 0.14 1759 0.25 0.26 0.042 GRMZM2G146627 (TIP4;1): tonoplast

intrinsic protein 4;1 S3_13528961 3 13528961 1.04E-05 0.14 1759 0.25 0.26 0.042 GRMZM2G447857 Tetratricopeptide repeat (TPR)-like

superfamily protein S3_17831379 3 17831379 1.41E-05 0.19 1759 0.25 0.26 0.046 GRMZM2G030784 (ATCTIMC,CYTOTPI,TPI): triosephosphate

isomerase S3_20175116 3 20175116 9.03E-07 0.36 1759 0.25 0.26 0.011 GRMZM2G412760 Protein kinase

superfamily protein S3_54117113 3 54117113 8.98E-06 0.50 1759 0.25 0.26 0.040 GRMZM2G103771 (ATOEP16-2,ATOEP16- S): Mitochondrial import inner membrane translocase subunit Tim17/Tim22/Tim23

family protein S3_54117113 3 54117113 8.98E-06 0.50 1759 0.25 0.26 0.040 GRMZM2G103755 RING/FYVE/PHD zinc finger superfamily

protein

376

377

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P value maf obs w/o SNP w/ SNP P-values of SNP Annotation S3_54117486 3 54117486 8.55E-06 0.27 1759 0.25 0.26 0.040 GRMZM2G103771 (ATOEP16-2,ATOEP16- S): Mitochondrial import inner membrane translocase subunit Tim17/Tim22/Tim23

family protein S3_54117486 3 54117486 8.55E-06 0.27 1759 0.25 0.26 0.040 GRMZM2G103755 RING/FYVE/PHD zinc finger superfamily

protein

S3_99501500 3 99501500 9.32E-06 0.48 1759 0.25 0.26 0.040 GRMZM2G395853 Lojap-related protein

S3_99531336 3 99531336 7.51E-06 0.30 1759 0.25 0.26 0.039 GRMZM2G395853 Lojap-related protein S3_156487519 3 156487519 1.03E-05 0.40 1759 0.25 0.26 0.042 GRMZM2G338259 (ARF1- BP,ARF2,HSS,ORE14):

auxin response factor 2 S3_156487532 3 156487532 1.99E-07 0.16 1759 0.25 0.26 0.005 GRMZM2G338259 (ARF1- BP,ARF2,HSS,ORE14):

auxin response factor 2 S3_156634936 3 156634936 1.28E-05 0.18 1759 0.25 0.26 0.044 GRMZM2G032132 (CRN,SOL2): Protein kinase superfamily

protein S3_156635092 3 156635092 5.53E-07 0.14 1759 0.25 0.26 0.008 GRMZM2G032132 (CRN,SOL2): Protein kinase superfamily

protein S3_156635147 3 156635147 5.70E-07 0.15 1759 0.25 0.26 0.008 GRMZM2G032132 (CRN,SOL2): Protein kinase superfamily

protein S3_156635152 3 156635152 1.24E-06 0.15 1759 0.25 0.26 0.014 GRMZM2G032132 (CRN,SOL2): Protein kinase superfamily

protein

377

378

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P value maf obs w/o SNP w/ SNP P-values of SNP Annotation S3_156637883 3 156637883 2.32E-06 0.12 1759 0.25 0.26 0.021 GRMZM2G032132 (CRN,SOL2): Protein kinase superfamily

protein S3_156637925 3 156637925 2.78E-07 0.14 1759 0.25 0.26 0.005 GRMZM2G032132 (CRN,SOL2): Protein kinase superfamily

protein S3_156638093 3 156638093 2.77E-06 0.14 1759 0.25 0.26 0.022 GRMZM2G032132 (CRN,SOL2): Protein kinase superfamily

protein S3_156795071 3 156795071 5.01E-08 0.13 1759 0.25 0.26 0.002 GRMZM2G336909 (KYP,SDG33,SUVH4):

SU(VAR)3-9 homolog 4 S3_156795071 3 156795071 5.01E-08 0.13 1759 0.25 0.26 0.002 GRMZM2G031584 DNAJ heat shock N- terminal domain-

containing protein S3_156795071 3 156795071 5.01E-08 0.13 1759 0.25 0.26 0.002 GRMZM2G031528 Heavy metal transport/detoxification

superfamily protein S3_156795071 3 156795071 5.01E-08 0.13 1759 0.25 0.26 0.002 GRMZM2G031493 Homeodomain-like

superfamily protein S3_156795077 3 156795077 6.08E-08 0.13 1759 0.25 0.26 0.002 GRMZM2G336909 (KYP,SDG33,SUVH4):

SU(VAR)3-9 homolog 4 S3_156795077 3 156795077 6.08E-08 0.13 1759 0.25 0.26 0.002 GRMZM2G031584 DNAJ heat shock N- terminal domain-

containing protein S3_156795077 3 156795077 6.08E-08 0.13 1759 0.25 0.26 0.002 GRMZM2G031528 Heavy metal transport/detoxification

superfamily protein S3_156795077 3 156795077 6.08E-08 0.13 1759 0.25 0.26 0.002 GRMZM2G031493 Homeodomain-like

superfamily protein S3_156795092 3 156795092 7.28E-07 0.11 1759 0.25 0.26 0.010 GRMZM2G336909 (KYP,SDG33,SUVH4):

378

SU(VAR)3-9 homolog 4

379

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P value maf obs w/o SNP w/ SNP P-values of SNP Annotation S3_156795092 3 156795092 7.28E-07 0.11 1759 0.25 0.26 0.010 GRMZM2G031584 DNAJ heat shock N- terminal domain-

containing protein S3_156795092 3 156795092 7.28E-07 0.11 1759 0.25 0.26 0.010 GRMZM2G031528 Heavy metal transport/detoxification

superfamily protein S3_156795092 3 156795092 7.28E-07 0.11 1759 0.25 0.26 0.010 GRMZM2G031493 Homeodomain-like

superfamily protein S3_156797381 3 156797381 5.49E-07 0.11 1759 0.25 0.26 0.008 GRMZM2G336909 (KYP,SDG33,SUVH4):

SU(VAR)3-9 homolog 4 S3_156797381 3 156797381 5.49E-07 0.11 1759 0.25 0.26 0.008 GRMZM2G031584 DNAJ heat shock N- terminal domain-

containing protein S3_156797381 3 156797381 5.49E-07 0.11 1759 0.25 0.26 0.008 GRMZM2G031528 Heavy metal transport/detoxification

superfamily protein S3_156797381 3 156797381 5.49E-07 0.11 1759 0.25 0.26 0.008 GRMZM2G031493 Homeodomain-like

superfamily protein S3_156797382 3 156797382 5.49E-07 0.11 1759 0.25 0.26 0.008 GRMZM2G336909 (KYP,SDG33,SUVH4):

SU(VAR)3-9 homolog 4 S3_156797382 3 156797382 5.49E-07 0.11 1759 0.25 0.26 0.008 GRMZM2G031584 DNAJ heat shock N- terminal domain-

containing protein S3_156797382 3 156797382 5.49E-07 0.11 1759 0.25 0.26 0.008 GRMZM2G031528 Heavy metal transport/detoxification

superfamily protein S3_156797382 3 156797382 5.49E-07 0.11 1759 0.25 0.26 0.008 GRMZM2G031493 Homeodomain-like

superfamily protein S3_156797642 3 156797642 1.11E-05 0.22 1759 0.25 0.26 0.042 GRMZM2G336909 (KYP,SDG33,SUVH4):

SU(VAR)3-9 homolog 4

379

380

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P value maf obs w/o SNP w/ SNP P-values of SNP Annotation S3_156797642 3 156797642 1.11E-05 0.22 1759 0.25 0.26 0.042 GRMZM2G031584 DNAJ heat shock N- terminal domain-

containing protein S3_156797642 3 156797642 1.11E-05 0.22 1759 0.25 0.26 0.042 GRMZM2G031528 Heavy metal transport/detoxification

superfamily protein S3_156797642 3 156797642 1.11E-05 0.22 1759 0.25 0.26 0.042 GRMZM2G031493 Homeodomain-like

superfamily protein S3_156798875 3 156798875 2.00E-08 0.13 1759 0.25 0.26 0.001 GRMZM2G336909 (KYP,SDG33,SUVH4):

SU(VAR)3-9 homolog 4 S3_156798875 3 156798875 2.00E-08 0.13 1759 0.25 0.26 0.001 GRMZM2G031584 DNAJ heat shock N- terminal domain-

containing protein S3_156798875 3 156798875 2.00E-08 0.13 1759 0.25 0.26 0.001 GRMZM2G031528 Heavy metal transport/detoxification

superfamily protein S3_156798875 3 156798875 2.00E-08 0.13 1759 0.25 0.26 0.001 GRMZM2G031493 Homeodomain-like

superfamily protein S3_156814328 3 156814328 7.19E-06 0.37 1759 0.25 0.26 0.039 GRMZM2G336909 (KYP,SDG33,SUVH4):

SU(VAR)3-9 homolog 4 S3_156814632 3 156814632 2.50E-06 0.36 1759 0.25 0.26 0.021 GRMZM2G336909 (KYP,SDG33,SUVH4):

SU(VAR)3-9 homolog 4 S3_156963615 3 156963615 9.73E-06 0.46 1759 0.25 0.26 0.041 GRMZM2G142315 Sec14p-like phosphatidylinositol

transfer family protein S3_157019682 3 157019682 5.14E-06 0.06 1759 0.25 0.26 0.034 GRMZM5G898668 (ATGUT1,GUT2,IRX10):

Exostosin family protein S3_157019682 3 157019682 5.14E-06 0.06 1759 0.25 0.26 0.034 GRMZM5G863364 (ATIPK2A,IPK2a): inositol polyphosphate

kinase 2 alpha

380

381

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P value maf obs w/o SNP w/ SNP P-values of SNP Annotation S3_157019691 3 157019691 1.13E-05 0.07 1759 0.25 0.26 0.042 GRMZM5G898668 (ATGUT1,GUT2,IRX10):

Exostosin family protein S3_157019691 3 157019691 1.13E-05 0.07 1759 0.25 0.26 0.042 GRMZM5G863364 (ATIPK2A,IPK2a): inositol polyphosphate

kinase 2 alpha S3_158348749 3 158348749 1.11E-05 0.43 1759 0.25 0.26 0.042 GRMZM2G139617 DEK domain-containing chromatin associated

protein S3_158978714 3 158978714 1.01E-05 0.21 1759 0.25 0.26 0.042 GRMZM2G171650 (AGL3,SEP4): K-box region and MADS-box transcription factor

family protein S3_158978714 3 158978714 1.01E-05 0.21 1759 0.25 0.26 0.042 GRMZM2G171622 CBS / octicosapeptide/Phox/B emp1 (PB1) domains-

containing protein S3_178847449 3 178847449 8.67E-06 0.30 1759 0.25 0.26 0.040 AC147602.5_FG004 (SBPASE): sedoheptulose-

bisphosphatase S3_179634298 3 179634298 6.17E-06 0.37 1759 0.25 0.26 0.036 GRMZM2G007928 BBTI13 - Bowman-Birk type bran trypsin inhibitor precursor,

expressed S3_179634298 3 179634298 6.17E-06 0.37 1759 0.25 0.26 0.036 GRMZM2G178533 NAD(P)-linked oxidoreductase

superfamily protein S3_179634298 3 179634298 6.17E-06 0.37 1759 0.25 0.26 0.036 GRMZM2G479423 NAD(P)-linked oxidoreductase

superfamily protein

381

382

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P value maf obs w/o SNP w/ SNP P-values of SNP Annotation S3_179634300 3 179634300 6.17E-06 0.37 1759 0.25 0.26 0.036 GRMZM2G007928 BBTI13 - Bowman-Birk type bran trypsin inhibitor precursor,

expressed S3_179634300 3 179634300 6.17E-06 0.37 1759 0.25 0.26 0.036 GRMZM2G178533 NAD(P)-linked oxidoreductase

superfamily protein S3_179634300 3 179634300 6.17E-06 0.37 1759 0.25 0.26 0.036 GRMZM2G479423 NAD(P)-linked oxidoreductase

superfamily protein S4_67740840 4 67740840 6.60E-06 0.16 1759 0.25 0.26 0.037 GRMZM2G400129 (CYP96A1): cytochrome P450, family 96, subfamily A,

polypeptide 1 S4_218286494 4 218286494 4.38E-06 0.12 1759 0.25 0.26 0.030 GRMZM2G376265 GDSL-like Lipase/Acylhydrolase

superfamily protein S4_218286495 4 218286495 4.38E-06 0.12 1759 0.25 0.26 0.030 GRMZM2G376265 GDSL-like Lipase/Acylhydrolase

superfamily protein S4_218286496 4 218286496 4.38E-06 0.12 1759 0.25 0.26 0.030 GRMZM2G376265 GDSL-like Lipase/Acylhydrolase

superfamily protein S5_172808199 5 172808199 7.99E-06 0.29 1759 0.25 0.26 0.039 GRMZM2G119517 (ACR3): ACT domain

repeat 3 S5_172808199 5 172808199 7.99E-06 0.29 1759 0.25 0.26 0.039 GRMZM2G119566 DNAJ heat shock N- terminal domain-

containing protein S6_2058651 6 2058651 1.40E-05 0.13 1759 0.25 0.26 0.046 GRMZM2G313321 AT5G36210.1: alpha/beta-Hydrolases

382

superfamily protein

383

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P value maf obs w/o SNP w/ SNP P-values of SNP Annotation S6_4799970 6 4799970 1.26E-05 0.37 1759 0.25 0.26 0.044 GRMZM2G144873 Galactosyltransferase

family protein S6_4799976 6 4799976 1.15E-05 0.37 1759 0.25 0.26 0.042 GRMZM2G144873 Galactosyltransferase

family protein S6_4804248 6 4804248 1.97E-06 0.33 1759 0.25 0.26 0.018 GRMZM2G144873 Galactosyltransferase

family protein S6_31419311 6 31419311 3.94E-06 0.47 1759 0.25 0.26 0.029 GRMZM2G099317 (ATRSZ33,RSZ33): arginine/serine-rich zinc knuckle-containing

protein 33 S6_31419311 6 31419311 3.94E-06 0.47 1759 0.25 0.26 0.029 GRMZM2G099186 (RSZ32): RNA-binding (RRM/RBD/RNP motifs) family protein with retrovirus zinc finger-

like domain S6_31419311 6 31419311 3.94E-06 0.47 1759 0.25 0.26 0.029 GRMZM2G099619 ABC-2 type transporter

family protein S6_93784130 6 93784130 1.12E-05 0.32 1759 0.25 0.26 0.042 GRMZM2G360081 (UFO): F-box family

protein S7_2663867 7 2663867 9.27E-06 0.29 1759 0.25 0.26 0.040 GRMZM2G040170 transcription elongation factor 1, putative,

expressed S7_118909908 7 118909908 9.03E-07 0.07 1759 0.25 0.26 0.011 GRMZM2G117244 (ATMYB68,MYB68):

myb domain protein 68 S7_118909928 7 118909928 9.25E-07 0.07 1759 0.25 0.26 0.011 GRMZM2G117244 (ATMYB68,MYB68):

myb domain protein 68 S7_118909940 7 118909940 6.68E-06 0.07 1759 0.25 0.26 0.037 GRMZM2G117244 AT5G65790.1(ATMYB68 ,MYB68): myb domain

protein 68 S7_122076227 7 122076227 1.15E-05 0.32 1759 0.25 0.26 0.042 GRMZM2G388045 (ATGEX1,GEX1): gamete

383

expressed protein 1

384

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P value maf obs w/o SNP w/ SNP P-values of SNP Annotation S7_122076227 7 122076227 1.15E-05 0.32 1759 0.25 0.26 0.042 GRMZM2G086714 (AT- RSH3,ATRSH3,RSH3):

RELA/SPOT homolog 3 S7_122076227 7 122076227 1.15E-05 0.32 1759 0.25 0.26 0.042 GRMZM2G050172 (AT- RSH3,ATRSH3,RSH3):

RELA/SPOT homolog 3 S7_122130368 7 122130368 2.08E-07 0.36 1759 0.25 0.26 0.005 GRMZM2G075348 E2F-related protein,

putative, expressed S7_128647678 7 128647678 7.60E-06 0.15 1759 0.25 0.26 0.039 GRMZM2G082653 (ATL6): RING/U-box

superfamily protein S7_128647678 7 128647678 7.60E-06 0.15 1759 0.25 0.26 0.039 GRMZM2G382038 (UXS6): UDP-XYL

synthase 6 S7_160440470 7 160440470 3.42E-06 0.29 1759 0.25 0.26 0.026 GRMZM2G054658 DEFL49 - Defensin and Defensin-like DEFL

family, expressed S8_135958143 8 135958143 1.48E-05 0.06 1759 0.25 0.26 0.048 GRMZM2G176707 (NAP1;2,NFA02,NFA2): nucleosome assembly

protein 1;2 S8_162756261 8 162756261 3.19E-06 0.06 1759 0.25 0.26 0.025 GRMZM2G170975 (EPFL9,STOMAGEN):

stomagen S8_162756261 8 162756261 3.19E-06 0.06 1759 0.25 0.26 0.025 GRMZM2G471051 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily

protein S8_162756261 8 162756261 3.19E-06 0.06 1759 0.25 0.26 0.025 GRMZM2G170969 LTPL38 - Protease inhibitor/seed storage/LTP family protein precursor,

expressed

384

S9_22098032 9 22098032 2.84E-07 0.06 1759 0.25 0.26 0.005 GRMZM2G064302 (ENO2,LOS2): Enolase

385

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P value maf obs w/o SNP w/ SNP P-values of SNP Annotation S9_22424947 9 22424947 1.33E-07 0.14 1759 0.25 0.26 0.004 GRMZM2G398341 (PI- 4KBETA1,PI4KBETA1): phosphatidylinositol 4-

OH kinase beta1

S9_22685747 9 22685747 9.60E-15 0.05 1759 0.25 0.28 0.000 GRMZM5G847362 F-box family protein S9_22685747 9 22685747 9.60E-15 0.05 1759 0.25 0.28 0.000 GRMZM5G877500 RNA 3\'-terminal phosphate cyclase/enolpyruvate

transferase, alpha/beta

S9_22781026 9 22781026 1.80E-06 0.09 1759 0.25 0.26 0.018 GRMZM2G033208 Transketolase S9_23280484 9 23280484 1.28E-07 0.10 1759 0.25 0.26 0.004 GRMZM2G171395 (ANAC043,EMB2301,NS T1): NAC (No Apical Meristem) domain transcriptional regulator superfamily

protein S9_23280484 9 23280484 1.28E-07 0.10 1759 0.25 0.26 0.004 GRMZM2G171376 (EDA38,SBP2): selenium-binding

protein 2 S9_23334850 9 23334850 2.48E-09 0.07 1759 0.25 0.27 0.000 GRMZM2G110158 Lung seven transmembrane

receptor family protein S9_23458161 9 23458161 7.00E-11 0.06 1759 0.25 0.27 0.000 GRMZM2G121333 alpha/beta-Hydrolases

superfamily protein

S9_105518929 9 105518929 2.43E-06 0.05 1759 0.25 0.26 0.021 GRMZM2G085218 (BBX32): B-box 32 S9_105518929 9 105518929 2.43E-06 0.05 1759 0.25 0.26 0.021 GRMZM2G085246 (SRF1): STRUBBELIG-

receptor family 1 S9_105518929 9 105518929 2.43E-06 0.05 1759 0.25 0.26 0.021 GRMZM2G384661 NC domain-containing protein-related 385

386

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P value maf obs w/o SNP w/ SNP P-values of SNP Annotation S10_134601466 10 134601466 1.29E-06 0.44 1759 0.25 0.26 0.014 GRMZM2G018485 (NGA1): AP2/B3-like transcriptional factor

family protein

S10_134601466 10 134601466 1.29E-06 0.44 1759 0.25 0.26 0.014 GRMZM2G018464 G10 family protein S10_135609893 10 135609893 7.51E-06 0.13 1759 0.25 0.26 0.039 GRMZM2G086541 (GIK): Predicted AT- hook DNA-binding

family protein

386

387

I-2 Maize Kernel Oil Candidate Genes

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values of SNP Annotation S1_286182550 1 286182550 3.35E-09 0.10 1747 0.30 0.32 0.001 GRMZM2G174136 DUF593 domain containing protein,

expressed S1_286182550 1 286182550 3.35E-09 0.10 1747 0.30 0.32 0.001 GRMZM2G174210 VQ motif-containing

protein S2_236293157 2 236293157 3.39E-06 0.32 1747 0.30 0.31 0.047 GRMZM2G104032 (FUT8):

fucosyltransferase 8 S2_236293157 2 236293157 3.39E-06 0.32 1747 0.30 0.31 0.047 GRMZM2G083572 H-BTB5 - Bric-a-Brac, Tramtrack, Broad Complex BTB domain with H family conserved

sequence, S2_236293157 2 236293157 3.39E-06 0.32 1747 0.30 0.31 0.047 GRMZM2G103955 Tetratricopeptide repeat (TPR)-like superfamily

protein S3_212029092 3 212029092 7.13E-07 0.24 1747 0.30 0.31 0.015 GRMZM2G382632 (HS,HWS): Galactose oxidase/kelch repeat

superfamily protein S3_212029092 3 212029092 7.13E-07 0.24 1747 0.30 0.31 0.015 GRMZM2G033576 Calcium-dependent lipid- binding (CaLB domain)

family protein S3_212029094 3 212029094 1.84E-06 0.24 1747 0.30 0.31 0.033 GRMZM2G382632 (HS,HWS): Galactose oxidase/kelch repeat

superfamily protein S3_212029094 3 212029094 1.84E-06 0.24 1747 0.30 0.31 0.033 GRMZM2G033576 Calcium-dependent lipid- binding (CaLB domain)

family protein

387

388

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values of SNP Annotation S5_128105944 5 128105944 9.49E-07 0.14 1747 0.30 0.31 0.019 GRMZM2G071089 (ATPCAP1,PCAP1): plasma-membrane associated cation-binding

protein 1 S6_104674381 6 104674381 1.22E-08 0.17 1747 0.30 0.31 0.001 GRMZM2G151015 (GAUT11): galacturonosyltransferas

e 11 S6_104674381 6 104674381 1.22E-08 0.17 1747 0.30 0.31 0.001 GRMZM2G449817 Protein kinase family protein with leucine-rich

repeat domain S6_104713425 6 104713425 2.02E-07 0.19 1747 0.30 0.31 0.006 GRMZM2G151015 (GAUT11): galacturonosyltransferas

e 11 S6_104713425 6 104713425 2.02E-07 0.19 1747 0.30 0.31 0.006 GRMZM2G109009 (nPAP,PAP(IV)): nuclear

poly(a) polymerase S6_104713426 6 104713426 2.02E-07 0.19 1747 0.30 0.31 0.006 GRMZM2G151015 (GAUT11): galacturonosyltransferas

e 11 S6_104713426 6 104713426 2.02E-07 0.19 1747 0.30 0.31 0.006 GRMZM2G109009 (nPAP,PAP(IV)): nuclear

poly(a) polymerase S6_104713427 6 104713427 2.02E-07 0.19 1747 0.30 0.31 0.006 GRMZM2G151015 (GAUT11): galacturonosyltransferas

e 11 S6_104713427 6 104713427 2.02E-07 0.19 1747 0.30 0.31 0.006 GRMZM2G109009 (nPAP,PAP(IV)): nuclear

poly(a) polymerase S6_104713428 6 104713428 2.02E-07 0.19 1747 0.30 0.31 0.006 GRMZM2G151015 (GAUT11): galacturonosyltransferas

e 11 S6_104713428 6 104713428 2.02E-07 0.19 1747 0.30 0.31 0.006 GRMZM2G109009 (nPAP,PAP(IV)): nuclear

poly(a) polymerase

388

389

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values of SNP Annotation S6_104713429 6 104713429 2.04E-07 0.19 1747 0.30 0.31 0.006 GRMZM2G151015 (GAUT11): galacturonosyltransferas

e 11 S6_104713429 6 104713429 2.04E-07 0.19 1747 0.30 0.31 0.006 GRMZM2G109009 (nPAP,PAP(IV)): nuclear

poly(a) polymerase S6_104713431 6 104713431 1.48E-07 0.20 1747 0.30 0.31 0.006 GRMZM2G151015 (GAUT11): galacturonosyltransferas

e 11 S6_104713431 6 104713431 1.48E-07 0.20 1747 0.30 0.31 0.006 GRMZM2G109009 (nPAP,PAP(IV)): nuclear

poly(a) polymerase S6_104756131 6 104756131 5.93E-07 0.26 1747 0.30 0.31 0.014 GRMZM2G103526 HAD superfamily, subfamily IIIB acid

phosphatase S6_104759005 6 104759005 6.32E-08 0.23 1747 0.30 0.31 0.003 GRMZM2G103526 HAD superfamily, subfamily IIIB acid

phosphatase S6_104759143 6 104759143 2.42E-07 0.24 1747 0.30 0.31 0.006 GRMZM2G103526 HAD superfamily, subfamily IIIB acid

phosphatase S6_104858735 6 104858735 5.51E-09 0.15 1747 0.30 0.31 0.001 GRMZM2G169089 (ABX45,AS11,ATDGAT,D GAT1,RDS1,TAG1): membrane bound O-acyl transferase (MBOAT)

family protein S6_104858735 6 104858735 5.51E-09 0.15 1747 0.30 0.31 0.001 GRMZM2G169114 (ATKEA4,KEA4): K+ efflux

antiporter 4 S6_104865217 6 104865217 1.10E-08 0.23 1747 0.30 0.31 0.001 GRMZM2G169089 (ABX45,AS11,ATDGAT,D GAT1,RDS1,TAG1): membrane bound O-acyl transferase (MBOAT)

389

family protein

390

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values of SNP Annotation S6_104865217 6 104865217 1.10E-08 0.23 1747 0.30 0.31 0.001 GRMZM2G169114 (ATKEA4,KEA4): K+ efflux

antiporter 4 S6_104865219 6 104865219 2.10E-06 0.23 1747 0.30 0.31 0.035 GRMZM2G169089 (ABX45,AS11,ATDGAT,D GAT1,RDS1,TAG1): membrane bound O-acyl transferase (MBOAT)

family protein S6_104865219 6 104865219 2.10E-06 0.23 1747 0.30 0.31 0.035 GRMZM2G169114 (ATKEA4,KEA4): K+ efflux

antiporter 4 S6_104865232 6 104865232 2.18E-06 0.23 1747 0.30 0.31 0.035 GRMZM2G169089 (ABX45,AS11,ATDGAT,D GAT1,RDS1,TAG1): membrane bound O-acyl transferase (MBOAT)

family protein S6_104865232 6 104865232 2.18E-06 0.23 1747 0.30 0.31 0.035 GRMZM2G169114 (ATKEA4,KEA4): K+ efflux

antiporter 4 S8_5919129 8 5919129 2.76E-06 0.37 1747 0.30 0.31 0.041 GRMZM2G024151 (ATSK13,SK13): shaggy-

like kinase 13 S8_5919129 8 5919129 2.76E-06 0.37 1747 0.30 0.31 0.041 GRMZM2G024655 C2H2 and C2HC zinc fingers superfamily

protein S8_7617214 8 7617214 4.70E-08 0.49 1747 0.30 0.31 0.003 GRMZM2G078941 (ATRER1A): Rer1 family

protein S8_161916833 8 161916833 2.78E-06 0.39 1747 0.30 0.31 0.041 GRMZM2G013060 (atnudt16,NUDT16): nudix hydrolase homolog

16 S8_161916833 8 161916833 2.78E-06 0.39 1747 0.30 0.31 0.041 GRMZM5G875238 (ATSPS3F,SPS3F): sucrose

phosphate synthase 3F S9_57188643 9 57188643 3.10E-06 0.19 1747 0.30 0.31 0.044 GRMZM2G076272 (ATH1): homeobox gene

390

391

R2 of R2 of FDR N Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values of SNP Annotation S9_125564283 9 125564283 1.75E-06 0.40 1747 0.30 0.31 0.032 GRMZM2G142999 (NGA2): AP2/B3-like transcriptional factor

family protein S9_130873039 9 130873039 7.19E-07 0.35 1747 0.30 0.31 0.015 GRMZM2G015280 Peroxidase superfamily

protein

391

392

I-3 Maize Kernel Protein Candidate Genes

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_2466879 1 2466879 5.59E-05 0.05 1760 0.35 0.36 0.039 GRMZM2G028870 RING/U-box

superfamily protein

S1_3734582 1 3734582 4.92E-05 0.27 1760 0.35 0.36 0.037 GRMZM2G030567 : expressed protein S1_3734582 1 3734582 4.92E-05 0.27 1760 0.35 0.36 0.037 GRMZM2G320111 ligA, putative,

expressed S1_3734582 1 3734582 4.92E-05 0.27 1760 0.35 0.36 0.037 GRMZM2G030299 Protein kinase

superfamily protein

S1_3734754 1 3734754 9.23E-05 0.23 1760 0.35 0.36 0.047 GRMZM2G030567 : expressed protein S1_3734754 1 3734754 9.23E-05 0.23 1760 0.35 0.36 0.047 GRMZM2G320111 ligA, putative,

expressed S1_3734754 1 3734754 9.23E-05 0.23 1760 0.35 0.36 0.047 GRMZM2G030299 Protein kinase

superfamily protein S1_17492505 1 17492505 4.06E-05 0.11 1760 0.35 0.36 0.034 GRMZM2G018984 (HRE1): Integrase- type DNA-binding

superfamily protein S1_17492539 1 17492539 4.06E-05 0.11 1760 0.35 0.36 0.034 GRMZM2G018984 (HRE1): Integrase- type DNA-binding

superfamily protein S1_19978920 1 19978920 5.07E-05 0.14 1760 0.35 0.36 0.037 AC166636.1_FG009 (APUM7,PUM7):

pumilio 7 S1_19978920 1 19978920 5.07E-05 0.14 1760 0.35 0.36 0.037 AC166636.1_FG008 (ATRAB6A,ATRABH1 B,RAB6,RAB6A): Ras-related small GTP-binding family

protein S1_19978930 1 19978930 9.18E-05 0.18 1760 0.35 0.36 0.047 AC166636.1_FG009 (APUM7,PUM7):

pumilio 7

392

393

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_19978930 1 19978930 9.18E-05 0.18 1760 0.35 0.36 0.047 AC166636.1_FG008 (ATRAB6A,ATRABH1 B,RAB6,RAB6A): Ras-related small GTP-binding family

protein S1_19979829 1 19979829 8.87E-05 0.25 1760 0.35 0.36 0.047 AC166636.1_FG009 (APUM7,PUM7):

pumilio 7 S1_19979829 1 19979829 8.87E-05 0.25 1760 0.35 0.36 0.047 AC166636.1_FG008 (ATRAB6A,ATRABH1 B,RAB6,RAB6A): Ras-related small GTP-binding family

protein S1_19979854 1 19979854 8.87E-05 0.25 1760 0.35 0.36 0.047 AC166636.1_FG009 (APUM7,PUM7):

pumilio 7 S1_19979854 1 19979854 8.87E-05 0.25 1760 0.35 0.36 0.047 AC166636.1_FG009 (APUM7,PUM7):

pumilio 7 S1_19979854 1 19979854 8.87E-05 0.25 1760 0.35 0.36 0.047 AC166636.1_FG008 (ATRAB6A,ATRABH1 B,RAB6,RAB6A): Ras-related small GTP-binding family

protein S1_19979854 1 19979854 8.87E-05 0.25 1760 0.35 0.36 0.047 AC166636.1_FG008 (ATRAB6A,ATRABH1 B,RAB6,RAB6A): Ras-related small GTP-binding family

protein S1_24941000 1 24941000 1.05E-04 0.07 1760 0.35 0.36 0.049 GRMZM2G032423 (FRL2): FRIGIDA like

2 S1_28964818 1 28964818 9.54E-05 0.48 1760 0.35 0.36 0.048 GRMZM2G153611 (ARI2,ATARI2): RING/U-box

393

superfamily protein

394

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_28964818 1 28964818 9.54E-05 0.48 1760 0.35 0.36 0.048 GRMZM2G469304 Protein of unknown

function, DUF547 S1_32088456 1 32088456 2.23E-05 0.49 1760 0.35 0.36 0.027 GRMZM2G152549 hydroxyproline-rich glycoprotein family

protein S1_32088456 1 32088456 2.23E-05 0.49 1760 0.35 0.36 0.027 GRMZM2G152663 Protein of unknown

function (DUF1423) S1_33883039 1 33883039 1.20E-06 0.25 1760 0.35 0.36 0.011 GRMZM2G035552 (ACR8): ACT domain

repeat 8 S1_33883039 1 33883039 1.20E-06 0.25 1760 0.35 0.36 0.011 GRMZM2G035461 AT2G31260.1(APG9, ATAPG9): autophagy

9 (APG9) S1_33956321 1 33956321 1.42E-05 0.33 1760 0.35 0.36 0.024 GRMZM2G321033 AT2G45560.1(CYP76 C1): cytochrome P450, family 76, subfamily C,

polypeptide 1 S1_33956480 1 33956480 1.41E-05 0.27 1760 0.35 0.36 0.024 GRMZM2G321033 AT2G45560.1(CYP76 C1): cytochrome P450, family 76, subfamily C,

polypeptide 1 S1_33956502 1 33956502 1.41E-05 0.27 1760 0.35 0.36 0.024 GRMZM2G321033 AT2G45560.1(CYP76 C1): cytochrome P450, family 76, subfamily C,

polypeptide 1 S1_39856880 1 39856880 2.07E-05 0.28 1760 0.35 0.36 0.027 GRMZM2G321033 AT2G45560.1(CYP76 C1): cytochrome P450, family 76,

394 subfamily C,

polypeptide 1

395

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_43110857 1 43110857 3.90E-06 0.24 1760 0.35 0.36 0.015 GRMZM2G338131 (GSTL2): glutathione transferase lambda

2 S1_43110857 1 43110857 3.90E-06 0.24 1760 0.35 0.36 0.015 GRMZM2G043291 (GSTL2): glutathione transferase lambda

2 S1_43110857 1 43110857 3.90E-06 0.24 1760 0.35 0.36 0.015 GRMZM2G042639 (GSTL2): glutathione transferase lambda

2 S1_46848758 1 46848758 6.90E-05 0.16 1760 0.35 0.36 0.042 GRMZM2G010328 (AGD2): Pyridoxal phosphate (PLP)- dependent transferases

superfamily protein

S1_46848758 1 46848758 6.90E-05 0.16 1760 0.35 0.36 0.042 GRMZM2G313934 : expressed protein S1_46848758 1 46848758 6.90E-05 0.16 1760 0.35 0.36 0.042 GRMZM2G010545 PLAC8 family

protein S1_46924149 1 46924149 9.64E-06 0.07 1760 0.35 0.36 0.023 GRMZM2G113364 zinc finger (MYND type) family protein / programmed cell death 2 C-terminal domain-containing

protein S1_46924228 1 46924228 6.15E-05 0.05 1760 0.35 0.36 0.040 GRMZM2G113364 zinc finger (MYND type) family protein / programmed cell death 2 C-terminal domain-containing

protein

395

396

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_49656821 1 49656821 1.97E-05 0.17 1760 0.35 0.36 0.027 GRMZM2G011483 Uncharacterized

protein S1_50864330 1 50864330 4.05E-05 0.12 1760 0.35 0.36 0.034 GRMZM5G851485 sequence-specific DNA binding

transcription factors S1_54125348 1 54125348 3.99E-05 0.34 1760 0.35 0.36 0.034 GRMZM2G003424 Zinc finger (CCCH- type) family protein / RNA recognition motif (RRM)-

containing protein S1_80767432 1 80767432 2.56E-05 0.14 1760 0.35 0.36 0.029 GRMZM2G049852 MATE efflux family

protein S1_88969303 1 88969303 5.15E-05 0.36 1760 0.35 0.36 0.037 GRMZM2G089291 (ATRBOH F,ATRBOHF,RBOH F,RBOHAP108,RBOH F): respiratory burst

oxidase protein F S1_88969306 1 88969306 5.15E-05 0.36 1760 0.35 0.36 0.037 GRMZM2G089291 (ATRBOH F,ATRBOHF,RBOH F,RBOHAP108,RBOH F): respiratory burst

oxidase protein F S1_90222083 1 90222083 4.60E-05 0.36 1760 0.35 0.36 0.036 GRMZM2G154580 CCT motif family

protein, expressed S1_90222083 1 90222083 4.60E-05 0.36 1760 0.35 0.36 0.036 GRMZM2G154565 Plant protein of unknown function (DUF828) with plant pleckstrin homology-like

region

396

397

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_90222083 1 90222083 4.60E-05 0.36 1760 0.35 0.36 0.036 GRMZM2G154487 Ribosomal L18p/L5e

family protein S1_90229651 1 90229651 8.40E-06 0.29 1760 0.35 0.36 0.021 GRMZM2G154565 Plant protein of unknown function (DUF828) with plant pleckstrin homology-like

region S1_90229651 1 90229651 8.40E-06 0.29 1760 0.35 0.36 0.021 GRMZM2G154487 Ribosomal L18p/L5e family

protein S1_90229671 1 90229671 8.40E-06 0.29 1760 0.35 0.36 0.021 GRMZM2G154565 Plant protein of unknown function (DUF828) with plant pleckstrin homology-like

region S1_90229671 1 90229671 8.40E-06 0.29 1760 0.35 0.36 0.021 GRMZM2G154487 Ribosomal L18p/L5e

family protein S1_92243089 1 92243089 1.06E-04 0.42 1760 0.35 0.36 0.049 GRMZM2G114772 Nucleotide- diphospho-sugar transferases

superfamily protein S1_92243089 1 92243089 1.06E-04 0.42 1760 0.35 0.36 0.049 GRMZM2G114707 Polynucleotidyl transferase, ribonuclease H-like

superfamily protein S1_92243089 1 92243089 1.06E-04 0.42 1760 0.35 0.36 0.049 GRMZM2G114667 ZOS10-02 - C2H2 zinc finger protein,

expressed

397

398

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_172880584 1 172880584 6.30E-05 0.23 1760 0.35 0.36 0.041 GRMZM5G865967 (PIF4,SRL2): phytochrome

interacting factor 4 S1_172880584 1 172880584 6.30E-05 0.23 1760 0.35 0.36 0.041 GRMZM2G087608 OsFBX436 - F-box domain containing

protein, expressed S1_176097717 1 176097717 3.75E-05 0.18 1760 0.35 0.36 0.033 GRMZM2G042313 (CAT2): cationic amino acid

transporter 2 S1_183998437 1 183998437 3.88E-05 0.25 1760 0.35 0.36 0.033 GRMZM2G080775 (ATPEX5,PEX5):

peroxin 5 S1_183998437 1 183998437 3.88E-05 0.25 1760 0.35 0.36 0.033 GRMZM2G080746 (EMB2777): Sas10/U3 ribonucleoprotein

(Utp) family protein S1_231278895 1 231278895 3.29E-05 0.26 1760 0.35 0.36 0.031 GRMZM2G147346 (ATMYB15,ATY19,M YB15): myb domain

protein 15 S1_231481655 1 231481655 3.07E-05 0.25 1760 0.35 0.36 0.030 GRMZM2G010362 ARM repeat

superfamily protein S1_231511049 1 231511049 6.43E-05 0.32 1760 0.35 0.36 0.041 GRMZM2G010362 ARM repeat

superfamily protein S1_232529212 1 232529212 9.39E-05 0.40 1760 0.35 0.36 0.047 GRMZM2G150179 NB-ARC domain- containing disease

resistance protein S1_236916133 1 236916133 5.26E-05 0.10 1760 0.35 0.36 0.037 GRMZM2G430675 (ATNAP12,NAP12): non-intrinsic ABC

protein 12 S1_236916133 1 236916133 5.26E-05 0.10 1760 0.35 0.36 0.037 GRMZM2G130897 retrotransposon protein, putative,

398 unclassified,

expressed

399

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_236916154 1 236916154 5.26E-05 0.10 1760 0.35 0.36 0.037 GRMZM2G430675 (ATNAP12,NAP12): non-intrinsic ABC

protein 12 S1_236916154 1 236916154 5.26E-05 0.10 1760 0.35 0.36 0.037 GRMZM2G130897 retrotransposon protein, putative, unclassified,

expressed S1_241481541 1 241481541 8.03E-05 0.48 1760 0.35 0.36 0.045 GRMZM2G064605 Pathogenesis- related thaumatin

superfamily protein S1_244825916 1 244825916 1.87E-05 0.22 1760 0.35 0.36 0.026 GRMZM2G145412 (JAZ11,TIFY3A): jasmonate-zim-

domain protein 11 S1_244825916 1 244825916 1.87E-05 0.22 1760 0.35 0.36 0.026 GRMZM2G145458 (JAZ11,TIFY3A): jasmonate-zim-

domain protein 11 S1_244834295 1 244834295 4.61E-07 0.29 1760 0.35 0.36 0.008 GRMZM2G145412 (JAZ11,TIFY3A): jasmonate-zim-

domain protein 11 S1_244834295 1 244834295 4.61E-07 0.29 1760 0.35 0.36 0.008 GRMZM2G145458 (JAZ11,TIFY3A): jasmonate-zim-

domain protein 11 S1_244978469 1 244978469 2.05E-05 0.19 1760 0.35 0.36 0.027 GRMZM2G083182 (ATGCN3,GCN3): general control non-

repressible 3 S1_244978469 1 244978469 2.05E-05 0.19 1760 0.35 0.36 0.027 GRMZM2G083156 (MOT1): molybdate

transporter 1 S1_244978469 1 244978469 2.05E-05 0.19 1760 0.35 0.36 0.027 GRMZM2G083091 Transmembrane

proteins 14C S1_244978478 1 244978478 7.39E-05 0.07 1760 0.35 0.36 0.043 GRMZM2G083182 (ATGCN3,GCN3):

399 general control non-

repressible 3

400

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_244978478 1 244978478 7.39E-05 0.07 1760 0.35 0.36 0.043 GRMZM2G083156 (MOT1): molybdate

transporter 1 S1_244978478 1 244978478 7.39E-05 0.07 1760 0.35 0.36 0.043 GRMZM2G083091 Transmembrane

proteins 14C S1_245035072 1 245035072 1.68E-05 0.33 1760 0.35 0.36 0.025 GRMZM2G174549 (ATPAP18,PAP18): purple acid

phosphatase 18 S1_245035072 1 245035072 1.68E-05 0.33 1760 0.35 0.36 0.025 GRMZM2G174574 AMP-dependent synthetase and

ligase family protein S1_245035072 1 245035072 1.68E-05 0.33 1760 0.35 0.36 0.025 GRMZM2G472403 histone-lysine N-

methyltransferases S1_245035242 1 245035242 4.23E-07 0.37 1760 0.35 0.36 0.008 GRMZM2G174549 (ATPAP18,PAP18): purple acid

phosphatase 18 S1_245035242 1 245035242 4.23E-07 0.37 1760 0.35 0.36 0.008 GRMZM2G174574 AMP-dependent synthetase and

ligase family protein S1_245035242 1 245035242 4.23E-07 0.37 1760 0.35 0.36 0.008 GRMZM2G472403 histone-lysine N-

methyltransferases S1_245035279 1 245035279 6.47E-07 0.38 1760 0.35 0.36 0.008 GRMZM2G174549 (ATPAP18,PAP18): purple acid

phosphatase 18 S1_245035279 1 245035279 6.47E-07 0.38 1760 0.35 0.36 0.008 GRMZM2G174574 AMP-dependent synthetase and

ligase family protein S1_245035279 1 245035279 6.47E-07 0.38 1760 0.35 0.36 0.008 GRMZM2G472403 histone-lysine N-

methyltransferases S1_245035313 1 245035313 8.03E-05 0.21 1760 0.35 0.36 0.045 GRMZM2G174549 (ATPAP18,PAP18): purple acid

400

phosphatase 18

401

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_245035313 1 245035313 8.03E-05 0.21 1760 0.35 0.36 0.045 GRMZM2G174574 AMP-dependent synthetase and

ligase family protein S1_245035313 1 245035313 8.03E-05 0.21 1760 0.35 0.36 0.045 GRMZM2G472403 histone-lysine N-

methyltransferases S1_245035347 1 245035347 2.24E-06 0.34 1760 0.35 0.36 0.013 GRMZM2G174549 (ATPAP18,PAP18): purple acid

phosphatase 18 S1_245035347 1 245035347 2.24E-06 0.34 1760 0.35 0.36 0.013 GRMZM2G174574 AMP-dependent synthetase and

ligase family protein S1_245035347 1 245035347 2.24E-06 0.34 1760 0.35 0.36 0.013 GRMZM2G472403 histone-lysine N-

methyltransferases S1_245035387 1 245035387 8.50E-06 0.34 1760 0.35 0.36 0.021 GRMZM2G174549 (ATPAP18,PAP18): purple acid

phosphatase 18 S1_245035387 1 245035387 8.50E-06 0.34 1760 0.35 0.36 0.021 GRMZM2G174574 AMP-dependent synthetase and

ligase family protein S1_245035387 1 245035387 8.50E-06 0.34 1760 0.35 0.36 0.021 GRMZM2G472403 histone-lysine N-

methyltransferases S1_252931947 1 252931947 1.08E-04 0.19 1760 0.35 0.36 0.050 GRMZM2G111269 Protein kinase

superfamily protein S1_257971543 1 257971543 5.93E-06 0.14 1760 0.35 0.36 0.018 GRMZM2G319281 Leucine-rich repeat

(LRR) family protein S1_257971543 1 257971543 5.93E-06 0.14 1760 0.35 0.36 0.018 GRMZM2G055037 SBP (S-ribonuclease binding protein)

family protein S1_258045844 1 258045844 8.40E-05 0.12 1760 0.35 0.36 0.046 GRMZM2G046101 O-Glycosyl hydrolases family 17

401

protein

402

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_258875029 1 258875029 4.87E-06 0.48 1760 0.35 0.36 0.016 GRMZM2G359127 2Fe-2S ferredoxin- like superfamily

protein S1_258875029 1 258875029 4.87E-06 0.48 1760 0.35 0.36 0.016 GRMZM2G704005 Lactoylglutathione lyase / glyoxalase I

family protein S1_258957508 1 258957508 1.28E-05 0.28 1760 0.35 0.36 0.024 GRMZM2G149238 (ATTBP2,TBP2): TATA binding

protein 2 S1_258957508 1 258957508 1.28E-05 0.28 1760 0.35 0.36 0.024 GRMZM2G149219 (ATWRKY49,WRKY4 9): WRKY DNA-

binding protein 49 S1_259219664 1 259219664 9.60E-05 0.12 1760 0.35 0.36 0.048 GRMZM2G165747 (ATCIMS,ATMETS,AT MS1): Cobalamin- independent synthase family

protein S1_259219664 1 259219664 9.60E-05 0.12 1760 0.35 0.36 0.048 GRMZM2G154151 Microsomal signal peptidase 12 kDa

subunit (SPC12) S1_259274478 1 259274478 8.85E-05 0.20 1760 0.35 0.36 0.047 GRMZM2G176605 Ankyrin repeat

family protein S1_260150212 1 260150212 6.51E-05 0.37 1760 0.35 0.36 0.042 GRMZM2G134976 Protein of unknown

function, DUF593 S1_260150212 1 260150212 6.51E-05 0.37 1760 0.35 0.36 0.042 GRMZM2G134982 Ribosomal protein S5/Elongation factor G/III/V family

protein S1_260150230 1 260150230 7.02E-06 0.38 1760 0.35 0.36 0.020 GRMZM2G134976 Protein of unknown

402

function, DUF593

403

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation

S1_260150230 1 260150230 7.02E-06 0.38 1760 0.35 0.36 0.020 GRMZM2G134982 Ribosomal protein S5/Elongation factor G/III/V family

protein S1_260150325 1 260150325 1.09E-05 0.38 1760 0.35 0.36 0.023 GRMZM2G134976 Protein of unknown

function, DUF593 S1_260150325 1 260150325 1.09E-05 0.38 1760 0.35 0.36 0.023 GRMZM2G134982 Ribosomal protein S5/Elongation factor G/III/V family

protein S1_262501900 1 262501900 9.75E-05 0.37 1760 0.35 0.36 0.048 GRMZM2G063133 Core-2/I-branching beta-1,6-N- acetylglucosaminyltr ansferase family

protein

S1_275776628 1 275776628 2.95E-05 0.36 1760 0.35 0.36 0.030 GRMZM2G171248 sterol isomerases S1_278451818 1 278451818 7.40E-07 0.38 1760 0.35 0.36 0.009 GRMZM2G047628 (ATRPA1A,ATRPA70 A,RPA1A,RPA70A): replication protein A

1A S1_286399806 1 286399806 8.02E-05 0.43 1760 0.35 0.36 0.045 GRMZM2G110295 (GATA2): GATA transcription factor

2 S1_288014744 1 288014744 3.11E-05 0.35 1760 0.35 0.36 0.030 GRMZM2G141244 zinc finger (C3HC4- type RING finger)

family protein S1_290309506 1 290309506 5.46E-05 0.42 1760 0.35 0.36 0.038 GRMZM2G082312 carboxyl-terminal peptidase, putative,

403 expressed

404

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_291901727 1 291901727 2.21E-05 0.16 1760 0.35 0.36 0.027 GRMZM5G831951 (AP19): associated

protein 19 S1_291901727 1 291901727 2.21E-05 0.16 1760 0.35 0.36 0.027 GRMZM2G027068 basic helix-loop- helix (bHLH) DNA- binding superfamily

protein S1_291901727 1 291901727 2.21E-05 0.16 1760 0.35 0.36 0.027 GRMZM2G087753 BRCA1 C Terminus domain containing

protein, expressed S1_295018890 1 295018890 1.09E-04 0.36 1760 0.35 0.36 0.050 GRMZM2G139041 (NPC1): non-specific

phospholipase C1 S1_295018890 1 295018890 1.09E-04 0.36 1760 0.35 0.36 0.050 GRMZM2G139123 Transcriptional coactivator/pterin

dehydratase S1_295018912 1 295018912 1.09E-04 0.36 1760 0.35 0.36 0.050 GRMZM2G139041 (NPC1): non- specific

phospholipase C1 S1_295018912 1 295018912 1.09E-04 0.36 1760 0.35 0.36 0.050 GRMZM2G139123 Transcriptional coactivator/pterin

dehydratase S1_295018933 1 295018933 1.09E-04 0.36 1760 0.35 0.36 0.050 GRMZM2G139041 (NPC1): non- specific

phospholipase C1 S1_295018933 1 295018933 1.09E-04 0.36 1760 0.35 0.36 0.050 GRMZM2G139123 Transcriptional coactivator/pterin

dehydratase S1_295306897 1 295306897 1.75E-05 0.21 1760 0.35 0.36 0.025 GRMZM5G840909 Cytidine/deoxycytid ylate deaminase

family protein

404

405

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_295306897 1 295306897 1.75E-05 0.21 1760 0.35 0.36 0.025 AC191575.2_FG001 Haloacid dehalogenase-like hydrolase (HAD)

superfamily protein S1_295306897 1 295306897 1.75E-05 0.21 1760 0.35 0.36 0.025 GRMZM5G882418 Pectin lyase-like

superfamily protein S1_295306910 1 295306910 1.75E-05 0.21 1760 0.35 0.36 0.025 GRMZM5G840909 Cytidine/deoxycytid ylate deaminase

family protein S1_295306910 1 295306910 1.75E-05 0.21 1760 0.35 0.36 0.025 AC191575.2_FG001 Haloacid dehalogenase-like hydrolase (HAD)

superfamily protein S1_295306910 1 295306910 1.75E-05 0.21 1760 0.35 0.36 0.025 GRMZM5G882418 Pectin lyase-like

superfamily protein S1_295349611 1 295349611 5.32E-05 0.17 1760 0.35 0.36 0.037 GRMZM5G840909 Cytidine/deoxycytid ylate deaminase

family protein S1_295349611 1 295349611 5.32E-05 0.17 1760 0.35 0.36 0.037 AC191575.2_FG001 Haloacid dehalogenase-like hydrolase (HAD)

superfamily protein S1_295349611 1 295349611 5.32E-05 0.17 1760 0.35 0.36 0.037 GRMZM5G882418 Pectin lyase-like

superfamily protein S1_295349612 1 295349612 1.54E-05 0.19 1760 0.35 0.36 0.025 GRMZM5G840909 Cytidine/deoxycytid ylate deaminase

family protein S1_295349612 1 295349612 1.54E-05 0.19 1760 0.35 0.36 0.025 AC191575.2_FG001 Haloacid dehalogenase-like hydrolase (HAD)

405

superfamily protein

406

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S1_295349612 1 295349612 1.54E-05 0.19 1760 0.35 0.36 0.025 GRMZM5G882418 Pectin lyase-like

superfamily protein S1_295349615 1 295349615 1.54E-05 0.19 1760 0.35 0.36 0.025 GRMZM5G840909 Cytidine/deoxycytid ylate deaminase

family protein S1_295349615 1 295349615 1.54E-05 0.19 1760 0.35 0.36 0.025 AC191575.2_FG001 Haloacid dehalogenase-like hydrolase (HAD)

superfamily protein S1_295349615 1 295349615 1.54E-05 0.19 1760 0.35 0.36 0.025 GRMZM5G882418 Pectin lyase-like

superfamily protein S1_300990544 1 300990544 3.02E-05 0.27 1760 0.35 0.36 0.030 GRMZM2G122267 Pleckstrin homology (PH) domain-

containing protein S1_300994650 1 300994650 1.45E-05 0.23 1760 0.35 0.36 0.024 GRMZM2G122267 Pleckstrin homology (PH) domain-

containing protein S1_300994672 1 300994672 1.88E-06 0.24 1760 0.35 0.36 0.012 GRMZM2G122267 Pleckstrin homology (PH) domain-

containing protein S1_300994674 1 300994674 1.88E-06 0.24 1760 0.35 0.36 0.012 GRMZM2G122267 Pleckstrin homology (PH) domain-

containing protein S2_3106376 2 3106376 5.30E-05 0.37 1760 0.35 0.36 0.037 GRMZM2G071333 ATP binding;leucine- tRNA ligases;aminoacyl- tRNA ligases;nucleotide binding;ATP binding;aminoacyl-

406

tRNA ligases

407

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S2_3106376 2 3106376 5.30E-05 0.37 1760 0.35 0.36 0.037 GRMZM2G035370 myb-like HTH

transcriptional regul S2_3106376 2 3106376 5.30E-05 0.37 1760 0.35 0.36 0.037 GRMZM2G035325 SWIB complex BAF60b domain-

containing protein S2_9314762 2 9314762 3.07E-05 0.19 1760 0.35 0.36 0.030 GRMZM2G041518 (HERK2): hercules

receptor kinase 2

S2_9314762 2 9314762 3.07E-05 0.19 1760 0.35 0.36 0.030 GRMZM2G337011 DNA binding S2_9314772 2 9314772 1.01E-04 0.15 1760 0.35 0.36 0.048 GRMZM2G041518 (HERK2): hercules

receptor kinase 2

S2_9314772 2 9314772 1.01E-04 0.15 1760 0.35 0.36 0.048 GRMZM2G337011 DNA binding S2_17790342 2 17790342 7.71E-05 0.24 1760 0.35 0.36 0.044 GRMZM2G101408 coiled-coil domain- containing protein 124, putative,

expressed S2_17790342 2 17790342 7.71E-05 0.24 1760 0.35 0.36 0.044 GRMZM2G101333 GDSL-like Lipase/Acylhydrolas e superfamily

protein S2_17790342 2 17790342 7.71E-05 0.24 1760 0.35 0.36 0.044 GRMZM2G101383 Pseudouridine synthase family

protein S2_17790343 2 17790343 7.71E-05 0.24 1760 0.35 0.36 0.044 GRMZM2G101408 coiled-coil domain- containing protein 124, putative,

expressed S2_17790343 2 17790343 7.71E-05 0.24 1760 0.35 0.36 0.044 GRMZM2G101333 GDSL-like Lipase/Acylhydrolas e superfamily

407 protein

408

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S2_17790343 2 17790343 7.71E-05 0.24 1760 0.35 0.36 0.044 GRMZM2G101383 Pseudouridine synthase family

protein S2_21008179 2 21008179 9.73E-05 0.14 1760 0.35 0.36 0.048 AC212835.3_FG007 placental protein 11 precursor, putative,

expressed S2_21008179 2 21008179 9.73E-05 0.14 1760 0.35 0.36 0.048 AC212835.3_FG008 Protein kinase

superfamily protein S2_21324760 2 21324760 1.02E-04 0.10 1760 0.35 0.36 0.049 GRMZM2G021530 (CYCP4,CYCP4;2):

CYCLIN P4;2 S2_22193603 2 22193603 9.40E-05 0.19 1760 0.35 0.36 0.047 GRMZM2G109244 (NDH-M): subunit NDH-M of NAD(P)H:plastoquin one dehydrogenase

complex S2_22193603 2 22193603 9.40E-05 0.19 1760 0.35 0.36 0.047 GRMZM2G109262 Lactoylglutathione lyase / glyoxalase I

family protein S2_22884845 2 22884845 1.36E-05 0.18 1760 0.35 0.36 0.024 GRMZM2G394450 Glycosyl hydrolases

family 32 protein S2_22974308 2 22974308 9.85E-05 0.15 1760 0.35 0.36 0.048 GRMZM2G034668 (ACYB-2): Cytochrome b561/ferric reductase transmembrane

protein family S2_22974308 2 22974308 9.85E-05 0.15 1760 0.35 0.36 0.048 GRMZM2G505380 DTA2, putative,

expressed

408

409

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S2_23765145 2 23765145 8.56E-05 0.40 1760 0.35 0.36 0.046 GRMZM2G026656 (FTRA2): ferredoxin/thioredo xin reductase subunit A (variable

subunit) 2 S2_25387853 2 25387853 3.50E-06 0.28 1760 0.35 0.36 0.015 GRMZM2G031360 Clathrin adaptor complexes medium subunit family

protein S2_25747245 2 25747245 1.28E-07 0.43 1760 0.35 0.36 0.004 AC212859.3_FG008 (ANAC030,VND7): vascular related NAC-domain protein

7 S2_25747245 2 25747245 1.28E-07 0.43 1760 0.35 0.36 0.004 AC212859.3_FG007 (DCAF1): DDB1- CUL4 associated

factor 1 S2_26717898 2 26717898 5.57E-07 0.48 1760 0.35 0.36 0.008 GRMZM2G113990 Endosomal targeting BRO1-like domain-

containing protein S2_26717898 2 26717898 5.57E-07 0.48 1760 0.35 0.36 0.008 GRMZM2G114153 GRAM domain- containing protein / ABA-responsive

protein-related S2_26717898 2 26717898 5.57E-07 0.48 1760 0.35 0.36 0.008 GRMZM2G114149 Mitochondrial substrate carrier

family protein S2_40011166 2 40011166 1.09E-04 0.34 1760 0.35 0.36 0.050 GRMZM2G327295 Copper transport

protein family S2_40011166 2 40011166 1.09E-04 0.34 1760 0.35 0.36 0.050 GRMZM2G022637 Heavy metal transport/detoxifica

409 tion superfamily

protein

410

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation

S2_40011166 2 40011166 1.09E-04 0.34 1760 0.35 0.36 0.050 GRMZM2G022797 putative, expressed S2_40508168 2 40508168 7.64E-05 0.10 1760 0.35 0.36 0.044 GRMZM2G042443 (RDR2,SMD1): RNA- dependent RNA

polymerase 2 S2_40508170 2 40508170 2.42E-05 0.10 1760 0.35 0.36 0.028 GRMZM2G042443 (RDR2,SMD1): RNA- dependent RNA

polymerase 2 S2_40508178 2 40508178 2.42E-05 0.10 1760 0.35 0.36 0.028 GRMZM2G042443 (RDR2,SMD1): RNA- dependent RNA

polymerase 2 S2_42001237 2 42001237 4.38E-07 0.16 1760 0.35 0.36 0.008 GRMZM2G137161 Transmembrane amino acid transporter family

protein S2_42001265 2 42001265 2.23E-05 0.12 1760 0.35 0.36 0.027 GRMZM2G137161 Transmembrane amino acid transporter family

protein S2_42001266 2 42001266 2.23E-05 0.12 1760 0.35 0.36 0.027 GRMZM2G137161 Transmembrane amino acid transporter family

protein S2_42001267 2 42001267 2.23E-05 0.12 1760 0.35 0.36 0.027 GRMZM2G137161 Transmembrane amino acid transporter family

protein S2_42001268 2 42001268 2.23E-05 0.12 1760 0.35 0.36 0.027 GRMZM2G137161 Transmembrane amino acid transporter family

protein 410

411

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S2_48739467 2 48739467 6.03E-05 0.19 1760 0.35 0.36 0.040 GRMZM2G064773 (EMB71,MAPKKK4,Y DA): Protein kinase

superfamily protein S2_48739467 2 48739467 6.03E-05 0.19 1760 0.35 0.36 0.040 GRMZM2G361100 (PUB25): plant U-

box 25 S2_49917746 2 49917746 1.09E-04 0.32 1760 0.35 0.36 0.050 GRMZM2G357660 Acyl-CoA N- acyltransferase with RING/FYVE/PHD- type zinc finger

protein S2_51285307 2 51285307 9.40E-05 0.17 1760 0.35 0.36 0.047 GRMZM5G806108 Protein kinase

superfamily protein S2_60659139 2 60659139 6.71E-05 0.13 1760 0.35 0.36 0.042 GRMZM2G069856 forkhead-associated domain-containing protein / FHA domain-containing

protein S2_60659139 2 60659139 6.71E-05 0.13 1760 0.35 0.36 0.042 GRMZM2G069708 NAD(P)-binding Rossmann-fold

superfamily protein S2_60659166 2 60659166 7.20E-05 0.13 1760 0.35 0.36 0.043 GRMZM2G069856 forkhead-associated domain-containing protein / FHA domain-containing

protein S2_60659166 2 60659166 7.20E-05 0.13 1760 0.35 0.36 0.043 GRMZM2G069708 NAD(P)-binding Rossmann-fold

superfamily protein S2_63670637 2 63670637 2.96E-05 0.11 1760 0.35 0.36 0.030 GRMZM2G436533 Homeodomain-like

superfamily protein

411 S2_63670859 2 63670859 6.83E-05 0.09 1760 0.35 0.36 0.042 GRMZM2G436533 Homeodomain-like

superfamily protein

412

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S2_63670892 2 63670892 2.92E-06 0.10 1760 0.35 0.36 0.014 GRMZM2G436533 Homeodomain-like

superfamily protein S2_63670904 2 63670904 2.92E-06 0.10 1760 0.35 0.36 0.014 GRMZM2G436533 Homeodomain-like

superfamily protein S2_63753407 2 63753407 2.27E-05 0.10 1760 0.35 0.36 0.028 GRMZM2G373849 (ATHSP93- V,CLPC,CLPC1,DCA1, HSP93-V): CLPC

homologue 1 S2_63753407 2 63753407 2.27E-05 0.10 1760 0.35 0.36 0.028 GRMZM2G373828 Calcium-binding EF-

hand family protein S2_82644737 2 82644737 1.07E-04 0.12 1760 0.35 0.36 0.050 GRMZM2G029211 (RPS2): NB-ARC domain-containing disease resistance

protein S2_82644743 2 82644743 1.07E-04 0.12 1760 0.35 0.36 0.050 GRMZM2G029211 (RPS2): NB-ARC domain-containing disease resistance

protein S2_115055708 2 115055708 1.42E-05 0.18 1760 0.35 0.36 0.024 GRMZM2G008649 : jasmonate- induced protein,

putative, expressed S2_143049728 2 143049728 1.10E-04 0.12 1760 0.35 0.36 0.050 GRMZM2G348866 (ATDCP1,DCP1):

decapping 1

S2_143049728 2 143049728 1.10E-04 0.12 1760 0.35 0.36 0.050 GRMZM2G348855 F-box family protein S2_148723161 2 148723161 5.45E-07 0.07 1760 0.35 0.36 0.008 GRMZM2G025002 (GATA12): GATA transcription factor

12 S2_149523377 2 149523377 3.58E-07 0.14 1760 0.35 0.36 0.008 GRMZM2G079236 (LACS8): AMP- dependent

synthetase and 412

ligase family protein

413

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S2_149523377 2 149523377 3.58E-07 0.14 1760 0.35 0.36 0.008 GRMZM2G079127 MATE efflux family

protein S2_149785808 2 149785808 5.48E-05 0.15 1760 0.35 0.36 0.038 GRMZM2G377797 Ribosomal protein S5 domain 2-like

superfamily protein S2_149786062 2 149786062 1.58E-05 0.14 1760 0.35 0.36 0.025 GRMZM2G377797 Ribosomal protein S5 domain 2-like

superfamily protein S2_150146615 2 150146615 2.09E-05 0.12 1760 0.35 0.36 0.027 GRMZM2G015080 (SCR,SGR1): GRAS family transcription

factor S2_150440091 2 150440091 1.60E-05 0.11 1760 0.35 0.36 0.025 GRMZM2G130049 (ATCHX15,CHX15): cation/hydrogen

exchanger 15 S2_150441036 2 150441036 1.02E-04 0.11 1760 0.35 0.36 0.049 GRMZM2G130049 (ATCHX15,CHX15): cation/hydrogen

exchanger 15 S2_150441156 2 150441156 6.43E-06 0.12 1760 0.35 0.36 0.019 GRMZM2G130049 (ATCHX15,CHX15): cation/hydrogen

exchanger 15 S2_150441180 2 150441180 1.57E-05 0.11 1760 0.35 0.36 0.025 GRMZM2G130049 (ATCHX15,CHX15): cation/hydrogen

exchanger 15 S2_150446773 2 150446773 1.40E-05 0.12 1760 0.35 0.36 0.024 GRMZM2G130049 (ATCHX15,CHX15): cation/hydrogen

exchanger 15 S2_150704513 2 150704513 2.35E-06 0.10 1760 0.35 0.36 0.013 GRMZM2G007283 Protein kinase

superfamily protein S2_150797209 2 150797209 1.14E-06 0.09 1760 0.35 0.36 0.011 GRMZM2G094535 Protein of unknown

function (DUF567)

413 S2_150803074 2 150803074 4.38E-05 0.13 1760 0.35 0.36 0.035 GRMZM2G094535 Protein of unknown

function (DUF567)

414

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S2_160962925 2 160962925 3.59E-05 0.32 1760 0.35 0.36 0.032 GRMZM2G171370 (AtbZIP16,bZIP16): basic region/leucine zipper transcription

factor 16 S2_186642390 2 186642390 1.08E-04 0.16 1760 0.35 0.36 0.050 GRMZM2G063723 DNAJ heat shock N- terminal domain-

containing protein S2_186642391 2 186642391 2.03E-05 0.16 1760 0.35 0.36 0.027 GRMZM2G063723 DNAJ heat shock N- terminal domain-

containing protein S2_186642421 2 186642421 7.99E-05 0.21 1760 0.35 0.36 0.045 GRMZM2G063723 DNAJ heat shock N- terminal domain-

containing protein S2_186642663 2 186642663 4.60E-06 0.16 1760 0.35 0.36 0.016 GRMZM2G063723 DNAJ heat shock N- terminal domain-

containing protein S2_193506687 2 193506687 4.05E-05 0.24 1760 0.35 0.36 0.034 GRMZM2G150533 (GLX2-5): glyoxalase

2-5 S2_193506687 2 193506687 4.05E-05 0.24 1760 0.35 0.36 0.034 GRMZM5G848608 C2 domain- containing protein / GRAM domain-

containing protein S2_193882732 2 193882732 2.81E-05 0.26 1760 0.35 0.36 0.030 GRMZM2G107560 (ATMYC2,JAI1,JIN1, MYC2,RD22BP1,ZBF 1): Basic helix-loop- helix (bHLH) DNA- binding family

protein

414

415

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S2_194355749 2 194355749 5.17E-05 0.31 1760 0.35 0.36 0.037 AC199782.5_FG002 (EMB2778,FKP1,HM GS,MVA1): hydroxymethylgluta ryl-CoA synthase / HMG-CoA synthase / 3-hydroxy-3- methylglutaryl coenzyme A

synthase S2_194355749 2 194355749 5.17E-05 0.31 1760 0.35 0.36 0.037 AC199782.5_FG003 TCP family

transcription factor S2_203257688 2 203257688 4.14E-05 0.08 1760 0.35 0.36 0.035 GRMZM2G169615 (ATRBP45B,RBP45B) : RNA-binding (RRM/RBD/RNP motifs) family

protein S2_203257688 2 203257688 4.14E-05 0.08 1760 0.35 0.36 0.035 GRMZM2G470075 MATE efflux family

protein S2_203257688 2 203257688 4.14E-05 0.08 1760 0.35 0.36 0.035 GRMZM2G169539 MATE efflux family

protein S2_208538475 2 208538475 2.56E-05 0.10 1760 0.35 0.36 0.029 GRMZM2G090274 (ERF1-3): eukaryotic

release factor 1-3 S2_208538475 2 208538475 2.56E-05 0.10 1760 0.35 0.36 0.029 GRMZM2G090493 ARM repeat

superfamily protein S2_210001112 2 210001112 4.30E-05 0.50 1760 0.35 0.36 0.035 GRMZM2G340048 (CRK25): cysteine- rich RLK (RECEPTOR- like protein kinase)

S2_216005119 2 216005119 7.85E-05 0.25 1760 0.35 0.36 0.044 GRMZM2G171068 CW-type Zinc Finger

415

416

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S2_216005119 2 216005119 7.85E-05 0.25 1760 0.35 0.36 0.044 GRMZM2G474525 retrotransposon protein, putative, unclassified,

expressed S2_224907521 2 224907521 9.67E-05 0.06 1760 0.35 0.36 0.048 GRMZM2G107945 (ADO3,FKF1): flavin- binding, kelch

repeat, f box 1 S2_224907521 2 224907521 9.67E-05 0.06 1760 0.35 0.36 0.048 GRMZM2G408768 (GF14 NU,GRF7): general regulatory

factor 7 S2_232987495 2 232987495 1.14E-05 0.19 1760 0.35 0.36 0.023 GRMZM2G082809 TPX2 (targeting protein for Xklp2)

protein family S3_4160924 3 4160924 1.71E-05 0.22 1760 0.35 0.36 0.025 GRMZM2G051043 (CID8): CTC- interacting domain

8 S3_4160924 3 4160924 1.71E-05 0.22 1760 0.35 0.36 0.025 GRMZM2G352891 RNA binding (RRM/RBD/RNP motifs) family

protein S3_4194021 3 4194021 8.67E-05 0.09 1760 0.35 0.36 0.047 GRMZM2G051327 (ATSYP43,SYP43):

syntaxin of plants 43 S3_4194021 3 4194021 8.67E-05 0.09 1760 0.35 0.36 0.047 GRMZM2G051262 Alg9-like mannosyltransferas

e family S3_4194021 3 4194021 8.67E-05 0.09 1760 0.35 0.36 0.047 GRMZM2G352926 transposable element protein, putative, containing Pfam profile: PF03732,

416 Retrotrans_gag,

expressed

417

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S3_4194030 3 4194030 1.79E-06 0.17 1760 0.35 0.36 0.012 GRMZM2G051327 (ATSYP43,SYP43):

syntaxin of plants 43 S3_4194030 3 4194030 1.79E-06 0.17 1760 0.35 0.36 0.012 GRMZM2G051262 Alg9-like mannosyltransferas

e family S3_4194030 3 4194030 1.79E-06 0.17 1760 0.35 0.36 0.012 GRMZM2G352926 transposable element protein, putative, containing Pfam profile: PF03732, Retrotrans_gag,

expressed S3_4194054 3 4194054 1.79E-06 0.17 1760 0.35 0.36 0.012 GRMZM2G051327 (ATSYP43,SYP43):

syntaxin of plants 43 S3_4194054 3 4194054 1.79E-06 0.17 1760 0.35 0.36 0.012 GRMZM2G051262 Alg9-like mannosyltransferas

e family S3_4194054 3 4194054 1.79E-06 0.17 1760 0.35 0.36 0.012 GRMZM2G352926 transposable element protein, putative, containing Pfam profile: PF03732, Retrotrans_gag,

expressed S3_4540263 3 4540263 6.19E-05 0.08 1760 0.35 0.36 0.041 GRMZM2G035256 alpha/beta- Hydrolases

superfamily protein S3_4540263 3 4540263 6.19E-05 0.08 1760 0.35 0.36 0.041 GRMZM2G035131 alpha/beta- Hydrolases

superfamily protein

417

418

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S3_4540263 3 4540263 6.19E-05 0.08 1760 0.35 0.36 0.041 GRMZM2G035278 Polyketide cyclase/dehydrase and lipid transport

superfamily protein S3_4862020 3 4862020 8.46E-05 0.15 1760 0.35 0.36 0.046 GRMZM2G471089 (AG): K-box region and MADS-box transcription factor

family protein S3_6977655 3 6977655 5.21E-05 0.17 1760 0.35 0.36 0.037 GRMZM2G371176 (IQD26): IQ-domain

26 S3_8304349 3 8304349 4.29E-06 0.09 1760 0.35 0.36 0.016 GRMZM2G015509 (ATSYP22,ATVAM3,S GR3,SYP22,VAM3): Syntaxin/t-SNARE

family protein S3_8304349 3 8304349 4.29E-06 0.09 1760 0.35 0.36 0.016 GRMZM2G314898 HXXXD-type acyltransferase family

protein S3_9580217 3 9580217 1.10E-04 0.20 1760 0.35 0.36 0.050 GRMZM2G363554 (IAGLU): indole-3- acetate beta-D-

glucosyltransferase S3_9580217 3 9580217 1.10E-04 0.20 1760 0.35 0.36 0.050 GRMZM2G363535 Enhancer of polycomb-like transcription factor

protein S3_9812918 3 9812918 9.69E-05 0.15 1760 0.35 0.36 0.048 GRMZM2G083518 (ATSYP32,SYP32):

syntaxin of plants 32 S3_9812918 3 9812918 9.69E-05 0.15 1760 0.35 0.36 0.048 GRMZM2G083374 (emb2410): embryo

defective 2410 S3_9812918 3 9812918 9.69E-05 0.15 1760 0.35 0.36 0.048 GRMZM2G083418 early fruit mRNA,

putative, expressed

418

419

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S3_9853649 3 9853649 6.52E-05 0.12 1760 0.35 0.36 0.042 GRMZM2G120296 (AIF1): AtBS1(activation- tagged BRI1 suppressor 1)-

interacting factor 1 S3_9853649 3 9853649 6.52E-05 0.12 1760 0.35 0.36 0.042 GRMZM2G305900 HXXXD-type acyltransferase family

protein S3_9853649 3 9853649 6.52E-05 0.12 1760 0.35 0.36 0.042 GRMZM2G421604 Major facilitator

superfamily protein S3_50606672 3 50606672 2.34E-06 0.44 1760 0.35 0.36 0.013 GRMZM2G170120 (CIPK1,SnRK3.16): CBL-interacting

protein kinase 1 S3_89038062 3 89038062 8.05E-05 0.16 1760 0.35 0.36 0.045 GRMZM2G164418 (UBP8): ubiquitin-

specific protease 8 S3_92542371 3 92542371 5.74E-05 0.24 1760 0.35 0.36 0.039 GRMZM2G163059 (RXW8): lipases;hydrolases, acting on ester

bonds S3_92542371 3 92542371 5.74E-05 0.24 1760 0.35 0.36 0.039 GRMZM2G163099 CAP (Cysteine-rich secretory proteins, Antigen 5, and Pathogenesis- related 1 protein)

superfamily protein S3_168004312 3 168004312 4.84E-05 0.12 1760 0.35 0.36 0.036 GRMZM2G392710 (CDC27b,HBT): CDC27 family

protein S3_187711101 3 187711101 9.58E-06 0.21 1760 0.35 0.36 0.023 GRMZM2G438551 (ATCYS6,ATCYSB,CYS

B): cystatin B

419

420

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S3_187711101 3 187711101 9.58E-06 0.21 1760 0.35 0.36 0.023 GRMZM2G138074 (CYP98A3): cytochrome P450, family 98, subfamily

A, polypeptide 3 S3_189700395 3 189700395 3.98E-05 0.27 1760 0.35 0.36 0.034 GRMZM2G085392 (AtENODL9,ENODL9 ): early nodulin-like

protein 9 S3_189700395 3 189700395 3.98E-05 0.27 1760 0.35 0.36 0.034 GRMZM2G386276 (PDF2): protodermal

factor 2 S3_189700395 3 189700395 3.98E-05 0.27 1760 0.35 0.36 0.034 GRMZM2G386261 Pentatricopeptide repeat (PPR)

superfamily protein S3_194739518 3 194739518 4.35E-05 0.22 1760 0.35 0.36 0.035 GRMZM2G162768 (PDCB3): plasmodesmata callose-binding

protein 3 S3_210977655 3 210977655 1.07E-05 0.13 1760 0.35 0.36 0.023 GRMZM2G151763 (ATWRKY28,WRKY2 8): WRKY DNA-

binding protein 28 S3_214853553 3 214853553 2.16E-05 0.19 1760 0.35 0.36 0.027 GRMZM2G126239 (ATHB- 17,ATHB17,HB17): homeobox-leucine

zipper protein 17 S3_214853589 3 214853589 2.16E-05 0.19 1760 0.35 0.36 0.027 GRMZM2G126239 (ATHB- 17,ATHB17,HB17): homeobox-leucine

zipper protein 17 S3_214854840 3 214854840 9.64E-05 0.16 1760 0.35 0.36 0.048 GRMZM2G126239 (ATHB- 17,ATHB17,HB17): homeobox-leucine

420

zipper protein 17

421

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S3_216648459 3 216648459 2.64E-05 0.28 1760 0.35 0.36 0.029 GRMZM2G464976 ZOS12-01 - C2H2 zinc finger protein,

expressed S3_216990765 3 216990765 1.05E-04 0.24 1760 0.35 0.36 0.049 GRMZM2G370745 (CYP72A14): cytochrome P450, family 72, subfamily

A, polypeptide 14 S3_216990773 3 216990773 8.75E-05 0.22 1760 0.35 0.36 0.047 GRMZM2G370745 (CYP72A14): cytochrome P450, family 72, subfamily

A, polypeptide 14 S3_217009770 3 217009770 5.28E-05 0.40 1760 0.35 0.36 0.037 GRMZM2G176943 (CYP72A15): cytochrome P450, family 72, subfamily

A, polypeptide 15 S3_217009771 3 217009771 5.28E-05 0.40 1760 0.35 0.36 0.037 GRMZM2G176943 (CYP72A15): cytochrome P450, family 72, subfamily

A, polypeptide 15 S3_219578255 3 219578255 1.96E-05 0.15 1760 0.35 0.36 0.027 GRMZM2G177693 (AtIDD7,IDD7): indeterminate(ID)-

domain 7 S3_219690630 3 219690630 5.72E-05 0.23 1760 0.35 0.36 0.039 GRMZM2G463032 (ftsh4): FTSH

protease 4 S3_219690630 3 219690630 5.72E-05 0.23 1760 0.35 0.36 0.039 GRMZM5G848696 (GLYR2,GR2): glyoxylate reductase

2 S3_219691484 3 219691484 2.72E-05 0.21 1760 0.35 0.36 0.029 GRMZM2G463032 (ftsh4): FTSH

protease 4 S3_219691484 3 219691484 2.72E-05 0.21 1760 0.35 0.36 0.029 GRMZM5G848696 (GLYR2,GR2):

421 glyoxylate reductase

422

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S3_222726588 3 222726588 6.76E-05 0.29 1760 0.35 0.36 0.042 GRMZM2G055578 CASC3/Barentsz

eIF4AIII binding S3_222726588 3 222726588 6.76E-05 0.29 1760 0.35 0.36 0.042 GRMZM2G055629 THION27 - Plant thionin family protein precursor,

expressed S3_222726589 3 222726589 2.06E-06 0.14 1760 0.35 0.36 0.012 GRMZM2G055578 CASC3/Barentsz

eIF4AIII binding S3_222726589 3 222726589 2.06E-06 0.14 1760 0.35 0.36 0.012 GRMZM2G055629 THION27 - Plant thionin family protein precursor,

expressed S3_222726607 3 222726607 7.59E-05 0.30 1760 0.35 0.36 0.044 GRMZM2G055578 CASC3/Barentsz

eIF4AIII binding S3_222726607 3 222726607 7.59E-05 0.30 1760 0.35 0.36 0.044 GRMZM2G055629 THION27 - Plant thionin family protein precursor,

expressed S3_222726628 3 222726628 2.06E-06 0.14 1760 0.35 0.36 0.012 GRMZM2G055578 CASC3/Barentsz

eIF4AIII binding S3_222726628 3 222726628 2.06E-06 0.14 1760 0.35 0.36 0.012 GRMZM2G055629 THION27 - Plant thionin family protein precursor,

expressed S3_224487288 3 224487288 8.64E-05 0.48 1760 0.35 0.36 0.046 GRMZM2G143139 (ABCG40,ATABCG40 ,ATPDR12,PDR12): pleiotropic drug

resistance 12 S3_224487297 3 224487297 8.64E-05 0.48 1760 0.35 0.36 0.046 GRMZM2G143139 (ABCG40,ATABCG40 ,ATPDR12,PDR12):

422 pleiotropic drug

resistance 12

423

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S3_225333995 3 225333995 8.40E-05 0.23 1760 0.35 0.36 0.046 GRMZM2G094428 HXXXD-type acyltransferase family

protein S3_225333995 3 225333995 8.40E-05 0.23 1760 0.35 0.36 0.046 GRMZM2G094418 Protein of unknown

function (DUF567) S3_231596457 3 231596457 7.37E-05 0.32 1760 0.35 0.36 0.043 GRMZM2G090722 Pyridoxal- dependent decarboxylase

family protein S4_30007 4 30007 2.21E-05 0.41 1760 0.35 0.36 0.027 GRMZM2G000510 (ATPUMP1,ATUCP1, PUMP1,UCP,UCP1): plant uncoupling mitochondrial

protein 1 S4_30007 4 30007 2.21E-05 0.41 1760 0.35 0.36 0.027 GRMZM2G397661 : Thioesterase

superfamily protein S4_2514655 4 2514655 2.30E-06 0.12 1760 0.35 0.36 0.013 GRMZM2G001160 (RECQI1): RECQ

helicase l1 S4_2514655 4 2514655 2.30E-06 0.12 1760 0.35 0.36 0.013 GRMZM2G001116 P-loop nucleoside triphosphate hydrolases superfamily protein with CH (Calponin

Homology) domain S4_2767078 4 2767078 7.01E-05 0.43 1760 0.35 0.36 0.042 GRMZM2G126601 (ATMHX,ATMHX1,M HX,MHX1): magnesium/proton

exchanger S4_2767078 4 2767078 7.01E-05 0.43 1760 0.35 0.36 0.042 GRMZM2G126541 (scpl50): serine carboxypeptidase-

423

like 50

424

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S4_2767078 4 2767078 7.01E-05 0.43 1760 0.35 0.36 0.042 GRMZM2G126552 (VIP3): Transducin/WD40 repeat-like

superfamily protein S4_2767078 4 2767078 7.01E-05 0.43 1760 0.35 0.36 0.042 GRMZM2G126453 AAA-type ATPase

family protein S4_2767079 4 2767079 5.17E-05 0.43 1760 0.35 0.36 0.037 GRMZM2G126601 (ATMHX,ATMHX1,M HX,MHX1): magnesium/proton

exchanger S4_2767079 4 2767079 5.17E-05 0.43 1760 0.35 0.36 0.037 GRMZM2G126541 (scpl50): serine carboxypeptidase-

like 50 S4_2767079 4 2767079 5.17E-05 0.43 1760 0.35 0.36 0.037 GRMZM2G126552 (VIP3): Transducin/WD40 repeat-like

superfamily protein S4_2767079 4 2767079 5.17E-05 0.43 1760 0.35 0.36 0.037 GRMZM2G126453 AAA-type ATPase

family protein S4_5405765 4 5405765 4.11E-06 0.10 1760 0.35 0.36 0.016 GRMZM2G154414 (ICK5,ICN6,KRP7): Cyclin-dependent kinase inhibitor

family protein S4_12584810 4 12584810 5.72E-05 0.12 1760 0.35 0.36 0.039 GRMZM2G030463 mRNA capping enzyme family

protein S4_12784637 4 12784637 3.20E-05 0.42 1760 0.35 0.36 0.031 GRMZM2G139533 NagB/RpiA/CoA transferase-like

superfamily protein S4_12784642 4 12784642 3.20E-05 0.42 1760 0.35 0.36 0.031 GRMZM2G139533 NagB/RpiA/CoA

424 transferase-like

superfamily protein

425

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S4_186841596 4 186841596 5.37E-06 0.26 1760 0.35 0.36 0.017 AC204868.3_FG004 Galactose oxidase/kelch repeat superfamily

protein S4_186841596 4 186841596 5.37E-06 0.26 1760 0.35 0.36 0.017 GRMZM2G076087 KOW domain-

containing protein S4_186841596 4 186841596 5.37E-06 0.26 1760 0.35 0.36 0.017 GRMZM2G353301 Pentatricopeptide repeat (PPR)

superfamily protein S4_186841596 4 186841596 5.37E-06 0.26 1760 0.35 0.36 0.017 GRMZM2G142777 Phosphoglycerate mutase family

protein S4_186841596 4 186841596 5.37E-06 0.26 1760 0.35 0.36 0.017 GRMZM2G075942 RNA-binding (RRM/RBD/RNP motifs) family

protein S4_188874694 4 188874694 1.72E-05 0.30 1760 0.35 0.36 0.025 GRMZM2G081794 Jacalin-like lectin domain containing protein, putative,

expressed S4_188874724 4 188874724 3.02E-06 0.42 1760 0.35 0.36 0.014 GRMZM2G081794 Jacalin-like lectin domain containing protein, putative,

expressed S4_191295476 4 191295476 1.75E-05 0.18 1760 0.35 0.36 0.025 GRMZM2G067865 SBP (S-ribonuclease binding protein)

family protein S4_191765044 4 191765044 6.64E-06 0.42 1760 0.35 0.36 0.019 GRMZM2G441541 (ATRBOHD,RBOHD): respiratory burst oxidase homologue

425

426

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S4_191765044 4 191765044 6.64E-06 0.42 1760 0.35 0.36 0.019 GRMZM2G142342 RmlC-like cupins

superfamily protein S4_191765044 4 191765044 6.64E-06 0.42 1760 0.35 0.36 0.019 GRMZM2G142344 SNARE associated

Golgi protein family S4_234406994 4 234406994 9.08E-05 0.11 1760 0.35 0.36 0.047 GRMZM2G336766 (AREB3,DPBF3): ABA-responsive element binding

protein 3 S4_234406994 4 234406994 9.08E-05 0.11 1760 0.35 0.36 0.047 GRMZM2G039848 alpha/beta- Hydrolases

superfamily protein S4_234406994 4 234406994 9.08E-05 0.11 1760 0.35 0.36 0.047 GRMZM2G336761 RING/U-box

superfamily protein S4_236082285 4 236082285 1.16E-05 0.39 1760 0.35 0.36 0.023 GRMZM2G051004 (GAPCP-2): glyceraldehyde-3- phosphate dehydrogenase of

plastid 2 S4_236082285 4 236082285 1.16E-05 0.39 1760 0.35 0.36 0.023 GRMZM2G351747 : transglycosylase SLT domain containing protein,

expressed S4_237323066 4 237323066 1.95E-05 0.17 1760 0.35 0.36 0.027 GRMZM2G153745 EMB1303, putative,

expressed S4_237323066 4 237323066 1.95E-05 0.17 1760 0.35 0.36 0.027 GRMZM2G451007 Leucine-rich receptor-like protein kinase

family protein S4_237323066 4 237323066 1.95E-05 0.17 1760 0.35 0.36 0.027 GRMZM2G450937 Ribosomal protein

L19e family protein

426 S4_237323072 4 237323072 4.55E-05 0.18 1760 0.35 0.36 0.035 GRMZM2G153745 EMB1303, putative,

expressed

427

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S4_237323072 4 237323072 4.55E-05 0.18 1760 0.35 0.36 0.035 GRMZM2G451007 Leucine-rich receptor-like protein kinase

family protein S4_237323072 4 237323072 4.55E-05 0.18 1760 0.35 0.36 0.035 GRMZM2G450937 Ribosomal protein

L19e family protein S4_237610718 4 237610718 9.68E-05 0.21 1760 0.35 0.36 0.048 GRMZM2G155384 (ATRPN1A,RPN1A): 26S proteasome regulatory subunit

S2 1A S4_237610718 4 237610718 9.68E-05 0.21 1760 0.35 0.36 0.048 GRMZM2G155370 (CIA2): chloroplast

import apparatus 2 S4_237686607 4 237686607 5.62E-05 0.15 1760 0.35 0.36 0.039 GRMZM2G117441 DNA/RNA-binding protein Kin17,

conserved region S4_237686607 4 237686607 5.62E-05 0.15 1760 0.35 0.36 0.039 AC196708.3_FG006 SAUR-like auxin- responsive protein

family S4_237686607 4 237686607 5.62E-05 0.15 1760 0.35 0.36 0.039 GRMZM2G117346 splicing factor,

putative S4_238120947 4 238120947 3.66E-05 0.13 1760 0.35 0.36 0.033 GRMZM2G389768 (CSDP1): cold shock

domain protein 1 S4_238991104 4 238991104 2.08E-06 0.26 1760 0.35 0.36 0.012 GRMZM2G019106 (AtbZIP16,bZIP16): basic region/leucine zipper transcription

factor 16 S4_238991104 4 238991104 2.08E-06 0.26 1760 0.35 0.36 0.012 GRMZM2G018697 (ATTIP49A,RIN1): P- loop containing nucleoside triphosphate

427 hydrolases

superfamily protein

428

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S4_238991104 4 238991104 2.08E-06 0.26 1760 0.35 0.36 0.012 GRMZM2G324956 HSP20-like chaperones

superfamily protein S4_239003429 4 239003429 9.82E-05 0.16 1760 0.35 0.36 0.048 GRMZM2G019106 (AtbZIP16,bZIP16): basic region/leucine zipper transcription

factor 16 S4_239003429 4 239003429 9.82E-05 0.16 1760 0.35 0.36 0.048 GRMZM2G018697 (ATTIP49A,RIN1): P- loop containing nucleoside triphosphate hydrolases

superfamily protein S4_239003429 4 239003429 9.82E-05 0.16 1760 0.35 0.36 0.048 GRMZM2G324863 (SUV2): protein

dimerizations S4_239003429 4 239003429 9.82E-05 0.16 1760 0.35 0.36 0.048 GRMZM5G893782 NAD(P)-linked oxidoreductase

superfamily protein S4_240322334 4 240322334 1.02E-04 0.06 1760 0.35 0.36 0.049 GRMZM2G054162 (IBM1): Transcription factor jumonji (jmjC) domain-containing

protein S4_240616519 4 240616519 1.08E-04 0.41 1760 0.35 0.36 0.050 GRMZM2G167103 (PGY2): Ribosomal

protein L6 family S4_240616519 4 240616519 1.08E-04 0.41 1760 0.35 0.36 0.050 GRMZM2G167149 Plant invertase/pectin methylesterase inhibitor

superfamily protein

428

429

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_929964 5 929964 7.77E-05 0.20 1760 0.35 0.36 0.044 GRMZM2G083346 (CPSF73-I): cleavage and polyadenylation specificity factor 73-

I S5_929964 5 929964 7.77E-05 0.20 1760 0.35 0.36 0.044 GRMZM2G082976 (DER2.2): DERLIN-

2.2 S5_929964 5 929964 7.77E-05 0.20 1760 0.35 0.36 0.044 GRMZM2G028955 (HTA6): histone H2A

6 S5_929964 5 929964 7.77E-05 0.20 1760 0.35 0.36 0.044 GRMZM2G083081 DUF565 domain containing protein,

putative, expressed S5_929964 5 929964 7.77E-05 0.20 1760 0.35 0.36 0.044 GRMZM2G028889 hydroxyproline-rich glycoprotein family

protein S5_929964 5 929964 7.77E-05 0.20 1760 0.35 0.36 0.044 GRMZM2G030858 transducin family protein / WD-40 repeat family

protein S5_1051375 5 1051375 1.40E-05 0.32 1760 0.35 0.36 0.024 GRMZM2G012229 (RIN4): RPM1

interacting protein 4 S5_1051375 5 1051375 1.40E-05 0.32 1760 0.35 0.36 0.024 GRMZM2G313460 brefeldin A-sensitive Golgi protein-like,

putative, expressed S5_1051375 5 1051375 1.40E-05 0.32 1760 0.35 0.36 0.024 GRMZM2G013042 NAD(P)-binding Rossmann-fold

superfamily protein S5_1051375 5 1051375 1.40E-05 0.32 1760 0.35 0.36 0.024 GRMZM2G313481 Nucleotide- diphospho-sugar transferase family

protein

429

430

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_1051375 5 1051375 1.40E-05 0.32 1760 0.35 0.36 0.024 GRMZM2G013200 Sec14p-like phosphatidylinositol transfer family

protein S5_1051375 5 1051375 1.40E-05 0.32 1760 0.35 0.36 0.024 GRMZM2G313656 Sterile alpha motif (SAM) domain-

containing protein S5_1051390 5 1051390 5.81E-05 0.35 1760 0.35 0.36 0.039 GRMZM2G012229 (RIN4): RPM1

interacting protein 4 S5_1051390 5 1051390 5.81E-05 0.35 1760 0.35 0.36 0.039 GRMZM2G313460 brefeldin A- sensitive Golgi protein-like,

putative, expressed S5_1051390 5 1051390 5.81E-05 0.35 1760 0.35 0.36 0.039 GRMZM2G013042 NAD(P)-binding Rossmann-fold

superfamily protein S5_1051390 5 1051390 5.81E-05 0.35 1760 0.35 0.36 0.039 GRMZM2G313481 Nucleotide- diphospho-sugar transferase family

protein S5_1051390 5 1051390 5.81E-05 0.35 1760 0.35 0.36 0.039 GRMZM2G013200 Sec14p-like phosphatidylinositol transfer family

protein S5_1051390 5 1051390 5.81E-05 0.35 1760 0.35 0.36 0.039 GRMZM2G313656 Sterile alpha motif (SAM) domain-

containing protein S5_1234691 5 1234691 2.90E-05 0.42 1760 0.35 0.36 0.030 GRMZM2G136854 (ALB4,ARTEMIS): OxaA/YidC-like membrane insertion

430

protein

431

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_1895033 5 1895033 7.47E-05 0.16 1760 0.35 0.36 0.044 GRMZM2G398668 5\'-3\' exonuclease

family protein S5_1895033 5 1895033 7.47E-05 0.16 1760 0.35 0.36 0.044 GRMZM2G100419 AT3G05940.1: Protein of unknown

function (DUF300) S5_2260025 5 2260025 9.74E-05 0.17 1760 0.35 0.36 0.048 GRMZM2G144008 (ATRAB- A2B,ATRABA2B,RAB -A2B,RABA2b): RAB GTPase homolog

A2B

S5_2260025 5 2260025 9.74E-05 0.17 1760 0.35 0.36 0.048 GRMZM2G144020 (Fes1A): Fes1A S5_2260025 5 2260025 9.74E-05 0.17 1760 0.35 0.36 0.048 GRMZM2G143998 Major facilitator

superfamily protein S5_2521558 5 2521558 9.93E-06 0.22 1760 0.35 0.36 0.023 GRMZM2G160064 Chloroplast- targeted copper

chaperone protein S5_2521558 5 2521558 9.93E-06 0.22 1760 0.35 0.36 0.023 GRMZM2G458266 Transducin/WD40 repeat-like

superfamily protein S5_2521581 5 2521581 1.60E-05 0.21 1760 0.35 0.36 0.025 GRMZM2G160064 Chloroplast- targeted copper

chaperone protein S5_2521581 5 2521581 1.60E-05 0.21 1760 0.35 0.36 0.025 GRMZM2G458266 Transducin/WD40 repeat-like

superfamily protein S5_2593784 5 2593784 7.71E-05 0.20 1760 0.35 0.36 0.044 GRMZM2G110881 NAD(P)-binding Rossmann-fold

superfamily protein S5_2593784 5 2593784 7.71E-05 0.20 1760 0.35 0.36 0.044 GRMZM2G410865 NAD(P)-binding

Rossmann-fold 431

superfamily protein

432

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_2593784 5 2593784 7.71E-05 0.20 1760 0.35 0.36 0.044 GRMZM2G110952 Pentatricopeptide repeat (PPR)

superfamily protein S5_3087242 5 3087242 4.57E-05 0.25 1760 0.35 0.36 0.035 GRMZM2G043453 (ALB- 1V,ALB1,CHLD,PDE1

66,V157): ALBINA 1 S5_3087242 5 3087242 4.57E-05 0.25 1760 0.35 0.36 0.035 GRMZM2G043802 DUF617 domain containing protein,

expressed S5_3087242 5 3087242 4.57E-05 0.25 1760 0.35 0.36 0.035 GRMZM5G854045 HIT zinc finger ;PAPA-1-like

conserved region S5_3087244 5 3087244 4.57E-05 0.25 1760 0.35 0.36 0.035 GRMZM2G043453 (ALB- 1V,ALB1,CHLD,PDE1

66,V157): ALBINA 1 S5_3087244 5 3087244 4.57E-05 0.25 1760 0.35 0.36 0.035 GRMZM2G043802 DUF617 domain containing protein,

expressed S5_3087244 5 3087244 4.57E-05 0.25 1760 0.35 0.36 0.035 GRMZM5G854045 HIT zinc finger ;PAPA-1-like

conserved region S5_3087246 5 3087246 4.57E-05 0.25 1760 0.35 0.36 0.035 GRMZM2G043453 (ALB- 1V,ALB1,CHLD,PDE1

66,V157): ALBINA 1 S5_3087246 5 3087246 4.57E-05 0.25 1760 0.35 0.36 0.035 GRMZM2G043802 DUF617 domain containing protein,

expressed S5_3087246 5 3087246 4.57E-05 0.25 1760 0.35 0.36 0.035 GRMZM5G854045 HIT zinc finger ;PAPA-1-like

conserved region

432

433

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_3087247 5 3087247 4.57E-05 0.25 1760 0.35 0.36 0.035 GRMZM2G043453 (ALB- 1V,ALB1,CHLD,PDE1

66,V157): ALBINA 1 S5_3087247 5 3087247 4.57E-05 0.25 1760 0.35 0.36 0.035 GRMZM2G043802 DUF617 domain containing protein,

expressed S5_3087247 5 3087247 4.57E-05 0.25 1760 0.35 0.36 0.035 GRMZM5G854045 HIT zinc finger ;PAPA-1-like

conserved region S5_23573589 5 23573589 7.45E-05 0.23 1760 0.35 0.36 0.043 GRMZM2G074543 AT2G45190.1(AFO, FIL,YAB1): Plant- specific transcription factor YABBY family

protein S5_30598740 5 30598740 5.90E-06 0.38 1760 0.35 0.36 0.018 GRMZM2G123550 CCT motif family

protein S5_30598740 5 30598740 5.90E-06 0.38 1760 0.35 0.36 0.018 GRMZM2G123495 Ribosomal protein L14p/L23e family

protein S5_30744716 5 30744716 6.87E-05 0.09 1760 0.35 0.36 0.042 GRMZM2G324540 (MAC3A): MOS4- associated complex

3A S5_30744716 5 30744716 6.87E-05 0.09 1760 0.35 0.36 0.042 GRMZM2G027232 (MRPL11): mitochondrial ribosomal protein

L11 S5_31881160 5 31881160 1.75E-05 0.07 1760 0.35 0.36 0.025 GRMZM2G326707 (ATPT2,PHT1;4): phosphate

transporter 1;4

433 S5_33783813 5 33783813 3.06E-06 0.16 1760 0.35 0.36 0.014 GRMZM2G137694 (KCS11): 3-ketoacyl-

CoA synthase 11

434

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_52761679 5 52761679 7.48E-05 0.07 1760 0.35 0.36 0.044 GRMZM2G061485 (ATRPA2,ATRPA32A, ROR1,RPA2,RPA32A)

: replicon protein A2 S5_52761679 5 52761679 7.48E-05 0.07 1760 0.35 0.36 0.044 GRMZM2G168920 Zinc finger protein

622 S5_54916355 5 54916355 6.68E-05 0.12 1760 0.35 0.36 0.042 GRMZM2G307400 (ATHB- 2,ATHB2,HAT4,HB- 2): homeobox

protein 2 S5_54916355 5 54916355 6.68E-05 0.12 1760 0.35 0.36 0.042 GRMZM2G307397 (HAT3): homeobox- leucine zipper

protein 3 S5_56901755 5 56901755 9.73E-06 0.30 1760 0.35 0.36 0.023 GRMZM2G135674 (ATHKT1,HKT1): high-affinity K+

transporter 1 S5_56901755 5 56901755 9.73E-06 0.30 1760 0.35 0.36 0.023 GRMZM2G329999 Protein of unknown

function, DUF617 S5_60927558 5 60927558 3.29E-05 0.40 1760 0.35 0.36 0.031 GRMZM2G361993 SAUR-like auxin- responsive protein

family S5_60989986 5 60989986 4.49E-05 0.49 1760 0.35 0.36 0.035 GRMZM2G457125 (ATRAB- A3,ATRABA3,RABA3 ): RAB GTPase

homolog A3

S5_60989986 5 60989986 4.49E-05 0.49 1760 0.35 0.36 0.035 GRMZM2G158131 ATPase, F1 complex, OSCP/delta subunit

protein

434

435

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_60989986 5 60989986 4.49E-05 0.49 1760 0.35 0.36 0.035 GRMZM2G158136 P-loop containing nucleoside triphosphate hydrolases

superfamily protein S5_60989986 5 60989986 4.49E-05 0.49 1760 0.35 0.36 0.035 GRMZM2G158103 Putative membrane

lipoprotein S5_60990903 5 60990903 5.11E-05 0.47 1760 0.35 0.36 0.037 GRMZM2G457125 (ATRAB- A3,ATRABA3,RABA3 ): RAB GTPase

homolog A3 S5_60990903 5 60990903 5.11E-05 0.47 1760 0.35 0.36 0.037 GRMZM2G158131 ATPase, F1 complex, OSCP/delta subunit

protein S5_60990903 5 60990903 5.11E-05 0.47 1760 0.35 0.36 0.037 GRMZM2G158136 P-loop containing nucleoside triphosphate hydrolases

superfamily protein S5_60990903 5 60990903 5.11E-05 0.47 1760 0.35 0.36 0.037 GRMZM2G158045 Protein kinase

superfamily protein S5_60990903 5 60990903 5.11E-05 0.47 1760 0.35 0.36 0.037 GRMZM2G158103 Putative membrane

lipoprotein S5_60995665 5 60995665 3.93E-06 0.32 1760 0.35 0.36 0.015 GRMZM2G457125 (ATRAB- A3,ATRABA3,RABA3 ): RAB GTPase

homolog A3 S5_60995665 5 60995665 3.93E-06 0.32 1760 0.35 0.36 0.015 GRMZM2G158131 ATPase, F1 complex, OSCP/delta subunit

protein

435

436

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_60995665 5 60995665 3.93E-06 0.32 1760 0.35 0.36 0.015 GRMZM2G158136 P-loop containing nucleoside triphosphate hydrolases

superfamily protein S5_60995665 5 60995665 3.93E-06 0.32 1760 0.35 0.36 0.015 GRMZM2G158045 Protein kinase

superfamily protein S5_60995665 5 60995665 3.93E-06 0.32 1760 0.35 0.36 0.015 GRMZM2G158103 Putative membrane

lipoprotein S5_63640217 5 63640217 9.92E-05 0.16 1760 0.35 0.36 0.048 GRMZM2G028501 (GAUT3): galacturonosyltransf

erase 3 S5_65116064 5 65116064 1.22E-05 0.10 1760 0.35 0.36 0.024 GRMZM2G057000 (CBB1,DIM,DIM1,D WF1,EVE1): cell elongation protein / DWARF1 /

DIMINUTO (DIM) S5_65116064 5 65116064 1.22E-05 0.10 1760 0.35 0.36 0.024 GRMZM2G313341 Spc97 / Spc98 family of spindle pole body

(SBP) component S5_65116064 5 65116064 1.22E-05 0.10 1760 0.35 0.36 0.024 GRMZM2G011998 Transcription elongation factor (TFIIS) family

protein S5_65116185 5 65116185 4.79E-05 0.10 1760 0.35 0.36 0.036 GRMZM2G057000 (CBB1,DIM,DIM1,D WF1,EVE1): cell elongation protein / DWARF1 /

DIMINUTO (DIM)

436

437

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_65116185 5 65116185 4.79E-05 0.10 1760 0.35 0.36 0.036 GRMZM2G313341 : Spc97 / Spc98 family of spindle pole body (SBP)

component S5_65116185 5 65116185 4.79E-05 0.10 1760 0.35 0.36 0.036 GRMZM2G011998 Transcription elongation factor (TFIIS) family

protein S5_65116186 5 65116186 4.79E-05 0.10 1760 0.35 0.36 0.036 GRMZM2G057000 (CBB1,DIM,DIM1,D WF1,EVE1): cell elongation protein / DWARF1 /

DIMINUTO (DIM) S5_65116186 5 65116186 4.79E-05 0.10 1760 0.35 0.36 0.036 GRMZM2G313341 Spc97 / Spc98 family of spindle pole body

(SBP) component S5_65116186 5 65116186 4.79E-05 0.10 1760 0.35 0.36 0.036 GRMZM2G011998 Transcription elongation factor (TFIIS) family

protein S5_65116188 5 65116188 4.79E-05 0.10 1760 0.35 0.36 0.036 GRMZM2G057000 (CBB1,DIM,DIM1,D WF1,EVE1): cell elongation protein / DWARF1 /

DIMINUTO (DIM) S5_65116188 5 65116188 4.79E-05 0.10 1760 0.35 0.36 0.036 GRMZM2G313341 Spc97 / Spc98 family of spindle pole body

(SBP) component S5_65116188 5 65116188 4.79E-05 0.10 1760 0.35 0.36 0.036 GRMZM2G011998 Transcription elongation factor

437 (TFIIS) family

protein

438

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_65116189 5 65116189 4.79E-05 0.10 1760 0.35 0.36 0.036 GRMZM2G057000 (CBB1,DIM,DIM1,D WF1,EVE1): cell elongation protein / DWARF1 /

DIMINUTO (DIM) S5_65116189 5 65116189 4.79E-05 0.10 1760 0.35 0.36 0.036 GRMZM2G313341 Spc97 / Spc98 family of spindle pole body

(SBP) component S5_65116189 5 65116189 4.79E-05 0.10 1760 0.35 0.36 0.036 GRMZM2G011998 Transcription elongation factor (TFIIS) family

protein S5_65124214 5 65124214 1.80E-05 0.08 1760 0.35 0.36 0.026 GRMZM2G057000 (CBB1,DIM,DIM1,D WF1,EVE1): cell elongation protein / DWARF1 /

DIMINUTO (DIM) S5_65124214 5 65124214 1.80E-05 0.08 1760 0.35 0.36 0.026 GRMZM2G313341 Spc97 / Spc98 family of spindle pole body

(SBP) component S5_65124214 5 65124214 1.80E-05 0.08 1760 0.35 0.36 0.026 GRMZM2G011998 Transcription elongation factor (TFIIS) family

protein S5_65222573 5 65222573 3.09E-05 0.43 1760 0.35 0.36 0.030 GRMZM2G131988 lysine ketoglutarate reductase trans- splicing related 1,

putative, expressed S5_65222573 5 65222573 3.09E-05 0.43 1760 0.35 0.36 0.030 GRMZM2G132060 proline-rich spliceosome-

438 associated (PSP)

family protein

439

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_65222594 5 65222594 3.09E-05 0.43 1760 0.35 0.36 0.030 GRMZM2G131988 lysine ketoglutarate reductase trans- splicing related 1,

putative, expressed S5_65222594 5 65222594 3.09E-05 0.43 1760 0.35 0.36 0.030 GRMZM2G132060 proline-rich spliceosome- associated (PSP)

family protein S5_65222604 5 65222604 3.09E-05 0.43 1760 0.35 0.36 0.030 GRMZM2G131988 lysine ketoglutarate reductase trans- splicing related 1,

putative, expressed S5_65222604 5 65222604 3.09E-05 0.43 1760 0.35 0.36 0.030 GRMZM2G132060 proline-rich spliceosome- associated (PSP)

family protein S5_65420665 5 65420665 7.42E-05 0.48 1760 0.35 0.36 0.043 GRMZM2G112805 Clathrin light chain

protein S5_65420665 5 65420665 7.42E-05 0.48 1760 0.35 0.36 0.043 GRMZM2G466292 Transcription factor jumonji (jmj) family protein / zinc finger (C5HC2 type) family

protein S5_65438199 5 65438199 5.70E-05 0.08 1760 0.35 0.36 0.039 GRMZM2G466292 Transcription factor jumonji (jmj) family protein / zinc finger (C5HC2 type) family

protein S5_65438199 5 65438199 5.70E-05 0.08 1760 0.35 0.36 0.039 GRMZM2G466270 transcription factor jumonji (jmjC)

439 domain-containing

protein

440

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_65450363 5 65450363 3.67E-05 0.08 1760 0.35 0.36 0.033 GRMZM2G165351 (ATSPPL2,SPPL2): SIGNAL PEPTIDE

PEPTIDASE-LIKE 2 S5_65450363 5 65450363 3.67E-05 0.08 1760 0.35 0.36 0.033 GRMZM2G466270 transcription factor jumonji (jmjC) domain-containing

protein S5_65457522 5 65457522 1.38E-05 0.28 1760 0.35 0.36 0.024 GRMZM2G165351 (ATSPPL2,SPPL2): SIGNAL PEPTIDE

PEPTIDASE-LIKE 2 S5_65457522 5 65457522 1.38E-05 0.28 1760 0.35 0.36 0.024 GRMZM2G466270 transcription factor jumonji (jmjC) domain-containing

protein S5_66038095 5 66038095 9.92E-05 0.22 1760 0.35 0.36 0.048 GRMZM2G033829 (ATPDI2,ATPDIL1- 4,PDI2,PDIL1-4):

PDI-like 1-4 S5_66038095 5 66038095 9.92E-05 0.22 1760 0.35 0.36 0.048 GRMZM2G034143 (UKL4): uridine

kinase-like 4 S5_68405850 5 68405850 2.97E-05 0.47 1760 0.35 0.36 0.030 AC215811.3_FG003 B-box type zinc finger protein with

CCT domain S5_68405850 5 68405850 2.97E-05 0.47 1760 0.35 0.36 0.030 GRMZM2G074957 Tetratricopeptide repeat (TPR)-like

superfamily protein S5_68405852 5 68405852 2.97E-05 0.47 1760 0.35 0.36 0.030 AC215811.3_FG003 B-box type zinc finger protein with

CCT domain S5_68405852 5 68405852 2.97E-05 0.47 1760 0.35 0.36 0.030 GRMZM2G074956 LOC_Os02g01970.1:

expressed protein

440

441

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_68405852 5 68405852 2.97E-05 0.47 1760 0.35 0.36 0.030 GRMZM2G074957 Tetratricopeptide repeat (TPR)-like

superfamily protein S5_68422121 5 68422121 5.65E-07 0.15 1760 0.35 0.36 0.008 GRMZM2G074896 Glycosyltransferase

family 61 protein S5_68422121 5 68422121 5.65E-07 0.15 1760 0.35 0.36 0.008 GRMZM2G074805 Tetratricopeptide repeat (TPR)-like

superfamily protein S5_68422128 5 68422128 6.08E-07 0.15 1760 0.35 0.36 0.008 GRMZM2G074896 Glycosyltransferase

family 61 protein S5_68422128 5 68422128 6.08E-07 0.15 1760 0.35 0.36 0.008 GRMZM2G074805 Tetratricopeptide repeat (TPR)-like

superfamily protein S5_68422150 5 68422150 6.61E-05 0.20 1760 0.35 0.36 0.042 GRMZM2G074896 Glycosyltransferase

family 61 protein S5_68422150 5 68422150 6.61E-05 0.20 1760 0.35 0.36 0.042 GRMZM2G074805 Tetratricopeptide repeat (TPR)-like

superfamily protein S5_68422159 5 68422159 5.65E-07 0.15 1760 0.35 0.36 0.008 GRMZM2G074896 Glycosyltransferase

family 61 protein S5_68422159 5 68422159 5.65E-07 0.15 1760 0.35 0.36 0.008 GRMZM2G074805 Tetratricopeptide repeat (TPR)-like

superfamily protein S5_68423010 5 68423010 7.89E-06 0.09 1760 0.35 0.36 0.020 GRMZM2G074896 Glycosyltransferase

family 61 protein S5_68423010 5 68423010 7.89E-06 0.09 1760 0.35 0.36 0.020 GRMZM2G074805 Tetratricopeptide repeat (TPR)-like

superfamily protein S5_68423966 5 68423966 6.26E-06 0.09 1760 0.35 0.36 0.019 GRMZM2G074896 Glycosyltransferase

family 61 protein

441

442

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_68423966 5 68423966 6.26E-06 0.09 1760 0.35 0.36 0.019 GRMZM2G074805 Tetratricopeptide repeat (TPR)-like

superfamily protein S5_68517421 5 68517421 1.37E-06 0.25 1760 0.35 0.36 0.011 GRMZM2G300866 (MOM,MOM1): ATP-dependent helicase family

protein S5_68517421 5 68517421 1.37E-06 0.25 1760 0.35 0.36 0.011 GRMZM2G063897 (NCRK): Protein kinase superfamily

protein S5_68517421 5 68517421 1.37E-06 0.25 1760 0.35 0.36 0.011 GRMZM2G000937 Alg9-like mannosyltransferas

e family S5_68523847 5 68523847 1.50E-05 0.33 1760 0.35 0.36 0.024 GRMZM2G300866 (MOM,MOM1): ATP-dependent helicase family

protein S5_68523847 5 68523847 1.50E-05 0.33 1760 0.35 0.36 0.024 GRMZM2G063897 (NCRK): Protein kinase superfamily

protein S5_68523847 5 68523847 1.50E-05 0.33 1760 0.35 0.36 0.024 GRMZM2G000937 Alg9-like mannosyltransferas

e family S5_68528175 5 68528175 2.62E-07 0.26 1760 0.35 0.36 0.007 GRMZM2G300866 (MOM,MOM1): ATP-dependent helicase family

protein S5_68528175 5 68528175 2.62E-07 0.26 1760 0.35 0.36 0.007 GRMZM2G000937 Alg9-like mannosyltransferas

e family

442

443

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_68528463 5 68528463 2.94E-05 0.24 1760 0.35 0.36 0.030 GRMZM2G300866 (MOM,MOM1): ATP-dependent helicase family

protein S5_68528463 5 68528463 2.94E-05 0.24 1760 0.35 0.36 0.030 GRMZM2G000937 Alg9-like mannosyltransferas

e family S5_69098216 5 69098216 3.28E-05 0.08 1760 0.35 0.36 0.031 GRMZM2G020146 (CPY,SCPL49): SERINE CARBOXYPEPTIDASE

-LIKE 49 S5_69102182 5 69102182 9.25E-07 0.08 1760 0.35 0.36 0.010 GRMZM2G020146 (CPY,SCPL49): SERINE CARBOXYPEPTIDASE

-LIKE 49 S5_69103411 5 69103411 2.87E-05 0.10 1760 0.35 0.36 0.030 GRMZM2G020146 (CPY,SCPL49): SERINE CARBOXYPEPTIDASE

-LIKE 49 S5_69303599 5 69303599 4.99E-05 0.14 1760 0.35 0.36 0.037 GRMZM2G088189 (ATMYB86,MYB86): myb domain protein

86 S5_69303599 5 69303599 4.99E-05 0.14 1760 0.35 0.36 0.037 GRMZM2G088114 Nucleic acid- binding, OB-fold-like

protein S5_69303599 5 69303599 4.99E-05 0.14 1760 0.35 0.36 0.037 GRMZM2G389155 Transducin/WD40 repeat-like

superfamily protein S5_69306720 5 69306720 6.63E-05 0.13 1760 0.35 0.36 0.042 GRMZM2G088189 (ATMYB86,MYB86): myb domain protein

443

444

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_69306720 5 69306720 6.63E-05 0.13 1760 0.35 0.36 0.042 GRMZM2G088114 Nucleic acid- binding, OB-fold-like

protein S5_69306720 5 69306720 6.63E-05 0.13 1760 0.35 0.36 0.042 GRMZM2G389155 Transducin/WD40 repeat-like

superfamily protein

S5_144284526 5 144284526 1.00E-04 0.11 1760 0.35 0.36 0.048 GRMZM2G049390 (PFD6): prefoldin 6 S5_186283488 5 186283488 2.69E-05 0.13 1760 0.35 0.36 0.029 GRMZM2G014560 (WAK5): wall

associated kinase 5 S5_186283527 5 186283527 9.95E-05 0.12 1760 0.35 0.36 0.048 GRMZM2G014560 (WAK5): wall

associated kinase 5 S5_186283633 5 186283633 2.53E-05 0.13 1760 0.35 0.36 0.029 GRMZM2G014560 (WAK5): wall

associated kinase 5 S5_186283676 5 186283676 2.53E-05 0.13 1760 0.35 0.36 0.029 GRMZM2G014560 (WAK5): wall

associated kinase 5 S5_186413892 5 186413892 8.90E-05 0.12 1760 0.35 0.36 0.047 GRMZM2G095904 (ATMYB15,ATY19,M YB15): myb domain

protein 15 S5_188652207 5 188652207 2.51E-05 0.35 1760 0.35 0.36 0.029 GRMZM2G139803 (FTRA2): ferredoxin/thioredo xin reductase subunit A (variable

subunit) 2 S5_188652207 5 188652207 2.51E-05 0.35 1760 0.35 0.36 0.029 GRMZM2G139773 Endosomal targeting BRO1-like domain-

containing protein S5_188652207 5 188652207 2.51E-05 0.35 1760 0.35 0.36 0.029 GRMZM2G139855 hydroxyproline-rich glycoprotein family

protein

S5_188652207 5 188652207 2.51E-05 0.35 1760 0.35 0.36 0.029 GRMZM2G139837 spliceosome 444

protein-related

445

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_188759802 5 188759802 7.18E-05 0.08 1760 0.35 0.36 0.043 GRMZM2G588223 (ATCPL1,CPL1,FRY2): C-terminal domain

phosphatase-like 1 S5_188759802 5 188759802 7.18E-05 0.08 1760 0.35 0.36 0.043 GRMZM2G073250 Protein kinase

superfamily protein S5_191625992 5 191625992 5.34E-05 0.47 1760 0.35 0.36 0.037 GRMZM2G056889 hydroxyproline-rich glycoprotein family

protein S5_191625992 5 191625992 5.34E-05 0.47 1760 0.35 0.36 0.037 GRMZM2G056903 Protein kinase

superfamily protein S5_193537504 5 193537504 1.08E-04 0.12 1760 0.35 0.36 0.050 GRMZM2G465957 (AGC2,AGC2- 1,AtOXI1,OXI1): AGC (cAMP-dependent, cGMP-dependent and protein kinase C) kinase family

protein S5_193537504 5 193537504 1.08E-04 0.12 1760 0.35 0.36 0.050 GRMZM2G165530 Major facilitator

superfamily protein S5_202819416 5 202819416 6.34E-05 0.21 1760 0.35 0.36 0.041 GRMZM2G180926 (XCP1): xylem

cysteine peptidase 1 S5_202819416 5 202819416 6.34E-05 0.21 1760 0.35 0.36 0.041 GRMZM2G180922 NAD(P)-binding Rossmann-fold

superfamily protein S5_202819416 5 202819416 6.34E-05 0.21 1760 0.35 0.36 0.041 GRMZM2G180930 Phosphoribosyltrans ferase family

protein S5_203035040 5 203035040 4.71E-06 0.28 1760 0.35 0.36 0.016 GRMZM2G056252 (FAD2): fatty acid

desaturase 2 S5_204229636 5 204229636 8.77E-05 0.14 1760 0.35 0.36 0.047 GRMZM2G394941 (OBP4): OBF binding

445

protein 4

446

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_204229636 5 204229636 8.77E-05 0.14 1760 0.35 0.36 0.047 GRMZM2G000280 Sucrase/ferredoxin-

like family protein S5_204800054 5 204800054 3.24E-05 0.36 1760 0.35 0.36 0.031 GRMZM2G075136 (ALMT9,AtALMT9): aluminum-activated malate transporter

9 S5_204800054 5 204800054 3.24E-05 0.36 1760 0.35 0.36 0.031 GRMZM2G075223 Fcf2 pre-rRNA

processing protein S5_204800054 5 204800054 3.24E-05 0.36 1760 0.35 0.36 0.031 GRMZM2G075260 NHL domain-

containing protein S5_204876427 5 204876427 8.03E-06 0.19 1760 0.35 0.36 0.020 GRMZM2G175875 Ribosomal protein

L17 family protein S5_213365813 5 213365813 8.30E-05 0.14 1760 0.35 0.36 0.046 GRMZM2G119691 Translation initiation

factor 3 protein S5_216602052 5 216602052 9.59E-05 0.40 1760 0.35 0.36 0.048 GRMZM2G445944 TCP family

transcription factor S5_216602052 5 216602052 9.59E-05 0.40 1760 0.35 0.36 0.048 GRMZM2G145128 Tetratricopeptide repeat (TPR)-like

superfamily protein S5_216602451 5 216602451 2.37E-05 0.19 1760 0.35 0.36 0.028 GRMZM2G445944 TCP family

transcription factor S5_216602451 5 216602451 2.37E-05 0.19 1760 0.35 0.36 0.028 GRMZM2G145128 Tetratricopeptide repeat (TPR)-like

superfamily protein S5_216693134 5 216693134 2.60E-05 0.17 1760 0.35 0.36 0.029 GRMZM5G842058 (ATBRK1,BRK1,HSPC 300): BRICK1,

putative S5_216693134 5 216693134 2.60E-05 0.17 1760 0.35 0.36 0.029 AC208348.3_FG012 Tetratricopeptide repeat (TPR)-like

superfamily protein

446

447

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S5_216693134 5 216693134 2.60E-05 0.17 1760 0.35 0.36 0.029 GRMZM2G133919 Zincin-like metalloproteases

family protein S5_217372609 5 217372609 7.45E-05 0.24 1760 0.35 0.36 0.043 GRMZM5G840560 (ATGSL12,gsl12): glucan synthase-like

12 S5_217609250 5 217609250 7.61E-05 0.39 1760 0.35 0.36 0.044 GRMZM2G375002 (ARAC3,ATROP6,RA C3,RHO1PS,ROP6):

RAC-like 3 S5_217609250 5 217609250 7.61E-05 0.39 1760 0.35 0.36 0.044 GRMZM2G077531 (ATSULA,GC1,SULA): NAD(P)-binding Rossmann-fold

superfamily protein

S5_217609250 5 217609250 7.61E-05 0.39 1760 0.35 0.36 0.044 GRMZM2G073609 ferredoxin-related S6_4609502 6 4609502 7.45E-05 0.15 1760 0.35 0.36 0.043 GRMZM2G032315 60S acidic ribosomal

protein family S6_6077100 6 6077100 5.51E-06 0.36 1760 0.35 0.36 0.017 GRMZM2G064174 (ATEXP11,ATEXPA11 ,ATHEXP ALPHA 1.14,EXP11,EXPA11)

: expansin 11 S6_24608229 6 24608229 7.77E-05 0.34 1760 0.35 0.36 0.044 GRMZM2G036908 (ATMTPA1,MTPA1): Cation efflux family

protein S6_31649787 6 31649787 6.61E-06 0.37 1760 0.35 0.36 0.019 GRMZM2G025959 Mannose-binding lectin superfamily

protein S6_34441673 6 34441673 1.22E-05 0.25 1760 0.35 0.36 0.024 GRMZM2G034598 (ATHEX2,HEXO1): beta-

hexosaminidase 1

447

448

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S6_34441673 6 34441673 1.22E-05 0.25 1760 0.35 0.36 0.024 GRMZM2G035502 (DHAR2): dehydroascorbate

reductase 2 S6_34441673 6 34441673 1.22E-05 0.25 1760 0.35 0.36 0.024 GRMZM2G034724 RmlC-like cupins

superfamily protein S6_34441700 6 34441700 1.22E-05 0.25 1760 0.35 0.36 0.024 GRMZM2G034598 (ATHEX2,HEXO1): beta-

hexosaminidase 1 S6_34441700 6 34441700 1.22E-05 0.25 1760 0.35 0.36 0.024 GRMZM2G035502 (DHAR2): dehydroascorbate

reductase 2 S6_34441700 6 34441700 1.22E-05 0.25 1760 0.35 0.36 0.024 GRMZM2G034724 RmlC-like cupins

superfamily protein S6_103857835 6 103857835 2.73E-05 0.13 1760 0.35 0.36 0.029 GRMZM2G335618 (ATGSTU25,GSTU25) : glutathione S-

transferase TAU 25 S6_104674381 6 104674381 7.93E-05 0.17 1760 0.35 0.36 0.045 GRMZM2G151015 (GAUT11): galacturonosyltransf

erase 11 S6_104674381 6 104674381 7.93E-05 0.17 1760 0.35 0.36 0.045 GRMZM2G449817 Protein kinase family protein with leucine-rich repeat

domain S6_104756165 6 104756165 8.61E-05 0.23 1760 0.35 0.36 0.046 GRMZM2G103526 HAD superfamily, subfamily IIIB acid

phosphatase S6_104756175 6 104756175 8.61E-05 0.23 1760 0.35 0.36 0.046 GRMZM2G103526 HAD superfamily, subfamily IIIB acid

phosphatase S6_104759143 6 104759143 1.08E-04 0.24 1760 0.35 0.36 0.050 GRMZM2G103526 HAD superfamily,

448 subfamily IIIB acid

phosphatase

449

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S6_108065144 6 108065144 1.10E-04 0.13 1760 0.35 0.36 0.050 GRMZM2G120371 (GCR1): G-protein-

coupled receptor 1 S6_108065144 6 108065144 1.10E-04 0.13 1760 0.35 0.36 0.050 GRMZM2G373435 Protein kinase

superfamily protein S6_108065144 6 108065144 1.10E-04 0.13 1760 0.35 0.36 0.050 GRMZM2G073150 Ribosomal S17

family protein S6_120136158 6 120136158 1.87E-05 0.43 1760 0.35 0.36 0.026 GRMZM2G036564 Ankyrin repeat

family protein S6_123156701 6 123156701 1.50E-05 0.11 1760 0.35 0.36 0.024 GRMZM2G426175 2-oxoglutarate (2OG) and Fe(II)- dependent oxygenase

superfamily protein S6_133817345 6 133817345 5.80E-05 0.36 1760 0.35 0.36 0.039 GRMZM2G476886 (LHT1): lysine histidine transporter

1 S6_133817345 6 133817345 5.80E-05 0.36 1760 0.35 0.36 0.039 GRMZM2G176655 Plant regulator RWP-RK family

protein S6_143959110 6 143959110 1.06E-05 0.29 1760 0.35 0.36 0.023 GRMZM2G308707 glycoside hydrolase

family 2 protein S6_143959110 6 143959110 1.06E-05 0.29 1760 0.35 0.36 0.023 GRMZM5G869788 Glycosyltransferase

family 61 protein S6_143959140 6 143959140 4.61E-06 0.37 1760 0.35 0.36 0.016 GRMZM2G308707 glycoside hydrolase

family 2 protein S6_143959140 6 143959140 4.61E-06 0.37 1760 0.35 0.36 0.016 GRMZM5G869788 Glycosyltransferase

family 61 protein

S6_144125412 6 144125412 6.03E-05 0.41 1760 0.35 0.36 0.040 GRMZM2G427337 glycine-rich protein

449

450

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S6_147880305 6 147880305 9.77E-05 0.37 1760 0.35 0.36 0.048 GRMZM2G180328 (ANAC002,ATAF1): NAC (No Apical Meristem) domain transcriptional regulator

superfamily protein S6_147880305 6 147880305 9.77E-05 0.37 1760 0.35 0.36 0.048 GRMZM2G018971 DUF803 domain containing, putative,

expressed S6_147880305 6 147880305 9.77E-05 0.37 1760 0.35 0.36 0.048 GRMZM2G456512 Protein of unknown function (DUF630 and DUF632) S6_147880323 6 147880323 9.77E-05 0.37 1760 0.35 0.36 0.048 GRMZM2G180328 (ANAC002,ATAF1): NAC (No Apical Meristem) domain transcriptional regulator

superfamily protein S6_147880323 6 147880323 9.77E-05 0.37 1760 0.35 0.36 0.048 GRMZM2G018971 DUF803 domain containing, putative,

expressed S6_147880323 6 147880323 9.77E-05 0.37 1760 0.35 0.36 0.048 GRMZM2G456512 Protein of unknown function (DUF630 and DUF632) S6_147887839 6 147887839 6.27E-05 0.16 1760 0.35 0.36 0.041 GRMZM2G456512 DUF630/DUF632 domains containing protein, putative,

expressed S6_147887839 6 147887839 6.27E-05 0.16 1760 0.35 0.36 0.041 GRMZM2G018971 DUF803 domain containing, putative,

450

expressed

451

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S6_147888459 6 147888459 4.28E-06 0.22 1760 0.35 0.36 0.016 GRMZM2G456512 DUF630/DUF632 domains containing protein, putative,

expressed S6_147888459 6 147888459 4.28E-06 0.22 1760 0.35 0.36 0.016 GRMZM2G018971 DUF803 domain containing, putative,

expressed S6_147968132 6 147968132 8.89E-05 0.21 1760 0.35 0.36 0.047 GRMZM2G058472 (GUX3,PGSIP2): plant glycogenin-like starch initiation

protein 2 S6_159013906 6 159013906 7.90E-05 0.20 1760 0.35 0.36 0.045 GRMZM2G127680 (ATOFP2,OFP2): ovate family protein 2 S6_159013906 6 159013906 7.90E-05 0.20 1760 0.35 0.36 0.045 GRMZM2G127648 (ATRABA1B,RAB11,R ABA1b): RAB GTPase

homolog A1B S6_161894988 6 161894988 9.88E-05 0.18 1760 0.35 0.36 0.048 GRMZM2G093441 alpha/beta- Hydrolases

superfamily protein S6_161894988 6 161894988 9.88E-05 0.18 1760 0.35 0.36 0.048 GRMZM2G093422 Cyclin/Brf1-like TBP-

binding protein S6_161894988 6 161894988 9.88E-05 0.18 1760 0.35 0.36 0.048 GRMZM2G093503 fiber protein Fb11,

putative, expressed S6_162009932 6 162009932 4.37E-05 0.20 1760 0.35 0.36 0.035 GRMZM2G079263 Pectin lyase-like

superfamily protein S6_162009932 6 162009932 4.37E-05 0.20 1760 0.35 0.36 0.035 GRMZM2G079617 Pectin lyase-like

superfamily protein S6_162561913 6 162561913 7.44E-06 0.11 1760 0.35 0.36 0.020 GRMZM2G059845 (ATGUT1,GUT2,IRX1 0): Exostosin family

451

protein

452

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S6_162561913 6 162561913 7.44E-06 0.11 1760 0.35 0.36 0.020 GRMZM2G059939 (EDF4,RAV1): related to ABI3/VP1

1 S6_162561913 6 162561913 7.44E-06 0.11 1760 0.35 0.36 0.020 GRMZM2G059825 (GUT1): Exostosin

family protein S6_162561913 6 162561913 7.44E-06 0.11 1760 0.35 0.36 0.020 GRMZM2G179797 (MTO2,TS): Pyridoxal-5\'- phosphate- dependent enzyme

family protein S6_162563498 6 162563498 4.45E-05 0.37 1760 0.35 0.36 0.035 GRMZM2G059845 (ATGUT1,GUT2,IRX1 0): Exostosin family

protein S6_162563498 6 162563498 4.45E-05 0.37 1760 0.35 0.36 0.035 GRMZM2G059939 (EDF2,RAP2.8,RAV2, TEM2): related to

ABI3/VP1 2 S6_162563498 6 162563498 4.45E-05 0.37 1760 0.35 0.36 0.035 GRMZM2G059825 (GUT1): Exostosin

family protein S6_162563507 6 162563507 4.00E-06 0.29 1760 0.35 0.36 0.015 GRMZM2G059845 (ATGUT1,GUT2,IRX1 0): Exostosin family

protein S6_162563507 6 162563507 4.00E-06 0.29 1760 0.35 0.36 0.015 GRMZM2G059939 (EDF2,RAP2.8,RAV2, TEM2): related to

ABI3/VP1 2 S6_162563507 6 162563507 4.00E-06 0.29 1760 0.35 0.36 0.015 GRMZM2G059825 (GUT1): Exostosin

family protein S6_162563514 6 162563514 4.00E-06 0.29 1760 0.35 0.36 0.015 GRMZM2G059845 (ATGUT1,GUT2,IRX1 0): Exostosin family

protein S6_162563514 6 162563514 4.00E-06 0.29 1760 0.35 0.36 0.015 GRMZM2G059939 (EDF2,RAP2.8,RAV2,

452 TEM2): related to

ABI3/VP1 2

453

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S6_162563514 6 162563514 4.00E-06 0.29 1760 0.35 0.36 0.015 GRMZM2G059825 (GUT1): Exostosin

family protein S6_162882956 6 162882956 1.55E-05 0.06 1760 0.35 0.36 0.025 GRMZM2G038032 (ATARCA,RACK1A,R ACK1A_AT): Transducin/WD40 repeat-like

superfamily protein S6_162882956 6 162882956 1.55E-05 0.06 1760 0.35 0.36 0.025 GRMZM2G037998 Galactosyltransferas

e family protein S6_164364329 6 164364329 6.02E-05 0.08 1760 0.35 0.36 0.040 GRMZM2G038284 Drought-responsive

family protein S6_164364329 6 164364329 6.02E-05 0.08 1760 0.35 0.36 0.040 GRMZM2G038183 Protein of unknown

function (DUF1421) S6_164369713 6 164369713 1.33E-05 0.13 1760 0.35 0.36 0.024 GRMZM2G039886 DNAJ heat shock

family protein S6_164369713 6 164369713 1.33E-05 0.13 1760 0.35 0.36 0.024 GRMZM2G038284 Drought-responsive

family protein S6_164369713 6 164369713 1.33E-05 0.13 1760 0.35 0.36 0.024 GRMZM2G038183 Protein of unknown

function (DUF1421) S6_165981766 6 165981766 6.76E-05 0.36 1760 0.35 0.36 0.042 GRMZM5G893630 DUF617 domain containing protein,

expressed S6_165981766 6 165981766 6.76E-05 0.36 1760 0.35 0.36 0.042 GRMZM5G847466 EF hand calcium- binding protein

family S7_126162868 7 126162868 1.09E-04 0.15 1760 0.35 0.36 0.050 GRMZM2G096268 (ATFT1,ATFUT1,FT1, MUR2):

fucosyltransferase 1 S7_133381306 7 133381306 6.25E-05 0.10 1760 0.35 0.36 0.041 GRMZM2G104299 AT hook motif DNA- binding family

453

protein

454

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S7_133381306 7 133381306 6.25E-05 0.10 1760 0.35 0.36 0.041 GRMZM2G103783 DNA-binding bromodomain-

containing protein S7_137515785 7 137515785 1.82E-05 0.15 1760 0.35 0.36 0.026 GRMZM2G066202 (AIR12): auxin- responsive family

protein S7_137515785 7 137515785 1.82E-05 0.15 1760 0.35 0.36 0.026 GRMZM2G066219 Auxin-responsive

family protein S7_137515785 7 137515785 1.82E-05 0.15 1760 0.35 0.36 0.026 GRMZM2G102181 DNA topoisomerase,

type IA, core S7_137515785 7 137515785 1.82E-05 0.15 1760 0.35 0.36 0.026 GRMZM2G065868 Ribosomal protein

L32e S7_145385488 7 145385488 6.14E-05 0.46 1760 0.35 0.36 0.040 GRMZM2G318849 ARM repeat

superfamily protein S7_157381776 7 157381776 2.57E-05 0.14 1760 0.35 0.36 0.029 GRMZM5G872502 uncharacterized secreted protein,

putative, expressed S7_158750056 7 158750056 1.30E-05 0.16 1760 0.35 0.36 0.024 GRMZM2G333980 (ATPGIP1,PGIP1): polygalacturonase

inhibiting protein 1 S7_158750056 7 158750056 1.30E-05 0.16 1760 0.35 0.36 0.024 GRMZM2G028086 (CPK7): calmodulin- domain protein

kinase 7 S7_158750071 7 158750071 9.65E-06 0.16 1760 0.35 0.36 0.023 GRMZM2G333980 (ATPGIP1,PGIP1): polygalacturonase

inhibiting protein 1 S7_158750071 7 158750071 9.65E-06 0.16 1760 0.35 0.36 0.023 GRMZM2G028086 (CPK7): calmodulin- domain protein

kinase 7 S7_160215587 7 160215587 9.07E-05 0.18 1760 0.35 0.36 0.047 GRMZM2G374971 (ATOSM34,OSM34):

454

osmotin 34

455

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S7_160215587 7 160215587 9.07E-05 0.18 1760 0.35 0.36 0.047 GRMZM2G374969 Transducin/WD40 repeat-like

superfamily protein S7_164079269 7 164079269 1.76E-05 0.45 1760 0.35 0.36 0.026 GRMZM2G136918 (PGL1): 6- phosphogluconolact

onase 1 S7_164079269 7 164079269 1.76E-05 0.45 1760 0.35 0.36 0.026 GRMZM2G136884 Eukaryotic aspartyl protease family

protein S7_164079269 7 164079269 1.76E-05 0.45 1760 0.35 0.36 0.026 GRMZM2G136872 Xanthine/uracil permease family

protein S7_165199390 7 165199390 4.23E-05 0.13 1760 0.35 0.36 0.035 GRMZM2G417072 (AT- RSH3,ATRSH3,RSH3) : RELA/SPOT

homolog 3 S7_165199390 7 165199390 4.23E-05 0.13 1760 0.35 0.36 0.035 GRMZM2G116426 alpha/beta- Hydrolases

superfamily protein S7_165242462 7 165242462 7.76E-06 0.17 1760 0.35 0.36 0.020 GRMZM2G030578 (PSD): ARM repeat

superfamily protein S7_165242462 7 165242462 7.76E-06 0.17 1760 0.35 0.36 0.020 GRMZM2G030731 Ribosomal protein L18e/L15

superfamily protein S7_165242464 7 165242464 7.76E-06 0.17 1760 0.35 0.36 0.020 GRMZM2G030578 (PSD): ARM repeat

superfamily protein S7_165242464 7 165242464 7.76E-06 0.17 1760 0.35 0.36 0.020 GRMZM2G030731 Ribosomal protein L18e/L15

superfamily protein S7_165300999 7 165300999 2.15E-05 0.13 1760 0.35 0.36 0.027 GRMZM2G127031 Protein kinase

455

superfamily protein

456

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S7_167944449 7 167944449 7.15E-06 0.36 1760 0.35 0.36 0.020 GRMZM5G867185 (ATSCL33,SCL33,SR3 3): SC35-like splicing

factor 33 S7_167944449 7 167944449 7.15E-06 0.36 1760 0.35 0.36 0.020 GRMZM2G060511 Mitochondrial ribosomal protein

L37 S7_168289936 7 168289936 1.35E-05 0.08 1760 0.35 0.36 0.024 GRMZM2G150841 (ATMYB86,MYB86): myb domain protein

86 S7_168290069 7 168290069 4.07E-05 0.17 1760 0.35 0.36 0.034 GRMZM2G150841 (ATMYB86,MYB86): myb domain protein

86 S7_168399484 7 168399484 3.52E-05 0.32 1760 0.35 0.36 0.032 GRMZM2G082365 (AtCBF5,AtNAP57,C BF5,NAP57): homologue of

NAP57 S7_168399484 7 168399484 3.52E-05 0.32 1760 0.35 0.36 0.032 GRMZM2G177715 (OTP84): Tetratricopeptide repeat (TPR)-like

superfamily protein S7_168399484 7 168399484 3.52E-05 0.32 1760 0.35 0.36 0.032 GRMZM2G477325 (RCI2A): Low temperature and salt responsive

protein family S7_168399484 7 168399484 3.52E-05 0.32 1760 0.35 0.36 0.032 GRMZM2G082318 : transcription regulator, putative,

expressed S7_168399576 7 168399576 4.70E-06 0.26 1760 0.35 0.36 0.016 GRMZM2G082365 (AtCBF5,AtNAP57,C BF5,NAP57): homologue of

456

NAP57

457

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S7_168399576 7 168399576 4.70E-06 0.26 1760 0.35 0.36 0.016 GRMZM2G177715 (OTP84): Tetratricopeptide repeat (TPR)-like

superfamily protein S7_168399576 7 168399576 4.70E-06 0.26 1760 0.35 0.36 0.016 GRMZM2G477325 (RCI2A): Low temperature and salt responsive

protein family S7_168399576 7 168399576 4.70E-06 0.26 1760 0.35 0.36 0.016 GRMZM2G082318 transcription regulator, putative,

expressed S7_168404877 7 168404877 8.96E-05 0.18 1760 0.35 0.36 0.047 GRMZM2G082365 (AtCBF5,AtNAP57,C BF5,NAP57): homologue of

NAP57 S7_168404877 7 168404877 8.96E-05 0.18 1760 0.35 0.36 0.047 GRMZM2G477325 (RCI2A): Low temperature and salt responsive

protein family S7_168404877 7 168404877 8.96E-05 0.18 1760 0.35 0.36 0.047 GRMZM2G082318 DNA-binding storekeeper protein-related transcriptional

regulator

S7_169452418 7 169452418 3.81E-05 0.29 1760 0.35 0.36 0.033 GRMZM2G120954 plectin-related S7_169452418 7 169452418 3.81E-05 0.29 1760 0.35 0.36 0.033 GRMZM2G120971 Transcription elongation factor (TFIIS) family

protein

S7_169455943 7 169455943 3.12E-05 0.34 1760 0.35 0.36 0.030 GRMZM2G120954 plectin-related 457

458

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S7_169455943 7 169455943 3.12E-05 0.34 1760 0.35 0.36 0.030 GRMZM2G120971 Transcription elongation factor (TFIIS) family

protein S7_169534765 7 169534765 7.83E-06 0.41 1760 0.35 0.36 0.020 GRMZM2G130398 (PAG1): 20S proteasome alpha

subunit G1 S7_169534766 7 169534766 7.83E-06 0.41 1760 0.35 0.36 0.020 GRMZM2G130398 (PAG1): 20S proteasome alpha

subunit G1 S7_169534864 7 169534864 1.05E-05 0.31 1760 0.35 0.36 0.023 GRMZM2G130398 (PAG1): 20S proteasome alpha

subunit G1 S7_169969340 7 169969340 2.44E-05 0.17 1760 0.35 0.36 0.028 GRMZM2G003172 ATP12 protein-

related S7_170835678 7 170835678 4.35E-05 0.17 1760 0.35 0.36 0.035 GRMZM2G136580 Glycosyltransferase

family 61 protein S7_170835678 7 170835678 4.35E-05 0.17 1760 0.35 0.36 0.035 GRMZM2G136578 TRAF-type zinc

finger-related S7_171046910 7 171046910 3.73E-05 0.12 1760 0.35 0.36 0.033 GRMZM2G031298 ankyrin repeat

family protein S7_171046910 7 171046910 3.73E-05 0.12 1760 0.35 0.36 0.033 GRMZM2G326270 Haloacid dehalogenase-like hydrolase (HAD)

superfamily protein S7_171046910 7 171046910 3.73E-05 0.12 1760 0.35 0.36 0.033 GRMZM2G326263 Pentatricopeptide repeat (PPR-like)

superfamily protein S7_172495590 7 172495590 1.14E-05 0.21 1760 0.35 0.36 0.023 GRMZM2G414460 (GH3.9): putative indole-3-acetic acid-

458 amido synthetase

GH3.9

459

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S7_172495590 7 172495590 1.14E-05 0.21 1760 0.35 0.36 0.023 GRMZM2G113863 Heavy metal transport/detoxifica tion superfamily

protein S7_172495623 7 172495623 1.74E-05 0.19 1760 0.35 0.36 0.025 GRMZM2G414460 (GH3.9): putative indole-3-acetic acid- amido synthetase

GH3.9 S7_172495623 7 172495623 1.74E-05 0.19 1760 0.35 0.36 0.025 GRMZM2G113863 Heavy metal transport/detoxifica tion superfamily

protein S7_172495737 7 172495737 2.87E-06 0.19 1760 0.35 0.36 0.014 GRMZM2G414460 (GH3.9): putative indole-3-acetic acid- amido synthetase

GH3.9 S7_172495737 7 172495737 2.87E-06 0.19 1760 0.35 0.36 0.014 GRMZM2G113863 Heavy metal transport/detoxifica tion superfamily

protein S7_172743650 7 172743650 4.51E-05 0.17 1760 0.35 0.36 0.035 GRMZM2G025441 Peroxidase

superfamily protein S7_172743650 7 172743650 4.51E-05 0.17 1760 0.35 0.36 0.035 GRMZM2G025182 Plant invertase/pectin methylesterase inhibitor

superfamily S7_172979391 7 172979391 8.43E-05 0.45 1760 0.35 0.36 0.046 GRMZM5G845472 (ATOFP3,OFP3): ovate family protein

459 S7_172979391 7 172979391 8.43E-05 0.45 1760 0.35 0.36 0.046 GRMZM2G053554 Melibiase family

protein

460

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S7_172979774 7 172979774 5.30E-05 0.23 1760 0.35 0.36 0.037 GRMZM5G845472 (ATOFP3,OFP3): ovate family protein

3 S7_172979774 7 172979774 5.30E-05 0.23 1760 0.35 0.36 0.037 GRMZM2G053554 Melibiase family

protein S7_174512457 7 174512457 4.33E-05 0.45 1760 0.35 0.36 0.035 GRMZM2G113056 (LON1,LON_ARA_AR

A): lon protease 1 S7_174512457 7 174512457 4.33E-05 0.45 1760 0.35 0.36 0.035 GRMZM2G113052 cAMP-regulated phosphoprotein 19-

related protein S7_174512457 7 174512457 4.33E-05 0.45 1760 0.35 0.36 0.035 GRMZM2G113036 Heat shock protein DnaJ with tetratricopeptide

repeat S7_174512457 7 174512457 4.33E-05 0.45 1760 0.35 0.36 0.035 GRMZM2G414141 transcription

coactivators S7_174512457 7 174512457 4.33E-05 0.45 1760 0.35 0.36 0.035 GRMZM2G113039 zinc finger (C3HC4- type RING finger)

family protein S7_174512510 7 174512510 3.48E-05 0.43 1760 0.35 0.36 0.032 GRMZM2G113056 (LON1,LON_ARA_AR

A): lon protease 1 S7_174512510 7 174512510 3.48E-05 0.43 1760 0.35 0.36 0.032 GRMZM2G113052 cAMP-regulated phosphoprotein 19-

related protein S7_174512510 7 174512510 3.48E-05 0.43 1760 0.35 0.36 0.032 GRMZM2G113036 Heat shock protein DnaJ with tetratricopeptide

repeat S7_174512510 7 174512510 3.48E-05 0.43 1760 0.35 0.36 0.032 GRMZM2G414141 transcription

coactivators

460

461

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S7_174512510 7 174512510 3.48E-05 0.43 1760 0.35 0.36 0.032 GRMZM2G113039 zinc finger (C3HC4- type RING finger)

family protein S7_174512525 7 174512525 3.39E-05 0.47 1760 0.35 0.36 0.032 GRMZM2G113056 (LON1,LON_ARA_AR

A): lon protease 1 S7_174512525 7 174512525 3.39E-05 0.47 1760 0.35 0.36 0.032 GRMZM2G113052 cAMP-regulated phosphoprotein 19-

related protein S7_174512525 7 174512525 3.39E-05 0.47 1760 0.35 0.36 0.032 GRMZM2G113036 Heat shock protein DnaJ with tetratricopeptide

repeat S7_174512525 7 174512525 3.39E-05 0.47 1760 0.35 0.36 0.032 GRMZM2G414141 transcription

coactivators S7_174512525 7 174512525 3.39E-05 0.47 1760 0.35 0.36 0.032 GRMZM2G113039 zinc finger (C3HC4- type RING finger)

family protein S8_6511776 8 6511776 7.83E-07 0.22 1760 0.35 0.36 0.009 GRMZM2G044636 (CYP72A9): cytochrome P450, family 72, subfamily

A, polypeptide 9 S8_6511776 8 6511776 7.83E-07 0.22 1760 0.35 0.36 0.009 GRMZM2G044553 rRNA processing

protein-related S8_18428004 8 18428004 6.79E-06 0.26 1760 0.35 0.36 0.020 GRMZM2G078267 (AIF1): AtBS1(activation- tagged BRI1 suppressor 1)-

interacting factor 1 S8_35002833 8 35002833 9.28E-05 0.08 1760 0.35 0.36 0.047 GRMZM2G331566 (AtGH9B13,GH9B13)

461 : glycosyl hydrolase

9B13

462

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S8_67972290 8 67972290 1.39E-05 0.11 1760 0.35 0.36 0.024 GRMZM2G399338 (ATBET10,BET10): bromodomain and extraterminal

domain protein 10 S8_68087117 8 68087117 9.29E-05 0.08 1760 0.35 0.36 0.047 GRMZM2G573324 (IAA8): indoleacetic acid-induced protein

8 S8_68087411 8 68087411 1.60E-05 0.09 1760 0.35 0.36 0.025 GRMZM2G573324 (IAA8): indoleacetic acid-induced protein

8 S8_72745120 8 72745120 5.73E-05 0.10 1760 0.35 0.36 0.039 AC234185.1_FG004 CTP synthase family

protein S8_73852614 8 73852614 9.47E-05 0.38 1760 0.35 0.36 0.048 GRMZM2G001991 NAD(P)-binding Rossmann-fold

superfamily protein S8_73852614 8 73852614 9.47E-05 0.38 1760 0.35 0.36 0.048 GRMZM2G002034 Pectin lyase-like

superfamily protein S8_74138238 8 74138238 8.24E-05 0.06 1760 0.35 0.36 0.046 GRMZM2G328438 (AtHB31,HB31): homeobox protein

31 S8_74138238 8 74138238 8.24E-05 0.06 1760 0.35 0.36 0.046 GRMZM2G029974 DNA glycosylase

superfamily protein S8_104821067 8 104821067 8.84E-05 0.09 1760 0.35 0.36 0.047 GRMZM2G471600 Homeodomain-like

superfamily protein S8_105571425 8 105571425 6.61E-05 0.08 1760 0.35 0.36 0.042 GRMZM2G080889 CUE domain containing protein,

expressed S8_106750616 8 106750616 1.03E-04 0.06 1760 0.35 0.36 0.049 GRMZM2G109354 (ATSPL7,SPL7): squamosa promoter binding protein-like

462

463

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S8_109938307 8 109938307 6.79E-05 0.18 1760 0.35 0.36 0.042 GRMZM2G312198 Sec14p-like phosphatidylinositol transfer family

protein S8_116858220 8 116858220 1.61E-06 0.20 1760 0.35 0.36 0.012 GRMZM2G336908 DHBP synthase RibB-like alpha/beta domain;GTP

cyclohydrolase II S8_116858220 8 116858220 1.61E-06 0.20 1760 0.35 0.36 0.012 GRMZM2G035202 Protein-tyrosine phosphatase-like,

PTPLA S8_116858220 8 116858220 1.61E-06 0.20 1760 0.35 0.36 0.012 GRMZM5G883149 SNARE-like

superfamily protein S8_132719065 8 132719065 3.21E-05 0.25 1760 0.35 0.36 0.031 GRMZM2G046520 Mannose-binding lectin superfamily

protein S8_132719089 8 132719089 7.62E-06 0.27 1760 0.35 0.36 0.020 GRMZM2G046520 Mannose-binding lectin superfamily

protein S8_132719090 8 132719090 7.62E-06 0.27 1760 0.35 0.36 0.020 GRMZM2G046520 Mannose-binding lectin superfamily

protein S8_133934643 8 133934643 2.49E-05 0.22 1760 0.35 0.36 0.029 GRMZM2G141922 (XBAT31): XB3 ortholog 1 in

Arabidopsis thaliana S8_133934643 8 133934643 2.49E-05 0.22 1760 0.35 0.36 0.029 GRMZM2G141873 Pectinacetylesterase

family protein S8_141293603 8 141293603 1.74E-05 0.19 1760 0.35 0.36 0.025 GRMZM2G028134 Heavy metal transport/detoxifica tion superfamily

463

protein

464

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S8_149897257 8 149897257 7.42E-06 0.36 1760 0.35 0.36 0.020 GRMZM2G060541 Homeodomain-like transcriptional

regulator S8_149897257 8 149897257 7.42E-06 0.36 1760 0.35 0.36 0.020 GRMZM2G359237 Homeodomain-like transcriptional

regulator S8_149897257 8 149897257 7.42E-06 0.36 1760 0.35 0.36 0.020 AC196465.3_FG006 Homeodomain-like transcriptional

regulator S8_149897257 8 149897257 7.42E-06 0.36 1760 0.35 0.36 0.020 GRMZM2G060516 Pentatricopeptide repeat (PPR)

superfamily protein S8_149982616 8 149982616 3.30E-06 0.47 1760 0.35 0.36 0.014 GRMZM2G160990 Protein of unknown

function (DUF1421) S8_149982624 8 149982624 1.28E-05 0.33 1760 0.35 0.36 0.024 GRMZM2G160990 Protein of unknown

function (DUF1421) S8_149982627 8 149982627 1.37E-05 0.33 1760 0.35 0.36 0.024 GRMZM2G160990 Protein of unknown

function (DUF1421) S8_149982630 8 149982630 1.37E-05 0.33 1760 0.35 0.36 0.024 GRMZM2G160990 Protein of unknown

function (DUF1421) S8_149982735 8 149982735 1.05E-05 0.46 1760 0.35 0.36 0.023 GRMZM2G160990 Protein of unknown

function (DUF1421) S8_149982739 8 149982739 1.05E-05 0.46 1760 0.35 0.36 0.023 GRMZM2G160990 Protein of unknown

function (DUF1421) S8_149982761 8 149982761 1.05E-05 0.46 1760 0.35 0.36 0.023 GRMZM2G160990 Protein of unknown

function (DUF1421) S8_149982925 8 149982925 1.16E-05 0.31 1760 0.35 0.36 0.023 GRMZM2G160990 Protein of unknown

function (DUF1421) S8_150040999 8 150040999 7.97E-05 0.43 1760 0.35 0.36 0.045 GRMZM2G160990 Protein of unknown

function (DUF1421)

464

465

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S8_155363827 8 155363827 8.07E-05 0.25 1760 0.35 0.36 0.045 GRMZM5G887216 Heavy metal transport/detoxifica tion superfamily

protein S8_156429243 8 156429243 7.35E-05 0.16 1760 0.35 0.36 0.043 GRMZM2G341404 (ATP58IPK,P58IPK): homolog of

mamallian P58IPK

S8_156429243 8 156429243 7.35E-05 0.16 1760 0.35 0.36 0.043 GRMZM2G341442 (TET6): tetraspanin6 S8_156429243 8 156429243 7.35E-05 0.16 1760 0.35 0.36 0.043 GRMZM2G045421 Tudor/PWWP/MBT

superfamily protein S8_159890544 8 159890544 3.64E-06 0.29 1760 0.35 0.36 0.015 GRMZM2G002147 ARM repeat

superfamily protein S8_159890544 8 159890544 3.64E-06 0.29 1760 0.35 0.36 0.015 GRMZM2G002304 NAD(P)-binding Rossmann-fold

superfamily protein S8_159890544 8 159890544 3.64E-06 0.29 1760 0.35 0.36 0.015 GRMZM2G002135 Phospholipid/glycer ol acyltransferase

family protein S8_159890544 8 159890544 3.64E-06 0.29 1760 0.35 0.36 0.015 GRMZM2G302045 Protein of unknown

function (DUF1624) S8_159890544 8 159890544 3.64E-06 0.29 1760 0.35 0.36 0.015 GRMZM2G302035 Protein of unknown

function (DUF567) S8_159954535 8 159954535 5.36E-05 0.21 1760 0.35 0.36 0.038 GRMZM2G460581 LEML1 - Anther- specific LEM1 family protein precursor, expressed S8_160096864 8 160096864 2.76E-05 0.28 1760 0.35 0.36 0.029 GRMZM2G116557 (ARF1- BP,ARF2,HSS,ORE14 ): auxin response

factor 2 465

466

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S8_160103448 8 160103448 3.57E-07 0.50 1760 0.35 0.36 0.008 GRMZM2G116557 (ARF1- BP,ARF2,HSS,ORE14 ): auxin response

factor 2 S8_160595838 8 160595838 8.14E-05 0.41 1760 0.35 0.36 0.045 GRMZM2G447436 (ATPAL1,PAL1): PHE

ammonia lyase 1 S8_160595838 8 160595838 8.14E-05 0.41 1760 0.35 0.36 0.045 GRMZM2G147226 ENTH/VHS family

protein S8_160595838 8 160595838 8.14E-05 0.41 1760 0.35 0.36 0.045 GRMZM2G447406 ENTH/VHS family

protein S8_160595841 8 160595841 8.14E-05 0.41 1760 0.35 0.36 0.045 GRMZM2G447436 (ATPAL1,PAL1): PHE

ammonia lyase 1 S8_160595841 8 160595841 8.14E-05 0.41 1760 0.35 0.36 0.045 GRMZM2G147226 ENTH/VHS family

protein S8_160595841 8 160595841 8.14E-05 0.41 1760 0.35 0.36 0.045 GRMZM2G447406 ENTH/VHS family

protein S8_161621735 8 161621735 5.57E-05 0.05 1760 0.35 0.36 0.039 GRMZM2G003518 (ATEXO70F1,EXO70F 1): exocyst subunit exo70 family protein

F1 S8_161621735 8 161621735 5.57E-05 0.05 1760 0.35 0.36 0.039 GRMZM2G003493 (KING1): SNF1- related protein kinase regulatory

subunit gamma 1 S8_163521766 8 163521766 1.87E-06 0.48 1760 0.35 0.36 0.012 GRMZM2G003518 (ATEXO70F1,EXO70F 1): exocyst subunit exo70 family protein

F1 S8_163521766 8 163521766 1.87E-06 0.48 1760 0.35 0.36 0.012 GRMZM2G003493 (KING1): SNF1- related protein

466 kinase regulatory

subunit gamma 1

467

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S8_163521767 8 163521767 2.99E-05 0.38 1760 0.35 0.36 0.030 GRMZM2G003518 (ATEXO70F1,EXO70F 1): exocyst subunit exo70 family protein

F1 S8_163521767 8 163521767 2.99E-05 0.38 1760 0.35 0.36 0.030 GRMZM2G003493 (KING1): SNF1- related protein kinase regulatory

subunit gamma 1 S8_163521776 8 163521776 2.99E-05 0.38 1760 0.35 0.36 0.030 GRMZM2G003518 (ATEXO70F1,EXO70F 1): exocyst subunit exo70 family protein

F1 S8_163521776 8 163521776 2.99E-05 0.38 1760 0.35 0.36 0.030 GRMZM2G003493 (KING1): SNF1- related protein kinase regulatory

subunit gamma 1 S8_163521793 8 163521793 2.99E-05 0.38 1760 0.35 0.36 0.030 GRMZM2G003518 (ATEXO70F1,EXO70F 1): exocyst subunit exo70 family protein

F1 S8_163521793 8 163521793 2.99E-05 0.38 1760 0.35 0.36 0.030 GRMZM2G003493 (KING1): SNF1- related protein kinase regulatory

subunit gamma 1 S8_163725413 8 163725413 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM5G817436 (ATPTR1,PTR1): peptide transporter

1 S8_163725413 8 163725413 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM2G091397 alpha/beta- Hydrolases

superfamily protein

467 S8_163725413 8 163725413 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM5G884972 Protein kinase

superfamily protein

468

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S8_163725416 8 163725416 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM5G817436 (ATPTR1,PTR1): peptide transporter

1 S8_163725416 8 163725416 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM2G091397 alpha/beta- Hydrolases

superfamily protein S8_163725416 8 163725416 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM5G884972 Protein kinase

superfamily protein S8_163725417 8 163725417 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM5G817436 (ATPTR1,PTR1): peptide transporter

1 S8_163725417 8 163725417 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM2G091397 alpha/beta- Hydrolases

superfamily protein S8_163725417 8 163725417 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM5G884972 Protein kinase

superfamily protein S8_163725418 8 163725418 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM5G817436 (ATPTR1,PTR1): peptide transporter

1 S8_163725418 8 163725418 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM2G091397 alpha/beta- Hydrolases

superfamily protein S8_163725418 8 163725418 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM5G884972 Protein kinase

superfamily protein S8_163725419 8 163725419 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM5G817436 (ATPTR1,PTR1): peptide transporter

1 S8_163725419 8 163725419 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM2G091397 alpha/beta- Hydrolases

superfamily protein

468 S8_163725419 8 163725419 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM5G884972 Protein kinase

superfamily protein

469

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S8_163725421 8 163725421 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM5G817436 (ATPTR1,PTR1): peptide transporter

1 S8_163725421 8 163725421 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM2G091397 alpha/beta- Hydrolases

superfamily protein S8_163725421 8 163725421 6.68E-05 0.08 1760 0.35 0.36 0.042 GRMZM5G884972 Protein kinase

superfamily protein S8_164899464 8 164899464 1.08E-06 0.32 1760 0.35 0.36 0.010 GRMZM2G368663 (CRK5,RLK6): cysteine-rich RLK (RECEPTOR-like

protein kinase) 5 S8_164899464 8 164899464 1.08E-06 0.32 1760 0.35 0.36 0.010 GRMZM2G068271 SNARE associated

Golgi protein family S8_165584643 8 165584643 3.48E-05 0.08 1760 0.35 0.36 0.032 GRMZM2G128248 DNAJ heat shock

family protein

S8_165584643 8 165584643 3.48E-05 0.08 1760 0.35 0.36 0.032 GRMZM2G128215 F-box family protein S8_165584643 8 165584643 3.48E-05 0.08 1760 0.35 0.36 0.032 GRMZM2G005483 Galactose-binding

protein S8_171180461 8 171180461 2.95E-05 0.16 1760 0.35 0.36 0.030 GRMZM2G028054 (ATMYB65,MYB65): myb domain protein

65 S8_171180461 8 171180461 2.95E-05 0.16 1760 0.35 0.36 0.030 GRMZM2G028346 (PAG1): 20S proteasome alpha

subunit G1 S8_171180461 8 171180461 2.95E-05 0.16 1760 0.35 0.36 0.030 GRMZM2G028266 serine protease inhibitor, Kazal-type

family protein S8_171713019 8 171713019 4.47E-06 0.36 1760 0.35 0.36 0.016 GRMZM2G106250 3-hydroxyacyl-CoA

dehydrogenase 469

family protein

470

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S8_171713019 8 171713019 4.47E-06 0.36 1760 0.35 0.36 0.016 GRMZM2G106344 DC1 domain-

containing protein S8_172458496 8 172458496 4.71E-05 0.12 1760 0.35 0.36 0.036 GRMZM2G111511 (ATNAP13,EMB2751 ): ABC transporter

family protein S8_172458496 8 172458496 4.71E-05 0.12 1760 0.35 0.36 0.036 GRMZM2G111501 thylakoid lumenal

P17.1 protein S8_172458497 8 172458497 1.13E-05 0.13 1760 0.35 0.36 0.023 GRMZM2G111511 (ATNAP13,EMB2751 ): ABC transporter

family protein S8_172458497 8 172458497 1.13E-05 0.13 1760 0.35 0.36 0.023 GRMZM2G111501 thylakoid lumenal

P17.1 protein S8_172458522 8 172458522 1.06E-04 0.13 1760 0.35 0.36 0.049 GRMZM2G111511 (ATNAP13,EMB2751 ): ABC transporter

family protein S8_172458522 8 172458522 1.06E-04 0.13 1760 0.35 0.36 0.049 GRMZM2G111501 thylakoid lumenal

P17.1 protein S8_175507972 8 175507972 5.16E-05 0.29 1760 0.35 0.36 0.037 GRMZM2G044070 (UGT71B6): UDP- glucosyl transferase

71B6 S8_175508003 8 175508003 5.16E-05 0.29 1760 0.35 0.36 0.037 GRMZM2G044070 (UGT71B6): UDP- glucosyl transferase

71B6 S9_2212339 9 2212339 6.50E-05 0.15 1760 0.35 0.36 0.042 GRMZM2G057611 Major facilitator

superfamily protein S9_5076236 9 5076236 1.80E-05 0.19 1760 0.35 0.36 0.026 GRMZM5G862101 (ATHVA22A,HVA22A ): HVA22

homologue A S9_5076237 9 5076237 1.80E-05 0.19 1760 0.35 0.36 0.026 GRMZM5G862101 (ATHVA22A,HVA22A ): HVA22

470

homologue A

471

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_5076249 9 5076249 1.80E-05 0.19 1760 0.35 0.36 0.026 GRMZM5G862101 (ATHVA22A,HVA22A ): HVA22

homologue A S9_5080062 9 5080062 2.41E-05 0.19 1760 0.35 0.36 0.028 GRMZM5G862101 (ATHVA22A,HVA22A ): HVA22

homologue A S9_6005483 9 6005483 8.97E-05 0.34 1760 0.35 0.36 0.047 GRMZM2G093772 (BST1,DER4,MRH3): DNAse I-like

superfamily protein S9_6005485 9 6005485 8.97E-05 0.34 1760 0.35 0.36 0.047 GRMZM2G093772 (BST1,DER4,MRH3): DNAse I-like

superfamily protein S9_6005486 9 6005486 8.97E-05 0.34 1760 0.35 0.36 0.047 GRMZM2G093772 (BST1,DER4,MRH3): DNAse I-like

superfamily protein S9_7870170 9 7870170 3.70E-06 0.19 1760 0.35 0.36 0.015 GRMZM2G343769 (ICK6,KRP3): inhibitor/interactor with cyclin-

dependent kinase S9_7956110 9 7956110 2.46E-05 0.17 1760 0.35 0.36 0.028 GRMZM2G038436 (CML38):

calmodulin-like 38 S9_7956110 9 7956110 2.46E-05 0.17 1760 0.35 0.36 0.028 GRMZM2G038532 Protein of unknown function DUF829,

transmembrane 53 S9_12333613 9 12333613 8.81E-05 0.12 1760 0.35 0.36 0.047 GRMZM2G455306 (GAE1): UDP-D- glucuronate 4-

epimerase 1 S9_12333613 9 12333613 8.81E-05 0.12 1760 0.35 0.36 0.047 GRMZM2G151923 (RSZP22,SRZ- 22,SRZ22): serine/arginine-rich

471

472

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_12333613 9 12333613 8.81E-05 0.12 1760 0.35 0.36 0.047 GRMZM2G151913 RING/U-box

superfamily protein S9_12333613 9 12333613 8.81E-05 0.12 1760 0.35 0.36 0.047 GRMZM2G151887 S-adenosyl-L- methionine- dependent methyltransferases

superfamily protein S9_12598772 9 12598772 5.18E-06 0.05 1760 0.35 0.36 0.017 GRMZM2G455306 (GAE1): UDP-D- glucuronate 4-

epimerase 1 S9_12598772 9 12598772 5.18E-06 0.05 1760 0.35 0.36 0.017 GRMZM2G151923 (RSZP22,SRZ- 22,SRZ22): serine/arginine-rich

22 S9_12598772 9 12598772 5.18E-06 0.05 1760 0.35 0.36 0.017 GRMZM2G151913 RING/U-box

superfamily protein S9_12598772 9 12598772 5.18E-06 0.05 1760 0.35 0.36 0.017 GRMZM2G151887 S-adenosyl-L- methionine- dependent methyltransferases

superfamily protein S9_12598979 9 12598979 1.39E-06 0.22 1760 0.35 0.36 0.011 GRMZM2G455306 (GAE1): UDP-D- glucuronate 4-

epimerase 1 S9_12598979 9 12598979 1.39E-06 0.22 1760 0.35 0.36 0.011 GRMZM2G151923 (RSZP22,SRZ- 22,SRZ22): serine/arginine-rich

22 S9_12598979 9 12598979 1.39E-06 0.22 1760 0.35 0.36 0.011 GRMZM2G151913 RING/U-box

superfamily protein

472

473

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_12598979 9 12598979 1.39E-06 0.22 1760 0.35 0.36 0.011 GRMZM2G151887 S-adenosyl-L- methionine- dependent methyltransferases

superfamily protein S9_12795227 9 12795227 7.66E-05 0.17 1760 0.35 0.36 0.044 GRMZM2G067053 (ENP,MAB4,NPY1): Phototropic- responsive NPH3

family protein S9_12795227 9 12795227 7.66E-05 0.17 1760 0.35 0.36 0.044 GRMZM2G067158 retrotransposon protein, putative, unclassified,

expressed S9_12795251 9 12795251 9.86E-05 0.29 1760 0.35 0.36 0.048 GRMZM2G067053 (ENP,MAB4,NPY1): Phototropic- responsive NPH3

family protein S9_12795251 9 12795251 9.86E-05 0.29 1760 0.35 0.36 0.048 GRMZM2G067158 retrotransposon protein, putative, unclassified,

expressed S9_13150222 9 13150222 1.47E-05 0.31 1760 0.35 0.36 0.024 GRMZM2G116491 WRKY family

transcription factor S9_13662469 9 13662469 2.25E-05 0.39 1760 0.35 0.36 0.027 GRMZM2G008326 PPPDE putative thiol peptidase family

protein S9_13662496 9 13662496 6.48E-05 0.16 1760 0.35 0.36 0.042 GRMZM2G008326 PPPDE putative thiol peptidase family

protein S9_13662517 9 13662517 2.80E-05 0.46 1760 0.35 0.36 0.030 GRMZM2G008326 PPPDE putative thiol

473 peptidase family

protein

474

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_13663290 9 13663290 3.03E-05 0.48 1760 0.35 0.36 0.030 GRMZM2G008326 PPPDE putative thiol peptidase family

protein S9_15692048 9 15692048 1.23E-05 0.10 1760 0.35 0.36 0.024 GRMZM5G810393 (CYP94D2): cytochrome P450, family 94, subfamily

D, polypeptide 2 S9_15908712 9 15908712 3.07E-06 0.09 1760 0.35 0.36 0.014 GRMZM2G576752 (WAK3): wall

associated kinase 3 S9_15908712 9 15908712 3.07E-06 0.09 1760 0.35 0.36 0.014 GRMZM2G007801 Protein kinase

superfamily protein S9_16253708 9 16253708 7.31E-06 0.15 1760 0.35 0.36 0.020 GRMZM2G301860 (DEAR3): DREB and

EAR motif protein 3 S9_16253708 9 16253708 7.31E-06 0.15 1760 0.35 0.36 0.020 GRMZM2G001799 (IAA14,SLR): indole- 3-acetic acid

inducible 14 S9_16318895 9 16318895 4.59E-05 0.19 1760 0.35 0.36 0.036 GRMZM2G099363 (CCoAOMT1): S- adenosyl-L- methionine- dependent methyltransferases

superfamily protein S9_16318895 9 16318895 4.59E-05 0.19 1760 0.35 0.36 0.036 GRMZM2G440198 PIF / Ping-Pong family of plant

transposases S9_16318895 9 16318895 4.59E-05 0.19 1760 0.35 0.36 0.036 GRMZM2G099324 S-locus lectin protein kinase

family protein

S9_16433307 9 16433307 1.08E-06 0.12 1760 0.35 0.36 0.010 GRMZM2G074611 dirigent, putative

474

475

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_17741346 9 17741346 1.84E-08 0.30 1760 0.35 0.37 0.001 GRMZM2G111903 (ATMRP14,MRP14): multidrug resistance- associated protein

14 S9_18241191 9 18241191 1.47E-06 0.14 1760 0.35 0.36 0.011 AC231745.1_FG004 (TPST): tyrosylprotein

sulfotransferase S9_19041867 9 19041867 2.71E-05 0.12 1760 0.35 0.36 0.029 GRMZM2G028594 (DBB3,LZF1,STH3): light-regulated zinc

finger protein 1 S9_19041867 9 19041867 2.71E-05 0.12 1760 0.35 0.36 0.029 GRMZM5G877388 (PFN3,PRF3): profilin

3 S9_19041867 9 19041867 2.71E-05 0.12 1760 0.35 0.36 0.029 GRMZM5G863550 Phosphotyrosine protein phosphatases

superfamily protein S9_19041869 9 19041869 2.71E-05 0.12 1760 0.35 0.36 0.029 GRMZM2G028594 (DBB3,LZF1,STH3): light-regulated zinc

finger protein 1 S9_19041869 9 19041869 2.71E-05 0.12 1760 0.35 0.36 0.029 GRMZM5G877388 (PFN3,PRF3): profilin

3 S9_19041869 9 19041869 2.71E-05 0.12 1760 0.35 0.36 0.029 GRMZM5G863550 Phosphotyrosine protein phosphatases

superfamily protein S9_19041871 9 19041871 2.71E-05 0.12 1760 0.35 0.36 0.029 GRMZM2G028594 (DBB3,LZF1,STH3): light-regulated zinc

finger protein 1 S9_19041871 9 19041871 2.71E-05 0.12 1760 0.35 0.36 0.029 GRMZM5G877388 (PFN3,PRF3): profilin

475

476

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_19041871 9 19041871 2.71E-05 0.12 1760 0.35 0.36 0.029 GRMZM5G863550 Phosphotyrosine protein phosphatases

superfamily protein S9_20606888 9 20606888 3.19E-05 0.33 1760 0.35 0.36 0.031 GRMZM5G899300 (BUB3.1): Transducin/WD40 repeat-like

superfamily protein S9_20606888 9 20606888 3.19E-05 0.33 1760 0.35 0.36 0.031 GRMZM2G103475 Pentatricopeptide repeat (PPR)

superfamily protein S9_22478909 9 22478909 2.43E-05 0.24 1760 0.35 0.36 0.028 GRMZM2G097313 Leucine-rich repeat protein kinase

family protein S9_22478943 9 22478943 2.43E-05 0.24 1760 0.35 0.36 0.028 GRMZM2G097313 Leucine-rich repeat protein kinase

family protein S9_22480282 9 22480282 2.67E-06 0.41 1760 0.35 0.36 0.014 GRMZM2G097313 Leucine-rich repeat protein kinase

family protein S9_22480284 9 22480284 2.67E-06 0.41 1760 0.35 0.36 0.014 GRMZM2G097313 Leucine-rich repeat protein kinase

family protein S9_22480343 9 22480343 2.29E-05 0.38 1760 0.35 0.36 0.028 GRMZM2G097313 Leucine-rich repeat protein kinase

family protein

S9_22681178 9 22681178 7.37E-07 0.36 1760 0.35 0.36 0.009 GRMZM5G847362 F-box family protein

476

477

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_22681178 9 22681178 7.37E-07 0.36 1760 0.35 0.36 0.009 GRMZM5G877500 RNA 3\'-terminal phosphate cyclase/enolpyruvat e transferase,

alpha/beta

S9_22681260 9 22681260 3.36E-06 0.29 1760 0.35 0.36 0.015 GRMZM5G847362 F-box family protein S9_22681260 9 22681260 3.36E-06 0.29 1760 0.35 0.36 0.015 GRMZM5G877500 RNA 3\'-terminal phosphate cyclase/enolpyruvat e transferase,

alpha/beta

S9_22685751 9 22685751 5.74E-05 0.20 1760 0.35 0.36 0.039 GRMZM5G847362 F-box family protein S9_22685751 9 22685751 5.74E-05 0.20 1760 0.35 0.36 0.039 GRMZM5G877500 RNA 3\'-terminal phosphate cyclase/enolpyruvat e transferase,

alpha/beta

S9_22780028 9 22780028 2.14E-05 0.18 1760 0.35 0.36 0.027 GRMZM2G033208 Transketolase

S9_22780117 9 22780117 3.85E-05 0.17 1760 0.35 0.36 0.033 GRMZM2G033208 Transketolase

S9_22780988 9 22780988 3.71E-05 0.44 1760 0.35 0.36 0.033 GRMZM2G033208 Transketolase

S9_22786319 9 22786319 1.26E-05 0.28 1760 0.35 0.36 0.024 GRMZM2G033208 Transketolase

S9_22788000 9 22788000 1.40E-05 0.18 1760 0.35 0.36 0.024 GRMZM2G033208 Transketolase S9_23008884 9 23008884 1.40E-05 0.38 1760 0.35 0.36 0.024 GRMZM2G147319 Zinc finger (C3HC4- type RING finger)

family protein S9_23009979 9 23009979 3.32E-06 0.38 1760 0.35 0.36 0.014 GRMZM2G147319 Zinc finger (C3HC4- type RING finger)

family protein 477

478

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_23054487 9 23054487 3.48E-05 0.10 1760 0.35 0.36 0.032 GRMZM2G010768 (ATIPS1,ATMIPS1,MI -1-P SYNTHASE,MIPS1): myo-inositol-1- phosphate synthase

1 S9_23054487 9 23054487 3.48E-05 0.10 1760 0.35 0.36 0.032 GRMZM2G010740 Zinc finger (C3HC4- type RING finger)

family protein S9_23054494 9 23054494 3.48E-05 0.10 1760 0.35 0.36 0.032 GRMZM2G010768 (ATIPS1,ATMIPS1,MI -1-P SYNTHASE,MIPS1): myo-inositol-1- phosphate synthase

1 S9_23054494 9 23054494 3.48E-05 0.10 1760 0.35 0.36 0.032 GRMZM2G010740 Zinc finger (C3HC4- type RING finger)

family protein S9_23059325 9 23059325 1.95E-05 0.27 1760 0.35 0.36 0.027 GRMZM2G010768 (ATIPS1,ATMIPS1,MI -1-P SYNTHASE,MIPS1): myo-inositol-1- phosphate synthase

1 S9_23059325 9 23059325 1.95E-05 0.27 1760 0.35 0.36 0.027 GRMZM2G010740 Zinc finger (C3HC4- type RING finger)

family protein

478

479

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_23060806 9 23060806 8.20E-07 0.35 1760 0.35 0.36 0.009 GRMZM2G010768 (ATIPS1,ATMIPS1,MI -1-P SYNTHASE,MIPS1): myo-inositol-1- phosphate synthase

1 S9_23060806 9 23060806 8.20E-07 0.35 1760 0.35 0.36 0.009 GRMZM2G010740 Zinc finger (C3HC4- type RING finger)

family protein S9_23334573 9 23334573 4.17E-05 0.26 1760 0.35 0.36 0.035 GRMZM2G110158 Lung seven transmembrane receptor family

protein S9_23334804 9 23334804 3.56E-05 0.35 1760 0.35 0.36 0.032 GRMZM2G110158 Lung seven transmembrane receptor family

protein S9_25060863 9 25060863 9.49E-06 0.20 1760 0.35 0.36 0.023 GRMZM2G029863 (ATBAG3,BAG3): BCL-2-associated

athanogene 3 S9_25060863 9 25060863 9.49E-06 0.20 1760 0.35 0.36 0.023 GRMZM2G030051 Disease resistance protein (CC-NBS-LRR

class) family S9_25063138 9 25063138 6.80E-05 0.11 1760 0.35 0.36 0.042 GRMZM2G029863 (ATBAG3,BAG3): BCL-2-associated

athanogene 3 S9_25063138 9 25063138 6.80E-05 0.11 1760 0.35 0.36 0.042 GRMZM2G030051 Disease resistance protein (CC-NBS-LRR

class) family S9_25063146 9 25063146 4.00E-05 0.11 1760 0.35 0.36 0.034 GRMZM2G029863 (ATBAG3,BAG3):

479 BCL-2-associated

athanogene 3

480

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_25063146 9 25063146 4.00E-05 0.11 1760 0.35 0.36 0.034 GRMZM2G030051 Disease resistance protein (CC-NBS-LRR

class) family S9_25069024 9 25069024 1.67E-05 0.11 1760 0.35 0.36 0.025 GRMZM2G029863 (ATBAG3,BAG3): BCL-2-associated

athanogene 3 S9_25069024 9 25069024 1.67E-05 0.11 1760 0.35 0.36 0.025 GRMZM2G030051 Disease resistance protein (CC-NBS-LRR

class) family S9_25070183 9 25070183 8.81E-05 0.11 1760 0.35 0.36 0.047 GRMZM2G029863 (ATBAG3,BAG3): BCL-2-associated

athanogene 3 S9_25070183 9 25070183 8.81E-05 0.11 1760 0.35 0.36 0.047 GRMZM2G030051 Disease resistance protein (CC-NBS-LRR

class) family S9_25070227 9 25070227 3.16E-06 0.13 1760 0.35 0.36 0.014 GRMZM2G029863 (ATBAG3,BAG3): BCL-2-associated

athanogene 3 S9_25070227 9 25070227 3.16E-06 0.13 1760 0.35 0.36 0.014 GRMZM2G030051 Disease resistance protein (CC-NBS-LRR

class) family S9_25073541 9 25073541 1.75E-07 0.20 1760 0.35 0.36 0.005 GRMZM2G029863 (ATBAG3,BAG3): BCL-2-associated

athanogene 3 S9_25073541 9 25073541 1.75E-07 0.20 1760 0.35 0.36 0.005 GRMZM2G030051 Disease resistance protein (CC-NBS-LRR

class) family S9_25088931 9 25088931 4.20E-05 0.12 1760 0.35 0.36 0.035 GRMZM2G335052 Malectin/receptor- like protein kinase

family protein

480

481

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_25250937 9 25250937 2.62E-05 0.34 1760 0.35 0.36 0.029 GRMZM2G071602 (BB,BB2): RING/U- box superfamily

protein

S9_25250937 9 25250937 2.62E-05 0.34 1760 0.35 0.36 0.029 GRMZM2G071491 (SLK2): SEUSS-like 2 S9_25258938 9 25258938 4.49E-05 0.09 1760 0.35 0.36 0.035 GRMZM5G825515 (ATOPT7,OPT7): oligopeptide

transporter 7 S9_25258938 9 25258938 4.49E-05 0.09 1760 0.35 0.36 0.035 GRMZM2G071602 (BB,BB2): RING/U- box superfamily

protein

S9_25258938 9 25258938 4.49E-05 0.09 1760 0.35 0.36 0.035 GRMZM2G071491 (SLK2): SEUSS-like 2 S9_25258938 9 25258938 4.49E-05 0.09 1760 0.35 0.36 0.035 GRMZM5G882758 Pentatricopeptide repeat (PPR)

superfamily protein S9_25809279 9 25809279 1.06E-04 0.18 1760 0.35 0.36 0.049 GRMZM2G344634 (ACBP,ACBP6): acyl- CoA-binding protein

6 S9_25809279 9 25809279 1.06E-04 0.18 1760 0.35 0.36 0.049 GRMZM2G042080 (FSD2): Fe superoxide

dismutase 2 S9_25809279 9 25809279 1.06E-04 0.18 1760 0.35 0.36 0.049 GRMZM2G042323 interacting protein of DMI3, putative,

expressed S9_25816294 9 25816294 1.09E-05 0.11 1760 0.35 0.36 0.023 GRMZM2G344634 (ACBP,ACBP6): acyl- CoA-binding protein

6 S9_25816294 9 25816294 1.09E-05 0.11 1760 0.35 0.36 0.023 GRMZM2G042080 (FSD2): Fe superoxide

dismutase 2

481

482

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_25816294 9 25816294 1.09E-05 0.11 1760 0.35 0.36 0.023 GRMZM2G042323 interacting protein of DMI3, putative,

expressed S9_25817796 9 25817796 6.26E-05 0.19 1760 0.35 0.36 0.041 GRMZM2G344634 (ACBP,ACBP6): acyl- CoA-binding protein

6 S9_25817796 9 25817796 6.26E-05 0.19 1760 0.35 0.36 0.041 GRMZM2G042080 (FSD2): Fe superoxide

dismutase 2 S9_25817796 9 25817796 6.26E-05 0.19 1760 0.35 0.36 0.041 GRMZM2G042323 interacting protein of DMI3, putative,

expressed S9_25817800 9 25817800 1.40E-06 0.27 1760 0.35 0.36 0.011 GRMZM2G344634 (ACBP,ACBP6): acyl- CoA-binding protein

6 S9_25817800 9 25817800 1.40E-06 0.27 1760 0.35 0.36 0.011 GRMZM2G042080 (FSD2): Fe superoxide

dismutase 2 S9_25817800 9 25817800 1.40E-06 0.27 1760 0.35 0.36 0.011 GRMZM2G042323 interacting protein of DMI3, putative,

expressed S9_25922741 9 25922741 2.67E-06 0.49 1760 0.35 0.36 0.014 GRMZM2G083716 (CPN60B,LEN1):

chaperonin 60 beta S9_25924081 9 25924081 4.55E-05 0.43 1760 0.35 0.36 0.035 GRMZM2G083716 (CPN60B,LEN1):

chaperonin 60 beta S9_25925883 9 25925883 4.94E-05 0.15 1760 0.35 0.36 0.037 GRMZM2G083716 (CPN60B,LEN1):

chaperonin 60 beta S9_26476559 9 26476559 6.26E-05 0.20 1760 0.35 0.36 0.041 GRMZM2G093291 (EMB976): Tetratricopeptide repeat (TPR)-like

482

superfamily protein

483

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_26476559 9 26476559 6.26E-05 0.20 1760 0.35 0.36 0.041 GRMZM2G393146 AMP-dependent synthetase and

ligase family protein S9_26477472 9 26477472 4.56E-05 0.34 1760 0.35 0.36 0.035 GRMZM2G093291 (EMB976): Tetratricopeptide repeat (TPR)-like

superfamily protein S9_26477472 9 26477472 4.56E-05 0.34 1760 0.35 0.36 0.035 GRMZM2G393146 AMP-dependent synthetase and

ligase family protein S9_26578146 9 26578146 2.16E-05 0.24 1760 0.35 0.36 0.027 GRMZM2G136838 (ATNACK1,HIK,NACK 1): ATP binding microtubule motor

family protein S9_26578147 9 26578147 1.92E-05 0.23 1760 0.35 0.36 0.026 GRMZM2G136838 (ATNACK1,HIK,NACK 1): ATP binding microtubule motor

family protein S9_26578322 9 26578322 5.59E-05 0.21 1760 0.35 0.36 0.039 GRMZM2G136838 (ATNACK1,HIK,NACK 1): ATP binding microtubule motor

family protein S9_26579522 9 26579522 1.18E-05 0.24 1760 0.35 0.36 0.023 GRMZM2G136838 (ATNACK1,HIK,NACK 1): ATP binding microtubule motor

family protein S9_26594985 9 26594985 5.69E-06 0.32 1760 0.35 0.36 0.018 GRMZM5G870176 (ATCSLD3,CSLD3,KJK ): cellulose

synthase-like D3

483

484

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_26594985 9 26594985 5.69E-06 0.32 1760 0.35 0.36 0.018 GRMZM2G136838 (ATNACK1,HIK,NACK 1): ATP binding microtubule motor

family protein S9_26594985 9 26594985 5.69E-06 0.32 1760 0.35 0.36 0.018 GRMZM5G847530 (DAD2): Defender against death (DAD

family) protein S9_26595039 9 26595039 1.38E-07 0.34 1760 0.35 0.36 0.004 GRMZM5G870176 (ATCSLD3,CSLD3,KJK ): cellulose

synthase-like D3 S9_26595039 9 26595039 1.38E-07 0.34 1760 0.35 0.36 0.004 GRMZM2G136838 (ATNACK1,HIK,NACK 1): ATP binding microtubule motor

family protein S9_26595039 9 26595039 1.38E-07 0.34 1760 0.35 0.36 0.004 GRMZM5G847530 (DAD2): Defender against death (DAD

family) protein S9_26611413 9 26611413 3.75E-05 0.09 1760 0.35 0.36 0.033 GRMZM5G870176 (ATCSLD3,CSLD3,KJK ): cellulose

synthase-like D3 S9_26611413 9 26611413 3.75E-05 0.09 1760 0.35 0.36 0.033 GRMZM2G051949 Phosphorylase

superfamily protein S9_26611413 9 26611413 3.75E-05 0.09 1760 0.35 0.36 0.033 GRMZM2G051890 RNA-binding (RRM/RBD/RNP motifs) family

protein S9_26611444 9 26611444 5.20E-06 0.31 1760 0.35 0.36 0.017 GRMZM5G870176 (ATCSLD3,CSLD3,KJK ): cellulose

synthase-like D3 S9_26611444 9 26611444 5.20E-06 0.31 1760 0.35 0.36 0.017 GRMZM2G051949 Phosphorylase

484

superfamily protein

485

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_26611444 9 26611444 5.20E-06 0.31 1760 0.35 0.36 0.017 GRMZM2G051890 RNA-binding (RRM/RBD/RNP motifs) family

protein S9_26612993 9 26612993 1.01E-04 0.24 1760 0.35 0.36 0.048 GRMZM5G870176 (ATCSLD3,CSLD3,KJK ): cellulose

synthase-like D3 S9_26612993 9 26612993 1.01E-04 0.24 1760 0.35 0.36 0.048 GRMZM2G051949 Phosphorylase

superfamily protein S9_26612993 9 26612993 1.01E-04 0.24 1760 0.35 0.36 0.048 GRMZM2G051890 RNA-binding (RRM/RBD/RNP motifs) family

protein S9_26713114 9 26713114 2.79E-08 0.11 1760 0.35 0.37 0.001 GRMZM2G093195 (ATKAO2,CYP88A4,K AO2): ent-kaurenoic

acid hydroxylase 2 S9_26715220 9 26715220 1.88E-05 0.07 1760 0.35 0.36 0.026 GRMZM2G093195 (ATKAO2,CYP88A4,K AO2): ent-kaurenoic

acid hydroxylase 2 S9_27096263 9 27096263 6.30E-05 0.09 1760 0.35 0.36 0.041 GRMZM2G084739 (PGY2): Ribosomal

protein L6 family S9_27096263 9 27096263 6.30E-05 0.09 1760 0.35 0.36 0.041 GRMZM2G084968 PPPDE putative thiol peptidase family

protein S9_33714950 9 33714950 2.17E-05 0.33 1760 0.35 0.36 0.027 AC216886.3_FG002 (TBL21): TRICHOME BIREFRINGENCE-

LIKE 21 S9_33714982 9 33714982 2.17E-05 0.33 1760 0.35 0.36 0.027 AC216886.3_FG002 (TBL21): TRICHOME BIREFRINGENCE-

LIKE 21

485

486

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_34704299 9 34704299 3.26E-05 0.11 1760 0.35 0.36 0.031 GRMZM2G065612 Armadillo/beta- catenin-like repeat

family protein S9_34704401 9 34704401 2.59E-05 0.11 1760 0.35 0.36 0.029 GRMZM2G065612 Armadillo/beta- catenin-like repeat

family protein S9_34704485 9 34704485 1.08E-04 0.11 1760 0.35 0.36 0.050 GRMZM2G065612 Armadillo/beta- catenin-like repeat

family protein S9_34704560 9 34704560 7.33E-05 0.10 1760 0.35 0.36 0.043 GRMZM2G065612 Armadillo/beta- catenin-like repeat

family protein S9_34704668 9 34704668 1.50E-05 0.11 1760 0.35 0.36 0.024 GRMZM2G065612 Armadillo/beta- catenin-like repeat

family protein S9_35913118 9 35913118 3.73E-05 0.09 1760 0.35 0.36 0.033 GRMZM2G408359 (ATPI4K GAMMA 7,PI4K GAMMA 7,UBDK GAMMA 7): phosphoinositide 4-

kinase gamma 7 S9_35913118 9 35913118 3.73E-05 0.09 1760 0.35 0.36 0.033 GRMZM2G408376 Protein kinase

superfamily protein S9_35915499 9 35915499 6.77E-05 0.09 1760 0.35 0.36 0.042 GRMZM2G408359 (ATPI4K GAMMA 7,PI4K GAMMA 7,UBDK GAMMA 7): phosphoinositide 4-

kinase gamma 7 S9_35915499 9 35915499 6.77E-05 0.09 1760 0.35 0.36 0.042 GRMZM2G408376 Protein kinase

superfamily protein S9_36406145 9 36406145 2.38E-05 0.08 1760 0.35 0.36 0.028 AC196437.3_FG001 Ribosomal protein

486

S24e family protein

487

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_45195770 9 45195770 5.20E-05 0.07 1760 0.35 0.36 0.037 GRMZM2G151414 pantothenate kinase 4, putative,

expressed S9_58451118 9 58451118 8.81E-05 0.21 1760 0.35 0.36 0.047 GRMZM2G173090 (ATHSFA2,HSFA2): heat shock transcription factor

A2 S9_58847195 9 58847195 3.15E-05 0.27 1760 0.35 0.36 0.030 GRMZM2G135236 ATPase E1-E2 type family protein / haloacid dehalogenase-like hydrolase family

protein S9_59160368 9 59160368 6.92E-05 0.27 1760 0.35 0.36 0.042 GRMZM2G104481 RNA-binding (RRM/RBD/RNP motifs) family

protein S9_61300467 9 61300467 1.72E-05 0.09 1760 0.35 0.36 0.025 GRMZM2G083841 (ATPPC2,PPC2): phosphoenolpyruva

te carboxylase 2 S9_61405838 9 61405838 1.93E-06 0.17 1760 0.35 0.36 0.012 GRMZM5G814159 (CID8): CTC- interacting domain

8 S9_62060483 9 62060483 1.63E-05 0.19 1760 0.35 0.36 0.025 GRMZM2G127266 RING/U-box

superfamily protein S9_73922636 9 73922636 9.19E-05 0.26 1760 0.35 0.36 0.047 GRMZM2G145989 (AAP1,NAT2): amino

acid permease 1 S9_75780129 9 75780129 1.22E-07 0.15 1760 0.35 0.36 0.004 GRMZM2G125441 (PDF1): protodermal

factor 1

487

488

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_76471131 9 76471131 5.90E-05 0.26 1760 0.35 0.36 0.039 GRMZM5G812774 (BEH4): BES1/BZR1

homolog 4

S9_76796966 9 76796966 5.69E-05 0.31 1760 0.35 0.36 0.039 GRMZM5G838496 : expressed protein S9_77023959 9 77023959 3.57E-05 0.20 1760 0.35 0.36 0.032 GRMZM2G001816 Ribosomal L5P

family protein S9_77023962 9 77023962 3.57E-05 0.20 1760 0.35 0.36 0.032 GRMZM2G001816 Ribosomal L5P

family protein S9_77023980 9 77023980 3.57E-05 0.20 1760 0.35 0.36 0.032 GRMZM2G001816 Ribosomal L5P

family protein S9_77024006 9 77024006 3.57E-05 0.20 1760 0.35 0.36 0.032 GRMZM2G001816 Ribosomal L5P

family protein S9_84245925 9 84245925 2.95E-06 0.48 1760 0.35 0.36 0.014 GRMZM2G163641 (OCP3): overexpressor of cationic peroxidase

3 S9_86399905 9 86399905 4.30E-05 0.10 1760 0.35 0.36 0.035 AC189879.3_FG003 (AGO10,PNH,ZLL): Stabilizer of iron transporter SufD / Polynucleotidyl

transferase S9_86530256 9 86530256 8.76E-06 0.39 1760 0.35 0.36 0.021 GRMZM2G004128 FAD/NAD(P)-binding oxidoreductase

family protein S9_86530570 9 86530570 8.10E-05 0.07 1760 0.35 0.36 0.045 GRMZM2G004128 FAD/NAD(P)-binding oxidoreductase

family protein S9_86530609 9 86530609 1.92E-05 0.08 1760 0.35 0.36 0.026 GRMZM2G004128 FAD/NAD(P)-binding oxidoreductase

family protein

488

489

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_86662298 9 86662298 4.28E-05 0.09 1760 0.35 0.36 0.035 GRMZM2G148940 (FRS5): FAR1-related

sequence 5 S9_86662298 9 86662298 4.28E-05 0.09 1760 0.35 0.36 0.035 GRMZM2G148872 SOUL heme-binding

family protein S9_86864208 9 86864208 1.06E-04 0.31 1760 0.35 0.36 0.049 GRMZM2G148940 (FRS5): FAR1-related

sequence 5 S9_86864208 9 86864208 1.06E-04 0.31 1760 0.35 0.36 0.049 GRMZM2G148872 SOUL heme-binding

family protein S9_86864564 9 86864564 2.49E-05 0.36 1760 0.35 0.36 0.029 GRMZM2G148940 (FRS5): FAR1-related

sequence 5 S9_86864564 9 86864564 2.49E-05 0.36 1760 0.35 0.36 0.029 GRMZM2G148872 SOUL heme-binding

family protein S9_86869084 9 86869084 8.56E-05 0.35 1760 0.35 0.36 0.046 GRMZM2G022558 (KCS11): 3-ketoacyl-

CoA synthase 11 S9_86869084 9 86869084 8.56E-05 0.35 1760 0.35 0.36 0.046 GRMZM2G022275 Transducin/WD40 repeat-like

superfamily protein S9_87131661 9 87131661 1.84E-05 0.08 1760 0.35 0.36 0.026 GRMZM2G158734 (AtDBP1,DBP1): DNA-binding protein

phosphatase 1 S9_87999506 9 87999506 2.94E-05 0.13 1760 0.35 0.36 0.030 GRMZM2G443953 Coatomer, beta\'

subunit S9_88001858 9 88001858 3.37E-05 0.13 1760 0.35 0.36 0.032 GRMZM2G443953 Coatomer, beta\'

subunit S9_88186195 9 88186195 2.82E-05 0.16 1760 0.35 0.36 0.030 GRMZM2G422948 (UGT89B1): UDP- glucosyl transferase

89B1 S9_88186645 9 88186645 6.80E-06 0.22 1760 0.35 0.36 0.020 GRMZM2G422948 (UGT89B1): UDP- glucosyl transferase

89B1

489

490

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_88448641 9 88448641 9.93E-05 0.11 1760 0.35 0.36 0.048 AC234524.1_FG005 UDP- Glycosyltransferase

superfamily protein S9_90041709 9 90041709 4.76E-06 0.13 1760 0.35 0.36 0.016 GRMZM2G416652 (ATM1,ATMYB101, MYB101): myb

domain protein 101 S9_90041709 9 90041709 4.76E-06 0.13 1760 0.35 0.36 0.016 GRMZM5G862017 Ribosomal protein

L1p/L10e family S9_90843373 9 90843373 9.20E-05 0.15 1760 0.35 0.36 0.047 GRMZM2G056166 TPX2 (targeting protein for Xklp2)

protein family S9_91420757 9 91420757 4.32E-05 0.16 1760 0.35 0.36 0.035 GRMZM2G074037 AAA-type ATPase

family protein S9_91420757 9 91420757 4.32E-05 0.16 1760 0.35 0.36 0.035 GRMZM2G372877 C2 calcium/lipid- binding and GRAM domain containing

protein S9_91475255 9 91475255 1.16E-05 0.13 1760 0.35 0.36 0.023 GRMZM2G074233 serine-rich protein-

related S9_95741674 9 95741674 6.97E-05 0.48 1760 0.35 0.36 0.042 GRMZM2G160730 (AP2,FL1,FLO2): Integrase-type DNA- binding superfamily

protein S9_96074410 9 96074410 5.53E-05 0.32 1760 0.35 0.36 0.038 GRMZM2G704277 Calcium-dependent lipid-binding (CaLB domain) family

protein S9_96077356 9 96077356 2.68E-05 0.23 1760 0.35 0.36 0.029 GRMZM2G704277 Calcium-dependent lipid-binding (CaLB domain) family

490

protein

491

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_96078039 9 96078039 1.41E-06 0.28 1760 0.35 0.36 0.011 GRMZM2G704277 Calcium-dependent lipid-binding (CaLB domain) family

protein S9_96078048 9 96078048 1.75E-06 0.27 1760 0.35 0.36 0.012 GRMZM2G704277 Calcium-dependent lipid-binding (CaLB domain) family

protein S9_96391130 9 96391130 8.70E-05 0.12 1760 0.35 0.36 0.047 GRMZM5G803308 (ATMYB73,MYB73): myb domain protein

73 S9_97022063 9 97022063 6.91E-05 0.08 1760 0.35 0.36 0.042 GRMZM5G830365 (DRN,ESR1): Integrase-type DNA- binding superfamily

protein S9_97035764 9 97035764 1.85E-05 0.08 1760 0.35 0.36 0.026 GRMZM2G104866 (ATERF12,ERF12): ERF domain protein

12 S9_97255258 9 97255258 4.69E-06 0.44 1760 0.35 0.36 0.016 GRMZM2G147856 (PUX4): plant UBX domain containing

protein 4 S9_97255258 9 97255258 4.69E-06 0.44 1760 0.35 0.36 0.016 GRMZM2G071573 (SRF8): STRUBBELIG-

receptor family 8 S9_97737229 9 97737229 5.61E-07 0.13 1760 0.35 0.36 0.008 GRMZM2G168690 RING/U-box

superfamily protein S9_97752211 9 97752211 9.10E-05 0.17 1760 0.35 0.36 0.047 GRMZM2G407631 PF00170: bZIP transcription factor , PF07716: Basic region leucine zipper

491

492

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_97752212 9 97752212 9.10E-05 0.17 1760 0.35 0.36 0.047 GRMZM2G407631 PF00170: bZIP transcription factor , PF07716: Basic region leucine zipper S9_99293255 9 99293255 1.67E-05 0.17 1760 0.35 0.36 0.025 GRMZM2G328578 (RPS15A): ribosomal

protein S15A S9_99293366 9 99293366 6.99E-05 0.36 1760 0.35 0.36 0.042 GRMZM2G328578 (RPS15A): ribosomal

protein S15A S9_99850154 9 99850154 9.69E-05 0.37 1760 0.35 0.36 0.048 GRMZM2G025812 (ATBZIP60,BZIP60): basic region/leucine

zipper motif 60 S9_100305577 9 100305577 5.40E-05 0.32 1760 0.35 0.36 0.038 GRMZM2G122447 VQ motif-containing

protein S9_100788531 9 100788531 2.06E-05 0.42 1760 0.35 0.36 0.027 AC211933.4_FG001 RD26, putative,

expressed S9_100788533 9 100788533 2.06E-05 0.42 1760 0.35 0.36 0.027 AC211933.4_FG001 RD26, putative,

expressed S9_100788973 9 100788973 3.96E-05 0.43 1760 0.35 0.36 0.034 AC211933.4_FG001 RD26, putative,

expressed S9_100887196 9 100887196 7.95E-05 0.28 1760 0.35 0.36 0.045 GRMZM2G108149 Calcium-dependent lipid-binding (CaLB domain) plant phosphoribosyltrans ferase family

protein S9_100887196 9 100887196 7.95E-05 0.28 1760 0.35 0.36 0.045 GRMZM2G108103 polyphenol oxidase,

putative, expressed S9_100887207 9 100887207 6.08E-05 0.28 1760 0.35 0.36 0.040 GRMZM2G108103 : polyphenol oxidase, putative,

492

expressed

493

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_100887207 9 100887207 6.08E-05 0.28 1760 0.35 0.36 0.040 GRMZM2G108149 Calcium-dependent lipid-binding (CaLB domain) plant phosphoribosyltrans ferase family

protein S9_102928135 9 102928135 8.84E-05 0.24 1760 0.35 0.36 0.047 GRMZM2G373578 alpha/beta- Hydrolases

superfamily protein S9_102928135 9 102928135 8.84E-05 0.24 1760 0.35 0.36 0.047 GRMZM2G452896 alpha/beta- Hydrolases

superfamily protein S9_102935540 9 102935540 4.42E-05 0.40 1760 0.35 0.36 0.035 GRMZM2G152120 (B120): S-locus lectin protein kinase

family protein S9_102935540 9 102935540 4.42E-05 0.40 1760 0.35 0.36 0.035 GRMZM2G373578 alpha/beta- Hydrolases

superfamily protein S9_102935540 9 102935540 4.42E-05 0.40 1760 0.35 0.36 0.035 GRMZM2G452896 alpha/beta- Hydrolases

superfamily protein S9_102942121 9 102942121 7.76E-05 0.14 1760 0.35 0.36 0.044 GRMZM2G152120 (B120): S-locus lectin protein kinase

family protein S9_102942121 9 102942121 7.76E-05 0.14 1760 0.35 0.36 0.044 GRMZM2G452896 alpha/beta- Hydrolases

superfamily protein S9_102962492 9 102962492 9.30E-05 0.24 1760 0.35 0.36 0.047 GRMZM2G152126 WRKY family

transcription factor S9_102962618 9 102962618 1.40E-05 0.17 1760 0.35 0.36 0.024 GRMZM2G152126 WRKY family

493

transcription factor

494

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_102963323 9 102963323 8.06E-06 0.28 1760 0.35 0.36 0.020 GRMZM2G152126 WRKY family

transcription factor S9_103070405 9 103070405 2.54E-05 0.36 1760 0.35 0.36 0.029 GRMZM2G111711 (ATWRKY40,WRKY4 0): WRKY DNA-

binding protein 40 S9_105187791 9 105187791 4.53E-06 0.35 1760 0.35 0.36 0.016 GRMZM2G029912 (CER3,FLP1,WAX2,Y RE): Fatty acid hydroxylase

superfamily

S9_105251296 9 105251296 3.15E-05 0.07 1760 0.35 0.36 0.030 GRMZM5G863602 (TET7): tetraspanin7

S9_105251297 9 105251297 3.15E-05 0.07 1760 0.35 0.36 0.030 GRMZM5G863602 (TET7): tetraspanin7

S9_105251298 9 105251298 3.15E-05 0.07 1760 0.35 0.36 0.030 GRMZM5G863602 (TET7): tetraspanin7

S9_105251302 9 105251302 3.15E-05 0.07 1760 0.35 0.36 0.030 GRMZM5G863602 (TET7): tetraspanin7 S9_107621535 9 107621535 7.64E-06 0.10 1760 0.35 0.36 0.020 GRMZM2G139082 (AIL5,CHO1,EMK): AINTEGUMENTA-

like 5 S9_108353397 9 108353397 4.33E-05 0.25 1760 0.35 0.36 0.035 GRMZM2G098423 (EDA9): D-3- phosphoglycerate

dehydrogenase S9_108353408 9 108353408 5.92E-05 0.25 1760 0.35 0.36 0.039 GRMZM2G098423 (EDA9): D-3- phosphoglycerate

dehydrogenase S9_109173765 9 109173765 3.98E-05 0.36 1760 0.35 0.36 0.034 GRMZM2G029407 Leucine-rich repeat protein kinase

family protein S9_109668134 9 109668134 1.00E-04 0.19 1760 0.35 0.36 0.048 GRMZM2G090849 LEM3 (ligand-effect modulator 3) family protein / CDC50

family protein

494

495

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_109687408 9 109687408 2.32E-05 0.20 1760 0.35 0.36 0.028 GRMZM2G151734 Haloacid dehalogenase-like hydrolase (HAD)

superfamily protein S9_109687408 9 109687408 2.32E-05 0.20 1760 0.35 0.36 0.028 GRMZM2G090849 LEM3 (ligand-effect modulator 3) family protein / CDC50

family protein S9_109687447 9 109687447 2.07E-05 0.21 1760 0.35 0.36 0.027 GRMZM2G151734 Haloacid dehalogenase-like hydrolase (HAD)

superfamily protein S9_109687447 9 109687447 2.07E-05 0.21 1760 0.35 0.36 0.027 GRMZM2G090849 LEM3 (ligand-effect modulator 3) family protein / CDC50

family protein S9_110319342 9 110319342 8.44E-05 0.33 1760 0.35 0.36 0.046 GRMZM2G333049 VQ motif-containing

protein S9_110455393 9 110455393 1.03E-04 0.27 1760 0.35 0.36 0.049 GRMZM2G124421 (ATHAP5B,HAP5B,N F-YC2): nuclear

factor Y, subunit C2 S9_110459755 9 110459755 9.98E-06 0.18 1760 0.35 0.36 0.023 GRMZM2G124421 (ATHAP5B,HAP5B,N F-YC2): nuclear

factor Y, subunit C2 S9_110578567 9 110578567 7.51E-05 0.07 1760 0.35 0.36 0.044 GRMZM2G009724 (ATBPM1,BPM1): BTB-POZ and MATH

domain 1 S9_110578567 9 110578567 7.51E-05 0.07 1760 0.35 0.36 0.044 GRMZM2G308884 (AtPRD1,PRD1): putative recombination

495

initiation defect 1

496

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_110578567 9 110578567 7.51E-05 0.07 1760 0.35 0.36 0.044 GRMZM2G308799 retrotransposon protein, putative, unclassified,

expressed S9_110578663 9 110578663 3.44E-05 0.25 1760 0.35 0.36 0.032 GRMZM2G009724 (ATBPM1,BPM1): BTB-POZ and MATH

domain 1 S9_110578663 9 110578663 3.44E-05 0.25 1760 0.35 0.36 0.032 GRMZM2G308884 (AtPRD1,PRD1): putative recombination

initiation defect 1 S9_110578663 9 110578663 3.44E-05 0.25 1760 0.35 0.36 0.032 GRMZM2G308799 retrotransposon protein, putative, unclassified,

expressed S9_110582905 9 110582905 6.23E-05 0.48 1760 0.35 0.36 0.041 GRMZM2G308884 (AtPRD1,PRD1): putative recombination

initiation defect 1 S9_110582905 9 110582905 6.23E-05 0.48 1760 0.35 0.36 0.041 GRMZM2G308799 retrotransposon protein, putative, unclassified,

expressed S9_110582969 9 110582969 5.51E-05 0.49 1760 0.35 0.36 0.038 GRMZM2G308884 (AtPRD1,PRD1): putative recombination

initiation defect 1 S9_110582969 9 110582969 5.51E-05 0.49 1760 0.35 0.36 0.038 GRMZM2G308799 retrotransposon protein, putative, unclassified,

496

expressed

497

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_113427558 9 113427558 1.07E-04 0.37 1760 0.35 0.36 0.050 GRMZM2G054634 (BSK2): BR-signaling

kinase 2 S9_114551355 9 114551355 5.18E-05 0.49 1760 0.35 0.36 0.037 GRMZM2G428470 Alcohol dehydrogenase transcription factor Myb/SANT-like

family protein S9_114551355 9 114551355 5.18E-05 0.49 1760 0.35 0.36 0.037 GRMZM2G150489 ARM repeat

superfamily protein S9_114552111 9 114552111 3.00E-05 0.48 1760 0.35 0.36 0.030 GRMZM2G428470 Alcohol dehydrogenase transcription factor Myb/SANT-like

family protein S9_114552111 9 114552111 3.00E-05 0.48 1760 0.35 0.36 0.030 GRMZM2G150489 ARM repeat

superfamily protein S9_114697240 9 114697240 1.03E-04 0.43 1760 0.35 0.36 0.049 GRMZM2G028796 (ARABIDILLO-1):

ARABIDILLO-1 S9_114778833 9 114778833 2.61E-05 0.39 1760 0.35 0.36 0.029 GRMZM2G093880 alpha/beta- Hydrolases

superfamily protein S9_114815584 9 114815584 9.69E-06 0.39 1760 0.35 0.36 0.023 GRMZM2G093880 alpha/beta- Hydrolases

superfamily protein S9_114919130 9 114919130 2.42E-05 0.43 1760 0.35 0.36 0.028 GRMZM2G125513 DUF630/DUF632 domains containing protein, putative,

expressed S9_114919563 9 114919563 5.91E-05 0.41 1760 0.35 0.36 0.039 GRMZM2G125513 DUF630/DUF632 domains containing

497 protein, putative,

expressed

498

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_114919645 9 114919645 2.18E-05 0.41 1760 0.35 0.36 0.027 GRMZM2G125513 DUF630/DUF632 domains containing protein, putative,

expressed S9_114962210 9 114962210 3.21E-05 0.46 1760 0.35 0.36 0.031 GRMZM2G067734 Protein kinase

superfamily protein S9_114962239 9 114962239 1.06E-05 0.46 1760 0.35 0.36 0.023 GRMZM2G067734 Protein kinase

superfamily protein S9_114962246 9 114962246 5.22E-05 0.44 1760 0.35 0.36 0.037 GRMZM2G067734 Protein kinase

superfamily protein S9_114964637 9 114964637 1.05E-04 0.44 1760 0.35 0.36 0.049 GRMZM2G067734 Protein kinase

superfamily protein S9_114979698 9 114979698 9.55E-07 0.38 1760 0.35 0.36 0.010 GRMZM2G368610 (PLA-I{beta]2): alpha/beta- Hydrolases

superfamily protein S9_114979743 9 114979743 1.48E-06 0.38 1760 0.35 0.36 0.011 GRMZM2G368610 (PLA-I{beta]2): alpha/beta- Hydrolases

superfamily protein S9_114980316 9 114980316 8.62E-05 0.44 1760 0.35 0.36 0.046 GRMZM2G368610 (PLA-I{beta]2): alpha/beta- Hydrolases

superfamily protein S9_119839045 9 119839045 2.84E-05 0.13 1760 0.35 0.36 0.030 GRMZM2G106172 O-methyltransferase

family protein S9_119839322 9 119839322 4.82E-05 0.12 1760 0.35 0.36 0.036 GRMZM2G106172 O-methyltransferase

family protein

498

499

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_119938060 9 119938060 1.07E-04 0.16 1760 0.35 0.36 0.050 GRMZM2G106172 O-methyltransferase

family protein S9_119947672 9 119947672 2.22E-05 0.25 1760 0.35 0.36 0.027 GRMZM2G035517 (scpl40): serine carboxypeptidase-

like 40 S9_120363261 9 120363261 6.66E-05 0.31 1760 0.35 0.36 0.042 GRMZM2G132238 (AMC1,ATMC1,ATM CPB1,LOL3,MCP1B):

metacaspase 1 S9_120363261 9 120363261 6.66E-05 0.31 1760 0.35 0.36 0.042 GRMZM2G431243 (CAMTA1,EICBP.B): ethylene induced calmodulin binding

protein S9_124765936 9 124765936 9.70E-05 0.23 1760 0.35 0.36 0.048 GRMZM2G113860 (AZF2,ZF2): zinc-

finger protein 2 S9_124765936 9 124765936 9.70E-05 0.23 1760 0.35 0.36 0.048 GRMZM2G113866 alpha/beta- Hydrolases

superfamily protein S9_124765938 9 124765938 5.16E-05 0.20 1760 0.35 0.36 0.037 GRMZM2G113860 (AZF2,ZF2): zinc-

finger protein 2 S9_124765938 9 124765938 5.16E-05 0.20 1760 0.35 0.36 0.037 GRMZM2G113866 alpha/beta- Hydrolases

superfamily protein S9_124965662 9 124965662 4.29E-05 0.21 1760 0.35 0.36 0.035 GRMZM2G137816 DUF1230 domain containing protein,

expressed

S9_124965662 9 124965662 4.29E-05 0.21 1760 0.35 0.36 0.035 GRMZM2G137869 Ovate family protein S9_125564660 9 125564660 9.44E-05 0.43 1760 0.35 0.36 0.047 GRMZM2G142999 (NGA2): AP2/B3-like transcriptional

factor family protein

499

500

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_127208636 9 127208636 1.44E-05 0.30 1760 0.35 0.36 0.024 GRMZM2G072573 (POL): Protein phosphatase 2C

family protein S9_127211736 9 127211736 1.05E-04 0.41 1760 0.35 0.36 0.049 GRMZM2G072573 (POL): Protein phosphatase 2C

family protein S9_127286556 9 127286556 7.76E-05 0.37 1760 0.35 0.36 0.044 GRMZM2G148969 (CYP709B2): cytochrome P450, family 709, subfamily B,

polypeptide 2 S9_128306318 9 128306318 1.50E-05 0.10 1760 0.35 0.36 0.024 GRMZM2G021483 Tudor/PWWP/MBT domain-containing

protein S9_128319334 9 128319334 4.35E-05 0.32 1760 0.35 0.36 0.035 GRMZM2G309995 Tetratricopeptide repeat (TPR)-like

superfamily protein S9_128319334 9 128319334 4.35E-05 0.32 1760 0.35 0.36 0.035 GRMZM2G021483 Tudor/PWWP/MBT domain-containing

protein S9_128419498 9 128419498 1.04E-05 0.29 1760 0.35 0.36 0.023 GRMZM2G309995 Tetratricopeptide repeat (TPR)-like

superfamily protein S9_128419498 9 128419498 1.04E-05 0.29 1760 0.35 0.36 0.023 GRMZM2G021483 Tudor/PWWP/MBT domain-containing

protein S9_128419663 9 128419663 4.33E-09 0.38 1760 0.35 0.37 0.001 GRMZM2G309995 Tetratricopeptide repeat (TPR)-like

superfamily protein S9_128419663 9 128419663 4.33E-09 0.38 1760 0.35 0.37 0.001 GRMZM2G021483 Tudor/PWWP/MBT

500 domain-containing

protein

501

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_128457999 9 128457999 5.56E-07 0.28 1760 0.35 0.36 0.008 GRMZM2G359566 (ATVLN2,VLN2):

villin 2 S9_128461819 9 128461819 2.90E-05 0.08 1760 0.35 0.36 0.030 GRMZM2G359566 (ATVLN2,VLN2):

villin 2 S9_128461819 9 128461819 2.90E-05 0.08 1760 0.35 0.36 0.030 GRMZM2G323479 (ATVLN2,VLN2):

villin 2 S9_129267714 9 129267714 5.16E-05 0.20 1760 0.35 0.36 0.037 GRMZM2G058522 (CSD1): copper/zinc superoxide

dismutase 1 S9_129403335 9 129403335 9.60E-06 0.44 1760 0.35 0.36 0.023 GRMZM2G125148 NOP56-like pre RNA processing

ribonucleoprotein S9_130088731 9 130088731 5.22E-05 0.14 1760 0.35 0.36 0.037 GRMZM2G121360 Heavy metal transport/detoxifica tion superfamily

protein S9_130088731 9 130088731 5.22E-05 0.14 1760 0.35 0.36 0.037 GRMZM2G421795 Ribosomal protein

S21e S9_130089569 9 130089569 7.32E-05 0.07 1760 0.35 0.36 0.043 GRMZM2G121360 Heavy metal transport/detoxifica tion superfamily

protein S9_130089569 9 130089569 7.32E-05 0.07 1760 0.35 0.36 0.043 GRMZM2G421795 Ribosomal protein

S21e S9_130089571 9 130089571 7.32E-05 0.07 1760 0.35 0.36 0.043 GRMZM2G121360 Heavy metal transport/detoxifica tion superfamily

protein S9_130089571 9 130089571 7.32E-05 0.07 1760 0.35 0.36 0.043 GRMZM2G421795 Ribosomal protein

S21e

501

502

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_133214273 9 133214273 1.68E-05 0.12 1760 0.35 0.36 0.025 GRMZM2G317584 (AtEIN3,EIN3): Ethylene insensitive

3 family protein S9_133214273 9 133214273 1.68E-05 0.12 1760 0.35 0.36 0.025 GRMZM2G022398 exostosin family

protein S9_135860135 9 135860135 3.70E-05 0.46 1760 0.35 0.36 0.033 GRMZM2G031637 Heat shock protein DnaJ with tetratricopeptide

repeat S9_135860168 9 135860168 4.18E-05 0.48 1760 0.35 0.36 0.035 GRMZM2G031637 Heat shock protein DnaJ with tetratricopeptide

repeat S9_135860229 9 135860229 6.74E-05 0.44 1760 0.35 0.36 0.042 GRMZM2G031637 Heat shock protein DnaJ with tetratricopeptide

repeat S9_135891509 9 135891509 7.38E-05 0.35 1760 0.35 0.36 0.043 GRMZM2G077895 cAMP-regulated phosphoprotein 19-

related protein S9_136179951 9 136179951 1.14E-05 0.33 1760 0.35 0.36 0.023 GRMZM2G022686 (ATMYB12,MYB12,P FG1): myb domain

protein 12 S9_136702333 9 136702333 3.65E-05 0.11 1760 0.35 0.36 0.033 GRMZM2G443785 (GATL7): galacturonosyltransf

erase-like 7 S9_136702342 9 136702342 3.65E-05 0.11 1760 0.35 0.36 0.033 GRMZM2G443785 (GATL7): galacturonosyltransf

erase-like 7 S9_136771503 9 136771503 5.18E-06 0.15 1760 0.35 0.36 0.017 GRMZM2G134476 Chaperone DnaJ-

502 domain superfamily

protein

503

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_136771503 9 136771503 5.18E-06 0.15 1760 0.35 0.36 0.017 GRMZM2G134471 transducin family protein / WD-40 repeat family

protein S9_136771503 9 136771503 5.18E-06 0.15 1760 0.35 0.36 0.017 GRMZM2G134424 zinc finger (MYND type) family protein / programmed cell death 2 C-terminal domain-containing

protein S9_137067368 9 137067368 7.49E-05 0.14 1760 0.35 0.36 0.044 GRMZM2G053639 catalytics;transferas es;[acyl-carrier- protein] S- malonyltransferases

;binding S9_137067368 9 137067368 7.49E-05 0.14 1760 0.35 0.36 0.044 GRMZM2G053652 Ribosomal protein

S7e family protein S9_137493675 9 137493675 1.85E-06 0.15 1760 0.35 0.36 0.012 GRMZM2G378852 (MAPKKK14): mitogen-activated protein kinase

kinase kinase 14 S9_137493675 9 137493675 1.85E-06 0.15 1760 0.35 0.36 0.012 GRMZM2G078933 (RANBP1): RAN

binding protein 1 S9_137744363 9 137744363 1.01E-04 0.25 1760 0.35 0.36 0.048 GRMZM2G047894 (ATG5,SAC8): SAC domain-containing

protein 8 S9_142207968 9 142207968 2.25E-06 0.17 1760 0.35 0.36 0.013 GRMZM2G031441 (ATRL6,RL6,RSM3):

RAD-like 6 S9_142207968 9 142207968 2.25E-06 0.17 1760 0.35 0.36 0.013 GRMZM2G030839 GHMP kinase family

protein

503 S9_142211144 9 142211144 9.36E-05 0.22 1760 0.35 0.36 0.047 GRMZM2G031441 (ATRL6,RL6,RSM3):

RAD-like 6

504

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_142211144 9 142211144 9.36E-05 0.22 1760 0.35 0.36 0.047 GRMZM2G030839 GHMP kinase family

protein S9_143187477 9 143187477 9.28E-05 0.38 1760 0.35 0.36 0.047 GRMZM2G147775 (ADF5,ATADF5): actin depolymerizing

factor 5 S9_143887199 9 143887199 1.01E-04 0.10 1760 0.35 0.36 0.048 GRMZM2G039919 (ATXTH28,EXGT- A2,XTH28,XTR2): xyloglucan endotransglucosylas

e/hydrolase 28 S9_143887199 9 143887199 1.01E-04 0.10 1760 0.35 0.36 0.048 GRMZM2G040161 2-oxoglutarate (2OG) and Fe(II)- dependent oxygenase

superfamily protein S9_144520558 9 144520558 1.43E-05 0.32 1760 0.35 0.36 0.024 GRMZM2G177982 Erythronate-4- phosphate dehydrogenase

family protein S9_144520558 9 144520558 1.43E-05 0.32 1760 0.35 0.36 0.024 GRMZM2G478876 Protein kinase

superfamily protein S9_145890592 9 145890592 4.30E-05 0.22 1760 0.35 0.36 0.035 GRMZM2G126834 (ARR2,RR2):

response regulator 2 S9_146340226 9 146340226 8.89E-07 0.30 1760 0.35 0.36 0.010 GRMZM2G051689 Sec14p-like phosphatidylinositol transfer family

protein

504

505

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_151644982 9 151644982 4.69E-05 0.32 1760 0.35 0.36 0.036 GRMZM2G127072 (ATEXLA2,ATEXPL2, ATHEXP BETA 2.2,EXLA2,EXPL2):

expansin-like A2 S9_151644982 9 151644982 4.69E-05 0.32 1760 0.35 0.36 0.036 GRMZM2G127101 ubiquitin family

protein S9_151654922 9 151654922 1.00E-05 0.28 1760 0.35 0.36 0.023 GRMZM2G127072 (ATEXLA2,ATEXPL2, ATHEXP BETA 2.2,EXLA2,EXPL2):

expansin-like A2 S9_151654922 9 151654922 1.00E-05 0.28 1760 0.35 0.36 0.023 GRMZM2G127050 (BSK1): BR-signaling

kinase 1 S9_151654922 9 151654922 1.00E-05 0.28 1760 0.35 0.36 0.023 GRMZM2G127101 ubiquitin family

protein S9_151654946 9 151654946 2.19E-06 0.29 1760 0.35 0.36 0.013 GRMZM2G127072 (ATEXLA2,ATEXPL2, ATHEXP BETA 2.2,EXLA2,EXPL2):

expansin-like A2 S9_151654946 9 151654946 2.19E-06 0.29 1760 0.35 0.36 0.013 GRMZM2G127050 (BSK1): BR-signaling

kinase 1 S9_151654946 9 151654946 2.19E-06 0.29 1760 0.35 0.36 0.013 GRMZM2G127101 ubiquitin family

protein

S9_151758419 9 151758419 6.79E-05 0.34 1760 0.35 0.36 0.042 GRMZM2G009808 (ACO3): aconitase 3 S9_151758419 9 151758419 6.79E-05 0.34 1760 0.35 0.36 0.042 GRMZM2G009770 Leucine-rich repeat protein kinase

family protein S9_151978410 9 151978410 8.93E-05 0.11 1760 0.35 0.36 0.047 GRMZM2G059937 (ATVDAC4,VDAC4): voltage dependent

anion channel 4

505

506

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_151978410 9 151978410 8.93E-05 0.11 1760 0.35 0.36 0.047 GRMZM2G358931 (ICK6,KRP3): inhibitor/interactor with cyclin-

dependent kinase S9_151978410 9 151978410 8.93E-05 0.11 1760 0.35 0.36 0.047 GRMZM2G059891 early-responsive to dehydration stress

protein (ERD4) S9_151978413 9 151978413 8.93E-05 0.11 1760 0.35 0.36 0.047 GRMZM2G059937 (ATVDAC4,VDAC4): voltage dependent

anion channel 4 S9_151978413 9 151978413 8.93E-05 0.11 1760 0.35 0.36 0.047 GRMZM2G358931 (ICK6,KRP3): inhibitor/interactor with cyclin-

dependent kinase S9_151978413 9 151978413 8.93E-05 0.11 1760 0.35 0.36 0.047 GRMZM2G059891 early-responsive to dehydration stress

protein (ERD4) S9_152080481 9 152080481 9.79E-05 0.24 1760 0.35 0.36 0.048 GRMZM2G057243 (ATCCD1,ATNCED1, CCD1,NCED1): carotenoid cleavage

dioxygenase 1 S9_152080481 9 152080481 9.79E-05 0.24 1760 0.35 0.36 0.048 GRMZM2G057491 Glutamyl/glutaminyl -tRNA synthetase,

class Ic S9_152757081 9 152757081 2.66E-05 0.33 1760 0.35 0.36 0.029 GRMZM5G891656 FAD/NAD(P)-binding oxidoreductase

family protein S9_152757081 9 152757081 2.66E-05 0.33 1760 0.35 0.36 0.029 GRMZM5G841893 FAD/NAD(P)-binding oxidoreductase

family protein

506

507

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_152757081 9 152757081 2.66E-05 0.33 1760 0.35 0.36 0.029 GRMZM5G832248 Splicing factor, CC1-

like S9_153453087 9 153453087 5.99E-05 0.09 1760 0.35 0.36 0.040 GRMZM2G374989 (ATBOR4,BOR4): HCO3- transporter

family S9_153453087 9 153453087 5.99E-05 0.09 1760 0.35 0.36 0.040 GRMZM2G075227 CPuORF24 - conserved peptide uORF-containing transcript,

expressed S9_153453087 9 153453087 5.99E-05 0.09 1760 0.35 0.36 0.040 GRMZM2G374986 Homeodomain-like

superfamily protein S9_155685865 9 155685865 5.79E-05 0.17 1760 0.35 0.36 0.039 GRMZM2G109624 (ASKTHETA,ATSK32, SK32): shaggy-like

protein kinase 32 S9_155685865 9 155685865 5.79E-05 0.17 1760 0.35 0.36 0.039 GRMZM2G434161 alpha/beta- Hydrolases

superfamily protein S9_155685881 9 155685881 1.27E-05 0.25 1760 0.35 0.36 0.024 GRMZM2G109624 (ASKTHETA,ATSK32, SK32): shaggy-like

protein kinase 32 S9_155685881 9 155685881 1.27E-05 0.25 1760 0.35 0.36 0.024 GRMZM2G434161 alpha/beta- Hydrolases

superfamily protein S9_155685883 9 155685883 1.14E-05 0.24 1760 0.35 0.36 0.023 GRMZM2G109624 (ASKTHETA,ATSK32, SK32): shaggy-like

protein kinase 32 S9_155685883 9 155685883 1.14E-05 0.24 1760 0.35 0.36 0.023 GRMZM2G434161 alpha/beta- Hydrolases

superfamily protein

507 S9_155793013 9 155793013 7.02E-05 0.30 1760 0.35 0.36 0.042 GRMZM2G159538 UBX domain-

containing protein

508

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S9_156413787 9 156413787 3.62E-05 0.20 1760 0.35 0.36 0.033 GRMZM2G168760 (MEE13): myosin

heavy chain-related S10_3190555 10 3190555 1.09E-05 0.29 1760 0.35 0.36 0.023 GRMZM2G058595 (RPT2): Phototropic- responsive NPH3

family protein S10_3190555 10 3190555 1.09E-05 0.29 1760 0.35 0.36 0.023 GRMZM2G058531 Phototropic- responsive NPH3

family protein S10_6067231 10 6067231 8.63E-05 0.06 1760 0.35 0.36 0.046 GRMZM5G805685 AP2/B3-like transcriptional

factor family protein S10_6067238 10 6067238 9.57E-05 0.06 1760 0.35 0.36 0.048 GRMZM5G805685 AP2/B3-like transcriptional

factor family protein S10_8356929 10 8356929 4.80E-05 0.32 1760 0.35 0.36 0.036 GRMZM2G343437 (ATEXO70C1,EXO70 C1): exocyst subunit exo70 family protein

C1 S10_8356929 10 8356929 4.80E-05 0.32 1760 0.35 0.36 0.036 GRMZM2G041317 cysteine proteinase inhibitor 8 precursor, putative,

expressed S10_10245128 10 10245128 9.04E-05 0.28 1760 0.35 0.36 0.047 GRMZM2G475197 (WAK3): wall

associated kinase 3 S10_10245128 10 10245128 9.04E-05 0.28 1760 0.35 0.36 0.047 GRMZM2G475170 Disease resistance- responsive (dirigent- like protein) family

protein S10_10245594 10 10245594 6.58E-05 0.27 1760 0.35 0.36 0.042 GRMZM2G475197 (WAK3): wall

associated kinase 3

508

509

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S10_10245594 10 10245594 6.58E-05 0.27 1760 0.35 0.36 0.042 GRMZM2G475170 Disease resistance- responsive (dirigent- like protein) family

protein S10_10247919 10 10247919 9.70E-05 0.41 1760 0.35 0.36 0.048 GRMZM2G475197 (WAK3): wall

associated kinase 3 S10_10247919 10 10247919 9.70E-05 0.41 1760 0.35 0.36 0.048 GRMZM2G475170 Disease resistance- responsive (dirigent- like protein) family

protein S10_12922800 10 12922800 2.00E-05 0.37 1760 0.35 0.36 0.027 GRMZM2G015869 PQ-loop repeat family protein / transmembrane

family protein S10_36259840 10 36259840 9.45E-05 0.37 1760 0.35 0.36 0.047 GRMZM2G472703 Leucine-rich repeat protein kinase

family protein S10_75814087 10 75814087 7.05E-06 0.14 1760 0.35 0.36 0.020 GRMZM2G068808 (ABC33,ATCPS1,CPS, CPS1,GA1): Terpenoid cyclases/Protein prenyltransferases

superfamily protein S10_77187331 10 77187331 4.32E-05 0.41 1760 0.35 0.36 0.035 GRMZM2G178014 alpha/beta- Hydrolases

superfamily protein S10_79138169 10 79138169 7.06E-05 0.33 1760 0.35 0.36 0.042 GRMZM2G123886 (ATMPK11,MPK11):

MAP kinase 11 S10_79138169 10 79138169 7.06E-05 0.33 1760 0.35 0.36 0.042 GRMZM5G806309 (ELF7): hydroxyproline-rich

509 glycoprotein family

protein

510

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S10_79138171 10 79138171 6.51E-05 0.33 1760 0.35 0.36 0.042 GRMZM2G123886 (ATMPK11,MPK11):

MAP kinase 11 S10_79138171 10 79138171 6.51E-05 0.33 1760 0.35 0.36 0.042 GRMZM5G806309 (ELF7): hydroxyproline-rich glycoprotein family

protein S10_80053282 10 80053282 1.08E-05 0.31 1760 0.35 0.36 0.023 GRMZM2G086496 (ATNRT1,B- 1,CHL1,CHL1- 1,NRT1,NRT1.1): nitrate transporter

1.1 S10_80053282 10 80053282 1.08E-05 0.31 1760 0.35 0.36 0.023 GRMZM2G385989 Plant VAMP (vesicle- associated membrane protein)

family protein S10_84263131 10 84263131 6.16E-05 0.09 1760 0.35 0.36 0.040 GRMZM2G170291 DNAse I-like

superfamily protein S10_102370515 10 102370515 3.73E-05 0.32 1760 0.35 0.36 0.033 AC204711.3_FG002 Glycosyl hydrolase

family 10 protein S10_113979996 10 113979996 4.87E-05 0.10 1760 0.35 0.36 0.036 AC217051.3_FG005 (ZPR3): protein

binding S10_117569900 10 117569900 8.32E-05 0.46 1760 0.35 0.36 0.046 GRMZM2G072322 late embryogenesis abundant domain- containing protein / LEA domain-

containing protein S10_117569900 10 117569900 8.32E-05 0.46 1760 0.35 0.36 0.046 GRMZM2G072337 Methylthiotransfera

se S10_117569900 10 117569900 8.32E-05 0.46 1760 0.35 0.36 0.046 GRMZM2G072174 Photosystem II reaction center PsbP

510

family protein

511

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S10_117569901 10 117569901 7.73E-05 0.46 1760 0.35 0.36 0.044 GRMZM2G072322 late embryogenesis abundant domain- containing protein / LEA domain-

containing protein S10_117569901 10 117569901 7.73E-05 0.46 1760 0.35 0.36 0.044 GRMZM2G072337 Methylthiotransfera

se S10_117569901 10 117569901 7.73E-05 0.46 1760 0.35 0.36 0.044 GRMZM2G072174 Photosystem II reaction center PsbP

family protein S10_117570602 10 117570602 9.50E-05 0.44 1760 0.35 0.36 0.048 GRMZM2G072322 late embryogenesis abundant domain- containing protein / LEA domain- containing protein S10_117570602 10 117570602 9.50E-05 0.44 1760 0.35 0.36 0.048 GRMZM2G072337 Methylthiotransfera

se S10_117570602 10 117570602 9.50E-05 0.44 1760 0.35 0.36 0.048 GRMZM2G072174 Photosystem II reaction center PsbP

family protein

S10_119916389 10 119916389 1.08E-05 0.07 1760 0.35 0.36 0.023 GRMZM2G092325 : expressed protein S10_119916389 10 119916389 1.08E-05 0.07 1760 0.35 0.36 0.023 GRMZM2G392168 sequence-specific DNA binding

transcription factors S10_125541348 10 125541348 6.31E-06 0.23 1760 0.35 0.36 0.019 GRMZM2G481373 (OTP82): Tetratricopeptide repeat (TPR)-like

superfamily protein S10_125541348 10 125541348 6.31E-06 0.23 1760 0.35 0.36 0.019 GRMZM2G180716 Cellulase (glycosyl

hydrolase family 5) 511

protein

512

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation

S10_130511473 10 130511473 4.02E-05 0.25 1760 0.35 0.36 0.034 GRMZM2G005859 : expressed protein S10_132371056 10 132371056 1.33E-05 0.18 1760 0.35 0.36 0.024 GRMZM2G017815 Transducin/WD40 repeat-like

superfamily protein S10_132539027 10 132539027 2.12E-05 0.42 1760 0.35 0.36 0.027 GRMZM2G468756 (RLK): receptor

lectin kinase

S10_132539027 10 132539027 2.12E-05 0.42 1760 0.35 0.36 0.027 GRMZM2G468688 : expressed protein S10_132539027 10 132539027 2.12E-05 0.42 1760 0.35 0.36 0.027 GRMZM2G468693 Aldolase-type TIM

barrel family protein S10_132539027 10 132539027 2.12E-05 0.42 1760 0.35 0.36 0.027 GRMZM2G168953 NAD(P)-binding Rossmann-fold

superfamily protein S10_132552876 10 132552876 8.31E-05 0.11 1760 0.35 0.36 0.046 GRMZM2G468756 (RLK): receptor

lectin kinase

S10_132552876 10 132552876 8.31E-05 0.11 1760 0.35 0.36 0.046 GRMZM2G468688 : expressed protein S10_132552876 10 132552876 8.31E-05 0.11 1760 0.35 0.36 0.046 GRMZM2G468693 Aldolase-type TIM

barrel family protein S10_132552876 10 132552876 8.31E-05 0.11 1760 0.35 0.36 0.046 GRMZM2G168953 NAD(P)-binding Rossmann-fold

superfamily protein S10_132559869 10 132559869 8.90E-05 0.13 1760 0.35 0.36 0.047 GRMZM2G168953 (RLK): receptor

lectin kinase S10_132559869 10 132559869 8.90E-05 0.13 1760 0.35 0.36 0.047 GRMZM2G168976 NAD(P)-binding Rossmann-fold

superfamily protein S10_132560022 10 132560022 9.71E-05 0.16 1760 0.35 0.36 0.048 GRMZM2G168953 (RLK): receptor

lectin kinase S10_132560022 10 132560022 9.71E-05 0.16 1760 0.35 0.36 0.048 GRMZM2G168976 NAD(P)-binding Rossmann-fold

512

superfamily protein

513

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S10_136705214 10 136705214 3.42E-05 0.14 1760 0.35 0.36 0.032 GRMZM2G077069 (AtPP2-A13,PP2- A13): phloem

protein 2-A13 S10_136705214 10 136705214 3.42E-05 0.14 1760 0.35 0.36 0.032 GRMZM2G077082 (TBL11): TRICHOME BIREFRINGENCE-

LIKE 11 S10_136705214 10 136705214 3.42E-05 0.14 1760 0.35 0.36 0.032 GRMZM2G077036 S-adenosyl-L- methionine- dependent methyltransferases

superfamily protein S10_136705238 10 136705238 2.21E-05 0.14 1760 0.35 0.36 0.027 GRMZM2G077069 (AtPP2-A13,PP2- A13): phloem

protein 2-A13 S10_136705238 10 136705238 2.21E-05 0.14 1760 0.35 0.36 0.027 GRMZM2G077082 (TBL11): TRICHOME BIREFRINGENCE-

LIKE 11 S10_136705238 10 136705238 2.21E-05 0.14 1760 0.35 0.36 0.027 GRMZM2G077036 S-adenosyl-L- methionine- dependent methyltransferases

superfamily protein S10_137282927 10 137282927 3.23E-06 0.42 1760 0.35 0.36 0.014 GRMZM2G094860 Aluminium activated malate transporter

family protein S10_137282927 10 137282927 3.23E-06 0.42 1760 0.35 0.36 0.014 GRMZM5G836567 Spc97 / Spc98 family of spindle pole body

(SBP) component S10_137286265 10 137286265 2.87E-06 0.30 1760 0.35 0.36 0.014 GRMZM2G094860 Aluminium activated malate transporter

513

family protein

514

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S10_137286265 10 137286265 2.87E-06 0.30 1760 0.35 0.36 0.014 GRMZM5G836567 Spc97 / Spc98 family of spindle pole body

(SBP) component S10_137460368 10 137460368 3.78E-05 0.49 1760 0.35 0.36 0.033 AC209206.3_FG014 polyphenol oxidase,

putative, expressed S10_137460396 10 137460396 6.49E-06 0.48 1760 0.35 0.36 0.019 AC209206.3_FG014 polyphenol oxidase,

putative, expressed S10_137460417 10 137460417 1.82E-05 0.49 1760 0.35 0.36 0.026 AC209206.3_FG014 polyphenol oxidase,

putative, expressed S10_137500425 10 137500425 8.98E-05 0.36 1760 0.35 0.36 0.047 GRMZM5G884137 (AtIDD5,IDD5): indeterminate(ID)-

domain 5 S10_138019498 10 138019498 9.06E-05 0.15 1760 0.35 0.36 0.047 GRMZM2G061287 (CYCB2;4): CYCLIN

B2;4 S10_138019498 10 138019498 9.06E-05 0.15 1760 0.35 0.36 0.047 GRMZM2G061398 DUF630/DUF632 domains containing protein, putative,

expressed S10_138217938 10 138217938 1.04E-04 0.31 1760 0.35 0.36 0.049 GRMZM2G112129 (AGAL2,AtAGAL2): alpha-galactosidase

2 S10_138217938 10 138217938 1.04E-04 0.31 1760 0.35 0.36 0.049 GRMZM2G112057 (CPK29): calcium- dependent protein

kinase 29 S10_138217938 10 138217938 1.04E-04 0.31 1760 0.35 0.36 0.049 GRMZM2G112100 Subtilase family

protein S10_138467901 10 138467901 6.85E-05 0.20 1760 0.35 0.36 0.042 GRMZM5G822829 (ATMYC- 2,EGL1,EGL3): basic helix-loop-helix (bHLH) DNA-binding

514

superfamily protein

515

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S10_138467929 10 138467929 6.85E-05 0.20 1760 0.35 0.36 0.042 GRMZM5G822829 (ATMYC- 2,EGL1,EGL3): basic helix-loop-helix (bHLH) DNA-binding

superfamily protein S10_139002222 10 139002222 2.37E-05 0.27 1760 0.35 0.36 0.028 GRMZM2G100940 (ARO2): armadillo

repeat only 2 S10_139002222 10 139002222 2.37E-05 0.27 1760 0.35 0.36 0.028 GRMZM2G100931 (ATEXPB2,ATHEXP BETA 1.4,EXPB2):

expansin B2 S10_139002222 10 139002222 2.37E-05 0.27 1760 0.35 0.36 0.028 GRMZM2G402027 C2H2-type zinc

finger family protein S10_139879397 10 139879397 5.73E-05 0.29 1760 0.35 0.36 0.039 GRMZM2G080516 (ATERF-1,ERF-1): ethylene responsive element binding

factor 1 S10_142077960 10 142077960 1.36E-05 0.33 1760 0.35 0.36 0.024 GRMZM2G019986 (GlcNAc1pUT1): N- acetylglucosamine- 1-phosphate

uridylyltransferase 1 S10_142077960 10 142077960 1.36E-05 0.33 1760 0.35 0.36 0.024 GRMZM2G019325 (RPS11-BETA): ribosomal protein

S11-beta S10_144528001 10 144528001 1.73E-05 0.15 1760 0.35 0.36 0.025 GRMZM2G445575 (OBF4,TGA4): TGACG motif-

binding factor 4 S10_146329291 10 146329291 1.12E-05 0.08 1760 0.35 0.36 0.023 GRMZM2G101179 nucleolar protein,Nop52 containing protein,

expressed

515 S10_146329291 10 146329291 1.12E-05 0.08 1760 0.35 0.36 0.023 GRMZM2G400109 RING/U-box

superfamily protein

516

R2 of R2 of FDR Model Model Adjusted Genes within 10 Kp SNP Chr Position P.value maf N obs w/o SNP w/ SNP P-values of SNP Annotation S10_146335890 10 146335890 2.49E-05 0.08 1760 0.35 0.36 0.029 GRMZM2G101179 nucleolar protein,Nop52 containing protein,

expressed S10_146335890 10 146335890 2.49E-05 0.08 1760 0.35 0.36 0.029 GRMZM2G400109 RING/U-box

superfamily protein S10_146336123 10 146336123 9.87E-05 0.31 1760 0.35 0.36 0.048 GRMZM2G101179 nucleolar protein,Nop52 containing protein,

expressed S10_146336123 10 146336123 9.87E-05 0.31 1760 0.35 0.36 0.048 GRMZM2G400109 RING/U-box

superfamily protein S10_146338328 10 146338328 6.72E-05 0.11 1760 0.35 0.36 0.042 GRMZM2G101179 nucleolar protein,Nop52 containing protein,

expressed S10_146338328 10 146338328 6.72E-05 0.11 1760 0.35 0.36 0.042 GRMZM2G400109 RING/U-box

superfamily protein

516

517

Appendix J Sorghum Kernel Composition NIR Calibration Correlations

Sorghum Calibrations for Mirror Cup and Breeders Cup

David Honigs, Ph.D. Perten Instruments, Springfield, IL 11/13/2013

Introduction The DA7250 NIR diode array can be used to measure a variety of properties in grains including sorghum. In this study the NIR spectra from a series of 100 samples were collected in two different methods designed for smaller quantity samples, and then the samples were analyzed for a variety of proximate constituents. The results of those data were analyzed individually and together with existing sorghum data that was collected from much larger samples.

Experimental A Perten DA7250 was used to collect NIR spectra of sorghum samples in the breeder’s cup and the mirror cup. The breeder’s cup is used to measure small sample quantities and the mirror cup measures spectra on even smaller sample sets. A series of 100 samples were used for this data collection. The spectral data was reviewed for its overall characteristics and then combined with data from other samples. A series of new calibrations were developed.

Small Sample Moisture Figure 1 shows the PLS calibration of the 100 sample spectra for moisture. Figure 1 - Breeders Cup NIR Calibration

517

The calibration error of 0.2% moisture is reasonably accurate, but the limited range of moistures makes the calibration value questionable. The RDP for the calibration is close to 1 which means that the

518 calibration is not much better than simply guessing the average moisture. The apparent accuracy comes from the fact that the moisture levels are not changing much.

Combined Data

Combining the data from the breeder’s cup, the mirror cup and the previous Perten data was evaluated by making a score v score plot of the principal component analysis of all the NIR spectra. This plot is shown in Figure 2. The data are colored with dark blue being the original Perten Data, light blue is the breeder’s cup data and yellow is the mirror cup data. The three distributions seem to overlap extremely well. 2 - Score v Score Plot

Putting all of the spectra together for the moisture calibration is shown in Figure 3.

518

519

Figure 3 - Moisture in Sorghum using All Data

By adding all of the data the error increased slightly, but the range of the calibration is much improved. The previous data had two groups widely separated in moisture. The added data falls between those extremes. By having a much wider range the coefficient of determination and the RPD values are much improved. This calibration should be much more robust over a wider range of moistures.

For the rest of the constituents the combined data set will be used for the calibration.

The protein calibration for the entire data set is shown in Figure 4. The previous data and the new data cover different protein ranges and the two complement each other well to improve the calibration range.

Figure 4 - Protein Calibration of Combined Data Sets

519

520

The calibration error of the combined protein sets was 0.55%. Breaking the error down by groups:

Previous data was 0.43%, Breeder’s cup was 0.59% Mirror cup was 0.62%

The bias between cups was not statistically significant and ranged between +/- 0.04% protein. These results confirm that the data fit together well in an unbiased way and that the accuracy of the breeder’s cup and mirror cup presentations are comparable.

The statistics for the remaining parameters are listed in the following figures.

Figure 5 Starch Calibration Combined Sets Data

For starch the range is limited the RPD value is 1.16 which is not much better than guessing the average. There were not many samples in the historical Perten data with starch values.

520

521

Figure 6 Fat Calibration Combined Sets Data

Once again, the RPD value is small. This calibration does not cover enough range as compared to the error for it to be reliable. The binning comes from the digitization of the lab values to the hundredths of a percent. There are not many historical samples with oil/fat values.

7 - ADF Calibration

521

522

Figure 8 - Total Digestible Nutrients Calibration

The TDN calibration is like the ADF calibration. Each of these calibrations is right on the edge of the RPD=1.75 cutoff point. If the data had a bit more range in the concentrations, the calibration statistics should improve and the RPD would increase. Several of the following calibrations are in this same condition of being very close to the 1.75 RPD level.

Figure 12 - Net Energy Main Calibration

522

523

Figure 13 - Net Energy Gain Calibration

Figure 14 - Net Energy of Lactation Calibration

523

524

Conclusions

The moisture and protein calibrations using the combined data sets are strong. Some of the energy calibrations are on the line between acceptable and unacceptable. The breeder’s cup and the mirror cup give comparable results.

524

525

Appendix K Sorghum Kernel Composition SAS Code for BLUP Analysis

Below is BLUP SAS code for the trait ADF, all other traits use similar code for BLUP calculations

/****** For Combined analysis of ADF*/ data WL; infile 'U:\Research Projects\Kernel Composition\Perten Sorghum Runs\Compiled Final File Sorghum NIR West Lafayette.csv ' dsd firstobs=2 missover; input Plot$ GroupID$ Name$ Range Row Block Moisture Protein Starch TDN ADF NEG NEL NEM treatn$ new loc; Loc = '1'; if GroupID= 'C1' then GroupID= '3000'; if GroupID= 'C2' then GroupID= '4000'; Data WLAVG; set WL; keep Plot Range Row GROUPID Block Protein Starch TDN ADF NEG NEL NEM treatn new loc; proc sort; by Block plot; run; Data WLAVG1; set WL; keep Block GROUPID treatn new ADF; rename Block =BlockWL; rename ADF = ADFWL; proc sort; by GroupID ; run; data EF; infile 'U:\Research Projects\Kernel Composition\Perten Sorghum Runs\Compiled Final File Sorghum NIR Champaign.csv' dsd firstobs=2 missover; input Plot$ GroupID$ Name$ Range Row Block Moisture Protein

Starch TDN ADF NEG NEL NEM treatn$ new loc; 525 Loc = '2';

if GroupID= 'C1' then GroupID= '3000'; if GroupID= 'C2' then GroupID= '4000'; Data EFAVG; set EF; keep Plot Range Row GROUPID Block Protein Starch TDN ADF NEG NEL NEM treatn new loc; proc sort; by Block plot; run; Data EFAVG1; set EF; keep Block GROUPID treatn new ADF; rename Block =BlockEF; rename ADF = ADFEF;

526 proc sort; by GroupID ; run;

data MN; infile 'U:\Research Projects\Kernel Composition\Perten Sorghum Runs\Compiled Final File Sorghum NIR Monmouth.csv' dsd firstobs=2 missover; input Plot$ GroupID$ Name$ Range Row Block Moisture Protein Starch TDN ADF NEG NEL NEM treatn$ new loc; Loc = '3'; if GroupID= 'C1' then GroupID= '3000'; if GroupID= 'C2' then GroupID= '4000'; Data MNAVG; set MN; keep Plot Range Row GROUPID Block Protein Starch TDN ADF NEG NEL NEM treatn new loc; proc sort; by Block plot; run; Data MNAVG1; set MN; keep Block GROUPID treatn new ADF; rename Block =BlockMN; rename ADF = ADFMN; proc sort; by GroupID ; run; Data SorgComb; set WLAVG EFAVG MNAVG; run; proc sort; by Block plot; run; Data SorgComb1; merge WLAVG1 EFAVG1 MNAVG1; by GroupID; keep BlockWL BlockEF BlockMN GroupID treatn new ADFWL ADFEF ADFMN; 526

run; proc print data=sorgcomb; run;

/* To run an ANOVA on Starch*/ proc glm data=sorgcomb; class groupid loc block; model ADF=groupid loc block(loc); random loc block(loc); run;

/*To calculate BLUP*/ proc mixed data=SorgComb; class loc Block GroupID treatn; model ADF = treatn /solution; random loc block(loc) GroupID*new/ solution;

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lsmeans treatn; ods listing exclude solutionr; ods output solutionr=sr LSMeans=lsm; run; proc sort data = sr; by effect loc;

/* Attempt to combine the Estimates for the different traits with the original data to compute BLUPs*/ Data LS; set lsm; rename Estimate=ADFuMean; proc sort Data=LS; By treatn; run; proc sort data=SorgComb1; By treatn; run; Data ADFREP; merge LS SorgComb1; By treatn; keep BlockWL BlockEF BlockMN treatn GROUPID ADFuMean ADFWL ADFEF ADFMN; Data ADFRan; set sr; if Effect= 'loc' then delete; if GroupID= " " then ADFRan=Estimate; else delete; Data ADFEST; set sr; if GroupID= '' then delete; keep GroupID Estimate; rename Estimate=ADFEst; run; Data ADFBlockWL; set ADFRan; if Loc=1 then ADFBlockWL=ADFRan; else delete; keep Effect Block ADFBlockWL; 527

rename Block=BlockWL; Proc sort data=ADFBLockWL; by BlockWL; run; Data ADFBLockEF; set ADFRan; if Loc=2 then ADFBLockEF=ADFRan; else delete; keep Effect Block ADFBLockEF; rename Block=BlockEF; Proc Sort data=ADFBLockEF; by BlockEF; run; Data ADFBLockMN; set ADFRan;

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if Loc=3 then ADFBLockMN=ADFRan; else delete; keep Effect Block ADFBLockMN; rename Block=BlockMN;

Proc Sort data=ADFBLockMN; by BlockMN; run; proc sort data=SorgComb1; by BlockWL; run; data ADFBlockWLComb; merge SorgComb1 ADFBlockWL; by BlockWL; keep BlockWL BlockEF BlockMN treatn GroupID ADFBLockWL ADFWL ADFEF ADFMN; proc sort data=SorgComb1; by BlockEF; run; data ADFBlockEFComb; merge SorgComb1 ADFBlockEF; by BlockEF; keep BlockWL BlockEF BlockMN treatn GroupID ADFBLockEF ADFWL ADFEF ADFMN; proc sort data=SorgComb1; by BlockMN; run; data ADFBlockMNComb; merge SorgComb1 ADFBlockMN; by BlockMN; keep BlockWL BlockEF BlockMN treatn GroupID ADFBLockMN ADFWL ADFEF ADFMN; proc sort data=ADFBlockWLComb; by GroupID; run; proc sort data=ADFBlockEFComb; by GroupID; run; proc sort data=ADFBlockMNComb; by GroupID; 528

run; data ADFBlockComb; merge ADFBlockWLComb ADFBlockEFComb ADFBlockMNComb; by GroupID; keep BlockWL BlockEF BlockMN treatn GroupID ADFBlockWL ADFBlockEF ADFBlockMN ADFWL ADFEF ADFMN; data combranrep; merge ADFBlockComb ADFRep; run; proc sort data=combranrep; by GroupID; run; proc sort data=ADFEst; by GroupID; run;

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Data CombinedADF; merge CombRanRep ADFEST; by GroupID; ADFBLUP= (ADFEST + ADFBlockWL + ADFBlockEF + ADFBlockMN + ADFuMean); if ADFWL='.' then ADFBLUP='.'; if ADFEF='.' then ADFBLUP='.'; if ADFMN='.' then ADFBLUP='.'; keep BlockWL BlockEF BlockMN treatn GROUPID ADFWL ADFEF ADFMN ADFEST ADFBlockWL ADFBlockEF ADFBlockMN ADFuMean ADFBLUP; run; proc print; run; /*To check for normality of the BLUP data*/ proc univariate data = combinedADF; qqplot ADFblup; histogram ADFBLUP; run;

/* To Check to see if transformations necessary*/ proc transreg data= combinedADF; model Box (ADFBLUP / lambda = 0 to 1 by 0.5)= class(GroupID); run; /*To Compute the transformed BLUP value based on the BOXCOX suggestions*/ Data ADFfinal; set combinedADF; ADFBLUP= (log(ADFBLUP)); keep groupid ADF ADFblup; run; /*To Confirm transformation went properly*/ proc univariate data = ADFfinal; qqplot ADFBLUP; histogram ADFBLUP; run; /*Using the NON-Transformed ADF Data*/ proc print data=CombinedADF;run; proc export DATA= CombinedADF outfile="U:\Research Projects\Kernel Composition\Perten Sorghum Runs\BLUPs Calculated\CombinedADF.csv" dbms=CSV 529

;run;

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Appendix L Sorghum Kernel Composition R Code for GWAS Analysis

Below is R GWAS code for the trait ADF, all other traits use similar code for GWAS analysis

##########FOR ADF TRAIT GWAS######### ##Load gapit libraries and genotype files rm(biocLite) source("http://www.bioconductor.org/biocLite.R") biocLite("multtest") install.packages("gplots") install.packages("LDheatmap") install.packages("genetics") library("multtest") library("gplots") library("LDheatmap") library("genetics") library("compiler") #this library is already installed in R source("http://www.maizegenetics.net/images/stories/bioinformatics/GAPIT/gapit_fun ctions.txt") source("http://www.maizegenetics.net/images/stories/bioinformatics/GAPIT/emma.txt ") load("~/Research Projects/GAPIT/Sorghum Geno Files/gapitsnps_sb_1797_140430.RData") load("~/Research Projects/GAPIT/Sorghum Geno

530 Files/gapitinfo_sb_1797_140430.RData") #rename and change format snps[,1]=as.character(snps[,1]) myGD = snps; rm(snps) myGM = snp_info;rm(snp_info)

##set paths to phenotype file and ouput directory ##Phenotype file should be tab-delimited text, with first column ("Taxa") that contains entry names exactly as they appear in the genotypes file, ##and an additional column for each phenotype. Each phenotype column should have a unique column name. Numeric only, with "NA" in empty cells

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pheno_file="~/Research Projects/Kernel Composition/Perten Sorghum Runs/GAPIT RUNS/Combined/ash/ash.txt" #output directory should be a new empty, appropriately named directory --this script will fill it up with files output_directory="~/Research Projects/Kernel Composition/Perten Sorghum Runs/GAPIT RUNS/Combined/ash"

##Load phenotypes and set working directory for gapit output myY = read.table(pheno_file, header = T,sep="\t",stringsAsFactors=F) myY=myY[order(myY[,1]),]

#only include lines for which we have both phenotypes and genotypes #ordering:myY automatically gets ordered alphabetically in the step above. myGD is already ordered alphabetically. #see which names don't match #myGD[,1][myGD[,1]%in%myY[,1]==F] #myY[,1][myY[,1]%in%myGD[,1]==F] myGDtemp=myGD[myGD[,1]%in%myY[,1],] myY=myY[myY[,1]%in%myGDtemp[,1],] myGDtemp=myGDtemp[order(myGDtemp[,1]),] myY[,1]==myGDtemp[,1]

##Prune SNPs to only include those with with maf >= 0.05 for your phenotype-genotype dataset maf=c() 531 for (i in 2:ncol(myGDtemp)){ maf[i]=mean(myGDtemp[,i])/2 print(i) } maf[1]=0.5 myGDtemp=myGDtemp[,maf>=0.05&maf<=0.95] maf=maf[2:length(maf)] myGMtemp=myGM[maf>=0.05&maf<=0.95,]

#Prune identical side-by-side SNPs within 64 bp

532 identical=c() for (i in 2:ncol(myGDtemp)){ identical[i]=sum(myGDtemp[,i]==myGDtemp[,(i-1)])==nrow(myGDtemp) & myGMtemp[i,3]-myGMtemp[(i-1),3]<64 print(i) } identical[1]=F myGDtemp=myGDtemp[,identical==F] identical=identical[2:length(identical)] myGMtemp=myGMtemp[identical==F,]

#run gapit with default options #setwd(output_directory) #myGAPIT <- GAPIT(Y=myY, GD=myGDtemp,GM=myGMtemp)

#run gapit using MLM instead of CMLM setwd(output_directory) myGAPIT <- GAPIT(Y=myY, GD=myGDtemp, GM=myGMtemp, group.from=100, group.to=710 )

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533

Appendix M Sorghum Kernel Composition ANOVA Outputs

M-1 Sorghum Kernel ADF ANOVA Source DF Sum of Squares Mean Square F Value Pr > F Model 921 3132.857 3.401582 9.24 <.0001 Error 1595 587.3011 0.368214 Corrected Total 2516 3720.158

R -Square Coeff Var Root MSE ADF Mean 0.84213 9.99463 0.606806 6.071323

Source DF Type I SS Mean Square F Value Pr > F GroupID 836 2290.382 2.739692 7.44 <.0001 loc 2 779.9954 389.9977 1059.16 <.0001 Block(loc) 83 62.47894 0.752758 2.04 <.0001

Source DF Type III SS Mean Square F Value Pr > F GroupID 836 2237.208 2.676087 7.27 <.0001 loc 2 780.9242 390.4621 1060.42 <.0001 Block(loc) 83 62.47894 0.752758 2.04 <.0001

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M-2 Sorghum Kernel NEG ANOVA Source DF Sum of Squares Mean Square F Value Pr > F Model 923 7872.16 8.528884 8.92 <.0001 Error 1561 1491.804 0.955672 Corrected Total 2484 9363.965

R -Square Coeff Var Root MSE ADF Mean 0.840687 1.62031 0.977585 60.33319

Source DF Type I SS Mean Square F Value Pr > F GroupID 838 6175.11 7.368866 7.71 <.0001 loc 2 1208.077 604.0384 632.06 <.0001 Block(loc) 83 488.9738 5.89125 6.16 <.0001

Source DF Type III SS Mean Square F Value Pr > F GroupID 838 6117.684 7.300339 7.64 <.0001 loc 2 1185.413 592.7063 620.2 <.0001 Block(loc) 83 488.9738 5.89125 6.16 <.0001

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M-3 Sorghum Kernel NEL ANOVA Source DF Sum of Squares Mean Square F Value Pr > F Model 923 217.4601 0.235601 9.89 <.0001 Error 1602 38.15546 0.023817

Corrected Total 2525 255.6155

R -Square Coeff Var Root MSE ADF Mean 0.850731 0.17356 0.154329 88.91941

Source DF Type I SS Mean Square F Value Pr > F GroupID 838 160.9665 0.192084 8.06 <.0001 loc 2 52.92801 26.464 1111.12 <.0001 Block(loc) 83 3.56551 0.042958 1.8 <.0001

Source DF Type III SS Mean Square F Value Pr > F GroupID 838 156.3301 0.186552 7.83 <.0001 loc 2 53.06933 26.53467 1114.09 <.0001 Block(loc) 83 3.56551 0.042958 1.8 <.0001

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M-4 Sorghum Kernel NEM ANOVA Source DF Sum of Squares Mean Square F Value Pr > F Model 925 14227.66 15.38126 11.15 <.0001 Error 1615 2228.409 1.37982

Corrected Total 2540 16456.07

R -Square Coeff Var Root MSE ADF Mean 0.864584 1.278756 1.174657 91.85939

Source DF Type I SS Mean Square F Value Pr > F GroupID 840 11022.55 13.12209 9.51 <.0001 loc 2 3000.837 1500.419 1087.4 <.0001 Block(loc) 83 204.2733 2.46112 1.78 <.0001

Source DF Type III SS Mean Square F Value Pr > F GroupID 840 10476.16 12.47162 9.04 <.0001 loc 2 3004.776 1502.388 1088.83 <.0001 Block(loc) 83 204.2733 2.46112 1.78 <.0001

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M-5 Sorghum Kernel Protein ANOVA Source DF Sum of Squares Mean Square F Value Pr > F Model 926 4998.536 5.397988 5.28 <.0001 Error 1622 1657.988 1.022188

Corrected Total 2548 6656.525

R -Square Coeff Var Root MSE ADF Mean 0.750923 7.842927 1.011033 12.89102

Source DF Type I SS Mean Square F Value Pr > F GroupID 841 4675.935 5.55997 5.44 <.0001 loc 2 133.9365 66.96826 65.51 <.0001 Block(loc) 83 188.6651 2.273073 2.22 <.0001

Source DF Type III SS Mean Square F Value Pr > F GroupID 841 4577.375 5.442777 5.32 <.0001 loc 2 136.0897 68.04486 66.57 <.0001 Block(loc) 83 188.6651 2.273073 2.22 <.0001

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M-6 Sorghum Kernel TDN ANOVA Source DF Sum of Squares Mean Square F Value Pr > F Model 924 8406.871 9.098345 12.7 <.0001 Error 1558 1115.776 0.716159

Corrected Total 2482 9522.647

R -Square Coeff Var Root MSE ADF Mean 0.882829 1.013702 0.846262 83.48228

So urce DF Type I SS Mean Square F Value Pr > F GroupID 839 5037.546 6.004227 8.38 <.0001 loc 2 3182.382 1591.191 2221.84 <.0001 Block(loc) 83 186.9422 2.252316 3.14 <.0001

Source DF Type III SS Mean Square F Value Pr > F GroupID 839 5110.956 6.091723 8.51 <.0001 loc 2 3188.829 1594.415 2226.34 <.0001 Block(loc) 83 186.9422 2.252316 3.14 <.0001

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Appendix N Sorghum Kernel Composition Candidate Genes

N-1 Sorghum Kernel Acid Detergent Fiber (ADF) Candidate Genes

R2 of R2 of FDR N Model Model Adjusted Gene within 20 SNP Chr Position P.value maf obs w/o SNP w/SNP P-values KB Annotation pstI_2_57617151 2 57617151 4.05E-07 0.26 682 0.24 0.27 0.023 Sb02g023750.1 hAT family C-terminal dimerisation region pstI_2_57617151 2 57617151 4.05E-07 0.26 682 0.24 0.27 0.023 Sb02g023790.1 ALPHA-AMYLASE pstI_2_57617151 2 57617151 4.05E-07 0.26 682 0.24 0.27 0.023 Sb02g023780.1 UNCHARACTERIZED

pstI_2_57617151 2 57617151 4.05E-07 0.26 682 0.24 0.27 0.023 Sb02g023770.1 Cytochrome P450 CYP2 subfamily pstI_2_57617151 2 57617151 4.05E-07 0.26 682 0.24 0.27 0.023 Sb02g023765.1 NA pstI_2_57617151 2 57617151 4.05E-07 0.26 682 0.24 0.27 0.023 Sb02g023760.1 NA pstI_2_57617151 2 57617151 4.05E-07 0.26 682 0.24 0.27 0.023 Sb02g023740.1 NA pstI_2_57617151 2 57617151 4.05E-07 0.26 682 0.24 0.27 0.023 Sb02g023730.1 Zinc finger, C3HC4 type (RING finger) pstI_2_57617151 2 57617151 4.05E-07 0.26 682 0.24 0.27 0.023 Sb02g023720.1 XANTHINE-URACIL / VITAMIN C PERMEASE FAMILY MEMBER pstI_2_57617151 2 57617151 4.05E-07 0.26 682 0.24 0.27 0.023 Sb02g023710.1 Protein of unknown function (DUF3353) pstI_2_57617151 2 57617151 4.05E-07 0.26 682 0.24 0.27 0.023 Sb02g023700.1 NA pstI_2_57617151 2 57617151 4.05E-07 0.26 682 0.24 0.27 0.023 Sb02g023690.1 AMP-binding enzyme

pstI_2_57617151 2 57617151 4.05E-07 0.26 682 0.24 0.27 0.023 Sb02g023680.1 Cytochrome P450 539

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540

R2 of R2 of FDR N Model Model Adjusted Gene within 20 SNP Chr Position P.value maf obs w/o SNP w/SNP P-values KB Annotation pstI_2_57617151 2 57617151 4.05E-07 0.26 682 0.24 0.27 0.023 Sb02g023660.1 Glycosyl hydrolase family 81 pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g028920.1 B-box zinc finger pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g028930.1 Mitochondrial carrier protein pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g028940.1 Plastocyanin-like domain pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g028950.1 NA pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g028960.1 SRF-type transcription factor (DNA-binding and dimerisation domain) pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g028970.1 PPR repeat pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g028980.1 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g028990.1 ASPARTYL PROTEASES pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029000.1 Aluminium activated malate transporter pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029010.1 UNCHARACTERIZED pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029020.1 NHL repeat pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029030.1 K+ potassium transporter pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029035.1 PRE-MRNA SPLICING FACTOR PRP31 pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029040.1 ALDEHYDE DEHYDROGENASE pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029050.1 Zinc finger, C3HC4 type

540 (RING finger)

540

541

R2 of R2 of FDR N Model Model Adjusted Gene within 20 SNP Chr Position P.value maf obs w/o SNP w/SNP P-values KB Annotation pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029060.1 Zinc finger, C3HC4 type (RING finger) pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029070.1 tRNA synthetases class I (M) pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029080.1 Homeobox associated leucine zipper pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029090.1 NA pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029100.1 Rhodanese-like domain pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029110.1 Arabidopsis proteins of unknown function pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029120.1 Arabidopsis proteins of unknown function pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029130.1 Arabidopsis proteins of unknown function pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029140.1 TETRASPANIN pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029150.1 RIBOSOMAL RNA PROCESSING PROTEIN 7- RELATED pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029160.1 Ribosomal protein L7Ae/L30e/S12e/Gadd4 5 family pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029170.1 LEUCINE-RICH REPEAT RECEPTOR-LIKE PROTEIN KINASE pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029180.1 GATA-4/5/6 transcription factors pstI_4_59095899 4 59095899 1.27E-06 0.36 682 0.24 0.27 0.036 Sb04g029190.1 LONGEVITY ASSURANCE FACTOR 1 (LAG1)

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N-2 Sorghum Kernel Net Energy of Lactation (NEL) Candidate Genes

R2 of R2 of FDR N Model Model Adjusted P- Gene within 200 SNP Chr Position P.value maf obs w/o SNP w/ SNP values KB Annotation pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g034918.1 NA pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g034930.1 Zinc finger, C3HC4 type (RING finger) pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g034940.1 NA pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g034950.1 X-BOX TRANSCRIPTION FACTOR-RELATED pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g034960.1 Protein of unknown function (DUF642) pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g034970.1 ALDO/KETO REDUCTASE pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g034980.1 VOLTAGE AND LIGAND GATED POTASSIUM CHANNEL pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g034990.1 NA pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035000.1 gibberellin 2-oxidase [EC:1.14.11.13] pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035010 ATP binding pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035010.1 ATPase family associated with various cellular activities (AAA) pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035020.1 Calcyclin-binding protein CacyBP pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035030.1 NA pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035040.1 PPR repeat pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035050.1 DNA REPAIR POLYMERASE UMUC / TRANSFERASE FAMILY MEMBER 542

542

543

R2 of R2 of FDR N Model Model Adjusted P- Gene within 200 SNP Chr Position P.value maf obs w/o SNP w/ SNP values KB Annotation pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035060.1 2-DEOXYGLUCOSE-6- PHOSPHATE PHOSPHATASE 2 pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035070.1 COPPER TRANSPORT PROTEIN ATOX1 (METAL TRANSPORT PROTEIN ATX1) pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035080.1 Dof domain, zinc finger pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035090.1 Phosphoenolpyruvate carboxylase pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035100.1 PHOSPHATIDATE CYTIDYLYLTRANSFERASE pstI_3_63184638 3 63184638 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035110.1 NA pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g034918.1 NA pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g034930.1 Zinc finger, C3HC4 type (RING finger) pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g034940.1 NA pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g034950.1 X-BOX TRANSCRIPTION FACTOR-RELATED pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g034960.1 Protein of unknown function (DUF642) pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g034970.1 ALDO/KETO REDUCTASE pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g034980.1 VOLTAGE AND LIGAND GATED POTASSIUM CHANNEL pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g034990.1 NA pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035000.1 gibberellin 2-oxidase [EC:1.14.11.13] pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035010 ATP binding

543

544

R2 of R2 of FDR N Model Model Adjusted P- Gene within 200 SNP Chr Position P.value maf obs w/o SNP w/ SNP values KB Annotation pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035010.1 ATPase family associated with various cellular activities (AAA) pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035020.1 Calcyclin-binding protein CacyBP pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035030.1 NA pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035040.1 PPR repeat pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035050.1 DNA REPAIR POLYMERASE UMUC / TRANSFERASE FAMILY MEMBER pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035060.1 2-DEOXYGLUCOSE-6- PHOSPHATE PHOSPHATASE 2 pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035070.1 COPPER TRANSPORT PROTEIN ATOX1 (METAL TRANSPORT PROTEIN ATX1) pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035080.1 Dof domain, zinc finger pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035090.1 Phosphoenolpyruvate carboxylase pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035100.1 PHOSPHATIDATE CYTIDYLYLTRANSFERASE pstI_3_63184681 3 63184681 7.88E-07 0.06 687 0.25 0.28 0.022 Sb03g035110.1 NA pstI_2_57617151 2 57617151 1.44E-06 0.26 687 0.25 0.28 0.022 Sb02g023750.1 hAT family C-terminal dimerisation region pstI_2_57617151 2 57617151 1.44E-06 0.26 687 0.25 0.28 0.022 Sb02g023790.1 ALPHA-AMYLASE pstI_2_57617151 2 57617151 1.44E-06 0.26 687 0.25 0.28 0.022 Sb02g023780.1 UNCHARACTERIZED pstI_2_57617151 2 57617151 1.44E-06 0.26 687 0.25 0.28 0.022 Sb02g023770.1 Cytochrome P450 CYP2 subfamily

544 pstI_2_57617151 2 57617151 1.44E-06 0.26 687 0.25 0.28 0.022 Sb02g023765.1 NA

544

545

R2 of R2 of FDR N Model Model Adjusted P- Gene within 200 SNP Chr Position P.value maf obs w/o SNP w/ SNP values KB Annotation pstI_2_57617151 2 57617151 1.44E-06 0.26 687 0.25 0.28 0.022 Sb02g023760.1 NA pstI_2_57617151 2 57617151 1.44E-06 0.26 687 0.25 0.28 0.022 Sb02g023740.1 NA pstI_2_57617151 2 57617151 1.44E-06 0.26 687 0.25 0.28 0.022 Sb02g023730.1 Zinc finger, C3HC4 type (RING finger) pstI_2_57617151 2 57617151 1.44E-06 0.26 687 0.25 0.28 0.022 Sb02g023720.1 XANTHINE-URACIL / VITAMIN C PERMEASE FAMILY MEMBER pstI_2_57617151 2 57617151 1.44E-06 0.26 687 0.25 0.28 0.022 Sb02g023710.1 Protein of unknown function (DUF3353) pstI_2_57617151 2 57617151 1.44E-06 0.26 687 0.25 0.28 0.022 Sb02g023700.1 NA pstI_2_57617151 2 57617151 1.44E-06 0.26 687 0.25 0.28 0.022 Sb02g023690.1 AMP-binding enzyme pstI_2_57617151 2 57617151 1.44E-06 0.26 687 0.25 0.28 0.022 Sb02g023680.1 Cytochrome P450 pstI_2_57617151 2 57617151 1.44E-06 0.26 687 0.25 0.28 0.022 Sb02g023660.1 Glycosyl hydrolase family 81 pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g028920.1 B-box zinc finger pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g028930.1 Mitochondrial carrier protein pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g028940.1 Plastocyanin-like domain pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g028950.1 NA pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g028960.1 SRF-type transcription factor (DNA-binding and dimerisation domain) pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g028970.1 PPR repeat pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g028980.1 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g028990.1 ASPARTYL PROTEASES pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029000.1 Aluminium activated malate transporter 545

545

546

R2 of R2 of FDR N Model Model Adjusted P- Gene within 200 SNP Chr Position P.value maf obs w/o SNP w/ SNP values KB Annotation pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029010.1 UNCHARACTERIZED pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029020.1 NHL repeat pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029030.1 K+ potassium transporter pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029035.1 PRE-MRNA SPLICING FACTOR PRP31 pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029040.1 ALDEHYDE DEHYDROGENASE pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029050.1 Zinc finger, C3HC4 type (RING finger) pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029060.1 Zinc finger, C3HC4 type (RING finger) pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029070.1 tRNA synthetases class I (M) pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029080.1 Homeobox associated leucine zipper pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029090.1 NA pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029100.1 Rhodanese-like domain pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029110.1 Arabidopsis proteins of unknown function pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029120.1 Arabidopsis proteins of unknown function pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029130.1 Arabidopsis proteins of unknown function pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029140.1 TETRASPANIN pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029150.1 RIBOSOMAL RNA PROCESSING PROTEIN 7- RELATED pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029160.1 Ribosomal protein L7Ae/L30e/S12e/Gadd45

546 family

546

547

R2 of R2 of FDR N Model Model Adjusted P- Gene within 200 SNP Chr Position P.value maf obs w/o SNP w/ SNP values KB Annotation pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029170.1 LEUCINE-RICH REPEAT RECEPTOR-LIKE PROTEIN KINASE pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029180.1 GATA-4/5/6 transcription factors pstI_4_59095899 4 59095899 1.56E-06 0.36 687 0.25 0.28 0.022 Sb04g029190.1 LONGEVITY ASSURANCE FACTOR 1 (LAG1)

547

548

N-3 Sorghum Kernel Net Energy of Maintenance (NEM) Candidate Genes

R2 of R2 of FDR N Model Model Adjusted Gene within 20 SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values KB Annotation pstI_2_57617151 2 57617151 1.42E-08 0.26 697 0.24 0.28 0.001 Sb02g023750.1 hAT family C-terminal dimerisation region pstI_2_57617151 2 57617151 1.42E-08 0.26 697 0.24 0.28 0.001 Sb02g023790.1 ALPHA-AMYLASE pstI_2_57617151 2 57617151 1.42E-08 0.26 697 0.24 0.28 0.001 Sb02g023780.1 UNCHARACTERIZED pstI_2_57617151 2 57617151 1.42E-08 0.26 697 0.24 0.28 0.001 Sb02g023770.1 Cytochrome P450 CYP2 subfamily

pstI_2_57617151 2 57617151 1.42E-08 0.26 697 0.24 0.28 0.001 Sb02g023765.1 NA pstI_2_57617151 2 57617151 1.42E-08 0.26 697 0.24 0.28 0.001 Sb02g023760.1 NA pstI_2_57617151 2 57617151 1.42E-08 0.26 697 0.24 0.28 0.001 Sb02g023740.1 NA pstI_2_57617151 2 57617151 1.42E-08 0.26 697 0.24 0.28 0.001 Sb02g023730.1 Zinc finger, C3HC4 type (RING finger) pstI_2_57617151 2 57617151 1.42E-08 0.26 697 0.24 0.28 0.001 Sb02g023720.1 XANTHINE-URACIL / VITAMIN C PERMEASE FAMILY MEMBER pstI_2_57617151 2 57617151 1.42E-08 0.26 697 0.24 0.28 0.001 Sb02g023710.1 Protein of unknown function (DUF3353) pstI_2_57617151 2 57617151 1.42E-08 0.26 697 0.24 0.28 0.001 Sb02g023700.1 NA pstI_2_57617151 2 57617151 1.42E-08 0.26 697 0.24 0.28 0.001 Sb02g023690.1 AMP-binding enzyme pstI_2_57617151 2 57617151 1.42E-08 0.26 697 0.24 0.28 0.001 Sb02g023680.1 Cytochrome P450 pstI_2_57617151 2 57617151 1.42E-08 0.26 697 0.24 0.28 0.001 Sb02g023660.1 Glycosyl hydrolase family 81 pstI_2_57604889 2 57604889 1.47E-07 0.35 697 0.24 0.27 0.004 Sb02g023750 hAT family C-terminal dimerisation region pstI_2_57604889 2 57604889 1.47E-07 0.35 697 0.24 0.27 0.004 Sb02g023740 NA

pstI_2_57604889 2 57604889 1.47E-07 0.35 697 0.24 0.27 0.004 Sb02g023790.1 ALPHA-AMYLASE 548

548

549

R2 of R2 of FDR N Model Model Adjusted Gene within 20 SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values KB Annotation pstI_2_57604889 2 57604889 1.47E-07 0.35 697 0.24 0.27 0.004 Sb02g023780.1 UNCHARACTERIZED pstI_2_57604889 2 57604889 1.47E-07 0.35 697 0.24 0.27 0.004 Sb02g023770.1 Cytochrome P450 CYP2 subfamily pstI_2_57604889 2 57604889 1.47E-07 0.35 697 0.24 0.27 0.004 Sb02g023765.1 NA pstI_2_57604889 2 57604889 1.47E-07 0.35 697 0.24 0.27 0.004 Sb02g023760.1 NA pstI_2_57604889 2 57604889 1.47E-07 0.35 697 0.24 0.27 0.004 Sb02g023730.1 Zinc finger, C3HC4 type (RING finger) pstI_2_57604889 2 57604889 1.47E-07 0.35 697 0.24 0.27 0.004 Sb02g023720.1 XANTHINE-URACIL / VITAMIN C PERMEASE FAMILY MEMBER pstI_2_57604889 2 57604889 1.47E-07 0.35 697 0.24 0.27 0.004 Sb02g023710.1 Protein of unknown function (DUF3353) pstI_2_57604889 2 57604889 1.47E-07 0.35 697 0.24 0.27 0.004 Sb02g023700.1 NA pstI_2_57604889 2 57604889 1.47E-07 0.35 697 0.24 0.27 0.004 Sb02g023690.1 Acyl-CoA synthetase pstI_2_57604889 2 57604889 1.47E-07 0.35 697 0.24 0.27 0.004 Sb02g023680.1 Cytochrome P450 pstI_2_57604889 2 57604889 1.47E-07 0.35 697 0.24 0.27 0.004 Sb02g023660.1 Glycosyl hydrolase family 81 pstI_2_57604889 2 57604889 1.47E-07 0.35 697 0.24 0.27 0.004 Sb02g023650.1 Homeobox associated leucine zipper pstI_2_57604889 2 57604889 1.47E-07 0.35 697 0.24 0.27 0.004 Sb02g023640.1 UDP-glucoronosyl and UDP- glucosyl transferase pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023765.1 NA pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023840.1 Helicase conserved C- terminal domain pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023680.1 Cytochrome P450 pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023690.1 AMP-binding enzyme pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023700.1 NA pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023710.1 Protein of unknown function

(DUF3353) 549

549

550

R2 of R2 of FDR N Model Model Adjusted Gene within 20 SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values KB Annotation pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023720.1 XANTHINE-URACIL / VITAMIN C PERMEASE FAMILY MEMBER pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023730.1 Zinc finger, C3HC4 type (RING finger) pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023740.1 NA pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023750.1 hAT family C-terminal dimerisation region pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023760.1 NA pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023770.1 Cytochrome P450 pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023780.1 UNCHARACTERIZED pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023790.1 ALPHA-AMYLASE pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023800.1 CYCLINE pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023810.1 NA pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023820.1 NA pstI_2_57649504 2 57649504 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023830.1 MITOGEN-ACTIVATED KINASE KINASE KINASE pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023765.1 NA pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023840.1 Helicase conserved C- terminal domain pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023680.1 Cytochrome P450 pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023690.1 AMP-binding enzyme pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023700.1 NA pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023710.1 Protein of unknown function (DUF3353) pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023720.1 XANTHINE-URACIL / VITAMIN C PERMEASE FAMILY

MEMBER 550

550

551

R2 of R2 of FDR N Model Model Adjusted Gene within 20 SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values KB Annotation pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023730.1 Zinc finger, C3HC4 type (RING finger) pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023740.1 NA pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023750.1 hAT family C-terminal dimerisation region pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023760.1 NA pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023770.1 Cytochrome P450 pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023780.1 UNCHARACTERIZED pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023790.1 ALPHA-AMYLASE pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023800.1 CYCLINE pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023810.1 NA pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023820.1 NA pstI_2_57649529 2 57649529 3.13E-07 0.33 697 0.24 0.27 0.004 Sb02g023830.1 MITOGEN-ACTIVATED KINASE KINASE KINASE pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023765.1 NA pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023840.1 Helicase conserved C- terminal domain pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023680.1 Cytochrome P450 pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023690.1 AMP-binding enzyme pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023700.1 NA pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023710.1 Protein of unknown function (DUF3353) pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023720.1 XANTHINE-URACIL / VITAMIN C PERMEASE FAMILY MEMBER pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023730.1 Zinc finger, C3HC4 type (RING finger) pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023740.1 NA 551

551

552

R2 of R2 of FDR N Model Model Adjusted Gene within 20 SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values KB Annotation pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023750.1 hAT family C-terminal dimerisation region pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023760.1 NA pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023770.1 Cytochrome P450 pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023780.1 UNCHARACTERIZED pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023790.1 ALPHA-AMYLASE pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023800.1 CYCLINE pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023810.1 NA pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023820.1 NA pstI_2_57649520 2 57649520 5.14E-07 0.33 697 0.24 0.27 0.006 Sb02g023830.1 MITOGEN-ACTIVATED KINASE KINASE KINASE pstI_2_57582078 2 57582078 8.57E-07 0.33 697 0.24 0.27 0.007 Sb02g023730 Zinc finger, C3HC4 type (RING finger) pstI_2_57582078 2 57582078 8.57E-07 0.33 697 0.24 0.27 0.007 Sb02g023720 Xanthine/uracil transporters pstI_2_57582078 2 57582078 8.57E-07 0.33 697 0.24 0.27 0.007 Sb02g023780.1 UNCHARACTERIZED pstI_2_57582078 2 57582078 8.57E-07 0.33 697 0.24 0.27 0.007 Sb02g023770.1 Cytochrome P450 pstI_2_57582078 2 57582078 8.57E-07 0.33 697 0.24 0.27 0.007 Sb02g023765.1 NA pstI_2_57582078 2 57582078 8.57E-07 0.33 697 0.24 0.27 0.007 Sb02g023760.1 NA pstI_2_57582078 2 57582078 8.57E-07 0.33 697 0.24 0.27 0.007 Sb02g023750.1 hAT family C-terminal dimerisation region pstI_2_57582078 2 57582078 8.57E-07 0.33 697 0.24 0.27 0.007 Sb02g023740.1 NA pstI_2_57582078 2 57582078 8.57E-07 0.33 697 0.24 0.27 0.007 Sb02g023710.1 NA pstI_2_57582078 2 57582078 8.57E-07 0.33 697 0.24 0.27 0.007 Sb02g023700.1 NA pstI_2_57582078 2 57582078 8.57E-07 0.33 697 0.24 0.27 0.007 Sb02g023690.1 AMP-binding enzyme pstI_2_57582078 2 57582078 8.57E-07 0.33 697 0.24 0.27 0.007 Sb02g023680.1 Cytochrome P450 pstI_2_57582078 2 57582078 8.57E-07 0.33 697 0.24 0.27 0.007 Sb02g023660.1 Glycosyl hydrolase family 81 pstI_2_57582078 2 57582078 8.57E-07 0.33 697 0.24 0.27 0.007 Sb02g023640.1 UDP-glucoronosyl and UDP- 552

glucosyl transferase

552

553

R2 of R2 of FDR N Model Model Adjusted Gene within 20 SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values KB Annotation pstI_2_57582078 2 57582078 8.57E-07 0.33 697 0.24 0.27 0.007 Sb02g023650.1 Homeobox associated leucine zipper pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023765 NA pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023680.1 Cytochrome P450 pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023690.1 AMP-binding enzyme pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023700.1 NA pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023710.1 Protein of unknown function (DUF3353) pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023720.1 XANTHINE-URACIL / VITAMIN C PERMEASE FAMILY MEMBER pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023840.1 Helicase conserved C- terminal domain pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023830.1 MITOGEN-ACTIVATED KINASE KINASE KINASE pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023820.1 NA pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023810.1 NA pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023800.1 CYCLINE pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023790.1 ALPHA-AMYLASE pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023780.1 UNCHARACTERIZED pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023770.1 Cytochrome P450 pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023760.1 NA pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023750.1 hAT family C-terminal dimerisation region pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023740.1 NA pstI_2_57649524 2 57649524 9.02E-07 0.33 697 0.24 0.27 0.007 Sb02g023730.1 Zinc finger, C3HC4 type (RING finger) pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g028920.1 B-box zinc finger 553 pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g028930.1 Mitochondrial carrier protein

553

554

R2 of R2 of FDR N Model Model Adjusted Gene within 20 SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values KB Annotation pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g028940.1 Plastocyanin-like domain pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g028950.1 NA pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g028960.1 SRF-type transcription factor (DNA-binding and dimerisation domain) pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g028970.1 PPR repeat pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g028980.1 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g028990.1 ASPARTYL PROTEASES pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029000.1 Aluminium activated malate transporter pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029010.1 UNCHARACTERIZED pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029020.1 NHL repeat pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029030.1 K+ potassium transporter pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029035.1 PRE-MRNA SPLICING FACTOR PRP31 pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029040.1 ALDEHYDE DEHYDROGENASE pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029050.1 Zinc finger, C3HC4 type (RING finger) pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029060.1 Zinc finger, C3HC4 type (RING finger) pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029070.1 tRNA synthetases class I (M) pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029080.1 Homeobox associated leucine zipper pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029090.1 NA pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029100.1 Rhodanese-like domain pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029110.1 Arabidopsis proteins of

unknown function 554

554

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R2 of R2 of FDR N Model Model Adjusted Gene within 20 SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values KB Annotation pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029120.1 Arabidopsis proteins of unknown function pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029130.1 Arabidopsis proteins of unknown function pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029140.1 TETRASPANIN pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029150.1 RIBOSOMAL RNA PROCESSING PROTEIN 7- RELATED pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029160.1 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029170.1 LEUCINE-RICH REPEAT RECEPTOR-LIKE PROTEIN KINASE pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029180.1 GATA-4/5/6 transcription factors pstI_4_59095899 4 59095899 2.09E-06 0.36 697 0.24 0.27 0.015 Sb04g029190.1 LONGEVITY ASSURANCE FACTOR 1 (LAG1)

555

556

N-4 Sorghum Kernel Protein Candidate Genes

R2 of R2 of FDR N Model Model Adjusted Gene within 20 SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values KB Annotation pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027900 NA pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027890 2Fe-2S iron-sulfur cluster binding domain pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027870 Protein phosphatase 2A regulatory B subunit (B56 family) pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027750.1 QUIESCIN Q6-RELATED SULFHYDRYL OXIDASE pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027760.1 UDP- GLUCOSYLTRANSFERASE pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027770.1 NA pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027780.1 NA pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027790.1 ATP synthase F1 beta subunit pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027800.1 Myb-like DNA-binding domain pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027810.1 SYNTAXIN pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027820.1 ANTI-SILENCING PROTEIN 1 pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027830.1 MULTIDRUG RESISTANCE PROTEIN pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027840.1 Rab5-interacting protein (Rab5ip) pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027850.1 PHOSPHATIDYLSERINE SYNTHASE pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027860.1 NA

556

557

R2 of R2 of FDR N Model Model Adjusted Gene within 20 SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values KB Annotation pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027870.1 SERINE/THREONINE PROTEIN PHOSPHATASE 2A (PP2A) REGULATORY SUBUNIT B pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027890.1 FERREDOXIN pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027900.1 NA pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027910.1 Glutamine amidotransferases class-II pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027920.1 NA pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027930.1 Ribosomal protein L35Ae pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027940.1 NA pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027945.1 OXIDOREDUCTASE, 2OG- FE(II) OXYGENASE FAMILY PROTEIN pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027950.1 OXIDOREDUCTASE, 2OG- FE(II) OXYGENASE FAMILY PROTEIN pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027960.1 Dynamin GTPase effector domain pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027970.1 Wax ester synthase-like Acyl-CoA acyltransferase domain pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027980.1 HEPATOCELLULAR CARCINOMA-ASSOCIATED ANTIGEN pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027983.1 Kinesin motor domain pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027986.1 NA pstI_9_56910830 9 56910830 6.03E-07 0.08 703 0.09 0.12 0.034 Sb09g027990.1 DOMON domain

557

558

N-5 Sorghum Kernel Total Digestible Nutrients (TDN) Candidate Genes

R2 of R2 of FDR N Model Model Adjusted Gene within 20 SNP Chr Position P.value maf obs w/o SNP w/ SNP P-values KB Annotation pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g028920.1 B-box zinc finger pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g028930.1 Mitochondrial carrier protein pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g028940.1 Plastocyanin-like domain pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g028950.1 NA pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g028960.1 SRF-type transcription factor (DNA-binding and dimerisation domain) pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g028970.1 PPR repeat pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g028980.1 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g028990.1 ASPARTYL PROTEASES pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g029000.1 Aluminium activated malate transporter pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g029010.1 UNCHARACTERIZED pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g029020.1 NHL repeat pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g029030.1 K+ potassium transporter pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g029035.1 PRE-MRNA SPLICING FACTOR PRP31 pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g029040.1 ALDEHYDE DEHYDROGENASE pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g029050.1 Zinc finger, C3HC4 type (RING finger) pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g029060.1 Zinc finger, C3HC4 type (RING finger) pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g029070.1 tRNA synthetases class I (M) pstI_4_59095899 4 59095899 8.22E-07 0.34 658 0.21 0.24 0.047 Sb04g029080.1 Homeobox associated leucine

zipper 558

558

559

VITA

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VITA

Raymond Scott Lindsey Ph.D. Candidate Department of Agronomy, Purdue University Education

2011-2015 Ph.D. in Plant Breeding and Genetics - Purdue University Dissertation: “Genetic Control of Kernel Composition and Leaf Nitrogen Remobilization in Diverse Populations of Zea mays and Sorghum bicolor”

2007-2011 B.S. in Crop and Soil Sciences – Michigan State University

2007-2011 B.A. in Political Science/Pre-Law – Michigan State University

Professional Experience

2015 Commercial Soybean Breeder - Dow AgroSciences (Grand Forks, ND)

2011-2015 Graduate Research Assistant - Purdue University (West Lafayette, IN) Advisor: Dr. Mitchell Tuinstra

2008-2011 Undergraduate Research Assistant - Michigan State University

Summer 2010 Germplasm Security and Protection Intern, Dupont Pioneer

Summer 2009 Maize Research Intern, Dupont Pioneer (Ithaca, MI)

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2003-2011 Equipment Operator, Harold Lindsey Farms (Otsego, MI)

Summer 2002 Corn detasseling crew member, Simmons’ Detasseling

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Teaching Experience

Fall 2014 Laboratory Instructor- Principles and Methods of Plant Breeding

Summer 2014 Course Design Assistant- Principles and Methods of Plant Breeding

Spring 2014 Lecture Teaching Assistant- World Crop Adaptation and Distribution

Fall 2013 Lecture Teaching Assistant- Introduction to Genetics

Spring 2013 Lecture Teaching Assistant- World Crop Adaptation and Distribution

Conference and Workshop Activity

April 2014 AFRI Partnership Advisory Council Meeting- West Lafayette, IN Poster Title: “Genetic Control of Kernel Composition and Leaf Nitrogen Remobilization in Diverse Populations of Maize and Sorghum”

December 2013 American Seed Trade Association Corn and Sorghum Seed Conference- Chicago, IL Poster Title: “Genetic Control of Kernel Composition and Leaf Nitrogen Remobilization in Diverse Populations of Maize and Sorghum”

March 2013 Maize Genetics Conference – St. Charles, IL

March 2013 Illinois Corn Breeders’ School – Champaign, IL

January 2013 Tucson Winter Plant Breeding Institute – Tucson, AZ

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June 2012 Marker-Assisted Plant Breeding Workshop – St. Paul, MN

March 2012 Maize Genetics Conference – Portland, OR Poster Title: “Examination of Low-N Tolerance in Tropical and Temperate Pools of Zea mays”

February 2012 AFRI Partnership Advisory Council Meeting – West Lafayette, IN Poster Title: “Examination of Low-N Tolerance in Tropical and Temperate Pools of Zea mays”

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December 2011 American Seed Trade Association Corn and Sorghum Seed Conference – Chicago, Il Poster Title: “Examination of Low-N Tolerance in Tropical and Temperate Pools of Zea mays”

Other Publications

Lindsey, Raymond S., Rachel Naegele, and Mitch McGrath. "Effect of NaCl on Germination of Sugar Beet." Beet Sugar Development Foundation Bluebook (2009).

Fellowships & Honors

2014 John D. Axtell Graduate Student Award in Plant Breeding and Genetics

2013-2014 Purdue Research Foundation Research Grant, Purdue University

2011-2013 Frederick N. Andrews Fellow, Purdue University

2013 Indiana Seed Industry Graduate Study Award

2013 Wyman E. Nyquist Scholarship in Agronomy

2011-2013 Perrigo Company Charitable Foundation Scholarship

Society Memberships

2010 - Present American Society of Agronomy, Soil Science Society of America,

Crop Science Society of America (ASA, SSSA, CSSA) 562

2013 – Present National Association of Plant Breeders (NAPB)

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Software Proficiency

R Statistical Software

Statistical Analysis Software (SAS)

Microsoft Office (Word, Powerpoint, Excel)

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