Agronomy Publications Agronomy 3-2019 Stability Analysis of Kernel Quality Traits in Exotic- Derived Doubled Haploid Maize Lines Adam Vanous Iowa State University, [email protected] Candice Gardner United States Department of Agriculture, [email protected] Michael Blanco United States Department of Agriculture Adam Martin-Schwarze Iowa State University Jinyu Wang Iowa State University, [email protected] SeFoe nelloxtw pa thige fors aaddndition addal aitutionhorsal works at: https://lib.dr.iastate.edu/agron_pubs Part of the Agriculture Commons, Agronomy and Crop Sciences Commons, and the Plant Breeding and Genetics Commons The ompc lete bibliographic information for this item can be found at https://lib.dr.iastate.edu/ agron_pubs/536. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Agronomy at Iowa State University Digital Repository. It has been accepted for inclusion in Agronomy Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Stability Analysis of Kernel Quality Traits in Exotic-Derived Doubled Haploid Maize Lines Abstract Variation in kernel composition across maize (Zea mays L.) germplasm is affected by a combination of the plant’s genotype, the environment in which it is grown, and the interaction between these two elements. Adapting exotic germplasm to the US Corn Belt is highly dependent on the plant’s genotype, the environment where it is grown, and the interaction between these components. Phenotypic plasticity is ill-defined when specific exotic germplasm is moved over large latitudinal distances and for the adapted variants being created. Reduced plasticity (or stability) is desired for the adapted variants, as it allows for a more rapid implementation into breeding programs throughout the Corn Belt. Here, doubled haploid lines derived from exotic maize and adapted through backcrossing exotic germplasm to elite adapted lines were used in conjunction with genome-wide association studies to explore stability in four kernel composition traits. Genotypes demonstrated a response to environments that paralleled the mean response of all genotypes used across all traits, with protein content and kernel density exhibiting the highest levels of Type II stability. Genes such as opaque10, empty pericarp 16, and floury 1 were identified as potential candidates within quantitative trait locus regions. The findings within this study aid in validating previously identified genomic regions and identified novel genomic regions affecting kernel quality traits. Disciplines Agriculture | Agronomy and Crop Sciences | Plant Breeding and Genetics Comments This article is published as Vanous, Adam, Candice Gardner, Michael Blanco, Adam Martin-Schwarze, Jinyu Wang, Xianran Li, Alexander E. Lipka et al. "Stability Analysis of Kernel Quality Traits in Exotic-Derived Doubled Haploid Maize Lines." The Plant Genome 12 (2018): 1-14. doi: 10.3835/plantgenome2017.12.0114. Rights Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The onc tent of this document is not copyrighted. Authors Adam Vanous, Candice Gardner, Michael Blanco, Adam Martin-Schwarze, Jinyu Wang, Xianran Li, Alexander E. Lipka, Sherry Flint-Garcia, Martin Bohn, Jode Edwards, and Thomas Lubberstedt This article is available at Iowa State University Digital Repository: https://lib.dr.iastate.edu/agron_pubs/536 Published online November 21, 2018 The Plant Genome ORIGINAL RESEARCH Stability Analysis of Kernel Quality Traits in Exotic-Derived Doubled Haploid Maize Lines Adam Vanous, Candice Gardner,* Michael Blanco, Adam Martin-Schwarze, Jinyu Wang, Xianran Li, Alexander E. Lipka, Sherry Flint-Garcia, Martin Bohn, Jode Edwards, and Thomas Lübberstedt A. Vanous, J. Wang, X. Li, T. Lübberstedt, Dep. of Agronomy, Iowa State Univ., Ames, IA 50011; M. Blanco, J. Edwards, C. Gardner, USDA- ARS and Dep. of Agronomy, Iowa State Univ., Ames, IA 50011; A. Martin-Schwarze, Dep. of Statistics, Iowa State Univ., Ames, IA 50011; S. Flint-Garcia, Division of Plant Sciences, Univ. of Missouri, Columbia, MO 65211; M. Bohn, Dep. of Crop Sciences and the Illinois Plant Breeding Center, Univ. of Illinois at Urbana-Champaign, Urbana, IL 61801; A. Lipka, Dep. of Crop Sciences, Univ. of Illinois at Urbana- Champaign, Urbana, IL 61801. ABSTRACT Variation in kernel composition across maize (Zea CORE IDEAS mays L.) germplasm is affected by a combination of the plant’s genotype, the environment in which it is grown, and the interaction • Exotic germplasm may be useful for altering between these two elements. Adapting exotic germplasm to the temperate kernel characteristics. US Corn Belt is highly dependent on the plant’s genotype, the • Single nucleotide polymorphism markers were environment where it is grown, and the interaction between these associated with composition traits. components. Phenotypic plasticity is ill-defined when specific • The stability and usefulness of exotic germplasm was exotic germplasm is moved over large latitudinal distances and demonstrated. for the adapted variants being created. Reduced plasticity (or stability) is desired for the adapted variants, as it allows for a more rapid implementation into breeding programs throughout the Corn Belt. Here, doubled haploid lines derived from exotic he overall fitness of a plant is highly dependent on maize and adapted through backcrossing exotic germplasm to Tthe plant’s ability to adapt to changing environmental elite adapted lines were used in conjunction with genome-wide factors through changes made in physiology, metabolism, association studies to explore stability in four kernel composition growth, and intermediate development (Lee et al., 2002; traits. Genotypes demonstrated a response to environments that Marais et al., 2013). These heritable changes are known paralleled the mean response of all genotypes used across as phenotypic plasticity, which can be selected for or all traits, with protein content and kernel density exhibiting the against with traditional plant breeding techniques (Gage highest levels of Type II stability. Genes such as opaque10, empty et al., 2017; Pigliucci, 2005). However, even with maize pericarp 16, and floury 1 were identified as potential candidates showing large amounts of phenotypic plasticity, relatively within quantitative trait locus regions. The findings within this little emphasis has been placed on introducing tropical study aid in validating previously identified genomic regions and germplasm to widen the U.S. germplasm pool (Pollak, identified novel genomic regions affecting kernel quality traits. 2003). Long daylength Corn Belt environments cause tropical maize to exhibit delayed flowering (Allison and Abbreviations: BGEM, inbred line from Iowa State University in the Daynard, 1979; Warrington and Kanemasu, 1983), which Germplasm Enhancement of Maize project; BLUP, best linear unbiased prediction; DH, doubled haploid; GWAS, genome-wide association study; LD, linkage disequilibrium; Meff, the effective number of independent tests; Citation: Wang, J., S. Li, A.E. Lipka, S. Flint-Garcia, M. Bohn, J. MLM, mixed linear model; NIRT, near-infrared transmission spectroscopy; Edwards, and T. Lübberstedt. 2019. Stability analysis of kernel quality QTL, quantitative trait locus; SNP, single nucleotide polymorphism. traits in exotic-derived double haploid maize lines. Plant Genome 12:170114. doi: 10.3835/plantgenome2017.12.0114 Received 15 Dec. 2017. Accepted 15 July 2018. *Corresponding author ([email protected]). This is an open access article distributed under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Copyright © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA THE PLANT GENOME VOL. 12, NO. 1 MARCH 2019 1 OF 14 makes adapting the germplasm to its new environment Vasal, 1992; Worral et al., 2015). Additional studies were precarious at best. Hallauer and Carena (2014) theorized, completed with the aim of finding additional protein however, that for some traits, the addition of tropical quality QTLs without yield reduction (Cook et al., 2012; germplasm could confer better characteristics than those Dudley et al., 2007, 2004; Laurie et al., 2004); however, of the 100% temperate germplasm currently being used yield reductions were still noted. in the Corn Belt. This is especially important, since maize Starch composition in maize kernels is well under- is an important food staple for many people around the stood (Wang et al., 2015). Shrunken1, shrunken2, brittle2, world, where it is directly consumed by humans or indi- waxy1, sugary2, dull1, amylose extender1, and sugary1 rectly through livestock consumption (Cook et al., 2012). (Hennen‐Bierwagen and Myers, 2013; Huang et al., Oil, starch, and protein content directly affect the 2014; Klösgen et al., 1986) are a few of the known genes quality of food and feed (Baker et al., 1969; Lewis et al., involved in starch biosynthesis. However, little is known 1982; Worral et al., 2015). Maize is also a popular fuel about the connections of these genes in the regula- source, as its starch content has become important in the tion of starch biosynthesis and starch accumulation in production of ethanol, potentially creating bottlenecks in maize (Wang et al., 2015). Many QTL studies have been the stable supply of sufficient