Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2014 Efficiency study of testing and selection in progeny- row yield trials and multiple-environment yield trials in soybean breeding Minghui Sun Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Agricultural Science Commons, Agriculture Commons, and the Agronomy and Crop Sciences Commons Recommended Citation Sun, Minghui, "Efficiency study of testing and selection in progeny-row yield trials and multiple-environment yield trials in soybean breeding" (2014). Graduate Theses and Dissertations. 13969. https://lib.dr.iastate.edu/etd/13969 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Efficiency study of testing and selection in progeny-row yield trials and multiple- environment yield trials in soybean breeding by Minghui Sun A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Plant Breeding Program of Study Committee: Reid G. Palmer, Co-major Professor Silvia R. Cianzio, Co-major Professor A. Susana Goggi Thomas Lubberstedt Kenneth J. Moore Kevin W. Matson Iowa State University Ames, Iowa 2014 Copyright © Minghui Sun, 2014. All rights reserved ii TABLE OF CONTENTS Page LIST OF FIGURES ………………………………………………...……………………………………………………… iv LIST OF TABLES …………………...…………………………………………………………………………………… vii ACKNOWLEDGEMENTS …………………………………………………………………………………………........ x ABSTRACT …………………………………………………………………………………………………………..……. xii CHAPTER 1 LITERATURE REVIEW …………………………………………………………………………. 1 Introduction of Soybean and Soybean Breeding ……………..………..…...……….. 1 PRYT Application in Soybean Breeding ………....……………………………………… 5 Non-genetic Factors Contributing to Yield Variation and Selection Accuracy in PRYT ……..…………………………………………………. 8 Experimental Designs and Spatial Statistical Modeling to Account for Spatial Variation in PRYT ……...…………............................ 11 Genotype by Environment Interaction and Predictability of Soybean Line Performance Based on Multiple Year and Location Trials ..………………………………………………………….. 16 Dissertation Organization ..…………………………………………………………………… 18 References …………………………………………………………………………………………... 22 CHAPTER 2 THIN PLATE SPLINE SPATIAL MODEL USED AT EARLY STAGE OF SOYBEAN BREEDING TO CONTROL FIELD SPATIAL VARIATION: THE STUDY OF TEST EFFICENCY IMPROVEMENT USING THREE CHECKS WITIN TEST-SETS ..….….…………………........... 28 Abstract …..…………………………………………………………………………………………. 28 Introduction ……………………………………………………………………………………….. 30 Materials and Methods ……………………………………………………………………….... 33 Results and Discussion …….....……………………………………………………………….. 42 Conclusions …..…………………………………………………………………………………….. 48 References …..………………………………………………………………………………………. 58 iii CHAPTER 3 PREDICTABILITY STUDY OF SOYBEAN LINE PERFORMANCE BASED ON MULTIPLE YEAR AND LOCATION TRIALS …………….…... 61 Abstract …..…………………………………………………………………………………………. 61 Introduction ………………………………………………………………………………………. 62 Materials and Methods ……………………………………………………………………….. 65 Results and Discussion …….....……………………………………………………………….. 69 Conclusions ….……………………………………………………………………………………. 76 References …..……………………………………………………………………………………… 86 CHAPTER 4 THIN PLATE SPLINE SPATIAL MODEL USED AT EARLY STAGE OF SOYBEAN BREEDING TO CONTROL FIELD SPATIAL VARIATION: THE STUDY OF TEST EFFICENCY IMPROVEMENT USING FIVE CHECKS WITHIN TEST-SETS ……..………………………….… 88 Abstract …..…………………………………………………………………………………………. 88 Introduction ……………………………………………………………………………………….. 90 Materials and Methods ……………...………………………………………………………… 92 Results and Discussion …….....……………………………………………………………… 100 Conclusions …..…………………………………………………………………………………… 105 References …..…………………………………………………………………………………….. 122 CHAPTER 5 GENERAL CONCLUSIONS ………………………………………..………………………….. 124 iv LIST OF FIGURES CHAPTER 1 Fig. 1 Soybean historic yield data (kg ha-1) from 1921 to 2014 in the United States (USDA data base) ………....……………………………………… 19 Fig. 2 Soybean relative maturity groups in the United States …...…………………….. 20 Fig. 3 Typical field lay-out of soybean PRYT test-set in North America ..………….. 21 CHAPTER 2 Fig. 1 Heat map for yield observations without the TPS spatial model adjustment (yield) of the Early Generation Tests in 2010 (left) and 2012 (right), respectively …....…………………………………….. 56 Fig. 2 Heat maps of check residuals and the predicted spatial effects ......…………. 57 CHAPTER 3 Fig. 1 Regressions between test locations and the mean yields of the locations measured by mean yields of testing lines within locations (location_codes were based on the alphabetical order of the first letter of test-location names across three trials) ..………………....…………………………………….. 85 CHAPTER 4 Fig. 1 Treatment 1 in Central IA. The heat map of check residuals estimated from the linear model with checks as fixed effects based on the yield of checks of the Spatial Study in 2013 (left), and the heat map of the predicted spatial pattern using the TPS spatial model based on the check residuals from the Spatial Study (right) ....………………………………… 112 v Fig. 2 Treatment 2 in Central IA. The heat map of check residuals estimated from the linear model with checks as fixed effects based on the yield of checks of the Spatial Study in 2013 (left), and the heat map of the predicted spatial pattern using the TPS spatial model based on the check residuals from the Spatial Study (right) …………………….. 113 Fig. 3 Treatment 3 in Central IA. The heat map of check residuals estimated from the linear model with checks as fixed effects based on the yield of checks of the Spatial Study in 2013 (left), and the heat map of the predicted spatial pattern using the TPS spatial model based on the check residuals from the Spatial Study (right) .…………………………………... 114 Fig. 4 Treatment 4 in Central IA. The heat map of check residuals estimated from the linear model with checks as fixed effects based on the yield of checks of the Spatial Study in 2013 (left), and the heat map of the predicted spatial pattern using the TPS spatial model based on the check residuals from the Spatial Study (right) ....………………………………… 115 Fig. 5 Treatment 1 in Southeast NE. The heat map of check residuals estimated from the linear model with checks as fixed effects based on the yield of checks of the Spatial Study in 2013 (left), and the heat map of the predicted spatial pattern using the TPS spatial model based on the check residuals from the Spatial Study (right) .…………………………………... 116 Fig. 6 Treatment 2 in Southeast NE. The heat map of check residuals estimated from the linear model with checks as fixed effects based on the yield of checks of the Spatial Study in 2013 (left), and the heat map of the predicted spatial pattern using the TPS spatial model based on the check residuals from the Spatial Study (right) .…………………………………... 117 Fig. 7 Treatment 3 in Southeast NE. The heat map of check residuals estimated from the linear model with checks as fixed effects vi based on the yield of checks of the Spatial Study in 2013 (left), and the heat map of the predicted spatial pattern using the TPS spatial model based on the check residuals from the Spatial Study (right) ....………………………………… 118 Fig. 8 Treatment 4 in Southeast NE. The heat map of check residuals estimated from the linear model with checks as fixed effects based on the yield of check’s checks of the Spatial Study in 2013 (left), and the heat map of the predicted spatial pattern using the TPS spatial model based on the check residuals from the Spatial Study (right) .…………………………………... 119 Fig. 9 Test-field 1 where treatments 1 and 3 were allocated in Central IA in the Spatial Study. The photo was taken on September 9, 2013. The plants with yellow leaves were underwent drought stress ………………………….……………………...……………………… 120 Fig. 10 Test-field 2 where treatments 2 and 4 were allocated in Central IA in the Spatial Study. The photo was taken on September 9, 2013. The plants with yellow leaves were underwent drought stress …………………………...…………………….……………………… 121 vii LIST OF TABLES CHAPTER 2 Table 1 Weather information for the research location of Monsanto Inc. In Central IA that was used in the conduct of the 2010 and 2012 Early Generation Tests ……………………………..………………... 51 Table 2 Variation within test-set in the yield observations recorded in the Uniformity Study, without the TPS spatial adjustment (yield), and with the TPS spatial adjustment (yld_adj) ..………………. 52 Table 3 Analysis of variance of the Uniformity Study based on yield observations without the TPS spatial adjustment (yield) and with the TPS spatial adjustment (yld_adj) …....……………………… 53 Table 4 Analysis of variance of the Early Generation Test combined over years with relative maturity (RM) as a covariate based on yield observations without the TPS spatial adjustment (yield) and with the TPS spatial adjustment (yld_adj) ……….…..……. 54 Table 5 Analysis on the basis of yield of bi-parental population performance for Pearson correlation coefficients (top) and P-values (bottom) between the Confirmation Study, and the Early Generation Tests. Correlations were calculated across the two years and by year, for yield without the TPS spatial adjustment (yield) and with the TPS spatial adjustment