Characterization of the Genetic and Environmental Effects Underlying Soybean Seed Protein Concentration in Two Recombinant Inbred Populations
in caps, centred) (triple space) CHARACTERIZATION OF THE GENETIC AND ENVIRONMENTAL EFFECTS UNDERLYING SOYBEAN SEED PROTEIN CONCENTRATION IN TWO RECOMBINANT INBRED POPULATIONS (triple space) Rachel Whaley Advisor(s) University of Guelph, 2018 Dr. Milad Eskandari Dr. Lewis Lukens (triple space) Soybean (Glycine max (L. Merrill) is a significant source of high quality plant based protein. An increased awareness of soybean health benefits has spurred a greater demand for soy based food products, which has attracted attention from researchers, soybean growers and food processors. Soybean seed protein concentration is a complex trait that is influenced by genotype, environment and genotype by environment interaction effects, and is negatively associated with seed yield. The main objectives of this study were to: (i) determine the effects of genotype and genotype by environment interaction on seed protein concentration; and (ii) identify quantitative trait loci (QTL) associated with seed protein concentration suitable for marker assisted selection. Genotypic and phenotypic data were collected from multi environment trials of two recombinant inbred line (RIL) populations, derived from the high protein cultivar, AC X790P (49% dry weight basis) and low protein commercial cultivars, S18 R6 (41% and S23 T5 (42% Genotype, environment and genotype by environment interaction effects significantly affected seed protein concentration and seed yield. Significant correlations between seed protein concentration and seed yield were not observed in either population, and GGE biplots made it possible to identify for competitive high protein genotypes. Seventy nine QTL associated with seed protein concentration (with R ranging from 4.1% to 24.4% were identified, 14 of which (with R ranging from 10.0% to 20.7% were deemed desirable for marker assisted selection. iii ACKNOWLEDGEMENTS I would like to thank my advisor, Dr. Milad Eskandari, for providing me with the opportunity to pursue my Master of Science degree at the University of Guelph, Ridgetown Campus. His incredible kindness, guidance and support were invaluable to me over the past two years. I would also like to thank my co advisor, Dr. Lewis Lukens; and, Dr. Frederic Marsolais, AAFC, who served on my advisory committee. Their experience and expertise were a great help to me over the course of my research. I am grateful for the assistance and expertise of Chris Grainger, Bryan Stirling, John Kobler, Lin Liao, Andre Passianotto and the entire Ridgetown Campus Field Crew. I would especially like to thank Bryan Stirling and John Kobler for improving my field research techniques, teaching me about the breeding program at every opportunity, and offering the full assistance of the Ridgetown Field Crew when I truly needed it. There are many members of the University of Guelph, Department of Plant Agriculture that have offered their knowledge and support over the course of my studies. I would like to thank Dr. Istvan Rajcan, who has been a great mentor since I was an undergraduate at Guelph. I would also like to thank my professors, Dr. Milad Eskandari, Dr. Istvan Rajcan, Dr. Ali Navabi and Dr. Stephen Bowley, for their insightful lectures in plant breeding, genotype by environment analysis and statistics. I would also like to thank Dr. Istvan Rajcan and Dr. Ali Navabi for serving on my defense examination committee. My time at the University of Guelph has been greatly influenced by my fellow graduate students. Thank you to Adam Carter and Ed MacDonell, who laid out the methodology for GxE and QTL analyses in soybean, and helped troubleshoot when issues arose in my own analyses. I especially want to thank my fellow graduate student and friend, Alexandra Ficht. Her assistance and conversations have been a constant source of support for me. I do not know what I would have done without her. Finally, thank you to my fiance, Michael Whiting, my parents, Missy Whaley and Dave Whaley, my soon to be in laws, Randy and Sherry Whiting, and the rest of my family and friends. Their constant love, understanding and support have carried me through the last two years. A special thank you to my grandmothers, Rita Whaley and Dr. Janet Scheetz, who are the most incredible role models. This project was funded with generous contributions from SeCan and the Grain Farmers of Ontario. iv TABLE OF CONTENTS Abstract ii Acknowledgements iii List of Tables vi List of Figures viii Chapter 1: Introduction 1 Chapter 2: Literature Review 3 2.1 Soybean [Glycine max (L. Merrill] 3 2.2 Economic Importance of Soybean 3 2.3 Food Grade Soybeans 4 2.4 Soybean Seed Protein 4 2.5 Relationship between Traits 5 2.6 Effects Influencing Soybean Seed Protein 5 2.7 Marker Assisted Selection 6 2.8 QTL Studies for Seed Protein in Soybean 7 2.9 Hypotheses and Objectives 11 Chapter 3: Genotype, Environment and Genotype by Environment Interaction Effects on Seed Protein Concentration in Two Recombinant Inbred Line Populations 12 3.1 Abstract 12 3.2 Introduction 12 3.3 Materials and Methods 14 3.3.1 Plant Materials 14 3.3.2 Experimental Design 15 3.3.3 Data Collection 15 3.3.4 Pearson Correlation Coefficients 15 3.3.5 Analysis of Variance 16 3.3.6 Classification of Genotypes and Mean Comparisons 16 3.3.7 Site Regression (SREG) Analysis and GGE Biplots 16 3.3.8 Interpretation of GGE Biplots 17 3.4 Results 18 3.4.1 Correlation between Traits 18 3.4.2 Analysis of Variance 18 3.4.3 Mean Comparisons by Trait Classification Group 19 3.4.4 Mean Comparisons by Environment 19 v 3.4.5 Transgressive Segregation 20 3.4.6 Test Environment Evaluation 20 3.4.7 Genotype Evaluation by Mega Environment 20 3.4.8 Genotype Evaluation by Sub Region 21 3.5 Discussion 22 3.6 Conclusion 24 Chapter 4: Identification and Validation of Environmentally Stable Quantitative Trait Loci Associated with Seed Protein Concentration in Two Recombinant Inbred Soybean Populations. 33 4.1 Abstract 33 4.2 Introduction 33 4.3 Materials and Methods 35 4.3.1 Plant Materials 35 4.3.2 Experimental Design 35 4.3.3 Phenotypic and Genotypi