Purdue University Purdue e-Pubs Open Access Dissertations Theses and Dissertations January 2016 NESTED ASSOCIATION MAPPING TO IDENTIFY SEED COMPOSITION QTL IN DIVERSE SOYBEAN LINES Mohammad Wali Salari Purdue University Follow this and additional works at: https://docs.lib.purdue.edu/open_access_dissertations Recommended Citation Salari, Mohammad Wali, "NESTED ASSOCIATION MAPPING TO IDENTIFY SEED COMPOSITION QTL IN DIVERSE SOYBEAN LINES" (2016). Open Access Dissertations. 1271. https://docs.lib.purdue.edu/open_access_dissertations/1271 This document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact [email protected] for additional information. Graduate School Form 30 Updated PURDUE UNIVERSITY GRADUATE SCHOOL Thesis/Dissertation Acceptance This is to certify that the thesis/dissertation prepared By Mohammad Wali Salari Entitled NESTED ASSOCIATION MAPPING TO IDENTIFY SEED COMPOSITION QTL IN DIVERSE SOYBEAN LINES For the degree of Doctor of Philosophy Is approved by the final examining committee: Katy Martin Rainey Chair Mitch Tuinstra Shaun N Casteel Kevin T McNamara To the best of my knowledge and as understood by the student in the Thesis/Dissertation Agreement, Publication Delay, and Certification Disclaimer (Graduate School Form 32), this thesis/dissertation adheres to the provisions of Purdue University’s “Policy of Integrity in Research” and the use of copyright material. Approved by Major Professor(s): Katy Martin Rainey Approved by: Joe M Anderson 7/18/2016 Head of the Departmental Graduate Program Date i NESTED ASSOCIATION MAPPING TO IDENTIFY SEED COMPOSITION QTL IN DIVERSE SOYBEAN LINES A Dissertation Submitted to the Faculty of Purdue University by Mohammad Wali Salari In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy i August 2016 Purdue University West Lafayette, Indiana ii I would like to dedicate this thesis to my parents who have always encouraged me to pursue my higher education. ii iii ACKNOWLEDGEMENTS I would like to thank my advisor, Dr. Katy Martin Rainey, for her guidance during all stages of my study. I am grateful for all her patience, advice, discussions and, giving me the opportunity to earn my Ph.D. degree with the Soybean Breeding Program. I am thankful to my advisory committee members: Dr. Mitch Tuinstra, Dr. Shaun Casteel and Dr. Kevin McNamara for their encouragement, advisory discussion, and help. I am grateful to USAID program for providing financial support for my Ph.D. program through the Strengthening Afghan Agriculture Faculties (SAAF) project. I would also like to give my deepest thanks to my close family members, my parents, my brothers, and sisters, who encouraged me to follow my Ph.D. program while away from them. Finally, I would like to thank all members of Dr. Rainey’s research program who helped me with various aspects of my research. iii iv TABLE OF CONTENTS Page LIST OF TABLES ........................................................................................................... viii LIST OF FIGURES ............................................................................................................ x LIST OF ABBREVIATIONS .......................................................................................... xiii ABSTRACT ...................................................................................................................... xv CHAPTER 1. GENERAL INTRODUCTION ............................................................. 1 1.1 Introduction .......................................................................................................... 1 1.2 Organization of the Dissertation ........................................................................... 2 CHAPTER 2. LITERATURE REVIEW ...................................................................... 4 2.1 Introduction .......................................................................................................... 4 2.2 Soybean Seed Composition .................................................................................. 7 2.3 Nutritional Value of Soybeans ............................................................................. 8 2.4 Soy Protein ........................................................................................................... 8 2.5 Soy Oil ................................................................................................................ 10 2.6 Sucrose ............................................................................................................... 12 2.7 Raffinose Family Oligosaccharides (RFOs) ....................................................... 14 2.8 Quantitative Trait Loci (QTL) Mapping ............................................................ 16 2.9 Linkage Mapping ................................................................................................ 17 iv 2.10 Association Mapping .................................................................................. 19 2.11 Type of Association Mapping ..................................................................... 21 2.12 Population Structure Issue Associated with Association Mapping ............ 23 2.13 Nested Association Mapping ...................................................................... 25 v CHAPTER 3. GENOME-WIDE ASSOCIATION STUDY OF SEED PROTEIN AND OIL CONTENT IN A SOYBEAN NESTED ASSOCIATION MAPPING POPULATION…. ............................................................................................................ 28 3.1 Abstract ............................................................................................................... 28 3.2 Introduction ........................................................................................................ 29 3.2.1 Plant Material, SoyNAM Structure, and Experimental Design .................. 32 3.3 Data Collection and Analysis ............................................................................. 33 3.3.1 Phenotypic Data Collection ........................................................................ 33 3.4 Phenotypic Data Analysis ................................................................................... 34 3.4.1 Variance and Stability Analyses ................................................................. 34 3.4.2 AMMI Analysis of GEI .............................................................................. 35 3.4.3 Estimation of Heritability and Correlation by Families .............................. 35 3.5 Linkage Disequilibrium (LD) Analysis .............................................................. 36 3.6 Population Structure ........................................................................................... 37 3.7 Genome Wide Association Study (GWAS) ....................................................... 37 3.7.1 Genotype and Phenotype Data .................................................................... 37 3.7.2 Association Analysis ................................................................................... 38 3.8 Result .................................................................................................................. 39 3.8.1 Mean Differences in Soybean Protein and Oil Content .............................. 39 3.8.2 Heritability Estimates and Correlations ...................................................... 44 v 3.8.3 Multi-Environment Assessment.................................................................. 46 3.8.4 Linkage Disequilibrium (LD) Analysis and Marker Distribution .............. 48 3.8.5 Population Structure.................................................................................... 52 3.8.6 Genome-Wide Association Study ............................................................... 53 3.8.7 Discussion ................................................................................................... 71 3.8.8 Phenotypic Differences, Heritability, and Correlation ............................... 71 3.8.9 Multi-Environment Analysis ...................................................................... 71 3.8.10 Linkage Disequilibrium .............................................................................. 73 3.8.11 Seed Protein and Oil Contents QTL ........................................................... 73 3.8.12 Refining the Candidate Region for Protein on Chromosome 9 .................. 74 vi 3.8.13 Conclusion .................................................................................................. 76 CHAPTER 4. MAPPING QTL CONTROLLING SOYBEAN SEED SUCROSE AND OLIGOSACCHARIDES IN A SINGLE FAMILY OF SOYBEAN NESTED ASSOCIATION MAPPING (SOYNAM) POPULATION .............................................. 77 4.1 Abstract ............................................................................................................... 77 4.2 Materials and Methods ....................................................................................... 79 4.2.1 Plant Material .............................................................................................. 79 4.2.2 Experimental Design ................................................................................... 81 4.2.3 Phenotype Data ........................................................................................... 81 4.2.3.1 Soluble Sugars Determination ................................................................. 81 4.2.4 Genotype Data ...........................................................................................