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Genome-Wide Association Mapping of Host Resistance to Stem Rust

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Genome-Wide Association Mapping of Host Resistance to Stem Rust GENOME-WIDE ASSOCIATION ANALYSIS OF HOST RESISTANCE TO STEM RUST, LEAF RUST, TAN SPOT, AND SEPTORIA NODORUM BLOTCH IN EMMER WHEAT A Dissertation Submitted to the Graduate Faculty of the North Dakota State University of Agriculture and Applied Science By Qun Sun In Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY Major Program: Genomics and Bioinformatics April 2015 Fargo, North Dakota North Dakota State University Graduate School Title GENOME-WIDE ASSOCIATION ANALYSIS OF HOST RESISTANCE TO STEM RUST, LEAF RUST, TAN SPOT, AND SEPTORIA NODORUM BLOTCH IN EMMER WHEAT By Qun Sun The Supervisory Committee certifies that this disquisition complies with North Dakota State University’s regulations and meets the accepted standards for the degree of DOCTOR OF PHILOSOPHY SUPERVISORY COMMITTEE: Steven S. Xu Chair Phillip E. McClean Xiwen Cai Justin D. Faris Marion O. Harris Approved: 4/7/2015 Phillip E. McClean Date Department Chair ABSTRACT Cultivated emmer wheat (Triticum turgidum ssp. dicoccum) is a good source of genes for resistance to several major diseases of wheat. The objectives of this study were to use genome- wide association analysis to detect genomic regions in cultivated emmer germplasm harboring novel resistance genes to four wheat diseases: stem rust, leaf rust, tan spot, and Septoria nodorum blotch (SNB). A natural population including 180 cultivated emmer accessions with a high level of geographic diversity was assembled as the association-mapping panel. This cultivated emmer panel was evaluated phenotypically by scoring reactions to stem rust, leaf rust, tan spot, and SNB and was genotyped using a 9K SNP Infinium array. After filtering for missing data points and minor allele frequency (MAF), 4,134 SNPs were used for association analysis using 178 emmer accessions. Based on principle component (PC) analysis, five subpopulations strongly associated with geographic origins were suggested by the first three PCs. Genome-wide association analysis revealed that 222, 42, 146, and 42 SNPs were significantly associated with resistance to stem rust, leaf rust, tan spot, and SNB, respectively, at the significant level of 1 percentile. Among the significant SNPs at the significant level of 0.1 percentile, ten, one, nine, and one co-located with known genes or QTL associated with resistance to the four diseases, respectively. The remaining significant SNPs were located in the genomic regions where no known resistance genes have been identified for the four diseases. This evidence suggests that some of the emmer wheat accessions carry novel genes conferring resistance to the four diseases. Additionally, 14, three, eight, and five LD blocks harboring at least one significant SNP were identified and might harbor putative QTL related to resistance to the four diseases, respectively. These studies provide information about the genomic regions in cultivated emmer that are associated with resistance to stem rust, leaf rust, tan spot, and SNB. Results from these studies provide guidance for selecting iii emmer accessions when decisions are being made about the parents that will be used for the development of new resistant germplasm and mapping populations for identifying novel genes conferring resistance to major wheat diseases. iv ACKNOWLEDGEMENTS I would like to acknowledge everyone who has assisted me throughout my doctoral studies over the years. I express the deepest appreciation to my major advisor Dr. Steven S. Xu, for agreeing to serve as my advisor and for his encouragement, support, and guidance during my graduate study. I express my sincere appreciation to my graduate committee, Dr. Phillip E. McClean, Dr. Xiwen Cai, Dr. Justin D. Faris, and Dr. Marion O. Harris for their guidance and advice, and also for helping to edit my dissertation. I express my sincere appreciation to Dr. Guangmin Xia at Shandong University for giving me this apportunity to study abroad. I also express my sincere thanks to Dr. Shiaoman Chao for her help with marker analysis, to Dr. Yue Jin, Dr. Maricelis Acevedo, Dr. Zhaohui Liu, and Dr. Timothy L. Friesen for their help with wheat disease testing, and to Dr. Samira Mafi Moghaddam, Dr. Sujan Mamidi, and Dr. Guotai Yu for their help with the data analysis. I extend my sincere thanks to Daryl L. Klindworth, Jason E. Axtman, Danielle J. Holmes, and Mary M. Osenga for their technical assistance. My thanks also go to Dr. Zhixia Niu, Dr. Chenggen Chu, and Dr. Qijun Zhang for their technical assistance in the lab. In addition, I am deeply grateful to Department of Plant Sciences, Program of Genomics and Bioinformatics, North Dakota State University (NDSU) for providing me with this great opportunity to pursue the Ph.D. degree. Specifically I wish to thank Dr. Richard D. Horsley, Dr. Michael C. Edwards, and Mrs. Eileen Buringrud for their support over the years. I thank the Chinese Scholarship Council (CSC) for funding my four years at NDSU. I am also grateful to Charles and Linda Moses for providing me with a scholarship. I especially thank my amazing family for the love, support, and constant encouragement over the years. In particular, I thank my parents and my husband. I undoubtedly could not have done this dissertation without their support. v TABLE OF CONTENTS ABSTRACT ................................................................................................................................... iii ACKNOWLEDGMENTS ............................................................................................................. v LIST OF TABLES ......................................................................................................................... ix LIST OF FIGURES ..................................................................................................................... xii LIST OF APPENDIX TABLES .................................................................................................. xiv CHAPTER 1. GENERAL INTRODUCTION ............................................................................... 1 Literature Cited ................................................................................................................... 5 CHAPTER 2. LITERATURE REVIEW ........................................................................................ 7 Modern Cultivated Wheat ................................................................................................... 7 Cultivated Emmer Wheat .................................................................................................. 10 Wheat Stem Rust............................................................................................................... 13 Wheat Leaf Rust ............................................................................................................... 19 Tan Spot and Septoria Nodorum Blotch ........................................................................... 22 Association Mapping ........................................................................................................ 29 Literature Cited ................................................................................................................. 45 CHAPTER 3. ASSOCIATION ANALYSIS OF STEM RUST RESISTANCE IN CULTIVATED EMMER WHEAT .............................................................................................. 69 Abstract ............................................................................................................................. 69 Introduction ....................................................................................................................... 70 Materials and Methods ...................................................................................................... 74 Results ............................................................................................................................... 80 Discussion ......................................................................................................................... 98 Supplementary Tables ..................................................................................................... 105 Supplementary Figures ................................................................................................... 121 vi Literature Cited ............................................................................................................... 126 CHAPTER 4. ASSOCIATION ANALYSIS OF LEAF RUST RESISTANCE IN CULTIVATED EMMER WHEAT ............................................................................................ 133 Abstract ........................................................................................................................... 133 Introduction ..................................................................................................................... 134 Materials and Methods .................................................................................................... 137 Results and Disscussion .................................................................................................. 139 Supplementary Tables ..................................................................................................... 149 Literature Cited ............................................................................................................... 151 CHAPTER 5. ASSOCIATION ANALYSIS OF TAN SPOT RESISTANCE IN CULTIVATED EMMER WHEAT ...........................................................................................
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