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UNDERSTANDING HOST RESISTANCE and PATHOGEN BIOLOGY in the WHEAT- FUSARIUM GRAMINEARUM PATHOSYSTEM a Dissertation Submitted to T

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UNDERSTANDING HOST RESISTANCE and PATHOGEN BIOLOGY in the WHEAT- FUSARIUM GRAMINEARUM PATHOSYSTEM a Dissertation Submitted to T UNDERSTANDING HOST RESISTANCE AND PATHOGEN BIOLOGY IN THE WHEAT- FUSARIUM GRAMINEARUM PATHOSYSTEM A Dissertation Submitted to the Graduate Faculty of the North Dakota State University of Agriculture and Applied Science By Bikash Poudel In Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY Major Department: Plant Pathology April 2020 Fargo, North Dakota North Dakota State University Graduate School Title UNDERSTANDING HOST RESISTANCE AND PATHOGEN BIOLOGY IN THE WHEAT-FUSARIUM GRAMINEARUM PATHOSYSTEM By Bikash Poudel 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: Dr. Shaobin Zhong Chair Dr. Luis Del Río Mendoza Dr. Zhaohui Liu Dr. Steven Xu Dr. Xuehui Li Dr. Gideon Francois Marais Approved: April 27, 2020 Jack Rasmussen Date Department Chair ABSTRACT Fusarium head blight (FHB) is a major challenge in global wheat production. In the United States, the disease is predominantly caused by the fungus Fusarium graminearum. Utilization of FHB-resistant wheat cultivars integrated with other measures such as fungicide application is the most effective approach for the management of this disease. This study aimed to 1) identify novel quantitative trait loci (QTL) for resistance to FHB in a Brazilian spring wheat cultivar ‘Surpresa’ through bi-parental mapping, 2) detect QTL for FHB resistance in a global panel of 233 spring wheat accessions by genome-wide association analysis (GWAS), and 3) localize genomic regions governing traits associated with virulence in Fusarium graminearum. Using phenotypic and genotypic data from 187 recombinant inbred lines derived from the cross between Surpresa and a susceptible spring wheat cultivar ‘Wheaton’, four QTL (Qfhb.ndwp-2AS, Qfhb.ndwp-2AL, Qfhb.ndwp-3B, and Qfhb.ndwp-4D) were mapped on chromosomes 2A, 3B, and 4D of Surpresa, respectively. Qfhb.ndwp-2AS, Qfhb.ndwp-2AL, and Qfhb.ndwp-3B were found to be novel based on physical locations of the markers tightly linked to these QTL. Two significant marker-trait associations (Qfhb.ndwp-3A and Qfhb.ndwp-2BL) were detected by GWAS of 233 spring wheat accessions, which conferred type II and type III FHB resistance and mapped on chromosomes 3A and 2B, respectively. Both QTL were novel based on the physical locations of markers tightly linked to them. GWAS using 183 F. graminearum isolates collected from North Dakota identified two significant marker-trait associations in chromosomes 1 and 3 for mycotoxin production, and one for fungicide sensitivity to each of the fungicides, respectively. The genes detected in this study associated with mycotoxin production were not previously reported. Identification of these novel genes in metabolic pathways of F. graminearum could help to develop new strategies for the management FHB. iii ACKNOWLEDGEMENTS My biggest gratitude goes to my major advisor Dr. Shaobin Zhong, from day 1 at NDSU till date, for his constructive suggestions and support in my professional and personal life. I am grateful to my committee members Drs. Luis del Río, Zhaohui Liu, Steven Xu, Xuehui Li, and Gideon Francois Marais for their time and input in my research. I wouldn’t have been able to complete my Ph.D. without the support and guidance of my lab members: Dr. Yueqiang Leng, Dr. Rui Wang, Dr. Subidhya Shrestha, Dr. Mingxia Zhao, Joseph Mullins, Anil Karmacharya, Shirley Zhong, Ti Wei, and Tracy Zhou. I cannot thank enough to Dr. Jason Fiedler who led me into bioinformatic analyses and performed genotyping of the fungal population. My sincere thanks go to Justin Hegstad for preparing the GBS-library for sequencing the Wheaton/Surpresa mapping population, and to Yuan Liu for helping me with all the genotypic analyses. I extend my sincere thanks to Dr. Kishore Chittem for teaching me how to use RStudio. I always extend my sincere thanks to Alex Knudson and Jesse Ostrander for letting me use the resources from the plant diagnostic lab. I am grateful to Alex who would go above and beyond to make the resources available for my research. My sincere thanks also go to Claire Poore for her support, help, and input in correcting my dissertation drafts. Most importantly, I am highly indebted to North Dakota State University, the department of plant pathology, Dr. Jack Rasmussen, the administrative staffs (Darla Bakko, Barbara Nilles, and Aimee Thapa) for providing me an opportunity to pursue my Ph.D. and taking care of all the academic issues. Last but not the least, I am very grateful to the North Dakota Wheat Commission, and the US Wheat and Barley Scab Initiative (USWBSI) for funding my research. iv DEDICATION This work is humbly dedicated to all the valuable treasures in my life: To, Grandparents: Dina Nath Poudel, Nanda Maya Poudel, Badri Maya Karanjit Parents: Moti Ram Paudel, Bimala Kumari Poudel, Laxmi Poudel, Hema Laxmi Karanjit Siblings/Cousins: Manish Poudel, Deepa Sharma, Bikesh Karanjit, Sara Karanjit In-laws: Late Mr. Hom Nath Bhattarai, Saraswati Bhattarai, Regan Bhattarai, Sneha Bhattarai, Biswas Bhattarai, Anita Khadka, Ronal Bhattarai, Surabhi Timilsina Fargo Family: Roshan Sharma Poudel, Subidhya Shrestha, Reya Sharma, Anil Karmacharya, Ravi Bhattarai, Sunanda Neupane, Nabin Karki, Prithvi Awasthi, Sunil Acharya, Subash Shivakoti, Enija Shrestha, Binu Rana, Sailesh Sigdel, Anuj Ghimire, Ranjan Sapkota, Prakash Pokhrel, Brett Haddaway For shaping me in a way that I am today. And, Kanchan Bhattarai, my better half, for your love, patience, faith, and inspiration. You are always beside me even for better for worse Bikash Poudel v TABLE OF CONTENTS ABSTRACT ................................................................................................................................... iii ACKNOWLEDGEMENTS ........................................................................................................... iv LIST OF TABLES ......................................................................................................................... ix LIST OF FIGURES ....................................................................................................................... xi LIST OF APPENDIX TABLES .................................................................................................. xiii LIST OF APPENDIX FIGURES................................................................................................. xiv LITERATURE REVIEW ............................................................................................................... 1 The Host: Spring Wheat .............................................................................................................. 1 Evolution and Domestication of Wheat .................................................................................. 2 Wheat Genome and Sequencing .............................................................................................. 3 The Disease: Fusarium Head Blight ............................................................................................ 5 History of Disease Epidemics ................................................................................................. 6 Symptoms, Disease Cycle, and Epidemiology ........................................................................ 8 Integrated Disease Management ............................................................................................ 10 Genetic Map and QTL Mapping ........................................................................................... 21 Breeding for Resistance to FHB ............................................................................................ 24 The Pathogen: Fusarium graminearum .................................................................................... 26 History, Taxonomy, and Classification ................................................................................. 26 Pathogen Biology .................................................................................................................. 29 Fusarium graminearum Genome .......................................................................................... 31 Pathogenicity and Virulence Factors in Fusarium graminearum ......................................... 32 References ................................................................................................................................. 34 MOLECULAR MAPPING OF QUANTITATIVE TRAIT LOCI FOR FUSARIUM HEAD BLIGHT RESISTANCE IN BRAZILIAN SPRING WHEAT CULTIVAR ‘SURPRESA’ ................................................................................................................................ 51 vi Abstract ..................................................................................................................................... 51 Introduction ............................................................................................................................... 52 Materials and Methods .............................................................................................................. 55 Plant Materials ....................................................................................................................... 55 Phenotypic Evaluation ........................................................................................................... 55 DNA Extraction and Two Enzyme Genotyping-by-Sequencing .........................................
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