Mapping Resistance to Stem Rust, Stripe Rust, and Powdery Mildew, and Genotype Screening of Breeding Germplasm for Disease Resistance
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ABSTRACT VANGESSEL, CARL JOSEPH. Disease Resistance in Winter Wheat: Mapping Resistance to Stem Rust, Stripe Rust, and Powdery Mildew, and Genotype Screening of Breeding Germplasm for Disease Resistance. (Under the direction of Dr. David Marshall). Wheat production worldwide faces many challenges including fungal pathogens which can reduce growth, nutrient content, and yield. As the global population continues to increase, it is important to maximize production of wheat which provides a significant proportion of the human diet. Wheat breeders and pathologists are addressing the pathogen threat to wheat by breeding cultivars with improved resistance. However, as pathogen populations mutate and overcome resistance, it is important to identify sources of resistance to new pathogen races and understand the genetics of resistance in commercial cultivars. Stem rust (Puccinia graminis), stripe rust (Puccinia striiformis), and powdery mildew (Blumeria graminis) are among the most common and aggressive pathogens of wheat occurring worldwide. The stem rust resistance gene Sr31 was reliably effective until being overcome in 1999 by the race Ug99. This new race of stem rust has since evolved to include 12 related races and are potentially virulent to a majority of commercially produced wheat globally. The soft red winter wheat (SRWW) line, MD01W28- 08-11, was identified as having adult plant resistance (APR) to Ug99 in Njoro, Kenya. This line was crossed with the susceptible SRWW cultivar Coker 9553 and the subsequent 279 doubled haploid (DH) population used for linkage mapping analysis to better characterize the source of stem rust APR. A linkage map with 3,159 SNPs was produced that identified a significant quantitative trait loci (QTL) on the short arm of chromosome 6D and two QTL on the long arms of chromosomes 2B and 4B. The 6DS QTL, QSr.nc-6D, was the most significant QTL in both environments using two scoring systems and which accounted for 7-13% of the phenotypic variation. This QTL lies on the proximal end of the chromosome where at least five other stem rust associated QTL have been identified. KASP assays were developed from this analysis which will help to better characterize resistance on 6DS as well as assess the level of established resistance to Ug99 races in the eastern United States. This mapping population was similarly assessed for stripe rust and powdery mildew resistance by linkage mapping analysis. This identified one stripe rust resistance associated QTL on the long arm of chromosome 4B from Coker 9553 and two QTL associated with powdery mildew resistance on the long arms of chromosome 2B and 6B from Coker 9553 and MD01W28-08-11, respectively. Together, these stem rust, stripe rust, and powdery mildew loci will be targeted for use in marker assisted selection (MAS) in winter wheat breeding programs. Another objective was to genotype winter wheat breeding germplasm for Ug99 effective Sr markers and other disease resistance relevant to the eastern U.S. The Ug99 stem rust race group has so far been detected only in eastern Africa and the Middle East. It is important for wheat producing countries including the United States to assess the level of established resistance in germplasm to Ug99 races in preparation of the potential arrival of the pathogen. Of the 65 numerically designated stem rust resistance genes, 27 have some resistance to Ug99 or its race group however many are undesirable due to associated reductions in yield. It is important to have sources of stem rust resistance available for wheat breeders in the U.S. In order to determine germplasm sources of resistance, 141 winter wheat experimental lines ranging from F4 to F7 were genotyped for ten Ug99 race group effective markers. These lines were also genotyped for barley yellow dwarf virus, leaf rust, fusarium head blight, and stagonospora nodorum blotch toxin resistance which are economically important pathogens in the eastern U.S. These lines will provide a source of stem rust and other disease resistance for breeders in the eastern U.S. © Copyright 2018 by Carl Joseph VanGessel All Rights Reserved Disease Resistance in Winter Wheat: Mapping Resistance to Stem Rust, Stripe Rust, and Powdery Mildew, and Genotype Screening of Breeding Germplasm for Disease Resistance by Carl Joseph VanGessel A thesis submitted to the Graduate Faculty of North Carolina State University in partial fulfillment of the requirements for the degree of Master of Science Plant Pathology Raleigh, North Carolina 2018 APPROVED BY: ____________________________ ____________________________ David Marshall Christina Cowger Committee Chair ____________________________ ___________________________ Gina Brown-Guedira Paul Murphy DEDICATION In dedication and gratitude to my Mom and Dad, and to Frank, Claudia, and Gladis whose support has made this journey possible. ii BIOGRAPHY Carl was born in 1994 and grew up on the Eastern Shore. He spent childhood running around Trees & Ponds with his siblings, playing sports, and reading every book he could and most of them twice. His parents brought him around the field trials and research stations so much that something eventually stuck. They fostered a deep appreciation of science, biology, and ultimately agriculture. After graduating from Delmar High School, Carl attended The Catholic University of America where he made great friends while working towards a Bachelor of Science in Biology. After undergraduate studies, he joined Dr. David Marshall and the USDA-ARS small grains breeding program in 2016 to study plant pathology and plant breeding for a Master of Science at North Carolina State University. iii ACKNOWLEDGEMENTS I’d like to thank Dave, for introducing me to the world of wheat and small grains pathology. I was naïve to breeding at first but I couldn’t ask for a smarter or more experienced mentor and advisor. Thank you also to Gina, you have always been helpful and patient while I began to grasp the complexities of wheat genetics. You both have been extremely supportive and my desire to further study wheat genetics and breeding is in large part thanks to you. Thank you also to all the wonderful people who I have met and worked with at North Carolina State University and the USDA-ARS. Thank you to Christina Cowger and Paul Murphy who have made sure I stayed on track. A special thanks to Lynda Whitcher, it has been a joy to learn from and work with you, from the bench to the single head thresher. Thank you as well to Al-Sayed Mashaheet, Jared Smith, Kim Howell, Myron Fountain, Charlie Glover, Bill Brown, Emily Myers, Gabe Supino, and all the NCSU students I have worked alongside at MidPines. My biggest thanks are to my family. Mom and Dad, I had no idea what great teachers I had guiding me until I wasn’t around to pester you with more questions every day and appreciate the patient replies. You have shown me what it means to excel at what you do. To my siblings Frank, Claudia, Gladis, and my parents, Thank You. iv TABLE OF CONTENTS LIST OF TABLES ...................................................................................................................................... vii LIST OF FIGURES ................................................................................................................................... viii Literature Review .......................................................................................................................................... 1 Origin and Production of Wheat ...................................................................................................... 2 Regions and Market Types ................................................................................................. 3 Puccinia graminis f.sp. tritici, Stem Rust of Wheat ........................................................................ 4 Conditions and Epidemic Potential ..................................................................................... 5 Control ................................................................................................................................ 6 Major and Minor Resistance ............................................................................................................ 7 Historical Sources of Resistance ......................................................................................... 8 Ug99................................................................................................................................................. 9 Resistant Germplasm Development .................................................................................. 10 Genetic Improvement..................................................................................................................... 11 Linkage Mapping ........................................................................................................................... 14 Literature Cited .............................................................................................................................. 17 Determining the Genetic Basis of Ug99 Stem Rust, Stripe Rust, and Powdery Mildew Resistance in a Double Haploid Soft Red Winter Wheat Population .................................................................................. 21 Introduction .................................................................................................................................... 22 Material and Methods ...................................................................................................................