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Identification, Validation, and Mapping of Phytophthora Sojae and Soybean

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Identification, Validation, and Mapping of Phytophthora Sojae and Soybean Identification, Validation, and Mapping of Phytophthora sojae and Soybean Mosaic Virus Resistance Genes in Soybean Colin L. Davis Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Crop and Soil Environmental Sciences M. A. Saghai Maroof, Committee Chair John M. McDowell Bingyu Zhao Song Li May 10, 2017 Blacksburg, Virginia Keywords: Phytophthora sojae, Soybean Mosaic Virus, effectors, Glycine max, Soybean, R-genes, gene mapping Copyright © 2017, Colin Davis Identification, Validation, and Mapping of Phytophthora sojae and Soybean Mosaic Virus Resistance Genes in Soybean Abstract (Academic) Estimated at approximately $43 billion annually, the cultivated soybean Glycine max (L.) Merr., is the second most valuable crop in the United States. Soybeans account for 57% of the world oil-seed production and are utilized as a protein source in products such as animal feed. The value of a soybean crop, measured in seed quality and quantity, is negatively affected by biotic and abiotic stresses. This research is focused on resistance to biotic disease stress in soybean. In particular, we are working on the Phytophthora soja (P. sojae) and Soybean Mosaic Virus (SMV) systems. For each of these diseases, we are working to develop superior soybean germplasm that is resistant to the devastating economic impacts of pathogens. The majority of this research is focused on screening for novel sources of P. sojae resistance with core effectors to identify resistance genes (R-genes) that will be durable under field conditions. Four segregating populations and two recombinant inbred line (RIL) populations have been screened with core effectors. Effector-based screening methods were combined with pathogen-based phenotyping in the form of a mycelium-based trifoliate screening assay. One RIL population has been screened with virulent P. sojae mycelium. Disease phenotyping has generated a preliminary genetic map for resistance in soybean accession PI408132. The identification of novel R-genes will allow for stacking of resistance loci into elite G. max cultivars. The second project covered in this dissertation describes the validation of the SMV resistance gene Rsv3. Utilizing a combination of transient expression and homology modeling; we provide evidence that Glyma14g38533 encodes Rsv3. Abstract (General Audience) Estimated at approximately $43 billion annually, the cultivated soybean Glycine max (L.) Merr., is the second most valuable crop in the United States. Soybeans account for 57% of the world oil-seed production and are utilized as a protein source in products such as animal feed. The value of a soybean crop, measured in seed quality and quantity, is negatively affected by pathogens and other stressors. This research is focused on resistance to pathogen disease stress in soybean. In particular, we are working on the Phytophthora soja (P. sojae) and Soybean Mosaic Virus (SMV) systems. For each of these diseases, we are working to develop superior soybean lines that are resistant to the devastating economic impacts of these pathogens. The majority of this research is focused on screening for new sources of P. sojae resistance, using certain pathogen virulence proteins called core effectors, to identify resistance genes (R-genes) that will be durable under field conditions. Four segregating populations and two recombinant inbred line (RIL) populations have been screened with core effectors. Effector-based screening methods were combined with pathogen-based phenotyping in the form of an assay that involved the use of P. sojae to infect detached soybean leaves. One RIL population has been screened with virulent P. sojae. Disease screening has generated a preliminary genetic map for resistance in soybean accession PI408132. The identification of novel R-genes will allow for stacking of resistance genes into elite G. max cultivars that can be grown by farmers. The second project covered in this dissertation describes the validation of the SMV resistance gene Rsv3. Utilizing a combination of a molecular assay and protein prediction software; we provide evidence that the soybean gene Glyma14g38533 encodes Rsv3. Dedicated to the memory of my grandfather, Virgil Wayne Russell v Acknowledgments I would like to thank everyone who contributed to the success of my work and acknowledge them for their support and inspiration. First, I would like to thank my professors and co-advisors, Dr. M. A. Saghai Maroof and Dr. John M. McDowell, for giving me the opportunity to work with them and pursue my doctorate degree. Dr. Maroof gave me the freedom to pursue my research interests and has been a constant source of support and encouragement throughout my time at Virginia Tech. Dr. McDowell has been a close mentor and has encouraged me to pursue opportunities to attend conferences and disseminate my research which are among the best memories of my graduate career. I would also like to acknowledge and thank my other committee members, Dr. Bingyu Zhao and Dr. Song Li, for their support and expertise. I would like to thank the graduate students that I worked with so closely over the last four years, especially Dr. Mike Fedkenheuer, Dr. Kevin Fedkenheuer, and Dr. Neelam Redekar who provided advice and guidance as I began my graduate career. I would like to thank Dr. Ruslan Biyashev and Dr. Joel Shuman for their technical expertise in the many experiments I conducted. I would like to thank my colleagues, Elizabeth Clevinger and Lindsay DeMers, who even during harvest made my time in the Maroof lab enjoyable. I would also like to thank my colleagues from the McDowell lab, John Herlihy, Kasia Dinkaloo, Unnati Sonawala, Wei Wang, Nick Dietz, and Dr. Bhadra Gunesekera for providing an endless source of assistance and support. Finally, I would like to thank all of my family and friends for their support, and I would especially like to thank my fiancée Katelin Smith who encouraged me to attend graduate school and has kept me motivated and inspired during my graduate career. vi Table of Contents Acknowledgments.......................................................................................................................... vi Table of Contents .......................................................................................................................... vii List of Figures ................................................................................................................................ xi List of Tables ............................................................................................................................... xiii List of Abbreviations .................................................................................................................... xv Attribution ................................................................................................................................... xvii Chapter 1: Molecular Function of Genes Underlying Host Resistance against Root and Seedling Diseases of Soybean ....................................................................................................................... 1 Abstract ....................................................................................................................................... 2 Introduction ................................................................................................................................. 3 Phytophthora sojae and Pythium ................................................................................................ 4 Soybean Cyst Nematode ............................................................................................................. 5 Layers of Plant Defense .............................................................................................................. 6 NLR Structure ............................................................................................................................. 8 Effector Recognition ................................................................................................................... 9 Soybean Resistance Genes against Oomycetes and Nematodes............................................... 11 Quantitative Trait Loci .............................................................................................................. 13 Conclusions ............................................................................................................................... 15 Figures and Tables .................................................................................................................... 17 Chapter 2: Identification and Mapping of Novel Resistance Genes in Glycine max and Glycine soja Lines Conferring Durable Resistance to the Oomycete Pathogen, Phytophthora sojae. ...... 19 Abstract ..................................................................................................................................... 20 Introduction ............................................................................................................................... 21 Results ....................................................................................................................................... 26 Population Development ....................................................................................................... 26 Overview of Effector Screen ...............................................................................................
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