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Molecular Genetic Characterization of Ptr Toxc-Tsc1 Interaction

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MOLECULAR GENETIC CHARACTERIZATION OF PTR TOXC-TSC1 INTERACTION AND COMPARATIVE GENOMICS OF PYRENOPHORA TRITICI-REPENTIS A Dissertation Submitted to the Graduate Faculty of the North Dakota State University of Agriculture and Applied Science By Gayan Kanishka Kariyawasam In Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY Major Department: Plant Pathology November 2018 Fargo, North Dakota North Dakota State University Graduate School Title MOLECULAR GENETIC CHARACTERIZATION OF PTR TOXC-TSC1 INTERACTION AND COMPARATIVE GENOMICS OF PYRENOPHORA TRITICI-REPENTIS By Gayan Kanishka Kariyawasam 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. Zhaohui Liu Chair Dr. Shaobin Zhong Dr. Justin D. Faris Dr. Phillip E. McClean Dr. Timothy L. Friesen Approved: November 7, 2018 Jack Rasmussen Date Department Chair ABSTRACT Tan spot of wheat, caused by Pyrenophora tritici-repentis, is an economically important disease worldwide. The disease system is known to involve three pairs of interactions between fungal-produced necrotrophic effectors (NEs) and the wheat sensitivity genes, namely Ptr ToxA- Tsn1, Ptr ToxB-Tsc2 and Ptr ToxC-Tsc1, all of which result in susceptibility. Many lines of evidence also suggested the involvement of additional fungal virulence and host resistance factors. Due to the non-proteinaceous nature, Ptr ToxC, has not been purified and the fungal gene (s) controlling Ptr ToxC production is unknown. The objective for the first part of research is to map the fungal gene (s) controlling Ptr ToxC production. Therefore, A bi-parental fungal population segregating for Ptr ToxC production was first developed from genetically modified heterothallic strains of AR CrossB10 (Ptr ToxC producer) and 86-124 (Ptr ToxC non-producer), and then was genotyped and phenotyped. Using the data, the gene (s) was mapped to the distal end of chromosome 2 in the reference genome of Pt-1c-BFP. The objective for the second part of my research is to develop genomic and genetic resources for the fungal pathogen. A high quality of genome sequence for AR CrossB10 and the first P. tritici-repentis genetic linkage map was generated. The AR CrossB10 genome and genetic linkage map is highly comparable to newly published reference genome except some noticeable chromosomal structural variations (SVs). Comparison of the genome sequences between parental isolates and twenty progeny isolates also revealed some SVs including deletion, insertion and inversion were detected that likely occurred during the fungal sexual reproduction. The objective for the third of my research is to characterize genetic resistance in Nebraskan winter wheat cultivar ‘Wesley’ using QTL mapping in a recombinant inbred line population. The results showed that resistance in Wesley is largely due to the lack of susceptibility genes Tsc1 and Tsn1. My Ph.D. research provides a further iii understanding of the genetics of host-pathogen interaction in wheat tan spot and contributes knowledge and tools for breeding tan spot resistant cultivars. iv ACKNOWLEDGEMENTS Foremost, I would like to express my deepest appreciation and gratitude to my advisor Dr. Zhaohui Liu for invaluable guidance and mentoring throughout my PhD study. There were many times when experiments were not working, but Dr. Zhaohui Liu’s words and encouragement and advice guided me through such rough time periods. I want to express my sincere gratitude to other members of my graduate study committee, including Drs. Timothy L. Friesen, Shaobin Zhong, Justin D. Faris, and Phillip E. McClean. Thank you all for valuable advice and helps on my Ph.D. research projects. My special thanks go to Dr. Shaobin Zhong for helping the fungal SSR project and to Dr. Timothy L. Friesen for correcting my dissertation. I would also like to thank Dr. Sanzhen Liu from Kansas State University for providing the bioinformatics expertise in discovering SNPs associated with chlorosis production using genome sequence data in Chapter 2. I would also like to thank Mr. Gokul Wimalanathan of Iowa State University for teaching me the basics of bioinformatics. A very special thank goes to Mr. Nathan Wyatt for his immense support and mentoring for all the bioinformatics work done for the third chapter. Furthermore, I extend my gratitude for all the members of Friesen’s Lab including Dr. Johnathan Richards, Danielle Holmes and Shaun Clare for all the support given through last few months. I also extend my sincere thanks to Dr. Gongjun Shi for his valuable support in validating my results in various experiments. In addition, I would like to thank all the former and current lab members of Liu’s lab including Jana Hansen, Gazala Ameen, Melody McConnell, Suraj Sapkota, Joseph Leard, Dr. Aimin Wen, Nelomie Galagedara, Malini Jayawardana, Jingwai Gao, and Yi Qi for their helps in research projects and for their ever-lasting friendship that makes this v journey more enjoyable. I also thank all the members in Department of Plant Pathology who have given me support, encouragement, and friendship throughout the last five years. Very special thank goes to my best friends Ms. Nicole Bacheller and Dr. Dulan Samarappulli who have supported me in every difficult period in last five years. I am ever so grateful to these two lovely soles. Most importantly, I would like to thank my parents Mr. Lalith Shantha Kariyawasam and Mrs. Chandani De Silva and my brother Mr. Dilshan Kariyawasam for their continuous support, encouragement and love. I am grateful to my loving wife Madushika Samarasekara to expresses my deepest gratitude for love, support, dedication and understanding she provided throughout this study. Finally, I would also like to thank my funding sources including, United States Department of Agriculture, National Institute of Food and Agriculture – Agriculture and Food Research Initiative (USDA NIFA-AFRI) and North Dakota Wheat Commission. vi DEDICATION I dedicate my disquisition to my loving parents Lalith and Chandani and my friend Nicole Bacheller. vii TABLE OF CONTENTS ABSTRACT ................................................................................................................................... iii ACKNOWLEDGEMENTS ............................................................................................................ v DEDICATION .............................................................................................................................. vii LIST OF TABLES ....................................................................................................................... xiii LIST OF FIGURES ..................................................................................................................... xiv LIST OF APPENDIX TABLES .................................................................................................. xvi GENERAL INTRODUCTION ....................................................................................................... 1 CHAPTER 1. LITERATURE REVIEW ........................................................................................ 4 1.1. Wheat ....................................................................................................................................4 1.1.1. Wheat classification....................................................................................................... 4 1.1.2. Wheat evolution............................................................................................................. 4 1.1.3. Wheat production and diseases in North Dakota .......................................................... 5 1.1.3.1. Wheat production and classes ................................................................................. 5 1.1.3.2. ND wheat production .............................................................................................. 6 1.1.4. Wheat diseases in ND .................................................................................................... 7 1.2. Tan spot of wheat ..................................................................................................................8 1.2.1. History ........................................................................................................................... 8 1.2.2. Economic importance .................................................................................................. 10 1.2.3. Host range .................................................................................................................... 11 1.2.4. Disease cycle and symptoms ....................................................................................... 12 1.2.5. Disease management ................................................................................................... 13 1.3. Host-parasite genetics .........................................................................................................14 1.3.1. Genetic variability in pathogen virulence .................................................................... 17 1.3.2. Race classification and distribution ............................................................................. 18 viii 1.3.3. NEs of P. tritici-repentis .............................................................................................. 20 1.3.3.1. Ptr ToxA ..............................................................................................................
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