PREDICTION OF DISEASE DAMAGE, DETERMINATION OF PATHOGEN SURVIVAL REGIONS, AND CHARACTERIZATION OF INTERNATIONAL COLLECTIONS OF WHEAT STRIPE RUST By DIPAK SHARMA-POUDYAL A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY WASHINGTON STATE UNIVERSITY Department of Plant Pathology MAY 2012 To the Faculty of Washington State University: The members of the Committee appointed to examine the dissertation of DIPAK SHARMA-POUDYAL find it satisfactory and recommend that it be accepted. Xianming Chen, Ph.D., Chair Dennis A. Johnson, Ph.D. Kulvinder Gill, Ph.D. Timothy D. Murray, Ph.D. ii ACKNOWLEDGEMENTS I would like to express my sincere gratitude to Dr. Xianming Chen for his invaluable guidance, moral support, and encouragement throughout the course of the study. I would like to thank Drs. Dennis A. Johnson, Kulvinder Gill, and Timothy D. Murray for serving in my committee and their valuable suggestions for my project. I also like to thank Dr. Mark Evans, Department of Statistics, for his statistical advice on model development and selection. I am grateful to Dr. Richard A. Rupp, Department of Crop and Soil Sciences, for his expert advice on using GIS techniques. I am thankful to many wheat scientists throughout the world for providing stripe rust samples. Thanks are also extended to Drs. Anmin Wan, Kent Evans, and Meinan Wang for their kind help in the stripe rust experiments. Special thanks to Dr. Deven See for allowing me to use the genotyping facilities in his lab. Suggestions on data analyses by Dr. Tobin Peever are highly appreciated. I also like to thank my fellow graduate students, especially Jeremiah Dung, Ebrahiem Babiker, Jinita Sthapit, Lydia Tymon, Renuka Attanayake, and Shyam Kandel for their help in many ways. I am grateful to office staffs in the Department of Plant Pathology, and colleagues in the USDA-ARS Wheat Genetics, Quality, Physiology, and Disease Research Unit for their support during my Ph.D. program. Lastly, I would like to extend my heartfelt appreciation to my wife Shanti, son Sudip, and daughter Simran for their patience, sacrifice, understanding, and love. iii PREDICTION OF DISEASE DAMAGE, DETERMINATION OF PATHOGEN SURVIVAL REGIONS, AND CHARACTERIZATION OF INTERNATIONAL COLLECTIONS OF WHEAT STRIPE RUST Abstract by Dipak Sharma-Poudyal, Ph.D. Washington State University May 2012 Chair: Xianming Chen Stripe rust of wheat (Triticum aestivum L.), caused by Puccinia striiformis Westend. f. sp. tritici Erikss., is an economically important disease worldwide. Three studies were conducted in regional, national, and international scopes, with a focus on the epidemiology of the disease. A series of models for predicting potential yield loss for the U.S. Pacific Northwest were developed using historical climatic and disease data. Simple and multiple linear regression models were developed to estimate yield loss using winter climatic variables that were significantly correlated with yield loss. These models allow forecasting of potential yield loss and improve management of stripe rust in the major wheat growing areas in the Pacific Northwest. Regions for overseasoning of the stripe rust pathogen were determined in the mainland U.S. using long-term means for temperature, relative humidity, rainfall, dew point, snow iv depth, and availability of plant hosts. The pathogen can oversummer in most regions north of 40oN and in the highlands of southern states either in the Rocky or Appalachian Mountains. Winter survival can occur in most regions south of 40oN and the Pacific rims. The fungus cannot survive both summer and winter in most wheat growing regions. It can oversummer and overwinter in the Pacific rims, highlands of southern states, and in the Appalachian Mountains. A total of 235 P. striiformis f. sp. tritici isolates from 13 countries were tested on 20 single Yr-gene lines and 20 wheat genotypes that are used to differentiate races of the pathogen in the U.S. Virulence to 13 Yr genes and 14 U.S. differentials were detected in all countries. At least 80% of the isolates were virulent on 15 wheat differentials. All isolates were avirulent to Yr5 and Yr15. Molecular characterization of 292 isolates from 18 countries was conducted using 17 simple sequence repeat markers, which separated the isolates into two genetic groups with some of admix genotypes. The greatest genetic variation was among isolates within countries. This information helps us understand virulence and genetic variation of the pathogen populations and should be useful for control of stripe rust using disease resistance in the world. v TABLE OF CONTENTS Page ACKNOWLEDGEMENTS ……………………………….………………….........................iii ABSTRACT …………………………………………………………………..........................iv LIST OF TABLES ………………………………………………………………………….....x LIST OF FIGURES …………………………………………………………………………xiii CHAPTER ONE. LITERATURE REVIEW 1. WORLD AND U.S. WHEAT PRODUCTION ………………………….…….…………...1 2. MAJOR DISEASES OF WHEAT .………………………………………………..………..2 3. STRIPE RUST …………………………………………………………………..………….3 3.1. Distribution …………………………………………………………………..………..3 3.2. Economic importance ………………………………………………………..………..4 3.3. Pathogen nomenclature and taxonomy……………………………….…..……………6 3.4. Symptoms and signs …………………………………………………………...………8 3.5. Similarities to other diseases on wheat ……………………………………..…………9 3.6. Disease development ……………………………………..…….…..……………...…10 3.7. Host range …………………………………………………………………..…..……11 3.8. Environment and the disease ………………………………………………...…….…13 3.8.1. Temperature ………………………………………………………….....………13 3.8.2. Moisture …………………………………………………………..……….……16 3.8.3. Wind ………………………………………………………………..……...……16 vi 3.8.4. Light ……………………………………………………………………..……...17 3.9. The pathogen survival ….….………………………………………………..……..…17 3.9.1. Summer survival …..…………………………………………………..……..…18 3.9.2. Winter survival …..…………………………………………………...…………20 3.10. Disease prediction …………………………………..………………………………22 3.11. Virulence variation ………………………………..…………...……………………24 3.12. Molecular variation ……………………………………………………..……..……27 3.13. Disease management ……………………………………………………..…………29 3.13.1. Cultural practices ………………………………………………..……….……30 3.13.2. Chemical control ……………………………………..…………..……………30 3.13.3. Genetic resistance …………………………………………………..…………31 4. RESEARCH INTRODUCTION AND OBJECTIVES ……………….……..……………33 4.1. Models for predicting potential yield loss of wheat caused by stripe rust in the U.S. Pacific Northwest ………………………………………………...…...………………33 4.2. Potential summer and winter survival regions of the stripe rust pathogen in the contiguous United States ……………………………..……………..…………………33 4.3. Virulence characterization of international collections of the wheat stripe rust pathogen …………………….…………........……………………………………..……34 4.4. Molecular characterization of international collections of the wheat stripe rust pathogen ………………………………….………………………………………..……35 LITERATURE CITED ………………………………………………………..……..………35 CONTRIBUTION PAGE ……………………………………………..………..……………53 vii CHAPTER TWO. MODELS FOR PREDICTING POTENTIAL YIELD LOSS OF WHEAT CAUSED BY STRIPE RUST IN THE US PACIFIC NORTHWEST ABSTRACT ………………………………………………………………...………..………54 INTRODUCTION ……………………………………………………….……..……………55 MATERIALS AND METHODS ………………………………………...………..…………58 RESULTS ………………………………………………………………………....…………62 DISCUSSION ………………………………………………………………………..………81 LITERATURE CITED ………………….………………..……...…………………..………86 CHAPTER THREE. POTENTIAL OVERSUMMERING AND OVERWINTERING REGIONS FOR THE WHEAT STRIPE RUST PATHOGEN IN THE CONTIGUOUS UNITED STATES ABSTRACT ………………………………………………………………………..………...91 INTRODUCTION ……………………………………………………….………………..…92 MATERIALS AND METHODS …………………………………………..……………...…97 RESULTS ……………………………………………………………………………..……114 DISCUSSION ………………………………………………………………………....……118 LITERATURE CITED …………………………………………………………………..…126 CHAPTER FOUR. VIRULENCE CHARACTERIZATION OF INTERNATIONAL COLLECTIONS OF THE WHEAT STRIPE RUST PATHOGEN ABSTRACT ……………………………………………………………………………...…134 INTRODUCTION ………………………………………………………………………….135 viii MATERIALS AND METHODS ……………………………………………………...……137 RESULTS ………………………………………………………………………………..…141 DISCUSSION ………………………………………………………………………………152 LITERATURE CITED …………………………………………………………………..…157 CHAPTER FIVE. MOLECULAR CHARACTERIZATION OF INTERNATIONAL COLLECTIONS OF THE WHEAT STRIPE RUST PATHOGEN ABSTRACT ……………………………………………………………………………...…174 INTRODUCTION ……………………………………………………………………….…175 MATERIALS AND METHODS ………………………………………………………...…179 RESULTS …………………………………………………………………………………..186 DISCUSSION ………………………………………………………………………………201 LITERATURE CITED ………………………………………………………………..……206 ix LIST OF TABLES CHAPTER TWO 1. Correlation coefficients obtained between weather variables and yield loss percentage of winter wheat (1993-2007) and spring wheat (1995-2007) caused by stripe rust in Pullman, Washington ………………………………………………………………………………64 2. Single variable and multiple-variable models obtained through stepwise and the best subset regression analyses for predicting winter wheat yield loss caused by stripe rust ...71 3. Single variable and multiple-variable models obtained through stepwise and the best subset regression analyses for predicting spring wheat yield loss caused by stripe rust ……...…73 4. Prediction accuracies and probabilities of χ² tests for selected stripe rust yield loss models for winter and spring wheat based on predicted and actual yield loss data winter wheat (1993-2009) and spring wheat (1995-2009) at Pullman, Washington ……………………76 CHAPTER THREE 1. Climatic parameters used for estimation of potential summer survival