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Phaseolus Vulgaris Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2016 Persistent RNA Viruses of Common Bean (Phaseolus vulgaris): Distribution and Interaction with the Host and Acute Plant Viruses Surasak Khankhum Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Plant Sciences Commons Recommended Citation Khankhum, Surasak, "Persistent RNA Viruses of Common Bean (Phaseolus vulgaris): Distribution and Interaction with the Host and Acute Plant Viruses" (2016). LSU Doctoral Dissertations. 838. https://digitalcommons.lsu.edu/gradschool_dissertations/838 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. PERSISTENT RNA VIRUSES OF COMMON BEAN (PHASEOLUS VULGARIS): DISTRIBUTION AND INTERACTION WITH THE HOST AND ACUTE PLANT VIRUSES A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Plant Pathology and Crop Physiology by Surasak Khankhum B.S., Mahasarakham University, Thailand, 2001 M.S., Kasetsart University, Thailand, 2007 May 2016 This dissertation is dedicated to my parents, Sou and Nimnual Khankhum, for their forever love and efforts to provide me the best education, as well as, to my sisters, Kochamol Kruawan, Sukumarl Khankhum, and Yupadee Kaewviset, for their support, encouragement, and motivation to live in another part of the world. I also dedicate this work to my extended family for their unwavering support to get through the tough times. ii ACKNOWLEDGMENTS I would like to express my sincere appreciation to my major professor Dr. Rodrigo A. Valverde for his patient guidance, understanding, advice, assistance, and encouragement throughout my doctoral study. I am also thankful to my graduate committee members Dr. Charles Overstreet, Dr. Jeffrey W. Hoy, and Dr. Jong H. Ham for their advice and helpful suggestions. A special thanks to Dr. Gregg Henderson for being my graduate school representative. I wish to express my appreciation to the faculty, the staff, and the graduate students of the department of Plant Pathology and Crop Physiology at LSU for their friendship, support, and motivation during my graduate studies. I would like to thank The Ministry of Science and Technology of Thailand, Royal Thai Government, and Mahasarakham University for their financial support that allowed the opportunity to pursue the study in a doctoral degree in the U.S.A. I also would like to thank the Office of Educational Affairs (OEA) staff at the Royal Thai Embassy in Washington DC for their help and care throughout my study. The partial support for the research from the USDA National Institute of Food and Agriculture (NIFA) and the US-Israel Binational Agricultural Research and Development Fund (BARD) is appreciated. Finally, I wish to express my appreciation to my former advisor Dr. Pissawan Chiemsombat for introducing me to plant virology. I am also thankful to all of my former teachers for their affection, patience, support, and encouragement. Your efforts are greatly appreciated. iii TABLE OF CONTENTS ACKNOWLEDGMENTS ............................................................................................................ iii LIST OF TABLES ........................................................................................................................ vi LIST OF FIGURES .................................................................................................................... viii ABSTRACT ................................................................................................................................... x CHAPTER 1. LITERATURE REVIEW......................................................................................... 1 1.1 Common Bean ....................................................................................................... 1 1.2 Common Bean Pathogens ................................................................................... .. 2 1.3 Common Bean Viruses .......................................................................................... 3 1.4 Endornaviruses ...................................................................................................... 5 1.5 Endornaviruses of Common Bean ......................................................................... 6 1.6 Detection of Plant Endornaviruses ........................................................................ 8 1.7 Interactions Between Plant Viruses and Their Hosts .......................................... 11 1.8 Interactions Between Endornaviruses and Plant Pathogens ................................ 12 1.9 Hypothesis ........................................................................................................... 13 1.10 Objectives .......................................................................................................... 13 CHAPTER 2. DEVELOPMENT OF A PRACTICAL DSRNA EXTRACTION METHOD FOR DETECTION OF RNA VIRUSES................................................................ 15 2.1 Introduction ......................................................................................................... 15 2.2 Objective ............................................................................................................. 16 2.3 Materials and Methods ........................................................................................ 16 2.4 Results ................................................................................................................. 20 2.5 Discussion ............................................................................................................ 23 CHAPTER 3. PHASEOLUS VULGARIS ENDORNAVIRUS 1 AND PHASEOLUS VULGARIS ENDORNAVIRUS 2 INFECTING COMMON BEAN (PHASEOLUS VULGARIS) GENOTYPES SHOW DIFFERENTIAL INFECTION PATTERNS BETWEEN COMMON BEAN GENE POOLS ........ 27 3.1 Introduction ......................................................................................................... 27 3.2 Objectives ............................................................................................................ 29 3.3 Materials and Methods ........................................................................................ 29 3.4 Results ................................................................................................................. 33 3.5 Discussion ........................................................................................................... 49 iv CHAPTER 4. ASSOCIATION OF PHASEOLUS VULGARIS ENDORNAVIRUS 1 AND PHASEOLUS VULGARIS ENDORNAVIRUS 2 WITH SEED GERMINATION, PLANT GROWTH, PIGMENT CONTENT, AND GRAIN YIELD OF BLACK TURTLE SOUP COMMON BEAN ...................... 53 4.1 Introduction ......................................................................................................... 53 4.2 Objective ............................................................................................................. 55 4.3 Materials and Methods ........................................................................................ 55 4.4 Results ................................................................................................................. 59 4.5 Discussion ........................................................................................................... 63 CHAPTER 5. INTERACTION OF PHASEOLUS VULGARIS ENDORNAVIRUS 1 AND PHASEOLUS VULGARIS ENDORNAVIRUS 2 WITH TOBACCO RINGSPOT VIRUS, TOBACCO MOSAIC VIRUS, AND SUNN-HEMP MOSAIC VIRUS ..................................................................................................... 72 5.1 Introduction ......................................................................................................... 72 5.2 Objectives ......................................................................................................... ... 74 5.3 Materials and Methods ........................................................................................ 74 5.4 Results ................................................................................................................. 80 5.5 Discussion ........................................................................................................... 84 CHAPTER 6. CONCLUSIONS ................................................................................................... 89 REFERENCES ............................................................................................................................. 96 APPENDIX PERMISSION LETTER ....................................................................................... 109 VITA .......................................................................................................................................... 113 v LIST OF TABLES 2.1. Plants infected with acute and persistent viruses and type of tissue tested. .......................... 17 3.1. Common bean genotypes of various market classes from breeding programs in the United States tested by gel electrophoresis and PCR for Phaseolus vulgaris endornavirus 1 (PvEV1) and Phaseolus vulgaris
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