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Mhora Udel 0060D 13546.Pdf A GENOMICS BASED APPROACH TO MANAGING DOWNY MILDEW OF LIMA BEAN by Terence Tariro Mhora A dissertation submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Plant and Soil Sciences Fall 2018 © 2018 Terence Tariro Mhora All Rights Reserved A GENOMICS BASED APPROACH TO MANAGING DOWNY MILDEW OF LIMA BEAN by Terence Tariro Mhora Approved: __________________________________________________________ Erik Ervin, Ph.D. Chair of the Department of Plant and Soil Sciences Approved: __________________________________________________________ Mark Rieger, Ph.D. Dean of the College of Agriculture and Natural Resources Approved: __________________________________________________________ Douglas J. Doren, Ph.D. Interim Vice Provost for the Office of Graduate and Professional Education I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Nicole M. Donofrio, Ph.D. Professor in charge of dissertation I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Thomas A. Evans, Ph.D. Professor in charge of dissertation I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Randall J. Wisser, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Blake C. Meyers, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ William E Fry, Ph.D. Member of dissertation committee ACKNOWLEDGMENTS Thank you to my family for supporting me throughout this journey, without you, I would not have made it through this challenge. I love you all!! I would like to especially thank my advisors for their constant support and for granting me this opportunity to grow, not only as a scientist. Thank you to my committee for helping to guide this research. Cheers to all the friends I made along the way, you all helped me grow and learn different life lessons along this journey. Credit to all the undergraduate students I got to mentor, your input towards this research was immense. Thank you to the University of Delaware, the United States Department of Agriculture (USDA) and the Delaware Department of Agriculture (DDA) for funding this research and giving me the opportunity to make contributions to science and to the state of Delaware. To all who read this, anything is possible, just put your mind to it, work hard and love hard. v TABLE OF CONTENTS LIST OF TABLES ........................................................................................................ ix LIST OF FIGURES ........................................................................................................ x ABSTRACT ................................................................................................................ xvi Chapter 1 LITERATURE REVIEW ................................................................................... 1 Background and Significance ............................................................................. 4 Lima Bean (Phaseolus lunatus) .......................................................................... 6 Diseases of Lima Bean ....................................................................................... 8 Plant Pathogenic Oomycetes .............................................................................. 9 History of Phytophthora phaseoli .................................................................... 10 Biology of Phytophthora phaseoli ................................................................... 12 Control of Downy Mildew ............................................................................... 13 Utilization of Genetic Diversity in Disease Management ................................ 16 Methods of Assessing Genetic Diversity ......................................................... 20 Project Hypotheses and Objectives .................................................................. 22 Objectives ......................................................................................................... 23 REFERENCES ............................................................................................................. 24 2 AN ASSESSMENT OF MEFENOXAM INSENSITIVITY IN PHYTOPHTHORA PHASEOLI IDENTIFIES RISKS TO PROFITABLE LIMA BEAN PRODUCTION IN DELAWARE ............................................. 33 Introduction ...................................................................................................... 33 Materials and Methods ..................................................................................... 39 Isolate Collection, Media Formulation and Mefenoxam Sensitivity Assays ......................................................................................................... 39 Genotyping of Isolates and Data Analysis ................................................. 43 Results .............................................................................................................. 44 Media Formulation and Mefenoxam Sensitivity Assays ............................ 44 GBS Data Analysis ..................................................................................... 52 vi Discussion ......................................................................................................... 55 REFERENCES ............................................................................................................. 64 3 GENOTYPING-BY-SEQUENCING TO PREDICT RESISTANCE TO LIMA BEAN DOWNY MILDEW IN A DIVERSITY PANEL ..................... 70 Introduction ...................................................................................................... 70 Materials and Methods ..................................................................................... 73 Results .............................................................................................................. 81 Discussion ......................................................................................................... 88 REFERENCES ............................................................................................................. 92 4 INROADS TO IMPROVING LIMA BEAN PRODUCTION IN THE US BY ASSESSING THE GENETIC DIVERSITY OF EXISTING CULTIVARS COMPARED TO A DIVERSITY PANEL .............................. 98 Introduction ...................................................................................................... 98 Materials and Methods ................................................................................... 103 Plant Material ........................................................................................... 103 Tissue Collection and DNA Extraction .................................................... 104 Genotyping-by-Sequencing (GBS) .......................................................... 105 GBS Data Processing and Analysis .......................................................... 107 Population Genomic Analyses ................................................................. 108 Results ............................................................................................................ 111 GBS Data Processing and Analysis .......................................................... 111 Population Genomic Analyses ................................................................. 116 Discussion ....................................................................................................... 129 REFERENCES ........................................................................................................... 138 5 DISCOVERY OF DIVERSE FORMS OF RESISTANCE TO DOWNY MILDEW OF LIMA BEAN IN DELAWARE .............................................. 144 Introduction .................................................................................................... 144 Materials and Methods ................................................................................... 147 Diversity Panel ......................................................................................... 147 Experimental Plan and Field Layouts ....................................................... 148 Inoculation ................................................................................................ 151 vii Disease Ratings ........................................................................................ 152 Dew Chamber Validation ......................................................................... 153 Selection Criteria and Disease Screening of a Diversity
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