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Rootstock Breeding for Resistance to the Peach Root-Knot Nematode (Meloidogyne Floridensis)

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Rootstock Breeding for Resistance to the Peach Root-Knot Nematode (Meloidogyne Floridensis) ROOTSTOCK BREEDING FOR RESISTANCE TO THE PEACH ROOT-KNOT NEMATODE (MELOIDOGYNE FLORIDENSIS) By MARY ANN DY MAQUILAN A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2017 © 2017 Mary Ann Dy Maquilan To my mother: Lilia Dy Maquilan ACKNOWLEDGMENTS I thank my advisors Dr. Mercy Olmstead and Dr. José Chaparro for their kindness, encouragement, and extensive patience with me throughout this work. The complementary contributions of my committee to ensure successful completion of my dissertation as well as their support in my personal and professional growth are gratefully acknowledged: To Dr. Mercy Olmstead for trusting me with this project, for granting me many opportunities to hone my research skills, and for the sustained support that extends beyond academia. To Dr. José Chaparro for helping me conceptualize and refine my research questions, for broadening my cognition beyond Mendelian genetics, for his meticulous review of the early drafts of my manuscript, and for the valuable life lessons imparted. To Dr. Donald Dickson for the warm and sincere support, for giving me the needed nematology training and providing the resources to successfully conduct the nematode resistance evaluations. To Dr. James Olmstead for teaching me to logically work through my genetic marker data. Special thanks to Dr. Thomas Beckman for providing seeds and cuttings of some of the rootstock materials for the field trial, for sharing his experience in rootstock breeding, and for the insightful discussions over the course of this work. To Dr. Andrew Nyczepir for his feedback into the design and evaluation of my nematology-related experiments. To Dr. Dario Chavez for teaching me the necessary skills to be able to conduct molecular characterization studies. To Dr. Maria Mendes for the valuable technical guidance and assistance in nematology work. To Dr. Edzard van Santen for assistance in statistical analysis of the rootstock trial data. To Drs. Wayne Sherman and Paul Lyrene for bolstering my interest in plant breeding by sharing their knowledge and showing passion in their work. 4 The completion of this research could not have been possible without the field logistics support of Matthew Ross during the initial stages of my research and the untiring assistance of Moshe Doron in field and greenhouse during the data gathering stages. I thank Werner Collante for lending me some needed lab supplies and teaching me some molecular marker techniques. I also thank Ashley Kreynin, James Haddix, Alec McCloud, and Lorenzo Collante who offered help as needed and went well beyond what was required of them by showing empathy to my plants, being willing to work long hours, and making work more enjoyable. I thank Mark Gal for the technical advice with regards to maintenance of plants in the greenhouse and trees in the field. Cecile Shine who helped me set up irrigation for my greenhouse plants and for sharing his experiences in growing plants. John Thomas for lending me nifty tools for pollen collection and cracking seeds. The staff at Citra PSREU especially Jim Boyer for coordinating assistance in the field, and Mark Kann for ensuring that the greenhouse was set up to provide optimum conditions for my resistance screening experiments. To my lab colleagues: Zilfina, Maraisa, Elizabeth, Carlos, Ben, Emily, Rachel, Daniel, Silvia, Sai, and Weimin, for their kind assistance and wonderful companionship. I thank my mother, Lilia, for being a role model of dedication and perseverance, and for her faith in me and pride in even my smallest successes that motivate me to keep moving toward my goals. This dissertation is possible thanks to funding from the Florida Department of Agriculture and Consumer Services under the Specialty Crop Block Grant Contract Nos.18004 and 20727. 5 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ............................................................................................................ 8 LIST OF FIGURES ........................................................................................................ 11 LIST OF ABBREVIATIONS ........................................................................................... 13 ABSTRACT ................................................................................................................... 16 CHAPTER 1 LITERATURE REVIEW ........................................................................................... 18 Rootstock Development for Southeastern United States ........................................ 18 Sources and Inheritance of Resistance .................................................................. 21 Location of Resistance Genes and Associated Markers ......................................... 26 Host-Plant and Nematode Interaction ..................................................................... 28 Screening for Resistance ........................................................................................ 32 The Peach Root-knot Nematode Threat in Florida ................................................. 33 Research Objectives ............................................................................................... 35 2 INHERITANCE OF RESISTANCE TO MELOIDOGYNE FLORIDENSIS IN INTERSPECIFIC PEACH X PRUNUS KANSUENSIS PROGENIES ..................... 37 Introduction ............................................................................................................. 37 Materials and Methods............................................................................................ 42 Nematode Isolate ............................................................................................. 42 Genetic Material ............................................................................................... 42 Growth Conditions ............................................................................................ 43 Resistance Evaluation ...................................................................................... 44 Data Analyses .................................................................................................. 45 Results .................................................................................................................... 46 Selection Criteria for Resistance ...................................................................... 46 Segregation Analyses of P. persica x P. kansuensis F2 Families ..................... 47 Testcross of F1 Hybrids with P. persica ............................................................ 48 Discussion .............................................................................................................. 49 3 GENETIC ANALYSES OF RESISTANCE TO THE PEACH ROOT-KNOT NEMATODE USING MICROSATELLITE MARKERS ............................................. 61 Introduction ............................................................................................................. 61 Materials and Methods............................................................................................ 64 Plant Material ................................................................................................... 64 6 Phenotyping ..................................................................................................... 65 Genotyping ....................................................................................................... 65 Map Construction ............................................................................................. 69 Data Analyses .................................................................................................. 71 Results .................................................................................................................... 73 Resistance Segregation ................................................................................... 73 Polymorphisms and Genotype Segregation at Microsatellite Loci .................... 74 Linkage Maps ................................................................................................... 76 Marker-trait Association .................................................................................... 78 Localization of Major Resistance Locus on LG 2 .............................................. 81 Discussion .............................................................................................................. 82 4 HORTICULTURAL EVALUATION OF POTENTIAL ROOTSTOCKS FOR LOW- CHILL PEACH PRODUCTION DURING INITIAL YEARS OF FIELD ESTABLISHMENT .................................................................................................. 95 Introduction ............................................................................................................. 95 Materials and Methods............................................................................................ 98 Rootstocks and Tree Preparation ..................................................................... 98 Field Site and Experimental Design ................................................................. 99 Cultural Management ..................................................................................... 100 Data Collection ............................................................................................... 100 Data Analyses ...............................................................................................
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