GENETICS OF TREE ARCHITECTURE IN PEACH (Prunus persica (L.) Batsch) By OMAR CARRILLO MENDOZA 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 2012 1 © 2012 Omar Carrillo Mendoza 2 To my wife Patricia and my Mom Marcela with love 3 ACKNOWLEDGMENTS I am thankful to my advisor Dr. Jose Chaparro and retired professor Dr. Wayne Sherman, it has been a pleasure to learn from them and be part of the Stone Fruit Breeding Program. To the members of my committee: Dr. Rebecca Darnell, Dr. Kevin Folta, Dr. Matias Kirst and Dr. Jeffrey Williamson for all the guidance during my research. To Dr. James W. Olmstead for allowing me and Patricia for teaching me how to use the real time PCR machine. To Bruce Topp, Jean-Clement Marceillou, Jose Gandia, Jorge Rodriguez, Mohamed Benzit, Paul Lyrene and Thomas Beckman for sharing their experience. To Mark Gal, Cecil Shine, and John Thomas for their valuable help on the farm. To Valerie for her support in the lab. To Elia Ulivi and Dario Chavez for helping me to take field data. To my friends, Andres, Aparna, Divya, Marga, Mitra, Octavio, Preeti, Silvia,Yuan and especially Kendra for their friendship and kindness. To my Mexican fellows: Alberto, Aurora, Miriam, Nicacio, Oscar, Paola, Paula and Sebastian for helping me to adjust to my new home and reminding me my beloved home country. I am especially grateful to CONACYT and the people of Mexico for granting me with a scholarship that made possible this achievement. 4 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ............................................................................................................. 7 LIST OF FIGURES ........................................................................................................ 10 LIST OF ABBREVIATIONS ........................................................................................... 12 ABSTRACT .................................................................................................................... 14 CHAPTER 1 LITERATURE REVIEW ........................................................................................... 16 Introduction .............................................................................................................. 16 Plant Architecture .................................................................................................... 16 Axillary Meristem Development and Branching ....................................................... 17 Apical Dominance.................................................................................................... 18 Plant Architecture and Agriculture ........................................................................... 20 Temperate Fruit Tree Architecture .......................................................................... 20 Peach Tree Architecture .......................................................................................... 22 2 DEVELOPMENT OF A BRANCHING INDEX FOR EVALUATION OF PEACH SEEDLINGS USING INTERSPECIFIC HYBRIDS ..................................... 26 Introduction .............................................................................................................. 26 Materials and Methods ............................................................................................ 27 Branching Index Formula .................................................................................. 27 Plant Material .................................................................................................... 29 Data Collection .................................................................................................. 29 Statistical Analysis ............................................................................................ 30 Results and Discussion ........................................................................................... 30 3 BRANCHING AND BLIND NODE INCIDENCE IN INTERSPECIFIC BACKCROSS FAMILIES OF PEACH ..................................................................... 44 Introduction .............................................................................................................. 44 Branching in different Prunus species ............................................................... 44 Blind nodes in peach ......................................................................................... 46 Materials and Methods ............................................................................................ 48 Plant Material .................................................................................................... 48 Plant Management ............................................................................................ 48 Branching Index Data Collection ....................................................................... 49 Blind node data collection ................................................................................. 50 5 Identification of Selfs ......................................................................................... 50 Statistical Analysis ............................................................................................ 51 Results and Discussion ........................................................................................... 52 Branching Index ................................................................................................ 52 Blind Nodes ....................................................................................................... 55 Heritability for Branching and Blind Nodes ........................................................ 57 4 MAPPING CANDIDATE GENES and QTLs ASSOCIATED WITH BRANCING AND BLIND NODES IN Prunus sp. INTERSPECIFIC BACKCROSS FAMILIES ......................................................................................... 66 Introduction .............................................................................................................. 66 Materials and Methods ............................................................................................ 71 Plant Material .................................................................................................... 71 DNA Extraction ................................................................................................. 72 Candidate Gene Primer Design ........................................................................ 73 Branching Index Data Collection ....................................................................... 73 Blind Node Data Collection ............................................................................... 73 Candidate Gene Primer PCR Optimization ....................................................... 74 Candidate Gene Sequencing ............................................................................ 74 Genotyping ........................................................................................................ 75 SSR markers .............................................................................................. 75 Candidate gene genotyping with restriction enzymes ................................. 76 Candidate gene genotyping with high resolution melt analysis ................... 77 Statistical Analysis ............................................................................................ 77 Results and Discussion ........................................................................................... 78 Phenotypic Differences within and among Backcross Families ........................ 78 Polymorphism in Branching and Blind Node Candidate Genes ........................ 79 Genetic Maps .................................................................................................... 82 Branching Index QTLs ...................................................................................... 86 Blind Node QTLs ............................................................................................... 88 Allelic effects from QTLs ................................................................................... 89 Relationships between Branching and Blind Node QTLs .................................. 91 QTLs Detection by Candidate Genes ............................................................... 92 5 CONCLUSIONS .................................................................................................... 110 APPENDIX: COMPLEMENTARY TABLES AND FIGURES ........................................ 115 LIST OF REFERENCES .............................................................................................. 136 BIOGRAPHICAL SKETCH .......................................................................................... 150 6 LIST OF TABLES Table page 2-1 Mean total branch number per tree and branching index values in peach x almond and peach x P. kansuensis F1 hybrid populations. ................... 36 2-2 Mean number of first order branches, and the mean number of second, third and fourth order branches. ............................................................ 36 2-3 Mean total branch number per tree and branching index means for first, second, third and fourth order branching clusters ....................................... 37 3-1 Total number of progeny and number of contaminating self-pollinated