QUANTIFYING EFFICIENCY AND ACCURACY IN THE WASHINGTON STATE UNIVERSITY APPLE BREEDING PROGRAM By JULIA MAE HARSHMAN A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY WASHINGTON STATE UNIVERSITY Department of Horticulture DECEMBER 2015 © Copyright by JULIA MAE HARSHMAN, 2015 All Rights Reserved © Copyright by JULIA MAE HARSHMAN, 2015 All Rights Reserved To the Faculty of Washington State University: The members of the Committee appointed to examine the dissertation of JULIA MAE HARSHMAN find it satisfactory and recommend that it be accepted. _____________________________________ Katherine M. Evans, Ph.D., Chair _____________________________________ Amit Dhingra, Ph.D _____________________________________ Craig M. Hardner, Ph.D _____________________________________ James P. Mattheis, Ph.D _____________________________________ Michael O. Pumphrey, Ph.D ii Acknowledgements I would first like to thank my advisor, Kate Evans. The serendipitous meeting in 2011 and the leap of faith on your part has led to this culmination of my education and graduate career. It has been an honor to be your student and the experiences you have shared will forever be invaluable to me. No one could have prepared me to be a plant breeder or a professional as well as you have, and I look forward to trying. I would like to thank Craig Hardner for his guidance and extreme patience in teaching me equation-based quantitative genetics, as well as the life-changing experience of living abroad in Australia. I would like to thank Amit Dhingra, Jim Mattheis and Mike Pumphrey for their input, guidance and frank conversations over the course of this doctoral program. A special thank you to Amit Dhingra who tried to persuade me to attend WSU as a doctoral student when I was an undergraduate in 2008. You were the first person to suggest I pursue my doctorate. I would like to thank two of my Masters committee members, Chris Walsh and Wayne Jurick II, for their continued support, guidance and “checking in” during my doctoral program. I would like to thank Jay Norelli for his technical guidance and hosting me at his research station. I would like to thank Lisa Brutcher, Nancy Buchanan, and Bonnie Schonberg for answering all of my infinite questions, and all of the fun times in the lab, field and outside of work. Lastly, I would like to thank my family and friends who have cheered me on all this time, as well as the rest of the Tree Fruit Research and Extension staff, students and professors. iii QUANTIFYING EFFICIENCY AND ACCURACY IN THE WASHINGTON STATE UNIVERSITY APPLE BREEDING PROGRAM Abstract by Julia Mae Harshman, Ph.D. Washington State University December 2015 Chair: Katherine M. Evans The Washington State University Apple Breeding Program just passed its 20th anniversary, released its third new variety and moved under new direction with breeder Kate Evans. The major program goal is to release a portfolio of new and improved cultivars suited to production in central Washington. Improved cultivars should have exceptional storability, to compliment the state’s unrivaled long term cold storage facilities, while engendering an exceptional consumer experience. Apple breeding is a long and expensive process and therefore exploring how well the program meets its goal—releasing the best new cultivars—can validate the expenditures of the program while also potentially finding methods that would improve discovery rate and cost efficiency. The three main subprojects and conclusions are as follows: 1) Quantify moldy core susceptibility in currently available germplasm to inform crossing decisions and discover predisposing characteristics to inform culling decisions. Factors that predispose iv selections for moldy core were confirmed and appear heritable. 2) Quantify fire blight resistance in wild relative Malus sieversii to further inform crossing decisions and provide data for future association mapping. Multiple M. sieversii accessions were found to be resistant and will be used in 2016 as parents. 3) Analyze the cost structure of the current breeding program and the accuracy of trait evaluations in the replicated data collection phase of the program to explore the most efficient design structure for identifying elite selections. An alternative design that would allow more selections to be evaluated in that phase was proposed and is under consideration for the 2016 planting. v TABLE OF CONTENTS Page ACKNOWLEDGEMENTS ........................................................................................................... iii ABSTRACT ................................................................................................................................... iv LIST OF TABLES ......................................................................................................................... ix LIST OF FIGURES ...................................................................................................................... xii LIST OF ABBREVIATIONS ...................................................................................................... xiv DEDICATION ............................................................................................................................. xvi CHAPTER ONE: Introduction ..................................................................................................... 1 Apple Origin and Cultivation ...................................................................................................... 1 Washington State University Apple Breeding Program ............................................................. 2 Storability .................................................................................................................................... 6 Resistance to Diseases ................................................................................................................. 7 Phase 2 Trial Design ................................................................................................................. 11 Dissertation Overview and Hypotheses .................................................................................... 14 Literature Cited ......................................................................................................................... 15 CHAPTER 2: Survey of Moldy Core Incidence in Germplasm from Three U.S. Apple Breeding Programs ..................................................................................................................... 26 Abstract ..................................................................................................................................... 26 vi Introduction ............................................................................................................................... 27 Materials and Methods .............................................................................................................. 29 Results ....................................................................................................................................... 31 Author Contributions................................................................................................................. 34 Acknowledgements ................................................................................................................... 34 Literature Cited ......................................................................................................................... 36 CHAPTER THREE: Resistance to Erwinia amylovora in Wild Accessions of Malus sieversii ....................................................................................................................................................... 42 Abstract ..................................................................................................................................... 42 Introduction ............................................................................................................................... 43 Materials and Methods .............................................................................................................. 47 Results ....................................................................................................................................... 51 Discussion ................................................................................................................................. 56 Conclusion ................................................................................................................................. 62 Author Contributions................................................................................................................. 62 Acknowledgements ................................................................................................................... 62 Literature Cited ......................................................................................................................... 64 CHAPTER FOUR: Consideration of cost and accuracy for advanced breeding trial designs in apple ......................................................................................................................................... 96 Abstract ..................................................................................................................................... 96 vii Introduction ..............................................................................................................................