Genome wide mapping of fruit quality traits in apple by Beatrice Amyotte A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Doctor of Philosophy in Plant Agriculture Guelph, Ontario, Canada © Beatrice Amyotte, July 2017 ABSTRACT GENOME WIDE MAPPING OF FRUIT QUALITY TRAITS IN APPLE Beatrice Amyotte Advisor: University of Guelph, 2017 Professor I. Rajcan This thesis is an investigation of the genetics of fruit quality in cultivated apple (Malus x domestica). M. x domestica is grown around the world as one of the most popular temperate fruit crop species. Fruit quality is an important trait in apples, and understanding the genetic architecture can accelerate breeding efforts. In recent years, several important quantitative trait loci have been discovered, including genetic regions controlling components of fruit texture, taste and flavour. The objective of this thesis was to identify genetic sources of variation in fruit quality traits with the potential for application in marker assisted apple breeding. This research was necessary to evaluate how previous findings corresponded with variation in genetically distinct apple germplasm, and to determine whether both previously and newly discovered fruit quality loci could be applied to improve the human perception of apple quality. The genetic relationships among 100 diverse apple cultivars were investigated using genotyping by sequencing, and revealed a high level of diversity. Signatures of selection were detected at genomic regions previously found to be associated with fruit quality and adaptation. A genome wide association study of 85 heritage and commercial cultivars detected significant associations with known quantitative trait loci for apple flavour and texture. A novel association for apple texture was detected on chromosome 13. The novel locus could not be validated in two large and diverse apple populations, but remains a strong candidate for use in apple breeding due to its association with the human perception of apple juiciness. The results of this thesis demonstrate the potential for applying marker assisted selection in apple breeding, and for including trained sensory evaluation panels in association studies. DEDICATION This thesis is dedicated to my advisors Dr. Daryl Somers and Dr. Istvan Rajcan whom I would like to sincerely thank for their guidance and mentorship throughout my graduate studies. Both of my advisors have been incredible teachers who have inspired me to build a strong academic foundation in the study of plant genetics, and to continually challenge my assumptions about science and experimentation. Dr. Somers took a wild chance when he invited me to be the first graduate student in his brand new apple breeding program. Since then, he has devoted countless hours to guiding me through the processes of conducting research, communicating results, and building the foundation for a lasting career. Despite having had many opportunities to question my capabilities, Dr. Somers has only ever expressed encouragement, positivity, and an unwavering confidence in my ability to succeed. Dr. Rajcan also took an ambitious chance when he agreed to advise me as a student of apple, a plant which was substantially removed from soybean, his crop of expertise. Since then, Dr. Rajcan has guided me through the academic and administrative processes of pursuing a graduate degree, given me the encouragement I needed to transition to a doctoral program, and offered me valuable advice for both practical and personal challenges. To Dr. Somers and Dr. Rajcan: Thank you both for putting your trust in me, for taking the time to teach me, and for your incredible patience along the way. iii ACKNOWLEDGEMENTS I would like to thank the members of my advisory committee, Dr. Daryl Somers, Dr. Istvan Rajcan, Dr. David Wolyn and Dr. Lewis Lukens, who have provided excellent council and thoughtful advice for my graduate research. Thank you as well to the faculty, administration and support staff of the Department of Plant Agriculture. I would also like to thank my examiners Dr. Elizabeth Lee and Dr. James Luby, who have taken the time to provide expert critiques of my thesis research and participate in my defense. I would like to thank the members of the Somers lab and our collaborators at Vineland. Thank you to Dr. Amy Bowen, Mr. Travis Banks, Ms. Rachael Leblanc, Ms. Amy Blake, Dr. David Liscombe and Dr. Michael Pautler who have dedicated their time, resources, and scientific expertise to the studies within this thesis. Thank you as well to Dr. Ashok Ghosh, Ms. Ingrid Giles, Ms. Karen Van Weerden, Ms. Jessica Turecek, Ms. Carly Flemming, Mr. Tom Hern, Ms. Rosalie Zielinski, Ms. Jaclyn Prystupa and Mr. Joseph O’Neill for their excellent technical work. Thank you to the Vineland managers and staff who have shown great enthusiasm and support for the apple program. Thank you as well to Ms. Ingrid Giles, Ms. Cindy Rouet, Ms. Erin Agro, Ms. Carolyn Dowling- Olson and Dr. Hanny Elsadr who have shared with me the experience of working at Vineland while studying at Guelph, and who I am now privileged to call my friends. I would also like to thank the funding sources who have made this thesis possible. Thank you to the Robert P. Knowles foundation, the Ontario Graduate Scholarship, and the donors of the Plant Agriculture and Ontario Agricultural College awards for the generous scholarships. Thank you as well to the Ontario Apple Growers, the University of Guelph, OMAFRA and AAFC for the generous research funding. Finally, I would like to thank my family. Thank you to my mother Marion, my father Daniel, and my brother Pascal, for providing me with lifelong unconditional support and the opportunity to follow an academic path. Most of all, thank you to my partner Flynn who has stood by me throughout the challenges and successes of my university career, and has been my most constant source of personal support. Thank you for keeping me at once highly motivated and firmly grounded. iv TABLE OF CONTENTS ABSTRACT .....................................................................................................................ii DEDICATION .................................................................................................................. iii ACKNOWLEDGEMENTS ...............................................................................................iv TABLE OF CONTENTS .................................................................................................. v LIST OF TABLES ........................................................................................................... x LIST OF FIGURES..........................................................................................................xi LIST OF ABBREVIATIONS ........................................................................................... xii CHAPTER 1: INTRODUCTION AND LITERATURE REVIEW ....................................... 1 1.1 Apple origins and domestication ....................................................................... 1 1.2 Apple cultivars and breeding .............................................................................. 2 1.2.1 Controlled crossing .......................................................................................... 2 1.2.2 Cultivar lifespan ............................................................................................... 3 1.2.3 Heritage cultivars ............................................................................................. 4 1.2.4 Modern cultivars .............................................................................................. 5 1.3 Apple breeding programs ................................................................................... 6 1.3.1 Worldwide apple breeding ............................................................................... 6 1.3.2 North American apple breeding ....................................................................... 7 1.3.3 RosBREED .................................................................................................... 10 1.4 Apple germplasm resources ............................................................................. 10 1.4.1 Diverse germplasm ........................................................................................ 10 1.4.2 Integration of diverse germplasm ................................................................... 11 1.4.3 Application of elite germplasm ....................................................................... 12 1.5 Apple genetic resources ................................................................................... 13 1.5.1 Genetic linkage mapping ............................................................................... 13 1.5.2 Mapping with microsatellites .......................................................................... 14 v 1.5.3 Mapping with single nucleotide polymorphisms ............................................. 15 1.5.4 Mapping in complex populations .................................................................... 16 1.5.5 Genome wide association mapping ............................................................... 17 1.5.6 Linkage disequilibrium ................................................................................... 18 1.5.7 QTL validation and marker development ....................................................... 21 1.5.8 Marker assisted selection .............................................................................