Enabling Marker-assisted Breeding for Fruit Texture Traits in Progeny of the Apple Cultivar Honeycrisp A Thesis SUBMITTED TO THE FACULTY OF UNIVERSITY OF MINNESOTA BY Cari Ann Schmitz IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE James J. Luby, James M. Bradeen July 2013 © Cari Ann Schmitz 2013 Acknowledgements I would like to acknowledge the generosity of many individuals in providing moral, material and technical support throughout the duration of this project. Dr. Nahla Bassil and her lab at the USDA Clonal Germplasm Repository were excellent hosts in the summers of 2011 and 2012. Dr. Cameron Peace of Washington State University hosted a highly informative workshop in the fall of 2011. Dr. Amy Iezzoni and her lab at Michigan State University were the generous hosts of annual workshops. The instruction gained under their guidance is invaluable. I am also grateful for the guidance I received from the greater RosBREED team, especially the apple team, and the camaraderie of the RosBREED breeding trainees (the “RosBREEDlings”). I want to extend my thanks to the apple crew at the University of Minnesota Horticultural Research Center and to Ken Mullen for his persistent, voluntary help each harvest season. The support of my colleges in the Applied Plant Sciences program has been substantial. I especially want to thank the ladies of 440 Alderman, Dr. Jennifer Boldt, Dr. Esther McGinnis, Diana Trujillo, Annie Doberstein, and Hannah Swegarden. Additionally, I am grateful for the support of my lab mates Matthew Clark, Luke Haggerty and Soon Li Teh and my former lab mate Dr. Steve McKay to whom I am indebted for so much sage advice during my first year and for providing data used in Chapter 4. This work was funded by USDA's National Institute of Food and Agriculture – Specialty Crop Research Initiative project, “RosBREED: Enabling marker-assisted breeding in Rosaceae” (2009-51181-05808). Chapter 2 was published in the March 2013 issue of HortScience. I am grateful for the contributions of the coauthors: Matthew Clark, Jim Luby and Jim Bradeen of the University of Minnesota; Yingzhu Guan, Kate Evans, Sujeet Verma and Cameron Pease of Washington State University; and Ben Orcheski and Susan Brown of Cornell University. Chapter 3 is in review and coauthors were Matthew Clark, Dr. Jim Bradeen and Dr. Jim Luby of the University of Minnesota and Dr. Umesh Rosyara of Michigan State University. I gratefully acknowledge Elisabeth Alperin, April Nyberg, and Dr. Nahla Bassil (the National Clonal Germplasm Repository, Corvallis, OR), Dr. Amy Iezzoni (Department of Horticulture, Michigan State University), the Michigan State University Infinium SNP Genotyping Lab, and the Minnesota Supercomputing Institute for providing advice, resources, and services integral to the third chapter. I have received additional funding through the Daniels Fellowship in Horticulture and travel grants to attend conferences from the American Society of Horticultural Science and the University of Minnesota Microbial and Plant Genomics Institute. I have been greatly blessed with the unwavering support of my friends and family. Finally, I thank my co-advisors, Dr. Jim Luby and Dr. Jim Bradeen and my committee member Dr. Cindy Tong for their ready availability and support. i Dedication This thesis is dedicated to the memory of my grandfather, Thomas Herman (1926-2012) of Clover Valley Farm in Harshaw, WI. ii Abstract Apple fruit texture is a major determinant of consumer acceptability. The cultivar Honeycrisp, a product of the University of Minnesota apple breeding program, is commercially successful and widely recognized for its exceptional fruit texture qualities. Many breeding programs have begun using ‘Honeycrisp’ as a parent, to develop new cultivars having superb fruit texture and adaptations to unique environmental pressures. This study quantifies fruit texture changes between years and from harvest through storage of fruit from individuals of the three major United States apple breeding programs. A broad range of texture quality was observed within these programs. Using three families with ‘Honeycrisp’ as a common parent, a ‘Honeycrisp’ parental linkage map was developed for use in detecting marker-trait-locus associations in the University of Minnesota apple breeding program. Three genomic regions associated with variation for firmness and crispness were identified as regions to target in implementing marker- assisted selection in ‘Honeycrisp’ descendants. iii Table of Contents Acknowledgements .............................................................................................................. i Dedication ........................................................................................................................... ii Abstract .............................................................................................................................. iii List of Tables ...................................................................................................................... v List of Figures .................................................................................................................... vi CHAPTER ONE: LITERATURE REVIEW ...................................................................... 1 Introduction ..................................................................................................................... 1 Apple Consumption, Preferences and Texture Perception ............................................. 3 Quantification of Fruit Texture Traits ............................................................................. 5 Physiology of Fruit Texture and Underlying Genetics ................................................... 9 Apple Genetics and Molecular Markers ....................................................................... 13 Mapping Marker-Locus-Trait Associations .................................................................. 16 Genotype by Environment Interactions ........................................................................ 20 Standardized Phenotyping ............................................................................................ 22 Marker Assisted Breeding, Marker Assisted Seedling Selection, etc ........................... 23 Minnesota Cultivar Honeycrisp .................................................................................... 27 CHAPTER TWO: FRUIT TEXTURE TRAITS OF THE RosBREED U.S. APPLE REFERENCE GERMPLASM SET ............................................................................ 29 Introduction ................................................................................................................... 29 Materials and Methods .................................................................................................. 32 Results and Discussion ................................................................................................. 38 Conclusions ................................................................................................................... 44 CHAPTER THREE: A CONSENSUS ‘HONEYCRISP’ APPLE (Malus × domestica) GENETIC LINKAGE MAP FROM THREE FULL-SIB PROGENY POPULATIONS ......................................................................................................... 66 Introduction ................................................................................................................... 66 Materials and Methods .................................................................................................. 71 Results ........................................................................................................................... 78 Discussion ..................................................................................................................... 81 Description of Supplementary Materials ...................................................................... 88 CHAPTER FOUR: QUANTITATIVE TRAIT LOCI AND FUNCTIONAL HAPLOTYPES FOR FRUIT TEXTURE TRAITS IN ‘HONEYCRISP’ PROGENY ................................................................................................................................... 107 Introduction ................................................................................................................. 107 Materials and Methods ................................................................................................ 111 Results ......................................................................................................................... 114 Discussion ................................................................................................................... 118 Conclusions ................................................................................................................. 122 CONCLUSIONS............................................................................................................. 136 LITERATURE CITED ................................................................................................... 139 iv List of Tables Table 2.1. Counts of individuals phenotyped by year, location, and storage duration for sensory and instrumental traits at the University of Minnesota (UMN), Washington State University (WSU) and Cornell University (CU). ........................................... 46 Table 2.2. Instrumental and sensory texture (firmness, crispness, juiciness) trait means ± standard errors and trait range (minimum, maximum) in 2010 and