Identification and Characterization of Important Quantitative Trait Loci for Soluble Solids and Titratable Acidity for Germplasm in the University of Minnesota Apple Breeding Program A Thesis SUBMITTED TO THE FACULTY OF UNIVERSITY OF MINNESOTA BY Baylee Ann Miller IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE James J. Luby December 2020 © Baylee Ann Miller 2020 Acknowledgements I would like to acknowledge the large group of individuals that provided the many years of data collection, moral support, and teaching throughout the duration of this project. Much of the data that was utilized in this project was collected years before I arrived, and for that I am grateful as it provided an opportunity to carry out a research project unlike those previously for the UMN apple breeding program. The consistent help, determination, and willingness of all involved is immensely appreciated. I greatly appreciate the ongoing efforts to neatly maintain the apple orchard performed by the apple crew at the University of Minnesota Horticultural Research Center, including Winford McIntosh, and many of whom I have had the pleasure of working with since 2016 and into the future. My colleagues and peers at the University of Minnesota, specifically fellow graduate students in the Applied Plant Sciences graduate program, have been a constant source of help, support, and laughter. My lab mates in the fruit breeding group, namely Elizabeth Blissett and Seth Wannemuehler, have provided countless hours of assistance and motivation, especially during the busy harvest seasons. My coworker and supervisor, John Tillman, has provided an immense amount of technical teaching, support, and encouragement throughout my undergraduate and graduate education as well as into the beginning of my career. The genetic analysis portion of this project would not have been possible without the help, teaching, and assistance that Nicholas Howard has provided to others and myself. There have been dozens of members in the fruit group prior to my arrival, and without their efforts, my project would not have been possible. This group has consistently encouraged and supported me in my academic and scientific growth and knowledge, and for that, I am thankful. This project was partially funded by the USDA's National Institute of Food and Agriculture – Specialty Crop Research Initiative project, “RosBREED: Enabling marker- assisted breeding in Rosaceae” (2009-51181-05808). Additional funding was provided by the royalty funds from the patented releases of cultivars. I have received additional financial support from the Daniels Fellowship in Horticulture and travel grants to attend the RosBREED annual meeting in 2018 and the Plant and Animal Genomics conference in 2019. My education experience at the University of Minnesota has been one of great opportunities and never-ending learning, and would not have been possible without my advisor, Dr James Luby. I had the pleasure of working in the fruit breeding group as an undergraduate student, which embraced me and inspired me to continue my education and ultimately attain a full-time researcher position with the same group. My time with this group has been nothing but wonderful, and for that I am incredibly thankful. The members of my committee, Dr Matthew Clark and Dr James Bradeen, have been greatly supportive of me and this research project, and have made the experience seamless. i Dedication This thesis is dedicated to my mother, Julee Miller, who has inspired, encouraged, and supported me in my academic endeavors. Without her, I would not have discovered this path and taken this journey that has filled my life with curiosity, wonderful friends, and a lifelong passion for science. ii Abstract Apple fruit acidity and sweetness are two of the major trait components involved in apple seedling sensory evaluation. Published studies have alluded to some of the genetic components of apple fruit acidity and sweetness, but few have included an array of germplasm relevant to the University of Minnesota apple breeding program. With the release and subsequent frequent use of ‘Honeycrisp’ and ‘Minneiska’ apple cultivars as parents at the University of Minnesota, the germplasm set deviates from other breeding programs. In order to increase breeding efficiency and increase overall quality of apple seedlings, this study describes the genetic components of apple fruit acidity and sweetness and provides breeding insights to negate the creation of undesirable apple seedlings. This study uses data from 2010 to 2018 to characterize a wide but relevant array of germplasm, using six major families, three of which have ‘Honeycrisp’ as a parent, and three of which have ‘Minneiska’ as a parent. Three major loci associated with variation in titratable acidity content on linkage groups 1, 8, and 16, and two loci associated with variation in soluble solids content on linkage groups 1 and 13 were identified, and haplotypes were characterized for each locus. The conclusions from this study provide insights for designing crosses that create seedlings with desirable ranges of acidity and sweetness characteristics. iii Table of Contents Acknowledgements .............................................................................................................. i Dedication ........................................................................................................................... ii Abstract .............................................................................................................................. iii List of Figures .................................................................................................................... vi List of Tables .................................................................................................................... vii CHAPTER 1: INTRODUCTION AND LITERATURE REVIEW ................................... 1 Introduction ..................................................................................................................... 1 Current Public U.S. Apple Breeding Programs............................................................... 2 Importance of Sugar and Acid for Consumers ................................................................ 3 Biological Development of Acid Content ....................................................................... 5 Biological Development of Sugar Content ..................................................................... 6 Interaction of Sugar and Acid during Fruit Development and Maturation ..................... 7 Apple Genetics and Genomics ........................................................................................ 7 RosBREED Projects ........................................................................................................ 9 Mapping QTLs in Apple ............................................................................................... 10 Genotype by Environment Effects ................................................................................ 19 Utilization of Genetic Markers ...................................................................................... 20 Thesis Objectives .......................................................................................................... 22 CHAPTER 2: GENETIC COMPONENTS OF SOLUBLE SOLIDS CONTENT IN IMPORTANT UNIVERSITY OF MINNESOTA APPLE GERMPLASM .................... 26 Introduction ................................................................................................................... 26 Materials and Methods .................................................................................................. 28 Results ........................................................................................................................... 35 Discussion ..................................................................................................................... 43 Conclusions ................................................................................................................... 55 CHAPTER 3: GENETIC COMPONENTS OF TITRATABLE ACIDITY CONTENT IN IMPORTANT UNIVERSITY OF MINNESOTA APPLE GERMPLASM .................... 82 Introduction ................................................................................................................... 82 Materials and Methods .................................................................................................. 84 Results ........................................................................................................................... 86 Discussion ..................................................................................................................... 97 Conclusions ................................................................................................................. 112 iv LITERATURE CITED ................................................................................................... 148 v List of Figures Figure 2.1. Distributions of SSC at Harvest across Years. ............................................... 57 Figure 2.2. Distributions of SSC at Harvest across BLUP Models .................................. 58 Figure 2.3. Distributions of SSC at Harvest across Families ............................................ 59 Figure 2.4. Distributions of SSC at 10-Weeks Post Storage across Families ................... 60 Figure 2.5. SSC at Harvest vs. 10-Weeks Post Storage. ..................................................