Genetic Analysis of Black Raspberry Breeding Germplasm Thesis Presented in Partial Fulfillment of the Requirements for the Degree of Master of Science in the Graduate School of The Ohio State University By Matthew Willman, B.S. Graduate Program in Horticulture and Crop Science The Ohio State University 2019 Thesis Committee: Jonathan Fresnedo Ramírez, Advisor Leah McHale Joseph Scheerens Copyright by Matthew Willman 2019 Abstract U.S. black raspberry (BR) production is currently limited by narrowly adapted, elite germplasm. Improved understanding of genetic control and stability of pomological traits will inform the development of improved BR germplasm and cultivars. To this end, analysis of a multiple-environment trial of two BR mapping populations derived from crosses of commercial cultivars with wild accessions has provided insights into genetic variation, genotype-by-environment interactions (GEI), quantitative trait loci (QTL), and QTL-by-environment interactions (QEI) of fruit quality traits among diverse field environments. Genetic components and stability of four fruit size traits and six fruit biochemistry were characterized in two mapping populations following their evaluation over three years at four distinct locations representative of current U.S. BR production. GEI of pomological traits were described using two methods: mixed model analysis and Bayesian Finlay-Wilkinson regression. Both methods revealed relatively stable genetic control of the four fruit size traits across the tested production environments and less stable genetic control of the six fruit biochemistry traits. Further, Finlay-Wilkinson regression revealed individuals contributing to GEI for each trait. Ten QTL associated with three fruit morphology traits and five QTL associated with two fruit biochemistry traits were identified. Of the fifteen total QTL, eleven exhibited significant QEI. Closely overlapping QTL revealed linkage of several fruit size traits: fruit mass, drupelet count, and seed fraction. Further, alignment of linked markers to the BR genome revealed genomic regions associated with these traits. These and related findings are expected to guide further genetic characterization of BR fruit quality, management of breeding germplasm, and development of improved BR cultivars for U.S. production. i Dedication To my parents, who inspired my pursuit of science. ii Acknowledgements Thank you to all those who worked on this project before me – those who gathered and continue to develop germplasm, who spent countless hours in the field and lab taking measurements, and who had the foresight to plan and conduct the trials which led to my master’s work. To those I had the pleasure to work with, thank you for your time and direction. Thank you to The Ohio State University Graduate School and Department of Horticulture and Crop Science for your fellowship and research associate funding, and to the Department of Horticulture and Crop Science and Hartman Excellence in Fruit Production Fund for helping me share my research at an international symposium. Thank you to the OARDC librarians, who were masters at finding any text and forgiving of overdue books. Thank you to my advisor, Jonathan, for your unwavering support and for keeping me on track, and to my thesis committee, Joe and Leah, for your thoughtful questions, feedback, and expertise. Thank you to my sister, Anne, for being a constant friend. Finally, thank you to my wife, Katie, for your patience, enthusiasm, and companionship. I look forward to many great adventures with you. iii Vita April 2013 A.S., Cincinnati State Technical and Community College December 2015 B.S. Sustainable Plant Systems, The Ohio State University 2017 Graduate Fellow, The Ohio State University 2018 to present Graduate Research Associate, Department of Horticulture and Crop Science, The Ohio State University Fields of Study Major Field: Horticulture and Crop Science iv Table of Contents Abstract ............................................................................................................................ i Dedication ....................................................................................................................... ii Acknowledgements ....................................................................................................... iii Vita .................................................................................................................................. iv List of Figures ................................................................................................................ ix List of Tables ............................................................................................................... xiii List of Abbreviations ................................................................................................. xviii Introduction .................................................................................................................... 1 Chapter 1. Literature Review ......................................................................................... 3 Black raspberry biology, cultivation, and domestication ................................................... 3 Biology ................................................................................................................................................. 3 Cultivation ............................................................................................................................................ 4 Commercial production ........................................................................................................................ 6 Breeding history and objectives .......................................................................................................... 7 Germplasm ........................................................................................................................................ 11 Statistical methods of genetic characterization ................................................................ 13 Analysis of variance components ...................................................................................................... 13 Quantitative trait loci mapping ........................................................................................................... 14 Description of genotype-by-environment interactions ....................................................................... 15 Genetic characterization of black raspberry and related crops ....................................... 17 Variance components in raspberry .................................................................................................... 18 Quantitative trait loci mapping in raspberry ....................................................................................... 20 v Genotype-by-environment interactions in raspberry and other perennial crops ................................ 21 References ............................................................................................................................ 23 Figures ................................................................................................................................... 32 Tables .................................................................................................................................... 34 Chapter 2. Genotype-by-environment interaction analysis of a multiple- environment black raspberry trial .............................................................................. 36 Introduction ........................................................................................................................... 36 Black raspberry biology and cultivation ............................................................................................. 36 Genotype-by-environment interaction ............................................................................................... 37 Fruit size and fruit chemistry .............................................................................................................. 39 Materials and methods ......................................................................................................... 40 Germplasm ........................................................................................................................................ 40 Phenotypic data ................................................................................................................................. 41 DNA marker data & relatedness analysis .......................................................................................... 42 Mixed model analysis ........................................................................................................................ 44 Finlay-Wilkinson regression ............................................................................................................... 45 Results ................................................................................................................................... 47 Marker data & relatedness analysis .................................................................................................. 47 Fruit size traits ................................................................................................................................... 48 Fruit chemistry traits .........................................................................................................................