AN ABSTRACT OF THE DISSERTATION OF Michael Dossett for the degree of Doctor of Philosophy in Horticulture presented on April 22, 2011 Title: Evaluation of Genetic Diversity in Wild Populations of Black Raspberry (Rubus occidentalis L.) Abstract approved: Chad E. Finn In recent years, there has been renewed interest in black raspberry ( Rubus occidentalis L.) breeding. This has been spurred, in part, by an increase in black raspberry consumption due to studies that have shown them to be particularly high in anthocyanin content indicating high levels of antioxidants. Present cultivars are ill adapted to the biotic and abiotic stresses of the Pacific Northwest, where the commercial black raspberry industry is centered, and fields must be replanted after 3- 5 seasons. Breeding progress in black raspberry has been limited by a lack of genetic diversity. This work is the first documented effort to systematically collect and evaluate wild R. occidentalis germplasm from across the native range of the species. Sources of strong resistance to the virus vector Amphorophora agathonica Hottes were identified from Maine, Michigan, and Ontario. Populations with outstanding vigor and possible resistance to Verticillium wilt were identified, as were two populations with a novel anthocyanin profile. In addition, variation was documented for morphological traits such as thorniness and cane architecture as well as fruit weight and gloss, and ripening times. Molecular analysis of genetic diversity using microsatellite markers in these populations showed that black raspberry cultivars are closely related to each other, but there is tremendous diversity in the wild populations. The data also support phenotypic evidence that several “wild” populations may be descended from feral cultivated plants. Overall, genetic diversity in wild black raspberry germplasm shows tremendous potential for use in breeding improved cultivars. Evaluation of Genetic Diversity in Wild Populations of Black Raspberry ( Rubus occidentalis L.) by Michael Dossett A DISSERTATION submitted to Oregon State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Presented April 22, 2011 Commencement June 2011 Doctor of Philosophy dissertation of Michael Dossett presented on April 22, 2011 . APPROVED: Major Professor, representing Horticulture Head of the Department of Horticulture Dean of the Graduate School I understand that my thesis will become part of the permanent collection of Oregon State University libraries. My signature below authorizes release of my thesis to any reader upon request. Michael Dossett, Author ACKNOWLEDGMENTS There are many people who have been instrumental in the completion of this project. First, I would like to thank Dr. Chad Finn, for his tireless support and advice, willingness to talk about small fruits at the drop of a hat, or just to listen, his constant encouragement, and seemingly endless enthusiasm and optimism. I would also like to thank Dr. Nahla Bassil for her guidance and support, enthusiasm, constant smile, and cheerful disposition. I owe a great deal of what I have learned over the last several years to them and appreciate all they have done to help me along the way. I would also like to thank my other committee members, Dr. Shawn Mehlenbacher, Dr. Rich Cronn and Dr. Ken Johnson, for their help in answering questions and addressing problems that have arisen during the course of this project, and for their insights that have helped point me in the right direction. I also owe a debt of gratitude to Mary Peterson and Ted Mackey. Aside from just plain putting up with me, their expertise in providing technical and field assistance has been invaluable and is greatly appreciated. Andy Livesay, Rob Livesay, Catherine Wright, Maeve Dempsey, Isaac Otto, and Alex Renn, all helped me out too many times to count with watering plants when I was away, picking fruit, and helping with field maintenance, for which I’m grateful. Erin Ortiz and Sumi Maristany, in addition to providing valuable summer help, taught me a great deal about how to manage my own time and supervise others, while being a joy to work with. I would also like to thank all the folks at the USDA-ARS Horticultural Crops Research Lab and the USDA-ARS National Clonal Germplasm Repository, particularly Bob Martin, Karen Keller, Jana Lee, Jerry Weiland, Paul Charron, Kim Hummer, Joe Snead, Jeanine DeNoma, Missy Fix, Jim Oliphant, and Joseph Postman. I would especially like to thank the past and present members of the Bassil lab, April, Barb, Wambui, and Ted, with whom I have had the pleasure of working over the last few years, for their help and camaraderie, as well as my fellow graduate students in the Horticulture department at Oregon State University. Horticulture department head Anita Azarenko, as well as Gina, LeeAnn, and Viki in the Horticulture office have all been supportive and tremendously helpful with travel and other paperwork. I would like to thank Dr. Jungmin Lee and Chris Rennaker in Parma, Idaho, who helped me with fruit chemistry analyses. In addition to letting me invade her lab and doing her best to make me feel at home while working in Idaho, Jungmin has been a great friend and colleague, given me advice whether I needed it or not, and has always been there to support me in my research and career. Brian Yorgey, with his good-natured humor, freezer space, and advice, also provided space and equipment that helped a great deal during the course of this project. I would also like to thank Dr. Chaim Kempler and Brian Harding with Agriculture and Agri-Foods Canada, and Karen Keller with the USDA-ARS in Corvallis, who helped me get started working with aphids, giving me advice, sharing their techniques, and giving me tips on how to work with them. Without the help of the following individuals sending me seed this project would not have been possible: W. Anderson (Illinois), M. Bathrick (Pennsylvania), C. Brown (New Jersey), P. Byers (Missouri), T. Cuff (Wisconsin), A. Dale (Ontario), R. Davis (New York), R. Geneve (Kentucky), J. Hancock (Michigan), D. Handley (Maine), A. Jamieson (New Brunswick), K. Kellogg (Connecticut), J. Lehman (Indiana), T. Leslie (Ohio), H. Love (Tennessee), J. Luby (Minnesota), C. Mauchline (Pennsylvania), R. Moyer (Virginia), G. Nonnecke (Iowa), M. Retter (Indiana), M. Stanton (Ohio), H. Swartz (Maryland), F. Takeda (West Virginia), E. Thompson (Arkansas), and C. Weber (New York). Financial support for this project was provided by grants from the USDA-ARS Plant Exchange Office, USDA-ARS Northwest Center for Small Fruits Research, and the Oregon Raspberry and Blackberry Commission. There are many others who have helped me and given their support and encouragement these last years and I wish there was the space to list them all, so I will finish by thanking my family, especially my wife Jaye, sisters Lisa and Michelle, and mom and dad. Your support and love has meant more to me than you know and was always there when I needed it the most; thank you. CONTRIBUTION OF AUTHORS Dr. Chad Finn oversaw and assisted with overall project conception, planning and design. Dr. Jungmin Lee oversaw and assisted with sample preparation and analysis of anthocyanins in black raspberry fruit (Chapter 4). Dr. Nahla Bassil oversaw and assisted in the collection and analysis of microsatellite data (Chapter 5). Dr. Kim Lewers provided primer sequences for EST-SSRs from an unpublished black raspberry EST library for use in studying black raspberry diversity (Chapter 5). All coauthors helped to edit and have approved the final version of the chapters with which they are associated. TABLE OF CONTENTS Page Chapter 1: Introduction ............................................................................................ 1 Chapter 2: Identification of Resistance to the Large Raspberry Aphid in Black Raspberry................................................................................................................. 7 Abstract........................................................................................................................................ 8 Introduction.................................................................................................................................. 8 Materials and Methods ............................................................................................................... 11 Plant Materials and Aphids ..................................................................................................... 11 Aphid Resistance Screening.................................................................................................... 12 F1 Populations ........................................................................................................................ 14 BC 1 Populations...................................................................................................................... 15 Statistics................................................................................................................................. 15 Results and Discussion ............................................................................................................... 15 References.................................................................................................................................. 21 Chapter 3: Morphology, Phenology, and Field Performance of Wild Black Raspberry Germplasm ...........................................................................................................