Genetic and Phenotypic Differentiation Between Winemaking and Wild Strains of Saccharomyces Cerevisiae Katie Hyma Washington University in St

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Genetic and Phenotypic Differentiation Between Winemaking and Wild Strains of Saccharomyces Cerevisiae Katie Hyma Washington University in St Washington University in St. Louis Washington University Open Scholarship All Theses and Dissertations (ETDs) 5-24-2010 Genetic and Phenotypic Differentiation between Winemaking and Wild Strains of Saccharomyces cerevisiae Katie Hyma Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/etd Recommended Citation Hyma, Katie, "Genetic and Phenotypic Differentiation between Winemaking and Wild Strains of Saccharomyces cerevisiae" (2010). All Theses and Dissertations (ETDs). 888. https://openscholarship.wustl.edu/etd/888 This Dissertation is brought to you for free and open access by Washington University Open Scholarship. It has been accepted for inclusion in All Theses and Dissertations (ETDs) by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS Division of Biology and Biomedical Sciences Evolution, Ecology, and Population Biology Dissertation Examination Committee: Justin Fay, Chair Jim Cheverud Barak Cohen Ken Olsen Barbara Schaal Heather True-Krob GENETIC AND PHENOTYPIC DIFFERENTIATION BETWEEN WINEMAKING AND WILD STRAINS OF SACCHAROMYCES CEREVISIAE by Katie Elizabeth Hyma A dissertation presented to the Graduate School of Arts and Sciences of Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy December 2010 Saint Louis, Missouri copyright by Katie Elizabeth Hyma 2010 Abstract Traditionally, Saccharomyces cerevisiae has been associated with wine, beer and bread production, yet wild strains have also been isolated from natural habitats. While all strains of S. cerevisiae as well as other Saccharomyces species are capable of wine fermentation, a genetically distinct group of S. cerevisiae strains is primarily used to produce wine. These strains exhibit an apparent genetic bottleneck, which led to the hypothesis that wine stains have been domesticated from ‘wild’ natural strains. However, it is unknown whether the genetic bottleneck was accompanied by selection for phenotypic differences. In this study we tested for phenotypes correlated with the genetic bottleneck observed for wine strains. First, growth and fitness parameters (e.g. growth rate) of yeast strains were evaluated on different media types that simulated winemaking and natural habitats. Results provided no evidence that ‘wine’ or ‘wild’ strains have greater fitness in their respective environments, and suggest that the putative domestication has not resulted in habitat specific growth adaptation. Second, we tested for phenotypes associated with human perception of wine aroma and flavor characteristics using discriminatory and descriptive sensory analysis. The results from this study established human perception as a selectable yeast phenotype, and demonstrated that divergence in wine aroma and flavor attributes is consistent with the domestication hypothesis. The isolates used to infer domestication are geographically broad, but ecologically undersampled. We tested the relevance of global population genetic patterns in S. cerevisiae by conducting a population genetic study of S. cerevisiae isolated from vineyard and non-vineyard locations in North America. We used genome-wide single nucleotide markers to determine if the domestication hypothesis is supported at a local scale. Results demonstrate that two distinct populations of S. cerevisiae exist in North America, corresponding to European ‘wine’ and North ii American ‘wild’ genotypes. We provide evidence for genetic exchange between populations, suggesting a lack of physical or temporal barriers to gene flow. While wine strains exhibit a population genetic pattern consistent with previous studies, we find that the wild population is dominated by a few clonal genotypes, identifying new questions regarding the domestication hypothesis and the genetic structure of other wild populations. iii Acknowledgement I gratefully acknowledge the financial support provided by the Division of Biology and Biomedical Sciences (Program in Ecology, Evolution and Population Biology), and the NIH Genome Analysis Training Fellowship. Numerous faculty, staff and students have provided support for this research in what seems like infinitely many ways. I would like to especially thank my advisor, Justin Fay, for welcoming me in to his lab and encouraging me to pursue this research project. He provided me with intellectual support throughout the project, provided great insight into all aspects of my research, and was even willing to wield a pipette when I couldn’t. In addition, I am indebted to my thesis committee members: Dr. Barbara Schaal, Dr. Ken Olsen, Dr. Heather True-Krob, Dr. Jim Cheverud, and Dr. Barak Cohen, all of whom were supportive of me and provided thoughtful comments throughout this project. My labmates Betsy Engle and Devjanee Swain demonstrated great patience while teaching me the ins and outs of the lab and the yeast system, making it a pleasure to work in the Fay lab. Justin Fay, Betsy Engle and Devi Swain also provided a tremendous amount of help during the 2009 sampling season, and also during sensory analysis experiments. I would also like to thank the other members of the Fay lab: Scott Doniger, Hyun Kim, Sung Chun, Katie Reed, Andrew Bergen, Sandeep Venkataram, Juyoung Huh, Adam Coster and Linda Riles for all of their help and support in the lab on many experiments, and for all of their useful comments and suggestions during the time we spent working together. I learned a great deal from my fellow students, and many of them provided specific support in regard to this dissertation. I would especially like to thank a few in particular. Kim Lorenz designed restriction associated DNA sequencing DNA barcodes, shared detailed protocols and reagents for genotyping. Justin Gerke was a sounding board during early stages of this project, providing invaluable advice and instruction. Vitas Wagner accompanied me to a hot iv mosquito infested vineyard to help collect samples while he was rotating in the Fay lab. Jeff Sabina fielded questions regarding enzymatic assays and cloning methods. Chris Hittinger shared S. cerevisiae and S. kudriavzevii strains, and patiently taught me how to do competition experiments using flow cytometry. I have had the pleasure of experiencing graduate school surrounded by students in the Evolution, Ecology and Population Biology program, all of whom are incredibly talented, providing lively discussions on interesting topics. In particular, Brad Oberle, Wayne Law, Jennifer Neuwald, James Beck, Thom Sanger, Michele Johnson, Brian Allan, Liam Revell, Josh Reece, Nick Griffin, and Nikki Miller all provided excellent academic and emotional support. The support teams that keep research moving forward at Washington University are absolutely incredible. In particular, both Debbie Peterson and Alice Gleason helped me find solutions to any problems that I ran in to while conducting research on this project, and were always happy to help. Without the help of Jessica Hoisington-Lopez the genotyping I did for this project would not have been completed. My graduate coordinators, Dana Sterbenz and Melissa Torres were an invaluable resource, providing both administrative and emotional support. Without support like theirs, this research could not have been completed. Although I cannot name them, I would like to thank all of the people who participated in the discriminatory sensory analysis of wines. They were incredibly generous with their time, and played the role of a truly invaluable measuring instrument. I would also like to thank those people who welcomed me onto their property to collect yeast samples, or provided technical assistance on various aspects of these projects. Specifically, I would like to thank Tony Saballa of Charleville Vineyard (Ste. Genevieve, MO) and Hank Johnson of Chaumette Vineyard (Ste. Genevieve, MO), Mark Baehman of Mt. Pleasant Vineyard (Augusta, MO), Tom and Celeste Symonette of Whistling Dog Cellars (Polk Co., OR), v Marilee Buchanan of Tyee Vineyards (Benton Co, OR), Matt Gross of the Wine and Cheese Place (St. Louis, MO), Dave Deaton of St. Louis Wine and Beer Making (St. Louis, MO), Denise Gardner of Vinquiry, Inc., Richard DeScenzo of ETS Lab services, Lidia Watrud and Mike Bollman. Many conversations with these individuals brought up some of the most interesting questions regarding my research. My undergraduate advisor, Tom Whittam, is the reason I entered graduate school, and although I can’t share this moment with him, his memory provides a constant source of inspiration and encouragement. My family and friends provided me with an incredible amount of support throughout this process. My Mom, Kathy Hyma, is always there when I need her and always has faith in me. She was ready to help whenever she could, and even got involved in my research by helping to wash and sterilize hundreds of wine bottles during an unfortunately timed visit. My Dad was thrilled to the point of embarrassing when I graduated the 8th grade, and I know that if he were able to have been a part of this process, he would have been equally proud. My wonderful friends Ana Jacobsen and Carrie Vodehnal, who have been a constant source of help and support, also generously donated their time to help with the execution of a post-experiment wine tasting for participants in the sensory analysis. There is one family member who deserves acknowledgement in almost area I’ve mentioned so far. Jason
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