Molecular and quantitative genetic analyses of hop (Humulus lupulus L.) Erin L. McAdam BBiotech (Hons) School of Plant Science Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy University of Tasmania, August 2013 Statements and Declarations Declaration of originality This thesis contains no material which has been accepted for a degree or diploma by the University of Tasmania or any other institution. To the best of my knowledge and belief, this thesis contains no material previously published or written by another person except where due acknowledgement is made in the text, nor does this thesis contain any material that infringes copyright. …………………….. Date: …………. Erin McAdam Statement regarding published work contained in thesis and authority of access The publishers of the papers comprising Chapters 2 and 3 hold the copyright for that content; access to the material should be sought from the respective journals. The remaining non- published content of this thesis may be made available for loan, limited copying and communication in accordance with the Copyright Act, 1968. …………………….. Date: ………….. Erin McAdam i Statement of co-authorship of published work The following people and institutions contributed to the publications of work undertaken as part of this thesis: Erin L. McAdam, School of Plant Science: Candidate, primary author of all chapters Andreja Cerenak, Slovenian Institute of Hop Research and Brewing: Co-author of papers comprising Chapters 2 and 3 Andrzej Kilian, Diversity Arrays Technology Pty Ltd.: Co-author of papers comprising Chapters 2 and 3 Anthony Koutoulis, University of Tasmania: Co-author of papers comprising Chapters 2 and 3 Branka Javornik, University of Ljubljana: Co-author of papers comprising Chapters 2 and 3 Cai-Hong Wang, Qingdao Agricultural University: Co-author of paper comprising Chapter 3 Dave Andersen, The New Zealand Institute for Plant & Food Research Ltd.: Co-author of paper comprising Chapter 3 Donna Graham, The New Zealand Institute for Plant & Food Research Ltd.: Co-author of paper comprising Chapter 3 Emily J Buck, The New Zealand Institute for Plant & Food Research Ltd.: Co-author of paper comprising Chapter 3 Gene Probasco, John I. Haas Inc: Co-author of paper comprising Chapter 2 ii Jason Carling, Diversity Arrays Technology Pty Ltd.: Co-author of papers comprising Chapters 2 and 3 Jernej Jakše, University of Ljubljana: Co-author of papers comprising Chapters 2 and 3 John A. Henning, Hop Genetics and Breeding Program USDA-ARS: Co-author of paper comprising Chapter 2 Jules S. Freeman, University of Tasmania and University of the Sunshine Coast: Co-author of paper comprising Chapter 3 Lawrence Graham, The New Zealand Institute for Plant & Food Research Ltd.: Co-author of paper comprising Chapter 3 Paul D. Matthews, S. S. Steiner Inc: Co-author of paper comprising Chapter 2 Peter Darby, Wye Hops Ltd.: Co-author of papers comprising Chapters 2 and 3 René E Vaillancourt, University of Tasmania: Co-author of paper comprising Chapter 3 Ron Beatson, The New Zealand Institute for Plant & Food Research Ltd.: Co-author of paper comprising Chapter 3 Simon P. Whittock, Hop Products Australia and University of Tasmania: Co-author of papers comprising Chapters 2 and 3 iii Howard EL, Whittock SP, Jakše J, Carling J, Matthews PD, Probasco G, Henning JA, Darby P, Cerenak A, Javornik B, Kilian A, Koutoulis A: High-throughput genotyping of hop (Humulus lupulus L.) utilising diversity arrays technology (DArT). Theoretical and Applied Genetics 2011, 122: 1265-1280. This paper comprises the entirety of Chapter 2. Erin McAdam was the primary author (70%), and analysed all data, interpreted the results and wrote the manuscript. The co-authors contributed a cumulative total of 30% to the published work. Simon Whittock assisted with analyses and interpretation of results and revised the manuscript. Andreja Cerenak, Anthony Koutoulis, Peter Darby, John Henning, Jernej Jakše, Branka Javornik, Paul Matthews, Gene Probasco and Simon Whittock contributed intellectual input into the appropriate selection of germplasm. Andreja Cerenak, Peter Darby, John Henning, Jernej Jakše, Gene Probasco and Simon Whittock provided plant materials. Jernej Jakše also extracted the DNA for DArT marker development and assisted with both data analysis and interpretation of results. Andrzej Kilian and Jason Carling performed the DArT marker discovery analysis, developed the DArT array and assessed marker quality. Anthony Koutoulis led the international hop DArT collaboration and, was the instigator and co-ordinator of the study and revised the manuscript. McAdam EL, Freeman JS, Whittock SP, Buck EJ, Jakše J, Cerenak A, Javornik B, Kilian A, Wang C-H, Andersen D, Vaillancourt RE, Carling J, Beatson R, Graham L, Graham D, Darby P, Koutoulis A: Quantitative trait loci in hop (Humulus lupulus L.) reveal complex genetic architecture underlying variation in sex, yield and cone chemistry. BMC Genomics 2013, 14: 360. This paper comprises the entirety of Chapter 3. Erin McAdam was the primary author (75%), and performed the linkage, correlation and QTL analyses, interpreted the data and wrote the manuscript. The co-authors contributed a cumulative total of 25% to the published work. Jules Freeman assisted with linkage and QTL analyses, assisted with the data interpretation and revised the manuscript. Simon Whittock assisted with the correlation analysis and revised the manuscript. Emily Buck, with help from Cai-Hong Wang, provided DNA for DArT marker development and DArT genotyping of the New Zealand mapping population, obtained the genotypic data for the non-DArT markers used in the New Zealand mapping iv population of this study and revised the manuscript. Dave Andersen contributed the chemical data for the New Zealand mapping population and revised the manuscript. Lawrence Graham and Donna Graham provided the sex phenotypic data for the New Zealand mapping population. Ron Beatson developed the New Zealand mapping population. Andreja Cerenak, Jernej Jakše and Branka Javornik provided DNA for DArT marker development. Andreja Cerenak also provided the phenotypic and chemical data for the Slovenian mapping population, while Jernej Jakše provided DNA for DArT genotyping of the Slovenian mapping population and Branka Javornik revised the manuscript. Andrzej Kilian and Jason Carling performed the DArT marker discovery analysis, developed the DArT array and genotyped the two mapping populations with the DArT markers. Peter Darby contributed to the DArT marker development. René Vaillancourt assisted with data interpretation and revised the manuscript. Anthony Koutoulis led the international hop DArT collaboration and was the instigator and co-ordinator of the study. We the undersigned agree with the above stated proportion of work undertaken for each of the above published peer-reviewed manuscripts contributing to this thesis: ………………. ………………. Date: ………….. Anthony Koutoulis René Vaillancourt Primary Supervisor Head of School School of Plant Science School of Plant Science University of Tasmania University of Tasmania v Acknowledgements This thesis would not have been possible without the valuable contributions of a number of people. Firstly, I would like to give an enormous thanks to Jules Freeman for the expert guidance in linkage and QTL analyses. Your enthusiasm and dedication to these topics has been very inspiring. I am also very appreciative of your thorough revisions and advice. Thank you to Simon Whittock for the many hours you spent assisting me with the quantitative genetics analysis and many of the other statistical procedures in this thesis, as well as sharing your extensive knowledge of hop with me. Thanks to René Vaillancourt for your general expertise and advice; and to Anthony Koutoulis for encouraging me to present my work at conferences. I would like to acknowledge the members of the hop DArT collaboration, Andreja Cerenak, Branka Javornik, Emily Buck, Gene Probasco, Jernej Jakše, John Henning, Paul Matthews, Peter Darby and Ron Beatson for your contributions to these studies and for your supportive collaboration. I would also like to thank Hop Products Australia for providing me with materials, data, access to their hop fields and assistance with sample collection. Thanks to Matthew Hamilton and Dorothy Steane for technological assistance, Aina Price for assistance with field work and Sascha Wise for assistance in the laboratory. Thanks to Andrzej Kilian and Jason Carling from DArT Pty Ltd. for performing DArT genotyping and for technical advice. I would like to thank the organisers of the IHGC 2009 and IHGC 2011 conferences for giving me the opportunity to present work from this thesis, as well as the School of Plant Science and the University of Tasmania for providing with funding so that I could attend the conferences. Thanks to all the other Plant Science post-grads, for sharing in the experience, the endless laughs and wildly enjoyable games of cards. I wish you all many diamond gins! I give special thanks to my Mum and Dad for your continuous support and encouragement as well as providing me with such a motivational example of the value of hard work. I always looked forward to our Sunday night phone conversations. The biggest thanks go to Scott, not only for the endless discussion of ideas, the tireless help in the field and for proofreading every last word of this thesis, but for keeping me so happy the entire time. Your passion for research and keen interest in the natural world were