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Investigating the Genetic and Genomic Basis of Osteochondrosis in Thoroughbred Horses from Australia and New Zealand

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Investigating the Genetic and Genomic Basis of Osteochondrosis in Thoroughbred Horses from Australia and New Zealand Investigating the genetic and genomic basis of osteochondrosis in Thoroughbred horses from Australia and New Zealand Kao Castle The University of Sydney A thesis submitted to the Faculty of Veterinary Science, The University of Sydney, in fulfilment of the requirements for the Degree of Doctor of Philosophy December 2012 i Declaration I declare that the work presented in this thesis is, to the best of my knowledge and belief, original, except as acknowledged in the text, and that the material has not been submitted, either in whole or in part, for a degree at this or any other university. (Kao Castle) 17 December 2012 ii Statement of Contributions The identities of the studs and horses that participated in the research described in this thesis are protected by confidentiality agreements. On this basis, the names of stud staff and veterinarians who provided data for this research are not listed as authors or named in the acknowledgements, although their input was invaluable. Chapter 2, Skeletal lesions and injuries in Australasian Thoroughbred weanling and yearling radiographs (draft manuscript). Castle K., Tammen I., Thomson P.C., Jeffcott L.B., Raadsma H.W. and Nicholas F.W. • Dr Tammen supervised components of this work, contributed to discussions, and provided feedback on the presentation of results. • Associate Professor Thomson provided advice on statistical techniques to compare results between the weanling and yearling populations, and provided feedback on the presentation of results. • Professors Jeffcott and Raadsma contributed to planning the data collection strategy, and provided feedback on the presentation of results. • Emeritus Professor Nicholas supervised components of this work, contributed to discussions and provided extensive feedback on the presentation of the results, and edited the manuscript. iii Chapter 3, Osteochondrosis and other common skeletal lesions in Australasian Thoroughbred yearlings: factors affecting prevalence, and genetic/phenotypic parameters (draft manuscript). Castle K., Thomson P.C., James J.W., Jeffcott L.B., Raadsma H.W., Wade C.M., Tammen, I., Wilson B.J. and Nicholas F.W. • Associate Professor Thomson and Honorary Professor James guided the selection of appropriate statistical techniques in this work. Associate Professor Thomson assisted in developing scripts and running some analyses in the computer programs ASReml 3 and ASReml-R. • Professor Jeffcott contributed to discussions and planning of this work. • Professor Raadsma contributed to discussions regarding the planning of this work, and the interpretation and presentation of results. • Professor Wade supervised components of this work, and contributed to extensive discussions of the statistical techniques in this work, and the interpretation and presentation of results. • Dr Tammen supervised components of this work. • Bethany Wilson contributed to extensive discussions of the statistical techniques in this work, and the interpretation and presentation of results. • Emeritus Professor Nicholas supervised components of this work, and made major contributions to extensive discussions of the statistical techniques in this work and the interpretation and presentation of results, and edited the manuscript. Chapter 4, Genome-wide association studies of skeletal lesion traits in Australasian Thoroughbred horses (draft manuscript). Castle K., Nicholas F.W., Jeffcott L.B., Raadsma H.W., Tammen I., and Wade C.M. iv • Emeritus Professor Nicholas provided useful suggestions regarding the presentation of results, and edited the manuscript. • Professor Jeffcott, Professor Raadsma, and Dr Tammen contributed to early discussions regarding the usefulness and feasibility of this work. • Professor Wade supervised this work, providing guidance on quality assurance for samples and for genotyping data, analysis techniques suited to the population, and the use of the PLINK computer software in which the analyses were carried out; and performed editing of the manuscript. Chapter 5, A pedigree analysis of Australian Thoroughbred horses (draft manuscript). Castle K., James J.W., Castle T., Thomson P.C., Jeffcott L.B., Tammen I., Raadsma H.W., Wade C.M., and Nicholas F.W. • Emeritus Professor Nicholas and Honorary Professor James provided guidance regarding which coefficients and parameters were appropriate to quantify aspects of this population, and, where relevant which computer programs could be used for their calculation. • Honorary Professor James provided assistance in modifying the Fortran code of the Pedig computer program. • Toen Castle discussed the project and provided assistance in using the computer program Mathematica to visualise the pedigree structure over time. • Associate Professor Thomson, Professor Jeffcott, Dr Tammen, Professor Raadsma, and Professor Wade contributed to discussions of the work in this chapter. • Emeritus Professor Nicholas supervised this work and edited the manuscript. v vi Acknowledgements This thesis and the work it describes relied on the support and input of the participating studs and veterinarians, who are remaining unnamed to protect the identities of the participating studs and horses. Their contribution was extensive, and scores of people were involved. This research and this thesis would not have been possible without their assistance and trust. Funding for this research and a scholarship was kindly provided by the Rural Industries Research and Development Corporation (RIRDC) of Australia. The RIRDC is the primary source of invaluable funding for research into horse health in this country. My supervisors (Emeritus Professor Frank Nicholas, Professor Claire Wade, Associate Professor Imke Tammen, Professor Leo Jeffcott and Professor Herman Raadsma) were exceptional. I have nothing but the highest praise for their patience, thoughtfulness and knowledge, shown through their consistent guidance and many instances of vital input throughout the project. Emeritus Professor Frank Nicholas put an enormous amount of work into providing feedback, even after his retirement, and despite the many other projects to which he was committed. Professor Claire Wade arrived part-way through the project, bringing the perfect experience and background to guide the genome-wide association study component of my project, as well as kind words and enthusiasm. Dr Imke Tammen provided useful feedback throughout the project and was primary supervisor for a portion of my project that included a very large amount of paperwork – thank-you for all the vii signatures. Professor Leo Jeffcott effectively launched this project by sharing his incredible depth of knowledge regarding equine osteochondrosis and providing a vital clinical perspective to help ensure that any results from this project would make sense to vets in the field. Finally, Professor Herman Raadsma was the project's devil's advocate, always providing the impetus to revisit assumptions and search for efficient ways to carry out this research. Importantly, all of my supervisors were generous enough to work well as a group! Honorary Professor John James and Associate Professor Peter Thomson provided invaluable guidance on statistical methodology appropriate to this research project. I deeply admire both men for their passion for statistical methods and their generosity with their knowledge. My colleagues and fellow students in the Faculty of Veterinary Science at the University of Sydney were a pleasure to work with. They were an ongoing source of invaluable advice and good humour. In particular I will cherish memories of time spent with Camilla Whittington, Hannah Siddle, Lee Miles, Karma Nidup, Bethany Wilson, Priscilla Spendlove and Jaclyn Aldenhoven. Colleagues and fellow students elsewhere in Australia and overseas also shared their knowledge and happily participated in energetic discussions about horse research and osteochondrosis: thank-you Else van Grevenhof, Kristin Olstad and Melissa Jackson. The Hunter Valley Equine Research Centre kindly provided accommodation throughout the data collection phase of this project. Helen Sinclair, the Secretary of the Hunter Valley Equine Foundation, took time to give me the keys at each visit. Michael Ford and Jacqueline Stewart of the Australian Stud Book generously provided the pedigree file that was the basis for the pedigree analysis of Australian Thoroughbred horses in this thesis. viii My friends, neighbours and family have been consistently patient and encouraging. Ryan Curnick, my partner, was my material support and just provided the right amount of humour and patience to get me to the point where this thesis could be submitted. My mother, Riki Davidson, provided encouragement and enormous assistance editing the chapters of this thesis, and my brother, Toen Castle provided sympathy - he is completing his own PhD. My father, Will Castle, was a steady source of gentle good humour and support. My sincere and heartfelt thanks go to all involved. Dedication For my family, near and far. ix Abstract Osteochondrosis (OC) is a skeletal disorder that occurs in young, growing animals. It is defined as a focal disturbance of endochondral ossification, visible as small, discrete areas of abnormal bone and/or cartilage tissue occurring at typical sites on the articular surfaces of joints. In the Australian and New Zealand Thoroughbred horse populations, OC is one of the most common skeletal lesions reported to occur in young horses. The presence of OC lesions can negatively affect a horse's welfare, monetary value, and athletic performance.
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