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Genetic Diversity Studies of Trifolium Species from the Extremes of the UK

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Genetic Diversity Studies of Trifolium Species from the Extremes of the UK Genetic diversity studies of Trifolium species from the extremes of the UK by SERENE HARGREAVES A thesis submitted to The University of Birmingham for the degree of DOCTOR OF PHILOSOPHY School of Biosciences College of Life and Environmental Sciences The University of Birmingham September 2010 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. ABSTRACT Crop wild relatives have been identified as ecologically and economically important plant genetic resources but are often a neglected resource. The recognition of the need for their specific conservation and their value for future use has been strengthened by the Convention on Biological Diversity and the International Treaty on Plant Genetic Resources for Food and Agriculture, both of which have been ratified by the UK. This thesis provides a detailed view of the ecological, geographic and genetic background to three crop wild relative species, Trifolium dubium, T. pratense and T. repens, of which the latter two are amongst some of the most economically important legume species in the UK. Assessments of ecogeography, amplified fragment polymorphism and single nucleotide polymorphism markers were employed to investigate the distribution of variation in these species across the UK, including outlying island sites. Based on this information it was possible to look for isolation by distance in populations in UK; identify areas containing unique variation; assess the conservation importance of island sites surrounding the UK and speculate on the causes of the observed patterns of diversity. Conservation recommendations were based on the cumulative data from this research to identify how the recommendations change with an increased focus on genetic diversity. These results provide insights into the use of different types of background information when setting conservation plans in widespread species, contributing to the development of conservation strategies for widespread species in general. ACKNOWLEDGMENTS I would like to start by expressing my gratitude to my supervisors Dr. Brian Ford- Lloyd and Dr. Nigel Maxted for their suggestions, support and for the opportunities they have given me throughout my project. I would like to thank the staff at IGER who made me welcome during my stay and who helped me learn the ropes in the lab and in the field; Mike Abberton, Sue Dalton, Charlotte Deakin, Galina Latypova, Kirsten Skøt, Leif Skøt and Ian Thomas. In particular I would like to acknowledge Kirsten Skøt for kindly allowing me to learn in her spotless genomics lab, and to Leif Skøt for helpful discussions and for providing T. pratense EST sequences. Many thanks are due to all my colleagues in S208 and W204 for their friendship, good advice and encouragement, especially Joana Magos Brehm, Cristina Sousa Correia, Marianne Mitchell and Fay Hughes for guiding me through the start of my PhD and Andrea Harper, Jennifer Preston and Claire Teeling for helpful discussions and support throughout the rest. Most importantly I would like to thank my family for their encouragement and for their faith in me throughout this project and David Jacoby for his help with the collecting mission to the Isles of Scilly and with his patience and constant support. Finally, I would also like to acknowledge the BBSRC and the BSBI who supplied the financial support for this project. TABLE OF CONTENTS Chapter 1. General Introduction ............................................................................................. 1 1.1 What is diversity and why conserve it? ...................................................................... 1 1.2 Biodiversity crisis and UK commitments ................................................................... 1 1.3 Genetic resources and crop wild relatives .................................................................. 2 1.4 Background to the current study ................................................................................. 4 1.5 A general introduction to genetic diversity studies .................................................... 6 1.5.1 SSRs ..................................................................................................................... 7 1.5.2 Focus on Amplified Fragment Length Polymorphism (AFLP) ........................... 8 1.5.3 Focus on SNPs .................................................................................................... 10 1.6 Quantifying genetic differences................................................................................ 31 1.7 Gene flow and genetic diversity ............................................................................... 32 1.7.1 The consequence of introgression in conservation ............................................. 32 1.7.2 Measurements of gene flow ................................................................................ 33 1.7.3 Landscape genetic analysis and its implications for population genetics .......... 35 1.8 Mainland versus island populations ......................................................................... 39 1.8.1 Previous studies of diversity in mainland versus island populations ................. 40 1.9 Thesis outline ............................................................................................................ 41 Chapter 2. An ecogeographic background to three Trifolium species in the UK................. 43 2.1 Ecogeography as a tool for conservation analyses ................................................... 43 2.2 Aims of ecogeographic survey ................................................................................. 43 2.3 Target taxa ................................................................................................................ 44 2.4 Trifolium genetics ..................................................................................................... 45 2.4.1 Trifolium repens genetic diversity ...................................................................... 46 2.4.2 Trifolium pratense genetic diversity ................................................................... 48 2.5 Trifolium dubium Sibth. ............................................................................................ 51 2.6 Trifolium pratense L. ................................................................................................ 56 2.7 Trifolium repens L. ................................................................................................... 61 2.8 Target Island Site - Isles of Scilly ............................................................................ 66 2.8.1 Environmental history ........................................................................................ 67 2.8.2 Conservation ....................................................................................................... 69 2.8.3 Presence of species ............................................................................................. 70 2.9 Target Island Site - Outer Hebrides .......................................................................... 71 2.9.1 Environmental history ........................................................................................ 73 2.9.2 Conservation ....................................................................................................... 74 2.9.3 Presence of species ............................................................................................. 75 2.10 Target Island Site - Shetland Isles ............................................................................ 76 2.10.1 Environmental history ........................................................................................ 78 2.10.2 Conservation ....................................................................................................... 79 2.10.3 Presence of target species ................................................................................... 80 2.11 Target Island Site - Skye, Inner Hebrides................................................................. 81 2.11.1 Environmental history ........................................................................................ 83 2.11.2 Conservation ....................................................................................................... 85 2.11.3 Presence of species ............................................................................................. 85 2.12 Target Island Site - St Kilda, Outer Hebrides ........................................................... 86 2.12.1 Environmental history ........................................................................................ 88 2.12.2 Conservation ....................................................................................................... 90 2.12.3 Presence of target species ................................................................................... 91 2.13 Current threat status .................................................................................................
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