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Linkage Mapping, QTL Analysis and Population Genomic Studies

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Linkage Mapping, QTL Analysis and Population Genomic Studies Eucalyptus genomics: Linkage mapping, QTL analysis and population genomic studies Corey James Hudson B. Sc. (Hons) Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy School of Plant Science, University of Tasmania, January 2012 Declaration This thesis contains no material which has been accepted for a degree or diploma by the University or any other institution, except by way of background information and duly acknowledged in the thesis, and to the best of the my knowledge and belief no material previously published or written by another person except where due acknowledgement is made in the text of the thesis, nor does the thesis contain any material that infringes copyright. Corey James Hudson This thesis may be made available for loan and limited copying and communication in accordance with the Copyright Act 1968. Corey James Hudson The research associated with this thesis abides by the Australian Government’s Office of the Gene Technology Regulator and the rulings of the Safety, Ethics and Institutional Biosafety Committees of the University. Corey James Hudson i Abstract This thesis reports on genomic studies conducted in five of the most commercially important species of Eucalyptus, all from subgenus Symphyomyrtus; E. globulus, E. nitens (section Maidenaria), E. grandis, E. urophylla (section Latoangulatae) and E. camaldulensis (section Exsertaria). These studies utilised Diversity Arrays Technology (DArT), a microarray-based genotyping system which provides high-throughput genome-wide genotyping. DArT markers, and in particular linkage maps constructed with these markers, formed the basis for most of the research conducted in this thesis. The DArT markers are highly transferable across species which facilitates the transfer of information between studies and as sequences are available for most of the 7680 markers contained on the eucalypt genotyping array it is possible to place these markers on the recently released E. grandis genome sequence. A 1060 DArT and microsatellite marker linkage map was constructed in a large E. globulus dwarf x tall ecotype out-crossed F2 family (n = 503) in Chapter 1. This is the highest density linkage map produced for E. globulus and together with other high density DArT maps constructed in E. grandis x E. urophylla it was used to assess genome similarity (e.g. synteny and colinearity) between species through comparative mapping. Despite the detection of two small putative translocations or duplications in the inter-sectional comparison, these species showed very high synteny and colinearity overall. This finding showed that it is possible to link the economically important E. globulus to the E. grandis genome sequence. The feasibility of constructing a multi-species composite linkage map for Symphyomyrtus was explored in Chapter 2. Seven independently constructed linkage maps (built in either E. globulus or E. grandis x E. urophylla mapping families) were integrated into a single map containing a total of 4135 markers (3909 DArT markers, 218 microsatellite markers and 8 candidate genes). This composite map will, (1) serve as a valuable reference map for Symphyomyrtus and related species, and (2) aid comparative research by enabling the relative positions of markers and quantitative trait loci (QTL) from different studies to be determined more easily. Quantitative trait loci analyses were used to examine the genetic architecture underlying differences between dwarf and tall E. globulus ecotypes in Chapter 3; with a particular focus on vegetative and reproductive phase-change traits. A total of 22 significant and ii 11 suggestive QTL were detected for the nine traits examined. A highly significant QTL was detected for vegetative phase-change (LOD 103, 62.8% phenotypic variation explained). A micro-RNA gene known to regulate vegetative phase-change was found near the peak of this QTL. It is hypothesised that a mutation in, or a deletion of, this gene may be responsible for the heterochronic evolution of early phase-change in dwarf ecotype populations and that this has allowed E. globulus to inhabit the exposed coastal environments in which the dwarf ecotype occurs. In Chapter 4, population genomic analyses were conducted using range-wide samples (84 to 93 individuals per species) of E. globulus, E. nitens, E. grandis, E. urophylla and E. camaldulensis. Genetic diversity parameters were calculated using a common set of 2207 markers. In each of ten pair-wise species comparisons, markers under putative directional selection were identified using FST outlier analyses. These outlier markers along with genetic diversity estimates were mapped on the composite map (Chapter 2) to produce a ‘genomic atlas’. This identified several genomic ‘hot-spots’ of species molecular differentiation and together with other genetic resources, such as the E. grandis genome sequence and QTL positional information, offers the potential to identify candidate genes underlying traits associated with species adaptation and speciation. iii Acknowledgements This thesis would not have been possible without the valuable assistance provided by many people. Foremost, I would like to thank my supervisors, René Vaillancourt, Brad Potts and Jules Freeman, for their excellent guidance, support and encouragement. Rebecca Jones, Dorothy Steane, Valérie Hecht and Jim Weller are acknowledged for sharing their expertise. Valuable field and or laboratory assistance was provided by James Marthick, Sascha Wise, Paul Tilyard, Justin Bloomfield and Adam Smolenski (CSL). I thank Dario Grattapaglia for providing materials, access to equipment, and the opportunity to conduct research in his laboratory at Embrapa Genetic Resources and Biotechnology, Brazil. A special thanks to Danielle Faria for her laboratory assistance and support during this time. Marilia Pappas and Juliana Sena are acknowledged for their laboratory assistance. Carolina Sansaloni and César Petroli are thanked for providing linkage mapping and DArT marker information. Samuel Paiva is also thanked for his support during my Brazil trip. Zander Myburg and Anand Kullan from the University of Pretoria are thanked for their contributions to the comparative mapping and composite map projects. They are also acknowledged along with Geoff Galloway at Sappi (South Africa) and Kitt Payn at Mondi (South Africa) for their assistance and contribution of E. grandis and E. urophylla DNA, respectively. Andrzej Kilian and Frank Dettering at DArT Pty Ltd, Canberra are thanked for assisting with DArT genotyping, linkage mapping and QTL analyses. Kelsey Joyce at Gunns Ltd., Dean Williams at Forestry Tasmania and Sandra Hetherington at Norske Skog provided access to field trials and materials. Simon Southerton, Penny Butcher and Charlie Bell at CSIRO Plant Industries, Canberra are thanked for their assistance and contribution of E. camaldulensis DNA. I would like to acknowledge the late Sir Harold Cuthbertson and Lady Cuthbertson whose generosity provided the stipend that allowed me to undertake this work, the Australian Research Council for providing funding to this project (DP0770506 & DP110101621) and the Co-operative Research Centre for Forestry for in-kind support. Finally, special thanks to my parents, Ron and Wendy Hudson, for their support throughout my many years of study. iv Publications arising from this project Journal Publications Hudson CJ, Kullan ARK, Freeman JS, Faria DA, Grattapaglia D, Kilian A, Myburg AA, Potts BM, Vaillancourt RE (2011) High synteny and colinearity among Eucalyptus genomes revealed by high-density comparative genetic mapping. Tree Genetics & Genomes (http://dx.doi.org/10.1007/s11295-011-0444-9) Conference proceedings Freeman JS, Potts BM, Downes GM, Thavamanikumar S, Pilbeam DJ, Hudson CJ, Vaillancourt RE (2011) QTL analysis for growth and wood properties across multiple pedigrees and sites in Eucalyptus globulus. BMC Proceedings 5 (Suppl 7). Hudson CJ, Kumar KAR, Freeman JS, Faria DA, Grattapaglia D, Kilian A, Potts BM, Myburg AA and Vaillancourt RE (2010). Comparative mapping with high marker density reveals high synteny and colinearity among Eucalyptus genomes. Oral presentation at Genetics Society of AustralAsia (GSA) Conference, Canberra, Australia 4-8th July 2010. Abstract page 14. Hudson CJ, Kumar KAR, Freeman JS, Potts BM, Myburg AA and Vaillancourt RE (2010) High genome homology between Eucalyptus species. Poster presentation at CRC for Forestry Annual Conference, Fremantle, Western Australia, 17-20th May 2010. Hudson CJ, Freeman JS, Faria DA, Grattapaglia D, Kilian A, Potts BM and Vaillancourt RE (2010). High-density linkage map in Eucalyptus globulus constructed with 500+ F2 progenies using Diversity Array Technology (DArT) and microsatellite markers. Poster presentation at Plant and Animal Genome (PAG) 18 Conference, 9-13th January 2010, San Diego, California. Abstract page 212. Steane, DA, Hudson, CJ, Nicolle, D, Sansaloni, CP, Petroli, CD, Carling, J, Kilian, A, Myburg, AA, Grattapaglia, D, Vaillancourt, RE (2011) DArT markers provide a powerful tool for population genetic analysis and phylogeny reconstruction in v Eucalyptus (Myrtaceae). Poster presentation at the 28th International Botanical Congress, 23rd - 30th July 2011, Melbourne, Australia. Poster abstract P0423 Vaillancourt, RE, Hudson, CJ, Kumar, AR, Myburg, AA, Faria, DA, Grattapaglia, D, Kilian, A (2011) Comparative mapping in Eucalyptus genomes. Oral presentation by RE Vaillancourt at the 28th International Botanical Congress, 23rd - 30th July 2011,
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