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Lincoln University Digital Thesis Lincoln University Digital Thesis Copyright Statement The digital copy of this thesis is protected by the Copyright Act 1994 (New Zealand). This thesis may be consulted by you, provided you comply with the provisions of the Act and the following conditions of use: you will use the copy only for the purposes of research or private study you will recognise the author's right to be identified as the author of the thesis and due acknowledgement will be made to the author where appropriate you will obtain the author's permission before publishing any material from the thesis. Germplasm exploration and phenotyping in Trifolium species for the improvement of agronomic traits and abiotic stress tolerance A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University by Lucy Marie Egan Lincoln University 2020 Abstract of a thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy. Abstract Germplasm exploration and phenotyping in Trifolium species for the improvement of agronomic traits and abiotic stress tolerance by Lucy Marie Egan Trifolium is the most important pastoral legume genus for temperate agriculture. However, there has been little effort into characterising variation in Trifolium accessions. A series of studies utilising pedigree and genomic data were conducted to analyse variation in Trifolium accessions in the Margot Forde Germplasm Centre and in white clover breeding populations. Pedigree analysis experiments were designed to develop pedigree maps, calculate inbreeding and kinship coefficients, calculate the effective number of founders and identify influencing founders and ancestors for Trifolium repens (white clover), Trifolium pratense (red clover), Trifolium arvense, Trifolium ambiguum, Trifolium dubium, Trifolium hybridum, Trifolium medium, Trifolium subterraneum and Trifolium repens x Trifolium occidentale interspecific hybrids. One of the earliest parental white clover accessions identified was ‘North Canterbury Type I’ from 1941. The Type 1 phenotype influenced the population structure of all white clover accessions in the genebank. The relatedness and inbreeding coefficients revealed distinct germplasm pools formed across time that are of interest to pre-breeding efforts. One germplasm pool contained the majority of commercial white clover cultivars, of which they had similar phenotypes. Inbreeding in red clover remained stable in the last three decades, and a relationship between inbreeding and new introductions into the collection was found (r = 0.62). Founding accessions were classed into three phenotype groups; English Broad, English Giant Hybrid and Cotswald Broad. The first synthetic form was identified from parental accessions from English Broad and English Giant Hybrid. ii Within the minor Trifolium species, kinship levels remained below 8%, and no inbreeding was found. T. ambiguum and T. medium had the highest cumulative kinship across the decades. The Australian cultivar ‘Monaro’ had a strong influence over all of the studied accessions in T. ambiguum. Two genome-wide associations studies were designed to test for phenotype-genotype associations. The Mainstay panel had 242 white clover half-sib families, and the Genetic Gain panel had 80 white clover cultivars. The Mainstay panel had stolon density and growth score phenotype data. In contrast, the Genetic Gain panel had yield, clover content, seed yield, flowering duration, the peak number of flowers, leaf size, seed per head, leaf marking, cyanogenesis, normalised transpiration rate and the fraction of transpirable soil water phenotype data. Population structure was identified in the Mainstay panel (k=2), but no subpopulation divergence was present in the Genetic Gain panel. Both panels had rapid linkage disequilibrium decay. A marker-trait association was identified in the Genetic Gain panel for cyanogenesis. However, when the marker was tested against the marker dosage, it was not significant. The results of the genome-wide association studies emphasise the highly variable and heterozygous nature of white clover populations and cultivars. Keywords: Trifolium, white clover, red clover, breeding, forage, pedigree, relatedness, inbreeding, founders, germplasm, pre-breeding, ancestors, transpiration, drought, white clover, normalised transpiration rate, fraction of transpirable soil water, genome-wide association, population structure. iii Acknowledgements I truly believe that it takes a village to get a PhD student across the line. This PhD research and thesis would not have been possible without many people, who I am extremely thankful to. Firstly, I would like to thank my supervisors, Dr Rainer Hofmann (Lincoln University) and Dr Valerio Hoyos-Villegas (McGill University, formerly AgResearch) for their immense knowledge, patience, guidance and support throughout my project. Their doors were always open, and nothing was ever a problem. Even when Valerio moved to Canada, his support and speed at replying never waned. I am very grateful for Dr Chris Winefield (Lincoln University) and Dr Ross Bicknell (Plant and Food Research) for teaching me the fundamentals of plant breeding, both practically and in theory. Without their passion and commitment to teaching, I do not believe I would be in this position. Throughout this PhD, I had help from many incredible staff at AgResearch. Thank you to Dr Aurelie Laugraud, Dr Ken Dodds, Dr Rachael Ashby, Dr Abdul Baten, Dr Ruy Jauregui, Paul MacLean and Dr Chikako van Koten for their help with bioinformatics and statistics. Thank you to Angus Heslop and Tony Hilditch for their help, practical advice and discussions regarding field trials. Thank you to Dr Andrew Griffiths and Dr Marty Faville for their advice and knowledge with the genome-wide association studies. Thank you to Dr Marcelo Carena and Dr Tony Conner for their continuous support with my project. I would like to thank AgResearch for allowing me to complete my PhD at the organisation. A special thanks to Dr Jeanne Jacobs for being a fantastic mentor and support person, and for always empowering women in science. I would like to thank Keith Widdup for awarding me an AgResearch summer studentship in 2014 and spiking my interest in plant breeding. His passion and encouragement have led me to pursue plant breeding as a career. Thank you to the Lincoln University staff who have provided me with assistance; Dr Dean O’Connell for statistics advice and Stephen Stilwell for help in the lab. Thank you to Dr Paul Shaw from the James Hutton Institute for help with his programme, Helium. Without him, there would be no pedigree maps. Thank you to the following companies and trusts for the financial support and awards throughout the PhD: the Foundation of Arable Research postgraduate scholarship, the Manning Seed award, the John W & Carrie McLean Trust scholarship, the Beef and Lamb NZ Generic Ag scholarship, the Graduate Women Canterbury Trust travel award and the Royal Society of New Zealand Canterbury branch travel grant. I would like to acknowledge the financial support from Pastoral Genomics+ and AgResearch. iv Finally, I wish to thank my close friends and family, parents, sister and brother-in-law, for their love and support. I dedicate this thesis to my nephew, Jack, in hopes that this will show him that anything is possible if you set your mind to it, and that growth is not possible in your comfort zone. v Table of Contents Abstract .................................................................................................................................................. ii Acknowledgements ............................................................................................................................... iv Table of Contents ................................................................................................................................. vi List of Tables ........................................................................................................................................ ix List of Figures ........................................................................................................................................ x Abbreviations ...................................................................................................................................... xiv Chapter 1 Introduction .....................................................................................................................1 1.1 The Trifolium genus ..................................................................................................................1 1.2 Germplasm centres and pre-breeding .......................................................................................1 1.2.1 Plant variation in breeding programmes ...................................................................... 2 1.3 Gaps in knowledge ....................................................................................................................3 1.4 Objectives .................................................................................................................................3 1.5 Outline of the thesis ..................................................................................................................4 Chapter 2 Literature review .............................................................................................................5 2.1 Introduction ...............................................................................................................................5
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