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The Characterisation of Genetic Diversity of a Collection of Perennial Ryegrass (Lolium Perenne L.)

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The Characterisation of Genetic Diversity of a Collection of Perennial Ryegrass (Lolium Perenne L.) The Characterisation of Genetic Diversity of a Collection of Perennial Ryegrass (Lolium perenne L.) Sarah Katherine McGrath September 2008 Submission for Ph.D. University of Dublin, Trinity College 1 Declaration I, the undersigned, hereby declare that I am the sole author of this dissertation and that the work presented in it, unless otherwise referenced, is my own. I also declare that the work has not been submitted, in whole or in part, to any other university or college for a degree or other qualification. I authorize the library of Trinity College Dublin to lend or copy this dissertation on request ________________________________ Sarah Katherine McGrath 2 Acknowledgements I would firstly like to thank the supervisors of my Ph.D. thesis, Drs Susanne Barth and Trevor Hodkinson. Without their patience, immense support and enormous knowledge, this thesis would not have been completed. I would like to thank Dr Nicolas Salamin, University of Lausanne, for his help with the design of chloroplast microsatellite markers, Dr Maeve Harbourne, Trinity College Dublin, for her help with population genetics software, Dr Andreas Frohlich, Teagasc Oak Park, for all his help with the biochemical analysis and HPLC, and Dr Jim Grant, Teagasc Kinseally, for his help with statistical analysis of biochemical data. I would also like to thank Monica Francioso and Simona Lamorte for their assistance with the biochemical analysis, Teresa Marie Charles for her help with genotyping and with the measurement of morphological traits, and Padhraig Hennessy, Alan Kelly and Daniele Zen for their help with the measurement of morphological traits. Thank you to Drs Radomir Capka and Vladimir Cernoch of the Hladke Zivotice Breeding Station, Czech Republic, Dr Alan Stewart of PGG Wrightson, New Zealand, and Dr Ian Thomas of the Genetic Resources Unit, IGER, Wales for providing seed material for the analysis performed in this study. Thanks to the Teagasc Walsh Fellowship Programme and the Irish Department of Agriculture, Fisheries and Food under the “Genetic Resources for Food and Agriculture Scheme” for partially funding this work. Finally I would like to thank Paul Fabre for his excellent help proofreading the manuscript and checking all the references and for all his valued support during my Ph.D. and also my parents who always believed I could do it. 3 Abstract Perennial ryegrass ( Lolium perenne L.) is a member of the Poaceae family, is native to Europe, the Near East and North Africa and is grown in all the temperate climate areas of the world as a forage and turf grass. Due to its persistence, palatability and nutritive value for ruminants, it is a principal component of pastures, and the most important forage species in Ireland. The primary aim of this thesis was to characterise the level of diversity in a large genetic resource collection of L. perenne germplasm held at Teagasc, Oak Park. Molecular markers, both chloroplast and nuclear SSRs, biochemical characters (water soluble carbohydrate, crude protein, and dry matter), and morphological characters (vegetative and flowering) were used to characterise this diversity, as well as population differentiation, and geographic patterns. Levels of diversity in all systems were found to be high in this collection. Primers to amplify microsatellite markers from the chloroplast genome of Lolium perenne were designed and optimized using de novo sequencing and in silico sequences. With one exception, each locus was polymorphic with a range from two to nine alleles in L. perenne . The newly developed primer pairs cross-amplified in different species of Lolium and in 50 other grass species representing nine grass subfamilies. These markers were then used to characterise chloroplast genetic diversity at allelic and haplotypic level in 104 accessions of Lolium perenne, other Lolium species, Festuca species and ×Festulolium cultivars. Furthermore, genetic relationships between the accessions and biogeographic distribution of haplotypes were investigated using a range of population genetic diversity measures and an Analysis of Molecular Variance (AMOVA). An extremely high number of 511 haplotypes was detected in 1,575 individuals possibly attributable to natural and anthropogenic migration. Much of the L. perenne European ecotype diversity (61%) could be attributed to within population variance. Plastid gene pools and maternal lineages for L. perenne could be clearly identified. Evidence was found showing a most likely migration route of L. perenne into Ireland from southern regions of Europe northwards. 4 Morphological variation of 13 vegetative and reproductive traits was characterised for 2,481 individuals from 50 L. perenne accessions, a mixture of Irish and European ecotypes and cultivars. Considerable levels of among and within population variation was found across traits. Principal component analysis and UPGMA dendrograms were able to separate ecotypes from cultivars. Cultivars generally had later dates of ear emergence, better spring and summer growth, longer rachis length and more spikelets per spike than ecotypes. Correlation and regression analysis were used to assess relationships between traits and strong positive relationships were seen between reproductive characters, i.e. rachis length with spikelets per spike, florets per spikelet and glume length. The strong relationship between rachis length and the other reproductive characters suggested that rachis length could be used as a predictor for reproductive performance. Later flowering was correlated with improved spring and summer growth. Water soluble carbohydrate (WSC; glucose and fructose determined by HPLC), crude protein (determined via LECO analysis), and dry matter contents were recorded for 1,320 individuals, pooled into 132 samples from 33 L. perenne ecotypes and cultivars at five different harvest time points across the 2004 growing season. While, in general, the cultivars had higher WSC contents than the ecotypes, individual ecotypes did show potential to be used in breeding programmes, as they showed higher values than all other accessions at particular cutting points. In correlation analyses, positive relationships were shown between dry matter and glucose both early and late in the growing season, and this was in agreement with the amount of leaves compared to stem at these times in the growing season. PCA analysis allowed the separation either between cultivars and ecotypes, or between tetraploid cultivars and the rest of the accessions at four out of five cutting points. In the ANOVA analysis, cutting point was the most significant factor influencing the variation in the traits. Eight nuclear SSR markers were used to characterize genetic diversity in 928 individuals from 40 diploid ecotypes and cultivars of L. perenne. High levels of genetic diversity (0.82, Nei’s gene diversity, over all accessions) and high numbers of alleles (22.25 average number of alleles per locus) was found. An average polymorphic information content (PIC) value of 0.81 across all loci was found. When deviations from Hardy-Weinberg equilibrium were tested, the majority of populations 5 had an excess of homozygotes. Very low levels of linkage disequilibrium were found between pairs of loci tested. AMOVA analysis and F statistics were used to test partitioning of variation, and most variation was found within populations (e.g. 31% for glume length in ecotypes). UPGMA, PCA and STRUCTURE analysis all gave similar patterns of relationships between populations, where relationships with high bootstrap support on the UPGMA dendrogram were also seen in the other analyses. The overall results of the thesis are discussed in the context of plant breeding programmes and natural population genetic variation. Strategies for incorporation of the results of the thesis (and the novel markers developed within) into plant breeding programmes are suggested. 6 Chapter 1 – General introduction to the characterisation of genetic diversity of a collection of perennial ryegrass ( Lolium perenne L.) 1.1 Introduction ............................................................................................................ 1 1.1.1 Lolium perenne and close relatives ................................................................... 1 1.1.2 Breeding varieties of Lolium perenne ............................................................... 3 1.1.3 Genetic resources .............................................................................................. 4 1.1.4 Diversity ............................................................................................................ 6 1.1.5 General aims of the thesis ................................................................................. 7 Chapter 2 - Characteristion of Lolium perenne L. and related species using chloroplast SSR markers 2.1 Introduction ............................................................................................................ 9 2.1.1 Chloroplast DNA .............................................................................................. 9 2.1.2 Chloroplast simple sequence repeat (SSR) Markers ......................................... 9 2.1.3 Use of chloroplast DNA markers to assess relationships in the Festuca/Lolium complex .................................................................................................................... 10 2.1.4 Use of chloroplast DNA markers to characterise genetic variation in Lolium perenne ....................................................................................................................
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