Construction and assessment of tools for comparative structural genomic studies in white clover (Trifolium repens L.)

Abstract

White clover is an allotetraploid legume with a genome size of ca 960 Mb and is widely used in Irish grasslands to improve the nutritional value of the forage by increasing the relative amounts of nitrogen present. White clover is closely related to Medicago truncatula, the diploid (genome size of ca 500 Mb) model legume chosen to study the symbiotic genetic programmes of plants and facilitate the genetics and breeding of important legume crops.
This thesis describes the construction of a genetic map of a white clover mapping population composed of 94 F1 progeny bred in the Institute of Grassland and Environmental Research (UK) from parents S1S4 and R3R4. The genetic map was constructed using amplified fragment length polymorphism markers and white clover microsatellite markers from previously published white clover maps. The thesis also details a glasshouse and field based phenotypic analysis carried out on morphological traits which allowed quantitative trait loci (QTL) to be detected on the genetic linkage map of white clover. Due to the high correlation between the traits measured, both conservation of QTLs across environments and co-localisation of QTLs for related traits were observed in this study.
A BAC library of one of the family parents, R3R4, was constructed using pIndigo BAC-5, consisting of over 37,000 clones with an average insert size of 85 Kb, representing a threefold genome coverage. A preliminary sequence analysis was carried out where 700 BAC clones were sequenced on both ends. Results showed that over 50% of the BAC-ends had a correspondence with the Medicago genome sequence; however only 16 of the BAC-end sequence pairs had homology within a span of 20 to 200 Kb in M. truncatula. The level of synteny between white clover and M. truncatula was assessed by comparative structural genomics, where five BAC clones of the white clover library were sequenced to sixfold coverage and their sequences were compared to the corresponding M. truncatula sequences.

Date of Award	14 Apr 2008
Original language	English
Awarding Institution	Aberystwyth University
Supervisor	Marilyn Elizabeth Allen (Supervisor), Glyn Jenkins (Supervisor), Dan Milbourne (Supervisor) & Michael Terence Abberton (Supervisor)