Linkage disequilibrium analysis of hexaploid wheat (Triticum aestivum L.)

Abstract

There has recently been a renewed interest in using a whole-genome approach for identifying regions with relatively small effect on a particular trait of interest. One method that has proven effective in human populations is association mapping or linkage disequilibrium (LD) mapping. With focus on identifying the statistical correlations between marker allele frequency and phenotypes, association mapping, as a result, typically requires a high density marker map and a firm understanding of the extent and patterns of LD in the population. This study assesses the feasibility of applying LD mapping in hexaploid wheat research for the fine mapping of traits. Adequate marker coverage of the large wheat genome was attained providing a framework enabling the examination of the extent of LD in this species. Results presented in this thesis illustrate how extensive LD is in locally adapted populations of hexaploid wheat, extending up to I00cM in some cases. It is also apparent that statistical associations are not limited only to markers on the same chromosome but include those on different genomes and chromosome groups. One of the main focuses of this study was to evaluate the effect of genetic and evolutionary factors on the levels of statistically significant LD. Type- I error rate was successfully reduced by accounting for population structure and the presence of rare alleles in the data sets. This research has provided a base from which patterns of LD can begin to be understood in other populations and subsequently assess the applications of association mapping in inbreeding crop species, specifically Triticum aestivum L.