1 Patterns of linkage disequilibrium in multiple populations

Application of association analyses in plant breeding populations has the potential to revolutionize crop genetics. To determine the optimal strategies for implementing association analysis in wheat (Triticum aestivum L. subsp. aestivum) we analysed the structure of linkage disequilibrium (LD) across the genome in two distinct populations of CIMMYT wheat breeding germplasm. LD within a total of 645 advanced lines bred during the last 2 decades and distributed via CIMMYT Elite Spring Wheat Yield Trials and 160 synthetic hexaploid wheat (SHW) have been examined. Plant materials were gentoyped with DArT markers plus additional microsatellite markers on a smaller set of lines to compare LD measures among marker technologies. Variable pattern of LD among chromosomes and the two marker technologies was scored. Different patterns of LD decay were observed for advanced wheat lines and SHW. LD dropped faster in SHW and a lower percentage of loci pairs in LD was detected demonstrating the usefulness of SHW for high-resolution association analyses