An integrated physical map of simple sequence repeats in bread wheat

Physical mapping of DNA-based markers in wheat has been greatly facilitated due to the availability of deletion stocks, which constitute an ideal material for mapping these markers to specific chromosomal regions or bins to create physical landmarks. In the present study, the available physical maps for wheat SSRs were enriched by addition of 128 new SSR loci that belonged to wheat gSSRs and brachypodium gSSRs and EST-SSRs. This led to the development of an integrated physical map of 2,031 wheat SSR loci. A maximum of 765 loci (37.67%) were mapped on sub-genome B followed by the 651 loci (32.05%) on sub-genome D and 615 loci (30.28%) on sub-genome A, thus giving a mean resolution of 7.8 Mb between any two SSR loci. Relative to genomic SSRs (gSSRs), the EST-SSRs of brachypodium showed greater transferability in cv. Chinese Spring. Using 704 SSR loci which were mapped genetically as well as physically, a comparison was made between genetic and physical maps to determine the distribution of recombination frequencies (cM/Mb) in different regions of the wheat genome. Recombination frequencies within the individual bins ranged from 0.01 cM/Mb (low recombination) to 13.16 cM/Mb (high recombination), suggesting an uneven distribution along the chromosomes or chromosome arms. Hopefully, the integrated physical map presented in this communication may prove useful in the currently on-going whole genome sequencing of wheat genome through alignment of BAC contigs. A comparison of integrated physical map with genetic linkage map will also facilitate on-going and future genomics research.