The 5DS Physical Map Provides Insights into the Wheat D-Genome Structure and Organization

We report the first high quality physical map of chromosome 5DS, with a density of 10.5 markers/Mb. The final map, constructed by LTC software, consisted of 164 contigs, of which 45 were organized into 21 supercontigs, and was estimated to cover 176 Mb of the 258 Mb-long chromosome arm. The largest contig spanned 6649 kb and the N50 value was 2173 kb, including short contigs with 5 or fewer clones. A total of 1864 molecular markers were assigned to the map, anchoring 100 of the 120 contigs (>5 clones) that constitute ~95% of the cumulative length of the map. Furthermore, 80 of the anchored contigs were ordered along 5DS deletion bins, which suggested small-scale breaks in syntenic blocks through comparative analyses. A discrepancy in cytogenetic estimates of the physical sizes of the deletion bins was observed, in which the cytogenetic size of the 0.63-0.67 bin was concluded to be significantly underestimated. The analysis of the gene space revealed an increasing gene density towards the telomere, organized into gene islands. The 5DS map provides a chromosome-specific view into the organization and evolution of the D genome of bread wheat.