A High-Density, SNP-Based Consensus Map of Tetraploid Wheat (Triticum turgidum L.). Useful for Durum and Bread Wheat Genomics and Breeding

Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map from 13 bi-parental populations obtained from durum wheat (Triticum turgidum ssp. durum), emmer (T. turgidum ssp. dicoccum) and wild emmer (T. turgidum ssp. dicoccoides). Component maps were recalculated from raw genotypic data using a common mapping procedure. The consensus map harbored 30,144 markers (including 26,626 genic-SNPs and 791 SSRs, among others), half of which were present in at least two component maps. The final map spanned 2,631 cM with complete genome coverage. Comparison with hexaploid wheat maps indicated that tetraploid wheat presents fewer regions with suppressed recombination, thus making this map valuable for the A and B genomes of wheat in general. Sequence similarity analysis allowed us to relate genic-SNPs to chromosome-specific transcripts from the Chinese Spring survey sequence. Dense patterns of homeologous relationships have been established between the A- and B-genome maps and between non-syntenic homeologous chromosome regions tracing to ancient translocation events. The map is thus valuable to infer the map location of target loci/QTL homeologs. The consensus map is being used as a framework for association mapping and meta-QTL analyses, the results of which are presented. Because most SNP and SSR markers were previously mapped in bread wheat, the consensus will facilitate a more effective integration and exploitation of genes and QTLs for wheat breeding purposes.