Towards an SNP-Based Consensus Map of Durum Wheat

High-density Single-Nucleotide Polymorphism (SNP) arrays are becoming the golden standard for genotyping, even in polyploid species with a large and complex genome such as durum wheat (T. turgidum spp. durum). While a growing collection of SNPs is available in bread wheat, limited information is available for durum wheat. Therefore, durum wheat genetics and breeding would greatly benefit from the availability of an SNP-based consensus map with robust links with bread wheat. The wheat Illumina iSelect 90k array (Akhunov et al. submitted) provides ca. 76,000 functional SNPs, 8,000 of which are durum-specific. This SNP array was used for genotyping six T. durum x T. durum mapping populations and four interspecific populations (T. durum x T. dicoccum or T. dicoccoides). The intraspecific populations allowed us to map from 5,500 up to 6,200 SNPs/population with an average SNP density of ca. 1 SNP/0.3 cM. These populations differed in local marker density, suggesting the presence of extended identical-by-descent regions, major selective sweeps and/or variation in crossing-over frequency. The T. durum x T. dicoccum or T. dicoccoides populations showed higher polymorphism, with up to 12,000 SNPs/population. The consensus map of chromosome 3B  (222 cM) includes 2,249 markers. While the order of SNP loci was highly consistent between the single maps as well as between the component and the consensus maps, a small number of loci deviated from perfect collinearity. The progress on the assembly of the consensus map for other chromosomes will be reported.