Ultra-dense genetic map of durum wheat x wild emmer wheat developed using the 90K iSelect SNP genotyping assay

Wild emmer wheat (T. turgidum ssp. dicoccoides, genome BBAA) gene pool is an important source for wheat research and improvement. To utilize this resource, we hybridized wild emmer wheat (subpopulation judaicum, accession Zavitan) with durum wheat (T. turgidum ssp. durum, cv. Svevo) and developed an F-6 recombinant inbred line (RIL) population. The wheat 90K iSelect SNP genotyping assay was used for genotyping of the RILs, detecting segregation for 16,387 polymorphic markers. The genetic map was constructed based on the genotypic data of 140 RILs and included a total of 14,088 markers grouped into 2,296 genetic loci in 14 linkage groups, corresponding to the 14 chromosomes of tetraploid wheat. The map was 2,110 cM long with an average distance of 0.92 cM between adjacent markers. The B genome was slightly more polymorphic (57 %) for co-dominant SNP markers than the A genome. The map included 1,012 null allele markers, in which only one SNP allele was detected, and the frequency of these markers in the B genome of wild emmer greatly exceeded that of the A genome (69 and 31 %, respectively), which may reflect a greater rate of genomic changes in the B genome. Comparison of our mapped SNP sequences with the barley genome revealed that most of the markers (92.4 %) were syntenic. This ultra-dense SNP-based genetic map with a high level of synteny to barley provides a useful framework for genetic analyses of important traits, positional cloning and marker-assisted selection, as well as for comparative genomics and genome organization studies in wheat and other cereals.