Development of Resources for Mapping, GWAS and Allele Mining in Tetraploid Wheat Based on Svevo Durum Reference Sequence

The assembled Svevo durum wheat genome and the iSelect wheat 90K SNP array were used as a base to characterize a world-wide tetraploid wheat collection. We report on the diversity pattern of 1,854 non-redundant accessions from all known Triticum turgidum subspecies. The genetic diversity survey relied on a common genotype-calling pipeline from AgriBio supported by 17 tetraploid linkage maps. The pipeline yielded 17,416 informative single-locus SNPs anchored to the Svevo genome. Among the wild emmer (WEW), domesticated emmer (DEW), durum wheat landraces (DWL) and durum wheat cultivars (DWC), WEW showed the highest and uniform diversity across the whole genome, providing a reference for cross-comparison with DEW, DWL and DWC. Extended diversity depletions associated to domestication were found particularly in pericentromeric regions. Some 38.2% of DW genome was affected by strong genetic bottleneck/selection events leading to diversity depletions. Six extended regions showed increased genetic diversity associated to DEW-DWL and DWL-DWC transitions. Population structure revealed multiple subsequent events of population differentiation associated to human-driven dispersal routes. This analysis provides the basis for a more informative re-sequencing towards a tetraploid pan-genome. Sub-panels have already been used for GWAS analysis, allowing us to identify GWAS-QTL that can be readily used in breeding. GWAS-QTLs for grain yield components (grain size and grain number per spike) and resistance to diseases have been identified using a subpanel of Mediterranean DW landraces. These resources allowed us to map QTLs at an improved resolution (1 cM confidence interval) and readily scan the genome for underlying candidate genes.