Tetraploid Wheat Germplasm Diversity Scan based on the Durum Wheat Genome Assembly

The genome of modern durum wheat (DW) cultivar Svevo has been assembled based on a combination of whole genome shotgun sequencing (270X), NRGene deNovoMagic assembler, high-resolution genetic mapping obtained from the cross between Svevo DW and Zavitan wild emmer wheat (WEW) and scaffold ordering based on chromosome conformation capture sequencing (Hi-C). The assembly consisted of 9.96 Gb of ordered sequences with 66,559 high-confidence (HC) genes. We used this resource to investigate the genetic diversity and ancestry of tetraploid wheat germplasm. iSelect 90K SNP array was used to genotype a global collection of 1,858 non-redundant accessions covering the whole range of tetraploid genetic resources from WEW, cultivated emmer (CEW), durum landraces (DWL) and modern durum cultivars (DWC). We performed a whole-genome scan for population genetic structure, selective sweeps together with the tetraploid QTLome projection. Average whole-genome genetic diversity were pWEW= 0.285, pCEW = 0.254, pDWL = 0.201, pDWC = 0.192, with an overall WEW-DWC decrease in diversity equal to 32.6%. Diversity depletions were more relevant in peri-centromeric regions (pWEW_C = 0.269, pDWC_C = 0.151) as compared to the highly-recombinogenic distal regions (pWEW_R = 0.287, pDWC_R = 0.250). From WEW to DWC, 68 chromosome regions were subjected to diversity depletion, affecting up to 38% of the genome in total: 19 of these were associated to WEW-CEW transition, 41 to CEW-DWL and 8 to DWL-DWC. The gene content of these regions is being explored in relation to known QTL content and haplotype analysis. Overall, the analysis pointed out the chromosome regions subjected to strong selective sweeps during the domestication and breeding selection, on one side, and those regions that would benefit from targeted genetic diversity restoration on the other side.