Exploiting Survey Sequences for SNP Discovery

In wheat, because of the lack of a reference sequence, the development of SNPs has long been limited to the coding fraction. However, this fraction represents less than 3% of the wheat genome, leaving a significant part of the genome largely unexploited in terms of SNP discovery. The recent development of a draft assembly of the hexaploid wheat genome by the International Wheat Genome Sequencing Consortium (IWGSC) changed this paradigm. Indeed, this assembly provides the community with the opportunity to mine for SNPs in the three different compartments of the wheat genome, namely genes, non-repetitive intergenic regions and repetitive fraction. To this aim, these sequences were used as a reference for the mapping of whole genome resequencing data from four European and four Australian wheat varieties. The genic fraction was identified using RNAseq data and a set of ~187,000 transcriptionally active regions covering 355 Mb was selected. Non-repetitive intergenic regions were defined as untranscribed regions showing no homology with known repeats. This represented roughly 6 Gb. The repetitive fraction was mined for SNPs through the design of ~2.5 million ISBP markers, with a cumulative length of 523 Mb. Eventually, almost four million SNPs were discovered with roughly 440,000 in genes, more than 2.6 million in non-repetitive intergenic regions and approximately 720,000 in ISBPs. The detailed outcomes of this initiative will be presented, including the patterns of SNP frequency and distribution in the different compartments, as well as the virtual ordering of gene-derived SNPs along the 21 wheat chromosomes.