High Throughput SNP Discovery and Genotyping in Hexaploid Wheat

In wheat, the deployment of marker-assisted selection has long been hampered by the lack of markers compatible with high-throughput cost-effective genotyping techniques. The recent advent of second generation sequencing changed this paradigm by allowing for the first time to access the giant 17-Gb bread wheat genome. In the framework of the International Wheat Genome Sequencing Consortium (IWGSC), a draft assembly of the hexaploid wheat genome was generated. This assembly provides the community with the opportunity to mine for SNPs in non-repetitive regions, either genic or non-genic, as well as in repeats. By combining whole-genome resequencing on eight wheat varieties with targeted sequence capture on 96 wheat accessions, more than three million SNPs were identified. In the framework of the BreedWheat project, a large public-private French collaborative initiative, an Affymetrix Axiom genotyping array containing approx. 423,000 SNPs was designed. This chip has been used to genotype a set of ~7,000 wheat accessions corresponding to elite varieties as well as genetic resources representing the world-wide diversity. Genotyping data are currently being used to perform genetic and LD mapping, association studies, genetic resources characterization as well as genomic selection.