High throughput marker development from the repetitive fraction of the wheat genome

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. In the past five years, many initiatives have been launched at the international level to develop SNP markers, mainly from genic regions. However, because of the reduced polymorphism level in coding regions and the low gene density, gene-derived SNPs do not allow to efficiently saturating the hexaploid wheat genome. By exploiting the repetitive fraction of the wheat genome, Insertion Site-Based Polymorphism (ISBP) markers can reach a density of one marker per 5-10 kb. In addition, ISBPs have been demonstrated to be an invaluable source of genome-specific SNPs that have the potential to complement gene-derived SNPs. The so-called ISBP-SNPs have been shown to meet the five main requirements for their utilization in marker-assisted selection: flexible and high-throughput detection methods, low quantity and quality of DNA required, low cost per assay, tight link to target loci and high level of polymorphism in breeding material. To fully benefit from the potential of these markers, we have implemented a new procedure for the high throughput discovery of ISBP-SNPs that led to the design of roughly 20,000 SNPs in elite cultivars. A subset of ~3500 SNPs was used to genotype wheat lines using the KASPar technology and the results have been used for genetic mapping, LD mapping and association studies. Here we report on the most recent results and future prospects, including new technologies for SNP discovery and genotyping.