High throughput SNP discovery and genotyping in hexaploid wheat

Because of their abundance and their amenability to high-throughput genotyping techniques, Single Nucleotide Polymorphisms ( SNPs) are powerful tools for efficient genetics and genomicsstudies, including characterization of genetic resources, genome-wide association studies and genomicselection. In wheat, most of the previous SNPdiscovery initiatives targeted the coding fraction, leaving almost 98% of the wheat genomelargely unexploited. Here we report on the use of whole- genomeresequencing data from eight wheat lines to mine for SNPsin the genic, the repetitive and non-repetitive intergenic fractions of the wheat genome. Eventually, we identified 3.3 million SNPs, 49% being located on the B- genome, 41% on the A- genomeand 10% on the D- genome. We also describe the development of the TaBW280K high-throughput genotyping array containing 280,226 SNPs. Performance of this chip was examined by genotyping a set of 96 wheat accessions representing the worldwide diversity. Sixty-nine percent of the SNPscan be efficiently scored, half of them showing a diploid-like clustering. The TaBW280K was proven to be a very efficient tool for diversity analyses, as well as for breeding as it can discriminate between closely related elite varieties. Finally, the TaBW280K array was used to genotype a population derived from a cross between Chinese Spring and Renan, leading to the construction a dense genetic map comprising 83,721 markers. The results described here will provide the wheat community with powerful tools for both basic and applied research.