High throughput SNP discovery and genotyping in hexaploid wheat

Abstract

Because of their abundance and their amenability to high-throughput genotyping techniques, Single Nucleotide Polymorphisms (SNPs) are powerful tools for efficient genetics and genomics studies, including characterization of genetic resources, genome-wide association studies and genomic selection. In wheat, most of the previous SNP discovery initiatives targeted the coding fraction, leaving almost 98% of the wheat genome largely unexploited. Here we report on the use of whole-genome resequencing data from eight wheat lines to mine for SNPs in 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-genome and 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 SNPs can 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.

Fig 1. Distribution of the TaBW280K SNPs along chromosome 3B.

Densities of Polymorphic High Resolution SNPs (light blue), Off-Target Variants (dark blue) and non-converted (grey) SNPs are computed in a 10-Mb sliding window (step 1 Mb). The X-axis represents the position on chromosome 3B pseudomolecule (in Mb).

Fig 2. Proportion of TaBW280K SNP clustering categories.

For each chromosomes, the percentage of each category is displayed: PHR (light blue), OTV (dark blue), MHR (green), NMH (purple), CRBT (yellow) and Others (red).

Fig 3. Phylogenetic relationships between 96 wheat accessions.

(A) Ward dendrogram showing phylogenetic relationships between wheat accessions revealed by PHR and OTV SNPs. (B) Neighbour-joining tree showing phylogenetic relationships revealed by OTV SNPs only. Accessions are numbered following the S2 Table and colored according to their geographical origins: Eastern Asia (orange), Caucasus (pink), Central Asia (red), Western Europe (blue), Eastern Europe (purple) and Mediterranean (green).