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Journal Articles PLoS ONE Year : 2018

High throughput SNP discovery and genotyping in hexaploid wheat

Magalie Leveugle
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Jorge Duarte
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Nathalie Rivière
Jacques Le Gouis

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.
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hal-02628543 , version 1 (26-05-2020)

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Hélène Rimbert, Benoît Darrier, Julien Navarro, Jonathan Kitt, Frédéric Choulet, et al.. High throughput SNP discovery and genotyping in hexaploid wheat. PLoS ONE, 2018, 13 (1), pp.1-19. ⟨10.1371/journal.pone.0186329⟩. ⟨hal-02628543⟩
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