High throughput SNP discovery and genotyping in hexaploid wheat

PLoS One. 2018 Jan 2;13(1):e0186329. doi: 10.1371/journal.pone.0186329. eCollection 2018.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genes, Plant
  • Genotype*
  • Phylogeny
  • Polymorphism, Single Nucleotide*
  • Polyploidy*
  • Triticum / classification
  • Triticum / genetics*

Grant support

The research leading to these results have received funding from the French Government managed by the Research National Agency (ANR) under the Investment for the Future programme (BreedWheat project ANR-10-BTBR-03)- www.agence-nationale-recherche.fr/ - JLG and CF, from FranceAgriMer- 2011-0971 and 2013-0544 - www.franceagrimer.fr - EP, French Funds to support Plant Breeding (FSOV) and from INRA- www.inra.fr - EP. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Magalie Leveugle, Jorge Duarte and Nathalie Rivire are employees of Biogemma. Alessandro Davassi is an employee of Affymetrix. Kellye Eversole is the president and founder of Eversole Associates. The funders provided support in the form of salaries for authors [ML, JD, NR, AD & KE], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.