High throughput SNP discovery and genotyping in hexaploid wheat

PloS One
Hélène RimbertEtienne Paux

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 var...Continue Reading

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Citations

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Datasets Mentioned

BETA
PRJEB16737

Methods Mentioned

BETA
genotyping
RNA-seq
Assay
chip
chips

Software Mentioned

IsbpFinder
HomRO
HomFLD
Affymetrix
BWA
RepeatMasker
SNPolisher [UNK]
POPseq
Affymetrix Power Tools ( APT )
Samtools

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