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.
Highlights
Because they are the most abundant type of polymorphism in plant and animal genomes and because they are amenable to high-throughput, cost effective genotyping technologies, Single Nucleotide Polymorphisms (SNPs) have been adopted as the markers of choice in genetics
Despite the fact that this technique has the potential to sample a higher fraction of the genome and especially intergenic regions that are not targeted by exome capture, the large amount of missing data limits SNP discovery
For SNPs located in low-copy regions, the repeat-masked contigs were used as a reference
Summary
Because they are the most abundant type of polymorphism in plant and animal genomes and because they are amenable to high-throughput, cost effective genotyping technologies, Single Nucleotide Polymorphisms (SNPs) have been adopted as the markers of choice in genetics. Despite the fact that this technique has the potential to sample a higher fraction of the genome and especially intergenic regions that are not targeted by exome capture, the large amount of missing data limits SNP discovery This approach was used by Jordan et al [10] on a set of 62 diverse hexaploid lines and Kobayashi et al [13] on the NIAS Japanese Wheat Core Collection consisting of 96 lines. Noticeable exceptions to complexity reduction approaches are the works conducted by Lai et al [14] and Montenegro et al [15] who used whole-genome resequencing data from 16 and 18 wheat accessions, respectively, to detect more than four million and 36.4 million SNPs on group 7 chromosomes and at the whole genome level, respectively These two studies included mainly cultivars from Australia, leaving a significant part of the genetic diversity unexplored
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