The recently developed 90K wheat SNP chip (Wang et al.
2014 Plant Biotech J 12, 787) has been used extensively to genotype bread, durum and synthetic wheat accessions from around the world. Besides assaying more than 80,000 gene-associated loci with high accuracy and genotype call rate, the 90K SNP chip provides an accurate and efficient way to compare genotypic datasets generated in different laboratories and to anchor genotypic information to other wheat genomic resources.
Current status of the 90K wheat SNP genotyping assay
- 72K SNP assays reveal polymorphism in worldwide wheat
- 65K SNP loci are genetically mapped
- Genotypes can be called for 55K of the mapped SNP loci in unrelated germplasm
- 10-15K polymorphic SNPs are typically called in bi-parental mapping crosses
- Genotype call rate per sample typically exceeds 95%
- 90K SNPs are gene-associated and connected to various international wheat genotyping and sequencing resources, including the IWGSC flow-sorted wheat chromosome contigs
One of the most intriguing features of the 90K wheat SNP chip is its transferability to related species, which results from its ability to discover and genotype new polymorphism. For example, we have used the 90K SNP chip to construct genetic maps for T. monococcum
and Ae. tauschii
, as well as to tag introgressed alien segments in wheat genetic backgrounds.
Within GRDC Project DAV00127, we are working to get more value out of the 90K SNP chip by developing a capability for imputation. This capability is based on exome sequences from >300 genetically diverse bread wheat accessions including cultivars, landraces and synthetic derivatives.
To illustrate the power of genotype imputation, we investigated its potential to improve genome-wide association studies (GWAS). Using 678 Watkins’ bread wheat accessions that had been phenotyped by Dr U Bansal (PBI Cobbitty) in the field over multiple seasons for response to rust diseases Yr, Lr and Sr, we performed separate GWAS using 31,000 SNPs from the 90K assay, and 344,544 imputed SNPs. Analysis of marker-trait associations at sites around validated loci for rust resistance showed that the imputed SNPs performed similarly to SNPs directly genotyped using the 90K assay, however the imputed SNPs significantly increased marker-density (Figure 1). This example demonstrates the potential of imputation to improve GWAS, as well as to facilitate map-based cloning.
Genotype imputations at a stem rust disease resistance locus on chromosome 7A (grey box). SNP sites directly genotyped using the 90K SNP array are shown as red dots. Imputed SNPs are shown as black dots. 48 genotyped NPS and 1178 imputed SNPs were associated with the resistance locus.
90K SNP genotyping is available to GRDC-funded pre-breeding projects through GRDC Project DAV000127. Contact Kerrie Forrest (firstname.lastname@example.org
) for further information.