Development and Application of Cost-Effective Illumina BeadXpress-Based SNP Assays for Diversity Analysis in Chickpea and Pigeonpea

Single nucleotide polymorphisms (SNPs) are ideal markers due to their greater abundance in the plant genomes. Several type of genotyping platforms for assaying a large number of SNPs are available especially for undertaking genome wide association studies (GWAS)  In cases like marker-assisted selection (MAS) where only few markers are required for genotyping a set of potential lines, high throughput SNP genotyping platform (e.g. iScan or Infinium) may not be cost-effective. In this scenario, GoldenGate assays based on VeraCode technology using Illumina BeadXpress platform seems to be the most cost-effective platform. Therefore, with an objective of developing cost-effective SNP genotyping platforms in chickpea and pigeonpea, two leading legumes crops of semi-arid tropic regions, ca. 10,000 SNPs in each species were analysed for polymorphism information content (PIC) and assay designing tool (ADT) scores. As a result, two sets of SNPs one each for chickpea (96 SNPs) and pigeonpea (48 SNPs) were selected and used for designing custom Oligo Pool Assays (OPAs) for Illumina BeadXpress genotyping platform. These assays were used for genotyping reference sets (ca. 300 genotypes) in each species. The mean PIC value of assayed SNP markers was 0.31 and 0.32 in chickpea and pigeonpea, respectively. In terms of grouping of genotypes, while no unique pattern was observed in chickpea reference set, two major groups are observed in the case of pigeonpea reference set. In summary, these assays are highly informative and cost-effective for undertaking diversity analysis and molecular breeding applications in these legume species.