“Axiom®CicerSNP Array”: A High-Throughput SNP Genotyping Platform for High Resolution Genetic Analysis and Breeding Applications in Chickpea

With an objective to develop a high-throughput SNP genotyping platform in chickpea, 70,463 high quality non redundant SNPs were selected using an assortment of the criterion from a pool of 4.9 million SNPs generated from several large-scale re-sequencing projects. Based on p-convert score ≥ 0.3, a set of 61,174 SNPs was selected of which 50,590 SNPs were tiled on Affymetrix® Axiom® genotyping array. Among the selected set of SNPs 22.18% SNPs represent coding region of 4,984 different genes. On an average 1,402.36 SNPs from coding region were selected with Ca4 accounting for maximum (3,280 SNPs) and Ca5 for minimum (764 SNPs). In order to validate and assess the effectiveness, the developed Axiom®CicerSNP array was used for genotyping two intra-specific chickpea recombinant inbred line viz. ICCRIL03 (ICC 4958 X ICC 1882) and ICCRIL04 (ICC 283 X ICC 8261). High success and polymorphic rate was observed on analysing the genotyping data, resulting in high-quality genotyping data for 13,099 (25.89%; ICCRIL03) and 18,059 (35.7%; ICCRIL04) SNPs. By using these data, high-density genetic maps comprising 13,679 SNPs spanning 1033.67 cM size for ICCRIL03 population and 7,769 SNPs spanning 1076.34 cM for ICCRIL04 population have been developed. Using multi-location, multi-season phenotyping data for drought tolearnce related traits on these RILs, QTL analysis identified several new as well as known QTLs for drought tolerance related traits. Higher precision and high-throughput genotyping of this arrays is expected to accelearte both genetic studies and molecular breeding applications in chickpea.