Development and evaluation of high-density Axiom (R) CicerSNP Array for high-resolution genetic mapping and breeding applications in chickpea

To accelerate genomics research and molecular breeding applications in chickpea, a high-throughput SNP genotyping platform 'Axiom (R) CicerSNP Array' has been designed, developed and validated. Screening of whole-genome resequencing data from 429 chickpea lines identified 4.9 million SNPs, from which a subset of 70463 high-quality nonredundant SNPs was selected using different stringent filter criteria. This was further narrowed down to 61174 SNPs based on p-convert score 0.3, of which 50590 SNPs could be tiled on array. Among these tiled SNPs, a total of 11245 SNPs (22.23%) were from the coding regions of 3673 different genes. The developed Axiom (R) CicerSNP Array was used for genotyping two recombinant inbred line populations, namely ICCRIL03 (ICC 4958 x ICC 1882) and ICCRIL04 (ICC 283 x ICC 8261). Genotyping data reflected high success and polymorphic rate, with 15140 (29.93%; ICCRIL03) and 20018 (39.57%; ICCRIL04) polymorphic SNPs. High-density genetic maps comprising 13679 SNPs spanning 1033.67 cM and 7769 SNPs spanning 1076.35 cM were developed for ICCRIL03 and ICCRIL04 populations, respectively. QTL analysis using multilocation, multiseason phenotyping data on these RILs identified 70 (ICCRIL03) and 120 (ICCRIL04) main-effect QTLs on genetic map. Higher precision and potential of this array is expected to advance chickpea genetics and breeding applications.