Abstract
SummaryTo accelerate genomics research and molecular breeding applications in chickpea, a high‐throughput SNP genotyping platform ‘Axiom® 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 70 463 high‐quality nonredundant SNPs was selected using different stringent filter criteria. This was further narrowed down to 61 174 SNPs based on p‐convert score ≥0.3, of which 50 590 SNPs could be tiled on array. Among these tiled SNPs, a total of 11 245 SNPs (22.23%) were from the coding regions of 3673 different genes. The developed Axiom® CicerSNP Array was used for genotyping two recombinant inbred line populations, namely ICCRIL03 (ICC 4958 × ICC 1882) and ICCRIL04 (ICC 283 × ICC 8261). Genotyping data reflected high success and polymorphic rate, with 15 140 (29.93%; ICCRIL03) and 20 018 (39.57%; ICCRIL04) polymorphic SNPs. High‐density genetic maps comprising 13 679 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.
Highlights
Ongoing climatic changes that are affecting crop yields drastically and increasing food demand from ever increasing world population would certainly make the scenario worst by 2050 when the world population would be crossing the count of 9 billion
The resequencing data generated from 429 genotypes were aligned to the chickpea reference genomes for SNP discovery
The alignment of sequencing data resulted in the identification of total 4.9 million SNPs distributed across genome
Summary
Ongoing climatic changes that are affecting crop yields drastically and increasing food demand from ever increasing world population would certainly make the scenario worst by 2050 when the world population would be crossing the count of 9 billion. With the impact of various abiotic and biotic stresses, current average chickpea productivity is
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