Open AccessDevelopment and evaluation of high‐density Axiom ® Cicer SNP Array for high‐resolution genetic mapping and breeding applications in chickpea
Author(s) -
Roorkiwal Manish,
Jain Ankit,
Kale Sandip M.,
Doddamani Dadakhalandar,
Chitikineni Annapurna,
Thudi Mahendar,
Varshney Rajeev K.
Publication year - 2018
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/pbi.12836
Subject(s) - snp , snp genotyping , biology , snp array , genotyping , genetics , tag snp , quantitative trait locus , molecular inversion probe , single nucleotide polymorphism , computational biology , gene , genotype
Summary To accelerate genomics research and molecular breeding applications in chickpea, a high‐throughput SNP genotyping platform ‘Axiom ® Cicer SNP Array’ has been designed, developed and validated. Screening of whole‐genome resequencing data from 429 chickpea lines identified 4.9 million SNP s, from which a subset of 70 463 high‐quality nonredundant SNP s was selected using different stringent filter criteria. This was further narrowed down to 61 174 SNP s based on p ‐convert score ≥0.3, of which 50 590 SNP s could be tiled on array. Among these tiled SNP s, a total of 11 245 SNP s (22.23%) were from the coding regions of 3673 different genes. The developed Axiom ® Cicer SNP Array was used for genotyping two recombinant inbred line populations, namely ICCRIL 03 ( ICC 4958 × ICC 1882) and ICCRIL 04 ( ICC 283 × ICC 8261). Genotyping data reflected high success and polymorphic rate, with 15 140 (29.93%; ICCRIL 03) and 20 018 (39.57%; ICCRIL 04) polymorphic SNP s. High‐density genetic maps comprising 13 679 SNP s spanning 1033.67 cM and 7769 SNP s spanning 1076.35 cM were developed for ICCRIL 03 and ICCRIL 04 populations, respectively. QTL analysis using multilocation, multiseason phenotyping data on these RIL s identified 70 ( ICCRIL 03) and 120 ( ICCRIL 04) main‐effect QTL s on genetic map. Higher precision and potential of this array is expected to advance chickpea genetics and breeding applications.