z-logo
open-access-imgOpen Access
Development 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.

The content you want is available to Zendy users.

Already have an account? Click here to sign in.
Having issues? You can contact us here