In:
Plant Biotechnology Journal, Wiley, Vol. 16, No. 4 ( 2018-04), p. 890-901
Abstract:
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.
Type of Medium:
Online Resource
ISSN:
1467-7644
,
1467-7652
DOI:
10.1111/pbi.2018.16.issue-4
Language:
English
Publisher:
Wiley
Publication Date:
2018
detail.hit.zdb_id:
2136367-5
SSG:
12
Permalink