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

Roorkiwal, M and Jain, A and Kale, S M and Doddamani, D and Chitikineni, A and Thudi, M and Varshney, R K (2017) Development and evaluation of high-density Axiom® CicerSNP Array for high-resolution genetic mapping and breeding applications in chickpea. Plant Biotechnology Journal. pp. 1-12. ISSN 14677644

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Abstract

To 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.

Item Type: Article
Divisions: Research Program : Genetic Gains
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Chickpea, Drought, Genotyping, Molecular breeding, QTLs, SNP array, Genetics, Next-generation sequencing, Genotyping technologies, Breeding applications
Subjects: Others > Genetic Engineering
Others > Plant Breeding
Mandate crops > Chickpea
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 09 Nov 2017 06:39
Last Modified: 09 Nov 2017 06:43
URI: http://oar.icrisat.org/id/eprint/10273
Official URL: http://dx.doi.org/10.1111/pbi.12836
Projects: UNSPECIFIED
Funders: Bill & Melinda Gates Foundation (Tropical Legumes III) and Department of Agriculture Cooperation & Farmer’s Welfare, Ministry of Agriculture & Farmer’s Welfare, Government of India
Acknowledgement: The authors are thankful to Bill & Melinda Gates Foundation (Tropical Legumes III) and Department of Agriculture Cooperation & Farmer’s Welfare, Ministry of Agriculture & Farmer’s Welfare, Government of India, for financial assistance. The work reported in this article was undertaken as a part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of the CGIAR.
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