Journal article
Development and evaluation of high-density Axiom® CicerSNP Array for high-resolution genetic mapping and breeding applications in chickpea
Plant Biotechnology Journal, Vol.16(4), pp.890-901
2017
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.
Details
- Title
- Development and evaluation of high-density Axiom® CicerSNP Array for high-resolution genetic mapping and breeding applications in chickpea
- Authors/Creators
- M. Roorkiwal (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsA. Jain (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsS.M. Kale (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsD. Doddamani (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsA. Chitikineni (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsM. Thudi (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsR.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
- Publication Details
- Plant Biotechnology Journal, Vol.16(4), pp.890-901
- Publisher
- Blackwell Publishing Inc.
- Identifiers
- 991005541216807891
- Copyright
- © 2017 The Authors.
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Biotechnology & Applied Microbiology
- Plant Sciences
- ESI research areas
- Plant & Animal Science