Journal article
Single nucleotide polymorphism genotyping for breeding and genetics applications in chickpea and pigeonpea using the BeadXpress platform
The Plant Genome, Vol.6(2), Art. plantgenome2013.05.0017
2013
Abstract
Single nucleotide polymorphisms (SNPs) are ideal molecular markers due to their higher abundance. Although several types of genotyping platforms for assaying large number of SNPs are available, in cases such as marker-assisted selection, where few markers are required for genotyping a set of potential lines, high-throughput SNP genotyping platforms (e.g., iScan or Infinium) may not be cost effective. In this scenario, GoldenGate assays based on VeraCode technology using Illumina BeadXpress seems to be the most cost-effective platform. The objective of this study was to develop cost-effective SNP genotyping platforms in chickpea (Cicer arietinum L.) and pigeonpea (Cajanus cajan L.). Two sets of SNPs, one each for chickpea (96 SNPs) and pigeonpea (48 SNPs), were developed and tested by genotyping 288 diverse genotypes from respective reference sets. The SNPs selected for the oligo pool assays had high transferability to crop wild relative species. The mean polymorphism information content value of assayed SNP markers was 0.31 and 0.32 in chickpea and pigeonpea, respectively. No unique pattern was observed in the chickpea reference set whereas two major groups were observed in the case of the pigeonpea reference set. The Illumina BeadXpress platform assays developed for chickpea and pigeonpea are highly informative and cost effective for undertaking genetic studies in these legume species.
Details
- Title
- Single nucleotide polymorphism genotyping for breeding and genetics applications in chickpea and pigeonpea using the BeadXpress platform
- Authors/Creators
- M. Roorkiwal (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsS.L. Sawargaonkar (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. Saxena (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsH.D. Upadhyaya (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsM.I. Vales (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsO. Riera‐Lizarazu (Author/Creator)R.K. Varshney (Author/Creator) - Centro Internacional de Mejoramiento de Maíz Y Trigo
- Publication Details
- The Plant Genome, Vol.6(2), Art. plantgenome2013.05.0017
- Publisher
- Wiley Periodicals LLC on behalf of Crop Science Society of America
- Identifiers
- 991005545561907891
- Copyright
- © 2013 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
- Genetics & Heredity
- Plant Sciences
- ESI research areas
- Plant & Animal Science