Single Nucleotide Polymorphism Genotyping for Breeding and Genetics Applications in Chickpea and Pigeonpea using the BeadXpress Platform

Roorkiwal, M and Sawargaonkar, S L and Chitikineni, A and Thudi, M and Saxena, R K and Upadhyaya, H D and Vales, M I and Riera-Lizarazu, O and Varshney, R K (2013) Single Nucleotide Polymorphism Genotyping for Breeding and Genetics Applications in Chickpea and Pigeonpea using the BeadXpress Platform. The Plant Genome, 6 (2). pp. 1-10. ISSN 1940-3372

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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.

Item Type: Article
Divisions: UNSPECIFIED
CRP: UNSPECIFIED
Subjects: Mandate crops > Chickpea
Mandate crops > Pigeonpea
Others > Genetics and Genomics
Depositing User: Mr Siva Shankar
Date Deposited: 11 Aug 2013 06:41
Last Modified: 13 Aug 2013 03:56
URI: http://oar.icrisat.org/id/eprint/7047
Official URL: http://dx.doi.org/10.3835/plantgenome2013.05.0017
Projects: Center of Excellence (CoE) scheme, CGIAR Research Program on Grain Legume
Funders: Department of Biotechnology, Government of India
Acknowledgement: UNSPECIFIED
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