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


  • 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 markerassisted selection, where few markers are required for genotyping a set of potential lines, highthroughput 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 costeffective platform. The objective of this study was to develop costeffective 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.

published proceedings

  • The Plant Genome

author list (cited authors)

  • Roorkiwal, M., Sawargaonkar, S. L., Chitikineni, A., Thudi, M., Saxena, R. K., Upadhyaya, H. D., ... Varshney, R. K.

citation count

  • 59

complete list of authors

  • Roorkiwal, Manish||Sawargaonkar, Shrikant L||Chitikineni, Annapurna||Thudi, Mahendar||Saxena, Rachit K||Upadhyaya, Hari D||Vales, M Isabel||Riera‚ÄźLizarazu, Oscar||Varshney, Rajeev K

publication date

  • July 2013