Computational  analysis of SNPs and INDELs in cluster bean cultivars involved in multiple trait expression

Sarika Sahu; Tanmaya Kumar Sahu; Sabri Ghosal; Kishor Gaikwad; A. R. Rao

Sarika Sahu ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110 012
Tanmaya Kumar Sahu ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110 012
Sabri Ghosal ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110 012
Kishor Gaikwad ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110 012
A. R. Rao ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110 012

Keywords: Single nucleotide polymorphism, indels (Insertions/Deletions), next generation sequencing, in silico analysis, cluster bean.

Abstract

SNPs (Single Nucleotide Polymorphisms) are extensively used in plant breeding programs because of their automation and high precision in allele calling. In the present study, transcriptomes of three cultivars of Cyamopsis tetragonoloba, namely, RGC-936, RGC-1066 and M-18 were analysed for the identification of SNPs and Indels using the recently assembled draft genome made available by National Institute of Plant Biotechnology, New Delhi. Besides, a comparison among the identified SNPs and indels of three cultivars was made to mine out the cultivar specific SNPs and indels as well as common markers among the cultivars. In addition, an online database, cbSIR, was developed based on the markers populated from the said cultivars of cluster bean (http://webapp.cabgrid.res.in/clb_ce/index.php). The results reveal that highest number of SNPs (10279) were present in cultivar RGC-1066 followed by RGC-1066 (9714) and M-18 (7933). The detected SNPs were subjected to functional annotation. In a similar way, Indels were also identified and functionally annotated. Predictions were made based on the involvement of SNP/Indel possessing genes in the expression of multiple traits such as gum production, auxin transport, disease resistance in the three cultivars of cluster bean.