Mining of gene-based SNPs from publicly available ESTs and their conversion to cost-effective genotyping assay in sorghum [Sorghum bicolor (L.) Moench]

Girma, Y and Doddamani, D and Fakrudin, B and Rajkumar, . and Ahmed, S A W and Sheweta Gujar, S and Patil, S and Hiremath, G (2014) Mining of gene-based SNPs from publicly available ESTs and their conversion to cost-effective genotyping assay in sorghum [Sorghum bicolor (L.) Moench]. Journal of Crop Science and Biotechnology, 17 (3). pp. 155-160. ISSN 1975-9479

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Abstract

Single Nucleotide Polymorphisms (SNPs) are the commonest type of nucleotide variation distributed throughout the genome and have enormous potential to saturate genetic maps. However, their identification is constrained by the huge investment required for their detection. In this study, we used publicly available EST (Expressed Sequence Tag) sequences to identify SNPs in Sorghum bicolor. A total of 12,421 putative SNPs were identified from 2,921 contiguous transcripts leading to an average SNP interval of one putative SNP for every 275.26 bp. The proportion of transition type mutations (0.598) was larger than transversion types conforming to biological expectations. In order to demonstrate the utility of the SNPs for development of markers with relatively cheap assays, we experimentally validated SNPs using Single Strand Conformation Polymorphism (SSCP) technique in sorghum accessions, which are used as parents for development mapping populations. Genotyping these parents of mapping populations with SSCP markers showed up to 33% polymorphism in the markers suggesting that the SNPs can be used as potential resource for S. bicolor crop improvement programs.

Item Type: Article
Divisions: RP-Dryland Cereals
CRPS: CGIAR Research Program on Dryland Cereals
Uncontrolled Keywords: Cheap genotyping assay, Cleaved Amplified Polymorphism Sequence (CAPS), SNP, SSCP
Subjects: Mandate crops > Sorghum
Others > Genetics and Genomics
Depositing User: Mr B K Murthy
Date Deposited: 12 May 2015 06:21
Last Modified: 12 May 2015 06:21
URI: http://oar.icrisat.org/id/eprint/8678
Official URL: http://dx.doi.org/10.1007/s12892-014-0022-4
Projects: UNSPECIFIED
Funders: UNSPECIFIED
Acknowledgement: UNSPECIFIED
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