Record Details

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

OAR@ICRISAT

View Archive Info
 
 
Field Value
 
Relation http://oar.icrisat.org/8678/
http://dx.doi.org/10.1007/s12892-014-0022-4
 
Title Mining of gene-based SNPs from publicly available ESTs and their conversion to cost-effective genotyping assay in sorghum [Sorghum bicolor (L.) Moench]
 
Creator Girma, Y
Doddamani, D
Fakrudin, B
Rajkumar, .
Ahmed, S A W
Sheweta Gujar, S
Patil, S
Hiremath, G
 
Subject Sorghum
Genetics and Genomics
 
Description 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.
 
Publisher The Korean Society of Crop Science
 
Date 2014
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights —
 
Identifier http://oar.icrisat.org/8678/1/JCropSciBiotech_17_3_155-160_2014.pdf
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