SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure.

ABSTRACT:

Background

Single nucleotide polymorphism (SNP) validation and large-scale genotyping are required to maximize the use of DNA sequence variation and determine the functional relevance of candidate genes for complex stress tolerance traits through genetic association in rice. We used the bead array platform-based Illumina GoldenGate assay to validate and genotype SNPs in a select set of stress-responsive genes to understand their functional relevance and study the population structure in rice.

Results

Of the 384 putative SNPs assayed, we successfully validated and genotyped 362 (94.3%). Of these 325 (84.6%) showed polymorphism among the 91 rice genotypes examined. Physical distribution, degree of allele sharing, admixtures and introgression, and amino acid replacement of SNPs

SUBMITTER: Parida SK 

PROVIDER: S-EPMC3562522 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature