Development and validation of single nucleotide polymorphism markers in the eastern oyster Crassostrea virginica Gmelin by mining ESTs and resequencing

Single nucleotide polymorphisms (SNPs) are useful markers for genetic and genomic studies. They are needed in the eastern oyster (Crassostrea virginica), a major aquaculture species, for the mapping of genes affecting economically important quantitative traits such as disease resistance. Here we report the discovery and characterization of 46 SNPs in the eastern oyster by mining expressed sequence tags (ESTs) and resequencing. Sixty-three putative SNPs were identified from existing ESTs, of which 27 were validated. Three hundred and thirty-six putative SNPs were discovered by resequencing 6.8 Kb from 19 genes, corresponding to a remarkably high density of one SNP per 20 bp. Twenty-one of the candidate SNPs identified by resequencing were tested, and 19 were validated. Thirty-three of the 46 validated SNPs segregated in two mapping families, with 28 (85%) in accordance to expected Mendelian ratios. These markers are derived from expressed genes and should be useful for genetic analyses including the mapping and characterization of the genes that they represent.