Development of single nucleotide polymorphism markers from ESTs for discrimination between domestic and imported manila clams, Ruditapes philippinarum

Large amounts of the manila clam, Ruditapes philippinarum, have been imported from Dalian (China) recently to meet the increasing demand in Korea. To ensure the quality and safety of the domestic marine product, it is necessary to be able to distinguish between domestic manila clams and clams that are imported from Dalian, China. We developed expressed sequence tags (ESTs)-derived single nucleotide polymorphism markers using 454 pyrosequencing. A total of 780,000 ESTs were assembled, and 49,540 putative SNPs were identified from 46,405 contigs. Twenty-one polymorphic SNPs from 11 primers were finally selected as diagnostic markers. Genotype analysis showed that 21 SNP markers had the opposite alleles (transitions or transversions) between domestic and imported samples, which were useful for distinguishing clam origins. The GENECLASS 2.0 program was used to estimate the ability of the markers in the discrimination between domestic and imported populations. The 21 SNP markers had 98.96% ability to discriminate domestic manila clams and 100% ability to identify those imported. These markers could be useful for discriminating between domestic and imported manila clams and can contribute to the prevention of falsified labeling of this species.