DNA Haplotype-Based Identification of Blood Cockle Species from the Western Coastal Waters of Peninsular Malaysia

One of the biggest problems in studying the larval ecology of marine bivalves in the field is specific identification.  Quantification of planktonic larval distributions is limited by processing time, given the large numbers of samples generated in extensive field surveys.  The only method available for reliable species identification of bivalve larvae is direct morphological observation.  The blood cockle Anadara granosa is an important resource for fisheries and aquaculture in Southeast Asia, especially in Malaysia.  In this study, we developed species-specific primer sets by using DNA haplotypes of A. granosa and some cockles collected from the western coastal waters of Peninsular Malaysia.  We extracted the genomic DNA from the adult samples that were identified morphologically.  To identify the sequences specific to A. granosa, we aligned partial ITS2 and 28S rDNA sequences of A. granosa to the sequences of other arctic bivalves available from GenBank.  We designed candidate primer sets of 150–400 bp amplification target length and carried out optimal PCR reactions to amplify A. granosa sequences.  The DNA extracted from target and non-target species was used as template to examine the specificity of these primer sets.  Our results indicate that this technique is simple, quick, and suitable for field application to discriminate between A. granosa and related species sympatrically occured in the culture grounds.  The developed primers will be useful for the larval identification of blood cockle in ecological researches.