The single nucleotide polymorphism (SNP) markers for the hard clam, Meretrix meretrix, are currently limited as the expressed sequence tags (ESTs), which are the main sequence resource, are insufficient. A massive amount of the ESTs generated from the transcriptome for this clam have made possible the rapid development of the high-throughput SNP markers. In the present study, we identified 135 SNPs from the transcriptome dataset of M. meretrix using high-resolution melting (HRM) analysis. The genetic parameter analysis of these markers showed that their observed heterozygosities ranged from 0.0000 to 0.7667 with an average of 0.3225, whereas their expected heterozygosities ranged from 0.3045 to 0.5085 with an average of 0.4615. The minor allele frequency of these markers varied from 0.1833 to 0.5000. Of the 135 SNPs, the nucleotides A/G (31.9%) and C/T (28.9%) accounted for a high percentage. 56 SNPs showed significant deviation from the Hardy-Weinberg equilibrium (P < 0.01) after Bonferroni correction. This study indicated that the transcriptome data provided an extremely invaluable resource for SNP discovery, and these novel SNPs could serve as useful markers for the genetic diversity assessment and molecular-assisted breeding of this species.
