Characterization of EST-SSR and genomic-SSR markers in the clam, Meretrix meretrix

We described and characterized 17 expressed sequence tag (EST)-derived simple sequence repeats (SSR) and 16 genomic-derived SSRs for the clam Meretrix meretrix. The EST-SSRs comprised 17.6% dinucleotide repeats, 35.3% trinucleotide repeats, and 47.1% tetranucleotide repeats; whereas the majority of the G-SSRs were dinuleotide repeats (75.0%). The number of alleles for the 33 SSR markers varied from 6 to 15, with a mean of 10.3 alleles per locus. Observed and expected heterozygosity (Ho and He) varied from 0.613 to 0.824, and 0.687 to 0.850, respectively. Polymorphic information content (PIC) ranged from 0.645 to 0.842. The mean values of number of alleles, Ho, He, and PIC of G-SSRs were higher than those of the EST-SSRs. No significant deviations from Hardy–Weinberg equilibrium or linkage disequilibrium were observed in the 33 loci. These loci are the first to be characterized in M. meretrix and should be useful in the investigation of genetic evaluation for conservation.