Comparative assessment of genomic SSR, EST-SSR and EST-SNP markers for evaluation of the genetic diversity of wild and cultured Pacific oyster, Crassostrea gigas Thunberg

A set of eight genomic simple sequence repeat (SSR), 10 expressed sequences tag (EST)-derived SSR and 10 EST-derived single nucleotide polymorphism (SNP) markers were analyzed on two wild and three cultured Pacific oyster (Crassostrea gigas Thunberg) populations to access their applicability for population genetic studies. Genomic SSR markers were found to be the most polymorphic, with an average PIC value of 0.870, higher than EST-SSRs (0.721) and SNPs (0.346). The Nei's gene diversity (HE) per locus for the genomic SSRs ranged from 0.821 to 0.936 (mean HE = 0.882), while that of the EST-SSRs ranged from 0.624 to 0.825 (mean HE = 0.755) and that of the EST-SNPs ranged from 0.372 to 0.499 (mean HE = 0.448). No significant differences in the number of alleles, HE and PIC values were identified between the wild and cultured populations in terms of all three types of markers. The effective marker index (EMI) was the highest (0.653) for the genomic SSR markers and the lowest (0.346) for the SNP markers, while the EST-SSR markers had an intermediate EMI (0.541). Comparable population pairwise estimates of FST were obtained for all marker types, but while the absolute values for the genomic and EST-SSRs were similar (FST = 0.041 and 0.032, respectively), the differentiation level was higher for EST-SNPs in pairwise and global comparisons (global EST-SNPs FST = 0.077). The dendrogram of the combined dataset, based on the shared-allele distance among populations, classified the wild and cultured population into two major clusters. Our results suggest 1) that genomic SSRs and EST-SSRs are more suitable for routine genetic diversity analysis than are EST-SNPs, and 2) that EST-SSR markers represent a useful addition to the tools available for population genetic analysis, particularly for aquaculture species with existing EST databases.