Epigenetic variation of wild populations of the Pacific oyster Crassostrea gigas determined by methylation-sensitive amplified polymorphism analysis

Epigenetic variation can provide insights into ecological and evolutionary processes of eukaryote well-being, and can also be useful information for the conservation and management of wildlife. DNA methylation, a major epigenetic mechanism, plays a central role in gene regulation and phenotype variation in eukaryote genomes. However, in natural invertebrate populations, the potential role of epigenetic variation in DNA methylation polymorphisms and the association between this and genetic profiles remains largely unknown. In this work, we estimated epigenetic diversity and differentiation of the Pacific oyster Crassostrea gigas, from seven natural Chinese and Korean populations using the fluorescent-labeled methylation-sensitive amplified polymorphism (F-MSAP) technique. In total, 636 MSAP loci revealed an unambiguous genome-wide methylation status (31.32–43.23% on average) as well as extensive epigenetic polymorphism (approximately 97%) at 5′-CCGG-3′ sites. The unweighted pair group method with arithmetic mean and principal coordinates analysis separated the seven C. gigas populations remarkably well, reflecting great epigenetic differentiation among populations, and in particular for the Korean population. Variation was higher in epigenetic structure than in genetic structure. Both multivariate analysis and a significantly different population molecular structure suggested that epigenetic variation might be determined by the combined effects of geographical barriers as well as current features and founder characteristics. A Mantel test showed a moderate but significant correlation between epigenetic and genetic profiles, indicating epigenetic variation coupled with genetic distribution in natural, wild C. gigas populations. This study provides some information on the role of DNA methylation in adaptive epigenetic divergence in wild marine bivalve populations.