Detailed insights into pan‐European population structure and inbreeding in wild and hatchery Pacific oysters (Crassostrea gigas) revealed by genome‐wide SNP data

Abstract

Cultivated bivalves are important not only because of their economic value, but also due to their impacts on natural ecosystems. The Pacific oyster ( Crassostrea gigas ) is the world's most heavily cultivated shellfish species and has been introduced to all continents except Antarctica for aquaculture. We therefore used a medium‐density single nucleotide polymorphism (SNP) array to investigate the genetic structure of this species in Europe, where it was introduced during the 1960s and has since become a prolific invader of coastal ecosystems across the continent. We analyzed 21,499 polymorphic SNPs in 232 individuals from 23 localities spanning a latitudinal cline from Portugal to Norway and including the source populations of Japan and Canada. We confirmed the results of previous studies by finding clear support for a southern and a northern group, with the former being indistinguishable from the source populations indicating the absence of a pronounced founder effect. We furthermore conducted a large‐scale comparison of oysters sampled from the wild and from hatcheries to reveal substantial genetic differences including significantly higher levels of inbreeding in some but not all of the sampled hatchery cohorts. These findings were confirmed by a smaller but representative SNP dataset generated using restriction site‐associated DNA sequencing. We therefore conclude that genomic approaches can generate increasingly detailed insights into the genetics of wild and hatchery produced Pacific oysters.

Genetic Characterization of Cupped Oyster Resources in Europe Using Informative Single Nucleotide Polymorphism (SNP) Panels

“…This might be the case for the Pacific oyster C. gigas, for which several repeated introductions from Canada and Japan of adults, but also high quantities of spat, happened by the end of the 1960s in Europe, especially in France and the Netherlands [23,84]. Hence our results confirm an absence of detection of clear differences between the source population and the French populations of C. gigas as several other studies did even with a far higher number of markers [21,42,50,61,85,86]. We failed at detecting differences between Asian and European populations within each species [42] because our 80 SNPs panel was not well adapted for detecting such structure if it exists.…”

“…Although HTS has allowed the development of medium-density SNP panelsand whole genome resequencing of hundreds of individuals in oysters [47,[60][61][62], those approaches do not always scale to specific questions that only require small SNP panels. The level of precision for inferring individual ancestry for species identification requires only a handful of ancestry informative markers, typically one or two per chromosome.…”

Relative genomic impacts of translocation history, hatchery practices, and farm selection in Pacific oysterCrassostrea gigasthroughout the Northern Hemisphere

“…Population genetic analyses to date have not found evidence for bottlenecks during Pacific oyster introductions in BC or France (Sun & Hedgecock, 2017; Vendrami et al, 2018). Very low genetic differentiation between translocated naturalized populations and Japanese populations has been observed (Vendrami et al, 2018).…”

“…Population genetic analyses to date have not found evidence for bottlenecks during Pacific oyster introductions in BC or France (Sun & Hedgecock, 2017; Vendrami et al, 2018). Very low genetic differentiation between translocated naturalized populations and Japanese populations has been observed (Vendrami et al, 2018). In regions that have been recently colonized with rapid expansion of oyster populations, such as the Wadden Sea of Denmark, lower genetic diversity is observed (Vendrami et al, 2018).…”

“…Very low genetic differentiation between translocated naturalized populations and Japanese populations has been observed (Vendrami et al, 2018). In regions that have been recently colonized with rapid expansion of oyster populations, such as the Wadden Sea of Denmark, lower genetic diversity is observed (Vendrami et al, 2018). In the North East Pacific ocean (e.g.…”