Genomic diversity of wild and cultured Yesso scallopMizuhopecten yessoensisfrom Japan and Canada

Abstract

The Yesso scallopMizuhopecten yessoensisis an important aquaculture species that was introduced to Western Canada from Japan to establish an economically viable scallop farming industry. This highly fecund species has been propagated in Canadian aquaculture hatcheries for the past 40 years, raising questions about genetic diversity and genetic differences among hatchery stocks. In this study, we compare cultured Canadian and wild Japanese populations of Yesso scallop using double-digest restriction site-associated DNA (ddRAD)-sequencing to genotype 21,048 variants in 71 wild-caught scallops from Japan, 65 scallops from the Vancouver Island University breeding population, and 37 scallops obtained from a commercial farm off Vancouver Island, British Columbia. The wild scallops are largely comprised of equally unrelated individuals, whereas cultured scallops are comprised of multiple families of related individuals. The polymorphism rate estimated in wild scallops was 1.7%, whereas in the cultured strains it varied between 1.35% and 1.07%. Interestingly, heterozygosity rates were highest in the cultured populations, which is likely due to shellfish hatchery practices of crossing divergent strains to gain benefits of heterosis and to avoid inbreeding. Evidence of founder effects and drift were observed in the cultured strains, including high genetic differentiation between cultured populations and between cultured populations and the wild population. Cultured populations had effective population sizes ranging from 9-26 individuals whereas the wild population was estimated at 25-50K individuals. Further, a depletion of low frequency variants was observed in the cultured populations. These results indicate significant genetic diversity losses in cultured scallops in Canadian breeding programs.

An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster

“…Using genetic markers, the effective population size and other measures of diversity such as allelic richness can be directly monitored in the breeding population (Gurney-Smith et al, 2017;Hedgecock & Sly, 1990). Allelic richness may be a v.0.2.1 more appropriate measure to monitor diversity than observed heterozygosity or per-individual inbreeding coefficients (Sutherland et al, 2023;Varney & Wilbur, 2020;Yu & Guo, 2004), in part because these other metrics can be skewed by crossing divergent genetic lines for heterosis, an approach sometimes applied within the bivalve aquaculture industry. When reduced diversity is detected, solutions may be needed to replenish diversity (Li et al, 2007).…”