Relative genomic impacts of translocation history, hatchery practices, and farm selection in Pacific oyster Crassostrea gigas throughout the Northern Hemisphere

Abstract

Pacific oyster Crassostrea gigas, endemic to coastal Asia, has been translocated globally throughout the past century, resulting in self‐sustaining introduced populations (naturalized). Oyster aquaculture industries in many parts of the world depend on commercially available seed (hatchery‐farmed) or naturalized/wild oysters to move onto a farm (naturalized‐farmed). It is therefore important to understand genetic variation among populations and farm types. Here, we genotype naturalized/wild populations from France, Japan, China, and most extensively in coastal British Columbia, Canada. We also genotype cultured populations from throughout the Northern Hemisphere to compare with naturalized populations. In total, 16,942 markers were identified using double‐digest RAD‐sequencing in 182 naturalized, 112 hatchery‐farmed, and 72 naturalized‐farmed oysters (n = 366). Consistent with previous studies, very low genetic differentiation was observed around Vancouver Island (mean FST = 0.0019) and low differentiation between countries in the Japan–Canada–France historical translocation lineage (France–Canada FST = 0.0024; Japan–Canada FST = 0.0060). Chinese populations were more differentiated (China–Japan FST = 0.0241). Hatchery‐propagated populations had higher interindividual relatedness suggesting family structure. Within‐population inbreeding was not detected on farms, but nucleotide diversity and polymorphism rate were lower in one farm population. Moving oysters from nature onto farms did not result in strong within‐generation selection. Private alleles at substantial frequency were identified in several hatchery populations grown in BC, suggesting nonlocal origins. Tests of selection identified outlier loci consistent with selective differences associated with domestication, in some cases consistently identified in multiple farms. Top outlier candidates were nearby genes involved in calcium signaling and calmodulin activity. Implications of potential introgression from hatchery‐farmed oysters depend on whether naturalized populations are valued as a locally adapted resource or as an introduced, invasive species. Given the value of the industry in BC and the challenges the industry faces (e.g., climate change, crop losses, biotic stressors), this remains an important question.

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.…”

Population Genomics, Transcriptional Response to Heat Shock, and Gut Microbiota of the Hong Kong Oyster Magallana hongkongensis

“…In the estuarine oyster Magallana ariakensis, Pacific oyster M. gigas, and Olympia oyster Ostrea lurida, populations and gene flow barriers could also be identified [20,29,68]. Future analyses on the population structure of M. hongkongensis across a wider geographical scale are needed, as hatchery and farming activities have been identified as influential in determining oyster population structure [69,70], and useful for the identification of novel targets for molecular breeding [71,72].…”

Identification of Main Oyster Species and Comparison of Their Genetic Diversity in Zhejiang Coast, South of Yangtze River Estuary

“…Oyster larvae have a long swimming period of up to 3 or 4 weeks, and there are many islands along the coast of Zhejiang; therefore, it is possible that ocean currents drive larvae to settle (Sekino and Yamashita, 2012;Sekino et al, 2016). Molecular markers at the genome-wide level may be needed to further determine their exact source, such as with Pacific oysters in the Northern Hemisphere, where a clear lineage of different populations has been provided (Sutherland et al, 2020) and oysters in Europe (Vendrami et al, 2018).…”