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

• Published in: Evolutionary Applications
• Main Authors: Vendrami, David L. J., Houston, Ross D., Gharbi, Karim, Telesca, Luca, Gutierrez, Alejandro P., Gurney-Smith, Helen, Hasegawa, Natsuki, Boudry, Pierre, Hoffman, Joseph I.
• Other Authors: Universität Bielefeld = Bielefeld University, The Roslin Institute, Biotechnology and Biological Sciences Research Council (BBSRC), University of Edinburgh, Edinburgh Genomics, Department of Earth Sciences Cambridge, UK, University of Cambridge UK (CAM), British Antarctic Survey (BAS), Natural Environment Research Council (NERC), Japan Fisheries Research and Education Agency (FRA), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), European Project: 605051,EC:FP7:PEOPLE,FP7-PEOPLE-2013-ITN,CACHE(2013)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2019
• Subjects: ACL; growth; aquaculture; Pacific oyster; Crassostrea gigas; shellfish; traits; microsatellite; performance; reproductive success; depression; genetic structure; high-density genotyping array; inbreeding; invasion genetics; r-package; restriction site-associated DNA (RAD) sequencing; single nucleotide polymorphism (SNP); tool set; [SDE.BE]Environmental Sciences/Biodiversity and Ecology; Canada; Pacific; Norway; Antarc*; Antarctica
• Online Access: https://hal.science/hal-02920588; https://hal.science/hal-02920588/document; https://hal.science/hal-02920588/file/Vendrami_etal_EA_2019.pdf; https://doi.org/10.1111/eva.12736

WOS:000459328300012 International audience 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.