Genome-wide association studies for resistance to viral nervous necrosis in three populations of European sea bass (Dicentrarchus labrax) using a novel 57k SNP array DlabChip
2021
Griot, Ronan | Allal, François | Phocas, Florence | Brard-Fudulea, Sophie | Morvezen, Romain | Bestin, Anastasia | Haffray, Pierrick | François, Yoannah | Morin, Thierry | Poncet, Charles | Vergnet, Alain | Cariou, Sophie | Brunier, Joseph | Bruant, Jean-Sébastien | Peyrou, Bruno | Gagnaire, Pierre-Alexandre | Vandeputte, Marc | Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF) | Génétique Animale et Biologie Intégrative (GABI) ; AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | Laboratoire Service d' Experimentations Aquacoles [Palavas les Flots] (LSEA MARBEC) ; MARine Biodiversity Exploitation and Conservation (UMR MARBEC) ; Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS) | Laboratoire de Ploufragan-Plouzané-Niort [ANSES] ; Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES) | Virologie, Immunologie et Ecotoxicologie des Poissons (VIMEP) ; Laboratoire de Ploufragan-Plouzané-Niort [ANSES] ; Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES) | Génétique Diversité et Ecophysiologie des Céréales (GDEC) ; Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA) | Ferme Marine de Douhet | Ecloserie Marine de Gravelines ; Aquanord | Institut des Sciences de l'Evolution de Montpellier (UMR ISEM) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE) ; Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS) | This work was partially financially supported by the GeneSea project (n° R FEA 4700 16 FA 100 0005) funded by the French Government and the European Union (EMFF, European Maritime and Fisheries Fund) at the “Appels à projets Innovants” managed by the France Agrimer Office. The doctoral scholarship of Ronan Griot was partially supported by the ANRT (doctoral scholarship n° 2017/0731) and EMG and FMD breeding companies through SYSAAF organisation. We are grateful to the INRAE genotyping platform Gentyane (INRAE, Clermont-Ferrand, France) for the production of genotype data and to the Fortior Genetics platform (ANSES, Plouzané, France) for the realization of the challenges. We especially thank Daniel Guémené for his implication in the creation of the Fortior Genetics platform as well as his implication in the conception of this project.
International audience
Mostrar más [+] Menos [-]Inglés. Viral Nervous Necrosis (VNN) is a major threat for the European sea bass (Dicentrarchus labrax) aquaculture industry. The improvement of disease resistance through selective breeding is a promising option to reduce outbreaks. With the development of high-throughput genotyping technologies, identification of genomic regions involved in the resistance could improve the efficiency of selective breeding. The aim of this study was to identify quantitative trait loci (QTL) involved in VNN resistance and to quantify their effect.Four experimental backcross families comprising 378, 454, 291 and 211 individuals and two commercial populations A and B comprising 1027 and 1042 individuals obtained from partial factorial crosses (59 male x 20 female for pop A; 39 male x 14 female for pop B) were submitted to a redspotted grouper nervous necrosis virus (RGNNV) challenge by bath. A high-density single nucleotide polymorphism (SNP) chip panel was designed to develop the ThermoFisher Axiom (TM) 57k SNP DlabChip, which was used for genotyping all individuals and building a high quality linkage map. In the backcross families, composite interval mapping was performed on 30,917, 23,592, 30,656 and 31,490 markers, respectively. In the commercial populations, 40,263 markers in pop A and 41,166 markers in pop B were used to perform genome-wide association studies (GWAS) using a GBLUP and a BayesC pi approach.One QTL was identified on chromosome LG12 in three of the four experimental backcross families, and one additional QTL on LG8 was detected in only one family. In commercial populations, QTL mapping revealed a total of seven QTLs, among which the previously mentioned QTL on LG12 was detected in both. This QTL, which was mapped to an interval of 3.45 cM, explained 9.21% of the total genetic variance in pop A, while other identified QTLs individually explained less than 1% of the total genetic variance.The identification of QTL regions involved in VNN resistance in European sea bass, with one having a strong effect, should have a great impact on the aquaculture industry. Future work could focus on the fine mapping of the causal mutation present on LG12 using whole genome sequencing.
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