Genome-wide association and genomic prediction of resistance to viral nervous necrosis in European sea bass (Dicentrarchus labrax) using RAD sequencing

• Published in: Genetics Selection Evolution
• Main Authors: Palaiokostas, Christos, Cariou, Sophie, Bestin, Anastasia, Bruant, Jean-Sebastien, Haffray, Pierrick, Morin, Thierry, Cabon, Joelle, Allal, Francois, Vandeputte, Marc, Houston, Ross D.
• Other Authors: Institute of Aquaculture, School of Natural Sciences, University of Stirling, Ferme Marine de Douhet, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Laboratoire de Ploufragan-Plouzané-Niort ANSES, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), 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), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Biotechnology and Biological Sciences Research Council Institute BBS/E/D/20002172, BBS/E/D/30002275, European Project: 613611,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,FISHBOOST(2014)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2018
• Subjects: disease resistance; genetic evaluation; challenges; discovery; selection; livestock; salmon salmo-salar; traits; aquaculture; population; [SDV]Life Sciences [q-bio]; [SDE.MCG]Environmental Sciences/Global Changes; [SDV.EE.ECO]Life Sciences [q-bio]/Ecology; environment/Ecosystems; Salmo salar
• Online Access: https://hal.science/hal-01826622; https://hal.science/hal-01826622/document; https://hal.science/hal-01826622/file/12711_2018_Article_401.pdf; https://doi.org/10.1186/s12711-018-0401-2

International audience AbstractBackgroundEuropean sea bass (Dicentrarchus labrax) is one of the most important species for European aquaculture. Viral nervous necrosis (VNN), commonly caused by the redspotted grouper nervous necrosis virus (RGNNV), can result in high levels of morbidity and mortality, mainly during the larval and juvenile stages of cultured sea bass. In the absence of efficient therapeutic treatments, selective breeding for host resistance offers a promising strategy to control this disease. Our study aimed at investigating genetic resistance to VNN and genomic-based approaches to improve disease resistance by selective breeding. A population of 1538 sea bass juveniles from a factorial cross between 48 sires and 17 dams was challenged with RGNNV with mortalities and survivors being recorded and sampled for genotyping by the RAD sequencing approach.ResultsWe used genome-wide genotype data from 9195 single nucleotide polymorphisms (SNPs) for downstream analysis. Estimates of heritability of survival on the underlying scale for the pedigree and genomic relationship matrices were 0.27 (HPD interval 95%: 0.14-0.40) and 0.43 (0.29–0.57), respectively. Classical genome-wide association analysis detected genome-wide significant quantitative trait loci (QTL) for resistance to VNN on chromosomes (unassigned scaffolds in the case of ‘chromosome’ 25) 3, 20 and 25 (P < 1e06). Weighted genomic best linear unbiased predictor provided additional support for the QTL on chromosome 3 and suggested that it explained 4% of the additive genetic variation. Genomic prediction approaches were tested to investigate the potential of using genome-wide SNP data to estimate breeding values for resistance to VNN and showed that genomic prediction resulted in a 13% increase in successful classification of resistant and susceptible animals compared to pedigree-based methods, with Bayes A and Bayes B giving the highest predictive ability.ConclusionsGenome-wide significant QTL were identified but each with relatively small ...