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

Type Article
Date 2018-06
Language English
Author(s) Palaiokostas Christos1, Cariou Sophie2, Bestin Anastasia3, Bruant Jean-Sebastien2, Haffray Pierrick3, Morin Thierry4, Cabon Joelle4, Allal FrancoisORCID5, Vandeputte Marc6, Houston Ross D.1
Affiliation(s) 1 : Univ Edinburgh, Roslin Inst, Royal Dick Sch Vet Studies, Easter Bush EH25 9RG, Midlothian, Scotland.
2 : Ferme Marine Douhet, BP 4, F-17840 La Bree Les Bains, France.
3 : LPGP INRA, SYSAAF, Campus Beaulieu, F-35042 Rennes, France.
4 : Bretagne Loire Univ, Viral Fish Pathol Unit,Technopole Brest Iroise, French Agcy Food Environm & Occupat Hlth & Safety, Natl Reference Lab Regulated Fish Dis,Ploufragan, BP 70, F-29280 Plouzane, France.
5 : Univ Montpellier, Ifremer CNRS IRD UM, MARBEC, Palavas Les Flots, France.
6 : Univ Paris Saclay, GABI, INRA, AgroParisTech, F-78350 Jouy En Josas, France.
Source Genetics Selection Evolution (0999-193X) (Biomed Central Ltd), 2018-06 , Vol. 50 , N. 30 , P. 11p.
DOI 10.1186/s12711-018-0401-2
WOS© Times Cited 21
Abstract

Background: European 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. Results: We 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. Conclusions: Genome-wide significant QTL were identified but each with relatively small effects on the trait. Tests of genomic prediction suggested that incorporating genome-wide SNP data is likely to result in higher accuracy of estimated breeding values for resistance to VNN. RAD sequencing is an effective method for generating such genomewide SNPs, and our findings highlight the potential of genomic selection to breed farmed European sea bass with improved resistance to VNN.

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Palaiokostas Christos, Cariou Sophie, Bestin Anastasia, Bruant Jean-Sebastien, Haffray Pierrick, Morin Thierry, Cabon Joelle, Allal Francois, Vandeputte Marc, Houston Ross D. (2018). Genome-wide association and genomic prediction of resistance to viral nervous necrosis in European sea bass (Dicentrarchus labrax) using RAD sequencing. Genetics Selection Evolution, 50(30), 11p. Publisher's official version : https://doi.org/10.1186/s12711-018-0401-2 , Open Access version : https://archimer.ifremer.fr/doc/00445/55676/