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

Abstract

BackgroundEuropean 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 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 genome-wide SNPs, and our findings highlight the potential of genomic selection to breed farmed European sea bass with improved resistance to VNN.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0401-2) contains supplementary material, which is available to authorized users.

Genome-scale comparative analysis for host resistance against sea lice between Atlantic salmon and rainbow trout

“…As has been previously reported for other disease resistance traits in aquaculture species 18,20,27–29 , our results suggest that sea lice resistance is mainly of polygenic nature (i.e. many genes with small effect are involved in the trait).…”

Potential of genomic selection for improvement of resistance to Ostreid Herpes virus in Pacific oyster (Crassostrea gigas)

“…The prediction accuracy values ranged from 0.678 to 0.758 for GBLUP (with SNP densities ranging from 500 to 18K), while PBLUP only reached an accuracy of 0.637. This result has been mirrored in other studies of genomic versus pedigree-based prediction of disease resistance breeding values for other important farmed fish species, e.g Atlantic salmon (Tsai et al 2015; Yoshida et al 2017; Ødegård et al 2014; Robledo et al 2018), rainbow trout (Vallejo et al 2017; Yoshida et al 2018), sea bream (Palaiokostas et al 2016) and sea bass (Palaiokostas et al 2018a). Further, in shellfish similar findings have been observed for prediction of breeding values for growth traits in scallop (Dou et al 2016) and Pacific oyster (Gutierrez et al 2018b).…”

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Potential of genomic selection for improvement of resistance to ostreid herpesvirus in Pacific oyster (Crassostrea gigas)

“…This result has been mirrored in other studies of genomic vs. pedigree‐based prediction of disease resistance breeding values for other important farmed fish species, e.g. Atlantic salmon (Ødegård et al ; Tsai et al ; Yoshida et al ; Robledo et al ), rainbow trout (Vallejo et al ; Yoshida et al ), sea bream (Palaiokostas et al ) and sea bass (Palaiokostas et al ). Further, in shellfish similar findings have been observed for prediction of breeding values for growth traits in scallop (Dou et al ) and Pacific oyster (Gutierrez et al ).…”