Viral nervous necrosis resistance in gilthead sea bream (Sparus aurata) at the larval stage: heritability and accuracy of genomic prediction with different training and testing settings.

BACKGROUND: The gilthead sea bream (Sparus aurata) has long been considered resistant to viral nervous necrosis (VNN), until recently, when significant mortalities caused by a reassortant nervous necrosis virus (NNV) strain were reported. Selective breeding to enhance resistance against NNV might be a preventive action. In this study, 972 sea bream larvae were subjected to a NNV challenge test and the symptomatology was recorded. All the experimental fish and their parents were genotyped using a genome-wide single nucleotide polymorphism (SNP) array consisting of over 26,000 markers. RESULTS: Estimates of pedigree-based and genomic heritabilities of VNN symptomatology were consistent with each other (0.21, highest posterior density interval at 95% (HPD95%): 0.1-0.4; 0.19, HPD95%: 0.1-0.3, respectively). The genome-wide association study suggested one genomic region, i.e., in linkage group (LG) 23 that might be involved in sea bream VNN resistance, although it was far from the genome-wide significance threshold. The accuracies (r) of the predicted estimated breeding values (EBV) provided by three Bayesian genomic regression models (Bayes B, Bayes C, and Ridge Regression) were consistent and on average were equal to 0.90 when assessed in a set of cross-validation (CV) procedures. When genomic relationships between training and testing sets were minimized, accuracy decreased greatly (r = 0.53 for a validation based on genomic clustering, r = 0.12 for a validation based on a leave-one-family-out approach focused on the parents of the challenged fish). Classification of the phenotype using the genomic predictions of the phenotype or using the genomic predictions of the pedigree-based, all data included, EBV as classifiers was moderately accurate (area under the ROC curve 0.60 and 0.66, respectively). CONCLUSIONS: The estimate of the heritability for VNN symptomatology indicates that it is feasible to implement selective breeding programs for increased resistance to VNN of sea bream larvae/juveniles. Exploiting genomic information offers the opportunity of developing prediction tools for VNN resistance, and genomic models can be trained on EBV using all data or phenotypes, with minimal differences in classification performance of the trait phenotype. In a long-term view, the weakening of the genomic ties between animals in the training and test sets leads to decreased genomic prediction accuracies, thus periodical update of the reference population with new data is mandatory.

Metapopulation patterns of additive and nonadditive genetic variance in the sea bass (Dicentrarchus labrax).

Describing and explaining the geographic within-species variation in phenotypes ("phenogeography") in the sea over a species distribution range is central to our understanding of a variety of eco-evolutionary topics. However, phenogeographic studies that have a large potential to investigate adaptive variation are overcome by phylogeographic studies, still mainly focusing on neutral markers. How genotypic and phenotypic data could covary over large geographic scales remains poorly understood in marine species. We crossed 75 noninbred sires (five origins) and 26 dams (two origins; each side of a hybrid zone) in a factorial diallel cross in order to investigate geographic variation for early survival and sex ratio in the metapopulation of the European sea bass (Dicentrarchus labrax), a highly prized marine fish species. Full-sib families (N = 1,950) were produced and reared in a common environment. Parentage assignment of 7,200 individuals was performed with seven microsatellite markers. Generalized linear models showed significant additive effects for both traits and pleiotropy between traits. A significant nonadditive genetic effect was detected. Different expression of traits and distinct relative performances were found for reciprocal crosses involving populations located on each side of the main hybrid zone located at the Almeria-Oran front, illustrating asymmetric reproductive isolation. The poor fitness performance observed for the Western Mediterranean population of sea bass is discussed as it represents the main source of seed hatchery production, but also because it potentially illustrates nonadaptive introgression and maladaptation.

A polygenic hypothesis for sex determination in the European sea bass Dicentrarchus labrax.

Polygenic sex determination, although suspected in several species, is thought to be evolutionarily unstable and has been proven in very few cases. In the European sea bass, temperature is known to influence the sex ratio. We set up a factorial mating, producing 5.893 individuals from 253 full-sib families, all reared in a single batch to avoid any between-families environmental effects. The proportion of females in the offspring was 18.3%, with a large variation between families. Interpreting sex as a threshold trait, the heritability estimate was 0.62 +/- 0.12. The observed distribution of family sex ratios was in accordance with a polygenic model or with a four-sex-factors system with environmental variance and could not be explained by any genetic model without environmental variance. We showed that there was a positive genetic correlation between weight and sex (r(A) = 0.50 +/- 0.09), apart from the phenotypic sex dimorphism in favor of females. This supports the hypothesis that a minimum size is required for sea bass juveniles to differentiate as females. An evolution of sex ratio by frequency-dependent selection is expected during the domestication process of Dicentrarchus labrax populations, raising concern about the release of such fish in the wild.