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.

Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream (Sparus aurata) Broodstock Nuclei.

The gilthead seabream (Sparus aurata) is a species of relevance for the Mediterranean aquaculture industry. Despite the advancement of genetic tools for the species, breeding programs still do not often include genomics. In this study, we designed a genomic strategy to identify signatures of selection and genomic regions of high differentiation among populations of farmed fish stocks. A comparative DNA pooling sequencing approach was applied to identify signatures of selection in gilthead seabream from the same hatchery and from different nuclei that had not been subjected to genetic selection. Identified genomic regions were further investigated to detect SNPs with predicted high impact. The analyses underlined major genomic differences in the proportion of fixed alleles among the investigated nuclei. Some of these differences highlighted genomic regions, including genes involved in general metabolism and development already detected in QTL for growth, size, skeletal deformity, and adaptation to variation of oxygen levels in other teleosts. The obtained results pointed out the need to control the genetic effect of breeding programs in this species to avoid the reduction of genetic variability within populations and the increase in inbreeding level that, in turn, might lead to an increased frequency of alleles with deleterious effects.

Integrated Management Strategies for Viral Nervous Necrosis (VNN) Disease Control in Marine Fish Farming in the Mediterranean.

Viral nervous necrosis (VNN) is the most important viral disease affecting farmed fish in the Mediterranean. VNN can affect multiple fish species in all production phases (broodstock, hatchery, nursery and ongrowing) and sizes, but it is especially severe in larvae and juvenile stages, where can it cause up to 100% mortalities. European sea bass has been and is still the most affected species, and VNN in gilthead sea bream has become an emerging problem in recent years affecting larvae and juveniles and associated to the presence of new nervous necrosis virus (NNV) reassortants. The relevance of this disease as one of the main biological hazards for Mediterranean finfish farming has been particularly addressed in two recent H2020 projects: PerformFISH and MedAID. The presence of the virus in the environment and in the farming systems poses a serious menace for the development of the Mediterranean finfish aquaculture. Several risks associated to the VNN development in farms have been identified in the different phases of the farming system. The main risks concerning VNN affecting gilthead seabream and European seabass have been identified as restocking from wild fish in broodstock facilities, the origin of eggs and juveniles, quality water supply and live food in hatcheries and nurseries, and infected juveniles and location of farms in endemic areas for on-growing sites. Due to the potential severe impact, a holistic integrated management approach is the best strategy to control VNN in marine fish farms. This approach should include continuous surveillance and early and accurate diagnosis, essential for an early intervention when an outbreak occurs, the implementation of biosecurity and disinfection procedures in the production sites and systematic vaccination with effective vaccines. Outbreak management practices, clinical aspects, diagnostic techniques, and disinfections methods are reviewed in detail in this paper. Additionally, new strategies are becoming more relevant, such as the use of genetic resistant lines and boosting the fish immune system though nutrition.