Introduction
Viral nervous necrosis (VNN) disease caused by the nervous necrosis virus (NNV) inflicts significant losses to seabass producers through mortalities and impaired growth of the infected fish (Barsøe et al. 2021) . Genetics studies have demonstrated the potential for improving resistance to the disease through selective breeding in different seabass populations (Palaiokostas et al. 2018; Griot et al. 2021) . Additionally, recent studies have identified genomic regions or markers with significant effect on VNN resistance in different European seabass populations (Palaiokostas et al. 2018; Griot et al. 2021; Vela-Avitúa et al. 2022) . However, precise genetic basis of VNN resistance in European seabass remains unknown. Therefore, in the current study we employed multi-omics tools to identify and functionally characterize genomic components underpinning resistance to VNN in farmed European seabass.
Materials and Methods
Approximately 1,500 European seabass from a full factorial cross of 25 dams and 25 sires were challenged with NNV. Mortality of the challenged fish was then recorded twice a day for a period of 29 days and used as the primary phenotype for resistance to the virus (binary survival) . T ime of death (in days) of the challenged fish was also recorded. A total of 1,066 fish (including the 50 parents and 1016 NNV challenged fish) were genotyped on the MedFish SNP array for 30K SNPs. The 50 parents and 40 offspring were full genome sequenced, and used as references for full genome imputation of all the offspring. Additionally, 322 offspring from the same parents were recruited in a transcriptome challenge experiment where 110 and 212 fish were mock- and NNV- challenged respectively. Tissue samples for RNA sequencing were collected from brain and head kidney. Whole genome GWAS was performed for both binary survival and days to death using GCTA software. Additionally, correlation analyses between gene expression and VNN resistance breeding values were performed. We subsequently performed expression QTL analyses for the main candidate genes identified in the QTL region.
Results
Our results showed moderate heritability estimates for VNN resistance of 0.400 ± 0.058 and 0.451 ± 0.058, for binary survival and days to death respectively, indicating the potential of selective breeding to reduce the impact of the disease. Of the 8.5M variants, 48,787 were associated with VNN resistance, with a large majority (90%) located on LG12 (scaffold CAJNNU010000003.1) as shown in Figure 1A. The most significant variant explained 37% of the total additive genetic variation in VNN resistance (Figure 1B) and showed a clear additive effect with individuals homozygous for the resistant allele showing 81 % survival upon infection. This demonstrates the potential of utilizing marker assisted selection to enhance selective breeding for resistance against VNN. The eight most significant variants were located in the IFI27L2A gene, and our results revealed a significant correlation between IFI27L2A expression and VNN resistance (Figure 1C) . Interestingly, variants with the strongest effect on VNN resistance also showed a clear association with the expression levels of IFI27L2A.
Conclusions
Our results provide a more refined insight into the genomic basis of resistance to VNN, which could be utilized for enhancing selective breeding or to design genome editing approaches to produce fish that are more resistant to the disease.
Funding
The study was conducted as part of the AQUA-FAANG project, which has received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No 817923.
References
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Palaiokostas C., Cariou S., Bestin A., Bruant J.-S., Haffray P., Morin T., Cabon J., Allal F., Vandeputte M. & Houston R.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, 1-11.
Vela-Avitúa S., Thorland I., Bakopoulos V., Papanna K., Dimitroglou A., Kottaras E., Leonidas P., Guinand B., Tsigenopoulos C.S. & Aslam M.L.J.F.i.G. (2022) Genetic Basis for Resistance Against Viral Nervous Necrosis: GWAS and Potential of Genomic Prediction Explored in Farmed European Sea Bass (Dicentrarchus labrax). Frontiers in Genetics 2022:508.