Viral Nervous Necrosis (VNN) is a major threat to sea bass populations, with mortality rates of up to 90% and an expected increased incidence with global warming . G enetic selection is a promising strategy to reduce the frequency and severity of epidemics that French hatcheries have been developing for several years, and which has recently benefited from the identification of a genomic region on chromosome 12, significantly involved in resistance to infection . The heritability of resistance to nervous necrosis viruses (NNV) was estimated to be 0.21, and in the studied population, the presence of the identified marker resulted in up to a 40% increase in survival rates. In this study, we investigate the impact on progeny survival to NNV infection when incorporating or omitting this marker in the genetic evaluation model.
To get the genomic estimated breeding values (GEBV) of 98 EMG-Ichtus males, we used genotypes obtained from a comprehensive dataset. Specifically, genotypes were available from 5251 siblings, all of which were genotyped on ThermoFisher’s 57,000-marker DlabCHIP SNP chip. Among these siblings , 1051 sibs of the candidate males had been assessed for VNN survival, allowing for a thorough investigation of their genetic resistance to this disease.
A total of 98 EMG-Ichtus males were then crossed with a group of 8 females. This mating strategy was designed to obtain precise progeny-based estimates of the breeding value of the 98 males . Subsequently, to evaluate the susceptibility of the 4210 offspring to NNV, an experimental challenge was conducted at Fortior Genetics. Mortalities were recorded and all offspring were genotyped with the AgriSeq ™ targeted genotyping-by-sequencing (tGBS ) technology comprising 563 SNP markers among which 199 were used for parentage assignment and 282 were chosen for their association to NNV resistance. A total of 3663 offspring were assigned to their parents, and each sire had from 17 to 70 offspring, except one sire with 3 offspring which was removed from the analysis.
Based on all this information, we observed a correlation r = 0.38 between the GEBV of the 98 males obtained by ssGBLUP (Single-Step Genomic Best Linear Unbiased Prediction, combining the use of pedigree and genotypes) and the survival of their offspring challenged for NNV resistance . When the genetic effect of the SNP marker most significantly associated with NNV resistance was integrated as a fixed effect in the evaluation model, the correlation between GEBV and offspring survival increased significantly (r = 0.52).
These results confirm that the genetic selection of parents increases the resistance of their offspring to NNV. They also show that the additional use of the information provided by the QTL marker explaining a large part of the resistance (marker-assisted selection) improves the efficiency of "simple" genomic selection using the 57,000 markers available. The synergy between marker-assisted selection and genomic evaluation underscores its potential for improving natural disease resistance in aquaculture populations.
This work was financially supported by the FEAMP MedMax project (no. FEA470020FA1000002) co-funded by the French government and the European Union.