Exploring genetic resistance to Infectious Salmon Anaemia Virus in Atlantic salmon by genome-wide association and RNA sequencing

Abstract

Infectious Salmonid Anaemia Virus (ISAV) causes a notifiable disease that poses a large threat for Atlantic salmon breeders and producers worldwide. There is no fully effective treatment or vaccine, and therefore selective breeding to increase resistance to ISAV in commercial strains of Atlantic salmon is a promising avenue for disease prevention. Genomic selection and potentially genome editing can be applied to enhance host resistance, and these approaches benefit from improved knowledge of the genetic and functional basis of the target trait. The aim of this study was to characterise the genetic architecture of resistance to ISAV in a commercial Atlantic salmon population and study its underlying functional genomic basis using RNA Sequencing. A total of 2,833 Atlantic salmon parr belonging to 194 families were exposed to ISAV in a cohabitation challenge in which cumulative mortality reached 63% over 55 days. A total of 1,353 animals were genotyped using a 55K SNP array, and the estimate of heritability for the trait of binary survival was 0.33 (±0.04). A genome-wide association analysis confirmed that resistance to ISAV was a polygenic trait, albeit a genomic region in chromosome 13 was significantly associated with resistance and explained 3% of the genetic variance. RNA sequencing of the heart of 16 infected (7 and 14 days post infection) and 8 control fish highlighted 4,927 and 2,437 differentially expressed genes at 7 and 14 days post infection respectively. The complement and coagulation pathway was down-regulated, while several metabolic pathways were up-regulated in infected fish compared to controls. The interferon pathway was mildly activated at 7 days and showed no sign of up-regulation at 14 days post infection, implying a crosstalk between host and virus. Comparison of the transcriptomic response of fish with high and low breeding values for resistance (4 high resistance and 4 low resistance animals per time point) highlighted TRIM25 as being up-regulated in resistant fish, suggesting it may be a key antiviral gene involved in the functional genetic basis of resistance to ISAV.

Transcriptomic response to ISAV infection in the gills, head kidney and spleen of resistant and susceptible Atlantic salmon

“…A previous study showed similar results during early infection, with a more important up-regulation of interferon genes in the head kidney than in other tissues [34]. However, the interferon response was previously shown to be up-regulated also in other tissues, for instance in liver [35], and in these animals we previously found it down-regulated in the heart [13].…”

“…In head kidney, two copies of the E3 ubiquitin-protein ligase HERC3 were upregulated in response to the virus at 14 dpi. In our previous study in the same population, a gene of the same family (HERC4) co-located with a putative QTL for resistance to ISAV [13]. Additionally, another gene of this family, HERC5, was previously described as an antiviral protein in Influenza virus infection, catalysing ISGylation of NS1 and avoiding its interaction with the antiviral protein kinase R (PKR), which reduces viral propagation [47].…”

“…The challenge experiment and sampling were conducted in the facilities of VESO Vikan (Norway). All the disease challenge and sampling protocol was previously described in detail in [13]. After acclimatation of the fish during three week, 300 carrier fish (Atlantic salmon from the same population) were intraperitoneally injected with 0.1 mL of ISAV (Glaesvær, 080411, grown in ASK-cells, 2 passage, estimated titre 10 6 PFU / mL [58]) and introduced to the challenge tank with naïve fish.…”

“…For each timepoint (control, 7 dpi and 14 dpi) 4 fish with high breeding values for resistance and 4 fish with low breeding values for resistance, representing 8 different families, were selected according to their estimated genomic breeding value for ISAV resistance [13]. Gills, head kidney and spleen RNA samples from the same fish were extracted from preserved tissue samples in TRI reagent (Sigma, UK) and RNA extracted following the manufacturer’s instructions (n= 24 per tissue; control = 8; 7 dpi = 8; 14 dpi = 8).…”

“…The challenge experiment and sampling were conducted in the facilities of VESO Vikan (Norway). All the disease challenge and sampling protocol was previously described in detail in [13].…”