Quantitative trait loci and genes associated with salmonid alphavirus load in Atlantic salmon: implications for pancreas disease resistance and tolerance

Abstract

Salmonid alphavirus infection results in pancreas disease causing severe economic losses for Atlantic salmon aquaculture. Knowledge about genes and pathways contributing to resistance is limited. A 54 K SNP panel was used to genotype 10 full-sibling families each consisting of ~ 110 offspring challenged with salmonid alphavirus subtype 3. Relative heart viral load was assessed at 4- and 10-weeks post-infection using quantitative PCR. A moderate genomic heritability of viral load at 4 weeks (0.15-0.21) and a high positive correlation with survival (0.91-0.98) were detected. Positions of QTL detected on chromosome 3 matched those for survival detected by other studies. The SNP of highest significance occurred in the 3' untranslated region of gig1, a fish-specific antiviral effector. Locus B of immunoglobulin heavy chain mapped to an area containing multiple SNPs with genome-wide association. Heart mRNA-seq comparing parr from families with high- versus low-genomic breeding value, and matching sample genotypes for SNPs, identified two eQTL for salmonid alphavirus load. Immune genes associated with trans-eQTL were numerous and spread throughout the genome. QTL regions contained several genes with known or predicted immune functions, some differentially expressed. The putative functional genes and variants identified could help improve marker-based selection for pancreas disease resistance.

Figure 1

Manhattan plots of GWAS p-values for relative SAV3 viral load (− C_t) distributed across all chromosomes and for positions across Ssa03. Markers crossing genome and/or chromosome wide Bonferroni threshold are dotted in green colour. Results from the CH challenge trial (A, C) and the IP trial (B, D) are shown for SNPs on all chromosomes (A, B) and for SNPs on Ssa03 (C, D).

Figure 2

Histograms showing counts of sequences of IGH locus mapping across Ssa03 (positions in Mega base pairs, Mbp). Location of immune genes and SNPs significantly associated with C_t (red asterisks) are indicated.

Figure 3

Map of the 88–93 Mb QTL region on Ssa03 showing Manhattan plot and genes that are differentially expressed in H-gEBV versus L-gEBV salmon (highlighted as red text) and trans-eQTL (highlighted in green text). SNP AX-88234566 at position 89963083 which was associated with relative SAV3 viral load (genome wide significance) mapped to a 3′UTR region of gig1 (highlighted in orange). The other two SNPs associated with relative SAV3 viral load mapped to intergenic regions (relative positions indicated by arrows).

Figure 4

Boxplot of changes in expression of grass carp reovirus-induced gene 1 (Gig1-like), mapping to approximately 90.0 Mb along Ssa03. Plots show count of fragments per kilobase million (FPKM) for H-gEBV (green dot) and L-gEBV (red dot) fish challenged by intraperitoneal injection (IP) or cohabitation (CH) and sampled at 0- (naïve), 4- or 10-weeks post-infection.