Dissecting the genetic basis of response to salmonid alphavirus in Atlantic salmon

Background The development of effective disease management strategies is crucial for the assurance of welfare and sustainability of the aquaculture industries. Pancreas disease (PD) is a major challenge faced by Atlantic salmon aquaculture with viral outbreaks resulting in substantial production losses and raising significant welfare concerns for farmed salmon populations. Previous research has identified several quantitative trait loci (QTL) associated with PD resistance accounting for a substantial additive genetic component. However, pinpointing the underlying causal variation remains challenging, partly due to the location of the QTL within duplicated regions of the Atlantic salmon genome that share high sequence similarity. The present study leverages the latest advancements in Atlantic salmon genomics in order to uncover the genetic landscape underlying PD resistance and identify genomic variation with putative functional impact on disease response. Results Association mapping and haplotype analysis of fish challenged with salmonid alphavirus (SAV3), either through peritoneal injection or infectious cohabitation, confirmed the presence of a major QTL region on chromosome Ssa03. Additionally, another QTL on Ssa07 was detected, linked to infection-specific response. Transcriptomics analysis of the genes overlapping the Ssa03 QTL region revealed significant expression differences among three tandemly duplicated gig1-like genes, whereas allele-specific expression analysis detected several SNPs with putative functional impact on the particular genes. Use of long-read sequencing and construction of disease-associated haplotypes identified more complex variation in the region and offering a detailed exploration of the genetic architecture underlying PD resistance. Finally, integration of the regulatory landscape of Atlantic salmon during viral infection response improved genomic resolution, providing novel insight into the potential causal variation underlying pancreas disease in Atlantic salmon. Conclusions This study provides a detailed investigation of the genetic architecture underlying PD resistance in farmed Atlantic salmon. Using advanced genomic resources, three copies of the gig1-like gene were identified as likely causal candidates for a major QTL associated with PD resistance. Additionally, genomic variations with potential functional impacts on gig1-like expression were uncovered. These findings hold promise for application in developing effective disease management strategies in Atlantic salmon aquaculture.