Genome-wide structural variants associated with resistance to Infectious Pancreatic Necrosis virus in rainbow trout

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Abstract
Infectious pancreatic necrosis (IPN) is one of the most economically important viral diseases affecting salmonid aquaculture worldwide. Resistance to infectious pancreatic necrosis virus (IPNV) has been widely studied in rainbow trout (Oncorhynchus mykiss) by using SNP-based approaches. For instance, genome-wide association studies have led to the identification of moderate- to major-effect quantitative trait loci (QTL) controlling the trait. However, causative mutations underlying IPNV resistance in rainbow trout remains poorly understood. The potential contribution of structural variants (SVs) to the genetic architecture of resistance has received little attention despite their recognized role in shaping phenotypic variation and complex traits. In this study, we used whole-genome sequencing combined with a multi-tool SV detection approach to identify structural variants associated with IPNV-resistant and susceptible rainbow trout. A total of 2,564 SVs (2,358 deletions, 206 insertions) were identified as highly associated between resistant and susceptible individuals. Functional annotation showed that twelve of these variants overlapped genes with known immune-related functions, suggesting that they may contribute to variation in host antiviral responses. These findings provide further evidence that structural variation may contribute to resistance-related phenotypes in rainbow trout. Further incorporation of SVs into genomic analyses may improve the resolution of association studies and support the development of more comprehensive genomic selection strategies for disease resistance in aquaculture breeding programs.