Meta-analysis of GWAS for Sea Lice Load in Atlantic Salmon

Sea lice (Caligus rogercresseyi) are ectoparasites that cause significant production losses in the salmon aquaculture industry. Atlantic salmon (Salmo salar) is an important salmonid species for the aquaculture industry and highly susceptible to sea lice infestation. Sea lice load has been shown to be a polygenic trait, controlled by several quantitative trait loci (QTL) with small to medium effects. To improve the detection of QTL associated with sea lice load, we imputed single nucleotide polymorphism (SNP) data from medium- to high-density and conducted genome-wide association studies (GWAS). The imputation from 50 K to 600 K SNP genotypes was performed on 6144 fish from four different populations, which were challenged against sea lice. A metaGWAS was carried out for lice count, lice density, and log-transformed lice density. We identified two genomic regions highly associated with sea lice load on chromosomes (ssa) 3 and 12. Important functional candidate genes are mucin-16-like (ssa3), filamentous-growth-regulator 23-like (ssa3) and fibroblast growth factor receptor-like 1 (ssa12). Several other genes found here suggest that tissue repair, cytoskeletal modification and immune response may play an important role in the genetic variation of sea lice load. Our results confirm the highly polygenic architecture of sea lice load and provide novel insights into the genomic regions and candidate genes underlying the genetic variation for this trait in Atlantic salmon.