Genome-scale comparative analysis for host resistance against sea lice between Atlantic salmon and rainbow trout

Sea lice (Caligus rogercresseyi) are ectoparasites that cause major production losses in the salmon aquaculture industry worldwide. Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) are two of the most susceptible salmonid species to sea lice infestation. The goal of this study was to identify common candidate genes involved in resistance against sea lice. For this, 2,626 Atlantic salmon and 2,643 rainbow trout from breeding populations were challenged with sea lice and genotyped with a 50k and 57k SNP panel. We ran two independent genome-wide association studies for sea lice resistance on each species and identified 7 and 13 windows explaining 3% and 2.7% respectively the genetic variance. Heritabilities were observed with values of 0.19 for salmon and 0.08 for trout. We identified genes associated with immune responses, cytoskeletal factors and cell migration. We found 15 orthogroups which allowed us to identify dust8 and dust10 as candidate genes in orthogroup 13. This suggests that similar mechanisms can regulate resistance in different species; however, they most likely do not share the same standing variation within the genomic regions and genes that regulate resistance. Our results provide further knowledge and may help establish better control for sea lice in fish populations.