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The health of both wild and farmed salmon can be severely impacted by sea lice that live on the skin of the salmonid fish. Lice infections can cause production costs of Canadian farmed salmon to soar up to $35 million per year to control these infestations. This project used genomics to understand the host-pathogen interaction between different salmon and louse species. The collected data, including a comprehensive compilation of gene lists (over 30,000 genes) for the salmon louse Lepeophtheirus salmonis and some species of Caligus, gene expression profiling of host-pathogen responses to infection, and expression profiling of louse genes under different environmental conditions, addresses the impact of environmental variables in the prevalence of infection, the origin of lice infections, and potential therapeutic (i.e., vaccine) targets and control possibilities. This research not only benefits agencies that regulate salmon fishing, but also improves scientific communication and understanding of the sea lice/salmon controversy.

A suite of several hundred variable genetic markers was developed within GiLS and applied to the identification of salmon louse migration patterns across the Pacific and among farm and wild populations in British Columbia, showing evidence of virtually unrestricted gene flow among populations within both Ocean basins. Comparative infection experiments revealed evidence for a diversity of response mechanisms to L. salmonis among salmon species, showing that several Pacific salmon species are highly resistant to salmon louse infections. Furthermore, modest reductions in salinity elicited a detrimental stress response in the larval dispersal stages of L. salmonis. Finally, the team observed a previously undescribed microsporidian parasite in the sea lice which is known to perturb host (louse) physiology, affecting the transcriptomic reponse to the pesticide emamectin benzoate (EB), currently used by industry to contol infection.