The USDA National Cold Water Marine Aquaculture Center (NCWMAC) has been evaluating families of North American Atlantic salmon (Salmo salar) for resistance to sea lice (Lepeophtheirus salmonis) since 2015 and are currently evaluating the second generation of families selected for sea lice resistance. With the spawning of the second generation in 2021, the USDA began several different efforts to evaluate the success of the selection program. One of the efforts was to identify if different strains of Atlantic salmon with discrete long-term exposure histories to sea lice had different levels of resistance. This effort was supplemented with fin and skin transcriptomic profiling of each strain at sites of infection and at parasite free locations to investigate what factors might explain phenotypic differences between the strains.
Three different strains of Atlantic salmon smolts were compared: the St. John River (SJR) strain of historical sea run Atlantic salmon with many generations of continual sea lice exposure and the primary commercial strain used in net pen culture in Maine; the Casco Lake (CAS) strain which has been historically land locked with no history of exposure to sea lice in modern history; and the Grand Lakes Stream (GLS) strain, which generally remains in freshwater lakes and rivers but does have access to the ocean where they could be exposed to sea lice. Smolts from all three strains were challenged in four replicate tanks with 30 fish from each strain per challenge tank. A two-way ANOVA accounting for strain and challenge tank showed a significant difference in lice density between strains with CAS fish being more susceptible to sea lice than either SJR or GLS. Transcriptomic analyses of skin and fin revealed that, although skin and fin had strikingly different transcriptomic profiles, sites with or without sea lice copepodid attachment were generally indistinguishable. This study indicates that selection for sea lice resistance can be made within Atlantic salmon; however, transcriptomic responses in all 3 strains indicated little to no parasite recognition, suggesting immune responsiveness to copepodid infestation may not be a significant pathway involved in observed variations in resistance.