| Summary: | Systems biology methods can provide novel insight into the responses of an organism to a suboptimal environment, an infection or exposure to a xenobiotic. In the interaction of salmon and salmon lice, there are several areas requiring further research. These include the impacts of lice infection on wild salmon, response mechanisms of different salmon species or life stages to lice infections, effects of environmental conditions on lice stress, and mechanisms underlying the emergence of resistance to important parasiticidal chemicals. Here, I combine global gene expression analyses with phenotypic and physiological responses of salmon or salmon lice to further our understanding of these topics. In the first chapter, I introduce the work by discussing relevant background material on the current knowledge of salmon and salmon lice interactions, salmon immunity, the state of salmon and louse genomics and the emerging field of ecological genomics. I also discuss how these approaches are applied to the study of non-model organisms and sustainable aquaculture development and fisheries conservation. In the second chapter, I present the first large-scale transcriptome profiling of a Pacific salmon to a salmon lice infection, identifying transcript signatures associated with an infection in a sensitive life stage of pink salmon Oncorhynchus gorbuscha. In the third chapter, I present the results of multiple co-habitation infections of three species of Pacific and Atlantic salmon to compare physiological and transcriptomic responses at the local (skin) and systemic levels (anterior kidney). In the fourth chapter, I explore louse transcriptome functioning during temperature and salinity perturbations to characterize the molecular stress response and coping strategies of lice, as well as provide stressor context to response genes. In the fifth chapter, I evaluate sensitive Pacific and resistant and sensitive Atlantic lice responses to emamectin benzoate, an important compound for louse control which has recently been evaded ...
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