High Throughput Genomics Applied to Identify Cumulative Impacts of Environmental and Biological Stressors on Salmon

Declines in productivity and abundance of wild salmon likely result from the cumulative and synergistic effects of multiple stressors.  Our research program applies molecular genetic and genomic technologies to build a greater understanding of factors that may undermine performance of wild salmon.  Functional genomic studies on wild-migrating salmon have revealed a high percentage of signatures involving strong differential immune stimulation; some may be associated with responses to infectious agents.  A microfluidic platform to quantitatively assess presence and load of over 90% of microparasites known to cause disease in salmon worldwide has been applied to identify pathogens potentially impacting wild salmon survival.  Microarrays and biomarkers to dozens of host immune- and stress-related genes are resolving the microbes associated with a strong host response, indicative of a disease state.   Biotelemetry studies have resolved viruses and parasites associated with reduced migration success.  The additional roles of predators and climate influencing population-level pathogen profiles are providing insight into ecological and evolutionary outcomes potentially associated with cumulative stressors.  In future, evolutionary drivers of variation in microparasite susceptibility will be incorporated into these “natural” studies by linking data on MHC variation or by taking a dQTL approach via NGS.