| Summary: | Declines in Pacific salmon stocks in recent decades have spurred much research into their physiology and survivorship, but comparatively little into their genomics. Sockeye salmon in particular are experiencing high levels of mortality during their migration upriver, and the numbers of returning sockeye have fluxuated wildly with respect to predictions in recent years. The goal of my project is to gain insight into the basic genomics of Pacific salmon stocks, including the sockeye, through bioinformatic approaches to gene expression profiling. Using microarray technology, I have conducted a large-scale analysis of over 1,000 samples from multiple tissues, stocks, and species of salmon. I identified tissue-specific and housekeeping genes and compared them to orthologs in mouse and human, respectively. I have also classified a number of microarray samples with a support vector machine (SVM) using qPCR data showing the presence of several common pathogens affecting Pacific salmon populations. Using identified housekeeping genes as normalizing factors, I modeled in silico a qPCR assay designed to identify salmon as infected or uninfected with a particular pathogen. With these data I hope to increase basic knowledge of the genomics of the Pacific salmon.
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