M.Sc. EXIT SEMINAR
Evan Morien
B.Sc., SUNY at Buffalo, US, 2007
Friday, June 15th, 2012 at 11 AM
LOCATION: Lecture Theatre, BCCRC
Characterization of the Wild Salmon Transcriptome
Abstract:
Pacific salmon are ecologically and economically important, but populations have been declining and fluctuating unpredictably for the past few decades. Sockeye salmon in particular have been experiencing high levels of mortality during their migration upriver. These declines have spurred much research into the physiology of salmon, but comparatively little research into their genetics and genomics. We are using expression profiling to gain new insights into the genomics of Pacific salmon stocks. I will describe work aimed at baseline characterization of the salmon transcriptome, and the development of approaches for sample classification based on gene expression. We conducted a large-scale transcriptome analysis of multiple tissues and species taken from the Fraser River and surrounding ocean water from 2007-2010. We identified tissue-specific and housekeeping genes in salmon, and validated them by comparison to mouse and human orthologues. The results suggest that many features of the transcriptome are conserved, and indicate the likely robustness of the markers we identified.
Supervised classification of samples using qPCR-derived pathogen data was successful with one of the pathogens tested. We found that for these data, using housekeeping genes to compute normalization factors (mimicking the procedures that would be used for practical implementation of assays using qPCR) had little effect.
The discovery of tissue-specific and housekeeping genes in salmon will prove useful for others researching salmon genomics and genetics, and the results of the classification experiment are encouraging. Future work will be aimed at incorporating our findings into assays used in fisheries management.
Supervisor: Dr. Paul Pavlidis, Associate Professor, Department of Psychiatry, UBC
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