Atlantic Salmon (Salmo salar) and Chinook Salmon (Oncorhynchus tshawytscha) are important culturally, recreationally, economically, and are a common aquaculture species in Canada and the United States. In the Pacific Northwest, blooms of toxic algae result in millions of dollars annually in losses for salmonid aquaculture producers. Blooms of harmful cyanobacteria produce microcystins which have been linked to net-pen liver disease which has large financial impacts on net pen salmon operations. Microcystin-LR, the most toxic variant, bioaccumulates in the liver and disrupts normal cellular activity by inhibiting protein phosphatases leading to deleterious effects on growth, immune status, and liver function. To minimize economic loss and improve animal welfare, salmonid producers have interest in using biomarkers of sub-lethal microcystin exposure to mitigate these impacts. RNA-sequencing was performed on liver samples from Atlantic and Chinook Salmon fed algal paste containing microcystin-LR in order to evaluate changes in gene expression caused by toxin exposure. The transcriptome response was examined at several time points following exposure to determine the most useful candidate biomarkers and to evaluate windows of detection. These biomarkers can serve as early warning signs that will allow aquaculture managers to decide to harvest early to avoid large mortality events caused by these algal toxins. Additionally, the biomarkers identified in this study have potential to be utilized across salmonid species for fish species broadly. Complementing previous microcystin research on fish, this study reports many differentially expressed genes related to the cell cycle, microtubule integrity, apoptosis, oxidative stress, inflammation, and metabolism.

Date of publication

Fall 11-15-2023

Document Type




Persistent identifier


Committee members

Ryan Shartau, Matthew Greenwold, and Katrin Kellner


Masters in Biology