Chinook salmon are an iconic species with significant economic, cultural and ecological importance in British Columbia. Fisheries and Oceans Canada (FOC) plays a crucial role in managing these salmon populations through the Salmonid Enhancement Program (SEP). SEP is a key component of the Pacific Salmon Strategy Initiative (PSSI), which aims to stabilize and restore Pacific salmon populations and their habitats. One of the primary activities within the SEP involves releasing millions of hatchery-reared salmon each year. Evaluating the success of these hatchery enhancement activities is thus critically important both ecologically and economically.

However, there are currently few molecular tools for monitoring hatchery-reared salmon. This is important because hatchery salmon often don't thrive in natural rivers as well as wild salmon, despite having very similar DNA.  Traditional genetic tests, which look for differences in DNA sequences, aren't effective at distinguishing between them. To address this issue, the research team for this project plans to identify epigenomic biomarkers – these are indicators in a salmon's genes that show how its environment has affected its genes – of hatchery rearing and develop fast, efficient tests for these biomarkers. If successful, this will provide a new way to tell hatchery-raised salmon apart from wild salmon and allow improved monitoring of their performance.

Unlike standard DNA tests, these new epigenomic markers detect chemical changes to the DNA, which do not change the DNA sequence. These changes are affected by the environment and differ between hatchery-origin and natural origin-salmon. So epigenomic markers are like fingerprints in the genome that can be used to distinguish between hatchery-raised and naturally spawned Chinook salmon. 

These new markers could offer many advantages. They’d allow for quick and efficient monitoring of hatchery and natural-origin salmon without needing extensive genetic testing or physical markings. They could also reveal which specific hatchery a salmon comes from, providing more detailed information than physical markings alone. Furthermore, understanding the epigenetic differences between hatchery and natural origin fish could help improve how we manage salmon populations in response to changing environmental conditions.