Coho salmon low-coverage whole genome re-sequencing

Reintroduction of salmonids to regions where they have been extirpated is a common conservation strategy, often implemented through natural recolonization, translocation of natural populations, or hatchery-based programs. Locally adapting to specific environmental conditions is critical for long-term population viability, particularly for species like Coho Salmon Oncorhynchus kisutch, which face diverse selective pressures during their migration. This study focuses on the Mid-Columbia River Coho Salmon reintroduction program, managed by the Yakama Nation Fisheries, which has successfully reintroduced Coho Salmon to the Wenatchee and Methow river basins. Notably, these populations have adapted to the longer migration route than those in the founding stock, with selection favoring individuals with an earlier arrival time and that can navigate a 15 km high-gradient canyon to reach optimal spawning grounds. The objectives of this study were to investigate whether specific genomic regions are under selection for traits associated with return location and timing in Coho Salmon. Low coverage whole genome re-sequencing data was used to screen for genomic regions associated with the phenotypes of interest. A weak, polygenic signal in female Coho Salmon was found to be associated with return group, with a subset of candidate adaptive regions across eight chromosomes. These findings provide insights into the genomic mechanisms underlying local adaptation in reintroduced salmon populations and inform broodstock selection strategies aimed at promoting natural production and long-term population sustainability.