Detecting genomic variation underlying phenotypic characteristics of reintroduced Coho salmon (Oncorhynchus kisutch)

Abstract

For species that have been extirpated from parts of their range, conservation managers often reintroduce individuals to these areas in hopes of restoring populations to pre-decline conditions. Coho salmon (Oncorhynchus kisutch) have been extirpated since the early 1900s in the interior reaches of the Columbia River watershed. Starting in the late 1990s, the Columbia River Treaty tribes were successful in starting a re-introduction program that has established an upper Columbia River Coho salmon stock. Fish are preferentially selected for broodstock to incorporate naturally occurring phenotypic characteristics to facilitate local adaptation. On the Wenatchee River in Washington, broodstock are preferentially selected at a lower and upper river dam, however, only ~ 32% of fish successfully ascend a 15 km high-gradient reach to the upper river dam. Fish that successfully ascend the reach generally arrive early in the season and have a better overall body condition. In other salmonids, phenotypic traits such as return timing has been shown to be under genetic control. To determine if there are genomic regions that underly the phenotypic traits found to impact migration success up a high-gradient reach, low-coverage whole genome re-sequencing (lcWGR) was performed on adult fish returning to the system. Genome-wide association tests revealed three genomic regions that are associated with fish return location. Results of the lcWGR suggest that candidate markers can be incorporated as a genetic screening tool during broodstock selection to preferentially breed fish that have the phenotypic characteristics that confer greater potential for steeper and longer migration distances.