Vol.:(0123456789) 1 3 Conservation Genetics https://doi.org/10.1007/s10592-020-01307-0 RESEARCH ARTICLE Detecting genomic variation underlying phenotypic characteristics of reintroduced Coho salmon (Oncorhynchus kisutch) Rebekah L. Horn 1  · Cory Kamphaus 2  · Keely Murdoch 2  · Shawn R. Narum 1 Received: 9 December 2019 / Accepted: 19 August 2020 © Springer Nature B.V. 2020 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 fsh 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 fsh returning to the system. Genome-wide association tests revealed three genomic regions that are associated with fsh return location. Results of the lcWGR suggest that candidate markers can be incorporated as a genetic screening tool during broodstock selection to preferentially breed fsh that have the phenotypic characteristics that confer greater potential for steeper and longer migration distances. Keywords Coho salmon · Pool-seq · GWAS · Reintroduction · Fisheries management Introduction Conservation management of species often requires the movement and reintroduction of individuals into regions previously extirpated (Seddon et al. 2007). Success of these programs can be hard to estimate, with the ultimate goal for populations to reach their carrying capacity and maintain viable population sizes (Robert et al. 2015). Most reintro- duction projects focus on mammals or birds with only 4% of projects focused on fsh (Seddon et al. 2007). In the Pacifc Northwest, almost a third of the salmonid populations have been lost since the arrival of Europeans, with most of those in the interior reaches (Gustafson et al. 2007). Dams operat- ing along the Columbia and Snake Rivers contributed to the decline of upriver stocks of Chinook salmon (Oncorhynchus tshawytscha) (Schaller et al. 1999) and led to the extirpation of interior river Coho salmon (O. kisutch) (Nehlsen et al. 1991). In salmonids, re-introduction programs are becoming more numerous to return fsh to habitat no longer volitionally accessible due to dams or other man-made barriers (Bosch et al. 2007; Anderson et al. 2014; Galbreath et al. 2014; Sard et al. 2015; Kozfkay et al. 2019; Matala et al. 2019). There is considerable diversity in salmonids with respect to their life history strategies which includes diferential migration timing, maturation rate, return timing (Smith et al. 2014), and return distance and/or location (Bennett et al. 2015; Keefer et al. 2018). This diversity is critical to understand when implementing reintroduction programs for salmonids to increase survival of transplanted fsh and preserve the underlying life history variations (Anderson Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10592-020-01307-0) contains supplementary material, which is available to authorized users. * Rebekah L. Horn rhorn@critfc.org 1 Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA 2 Yakama Nation Fisheries, Toppenish, WA, USA