Linking Genotype and Phenotype: Identifying Fitness Traits That Respond to Genetic Adaptation to Captivity in Chinook Salmon

The success of conservation hatcheries may be limited if hatchery fish have reduced reproductive success in the wild. Genetic adaptation to captivity has been identified as one mechanism of this fitness reduction. Therefore, it is important to identify the specific traits that respond to selection in the captive environment and quantify the rate of genetic change, because this data can inform actions that maximize the effectiveness and longevity of hatchery programs. Previous work on hatchery Chinook salmon from the Cle Elum Supplementation and Research Facility surveyed 9410 restriction site-associated loci and identified genomic signatures in a segregated line that are consistent with adaptation to captivity. Here, we link key fitness traits that have been measured in five generations of returning adults to molecular markers using Genome Wide Association Studies and Random Forest analyses. We then perform tests of selection on associated markers to determine which traits respond to genetic adaptation to captivity. We compare our results to an integrated line to determine whether gene flow between hatchery and naturally spawned fish limits directional change at fitness loci. This study will inform management practices aimed at reducing selection in the captive environment, thus minimizing its effect in supportive breeding programs.