Single-Nucleotide Polymorphism (SNP) Loci Correlated with Run Timing in Adult Chinook Salmon from the Columbia River Basin

Run timing in Chinook salmon Oncorhynchus tshawytscha is a life history trait that varies among populations throughout the Columbia River basin and has a demonstrated genetic basis. In this study, we used 92 single-nucleotide polymorphic (SNP) markers linked to at least 75 different functional genes (including OtsClock1a) to test for correlations with run timing. We obtained samples of adult Chinook salmon on a weekly basis as they passed a fixed point (Bonneville Dam) on the lower Columbia River main stem during the majority of the migratory run from April to October for three sequential years from 2007 to 2009 (n = 2,731, 3,479, and 2,960, respectively). Since these fish represented unknown mixtures of the three major genetic lineages in the Columbia River basin, we used genetic stock identification to assign individuals to their likely stock of origin. We then determined whether allelic variation at the SNP loci was correlated with the date of passage of fish in the context of stock of origin. Nine SNP loci were identified as candidates based on significant correlations with date of passage using the spatial analysis method. A multivariate analysis was then used to rank these eight candidate loci according to the proportion of genetic variation that day of passage explained relative to two other predictor variables: population structure and temperature. The three top-ranked loci were Ots_TAPBP, Ots_97077-179R, and Ots_myoD-364, which have known involvement in immunological functioning and muscle differentiation. Future work will test candidate SNPs using run-timing information from fish of known origin within particular Columbia River subbasins to help validate the role of these genetic linkage groups in this important life history trait.