Genetic variation associated with adult migration timing in lineages of Steelhead and Chinook Salmon in the Columbia River

Abstract

With the discovery of a major effect region (GREB1L, ROCK1) for adult migration timing in genomes of both Chinook Salmon and Steelhead, several subsequent studies have investigated the effect size and distribution of early and late migration alleles among populations in the Columbia River. Here, we synthesize the results of these studies for the major lineages of Chinook Salmon and Steelhead that include highly distinct groups in the interior Columbia River that exhibit atypical life histories from most coastal lineage populations of these two species. Whole‐genome studies with high marker density have provided extensive insight into SNPs most associated with adult migration timing, and suites of markers for each species have been genotyped in large numbers of individuals to further validate phenotypic effects. For Steelhead, the largest phenotypic effect sizes have been observed in the coastal lineage (36% of variation for passage timing at Bonneville Dam; 43% of variation for tributary arrival timing) compared to the inland lineage (7.5% of variation for passage timing at Bonneville Dam; 8.4% of variation for tributary arrival timing) that overwinter in freshwater prior to spawning. For Chinook Salmon, large effect sizes have been observed in all three lineages for multiple adult migration phenotypes (Coastal lineage: percentage of variation of 27.9% for passage timing at Bonneville Dam, 28.7% for arrival timing for spawning; Interior ocean type: percentage of variation of 47.6% for passage timing at Bonneville Dam, 39.6% for tributary arrival timing, 77.9% for arrival timing for spawning; Interior stream type: percentage of variation of 35.3% for passage at Bonneville Dam, 9.8% for tributary arrival timing, 4.7% for arrival timing for spawning). Together, these results have extended our understanding of genetic variation associated with life history diversity in distinct populations of the Columbia River, however, much research remains necessary to determine the causal mechanism for this major effect region on migration timing in these species.

Advances in salmonid genetics—Insights from Coastwide and beyond

“…Several studies in this Special Issue investigated the crucial role of genomic diversity in maintaining life history variation and enabling natural populations to adapt to local environments. Three papers investigated genomic variation associated with locally adapted traits across populations (Lecomte et al, 2024;Narum et al, 2024;Willis et al, 2024), two others focused on genomic variation to adapt under scenarios of climate change (Tigano et al, 2024) or persist through ecological disturbance (Frei et al, 2024), and another on genomic differences between hatchery reared versus wild stocks (Howe et al, 2024). Lecomte et al (2024) examined SNPs, structural variants (SVs), and small indels between two populations of Atlantic Salmon in North America with differences in life history traits (i.e., age at smoltification and maturity).…”

“…Narum et al. ( 2024 ) synthesized multiple studies investigating genomic variation associated with adult migration timing in Steelhead and Chinook Salmon. A conserved genomic region of major effect (GREB1L/ROCK1) has been demonstrated to be highly associated with adult migration timing in both species.…”