Data from: Genomic region associated with run-timing has similar haplotypes and phenotypic effects across three lineages of Chinook salmon

Conserving life history variation is a stated goal of many management
programs, but the most effective means by which to accomplish this are
often far from clear. Early, premature migrating and late, mature
migrating forms of Chinook salmon face unequal pressure from natural and
anthropogenic forces. These forces may result in the diminishment of
migration variation in some stocks because migration timing is known to be
highly heritable. Genomic regions of chromosome 28 are known to be
strongly associated with migration variation in adult Chinook salmon, but
it remains unclear whether there is consistent association among the
diverse populations of Chinook salmon. Therefore, application of
this association for management may be premature. We examined the
association of genetic variation in 28 markers on chromosome 28 surveyed
with high-throughout genotyping (GT-seq) with individual run timing
characteristics gleaned from passive integrated transponder recordings of
over 5,000 Chinook salmon from the three phylogeographic lineages that
inhabit the Columbia River Basin. Despite the strong genetic differences
among them, the three lineages exhibited very similar genetic variants in
the chromosome 28 region and moderate to strong association of these
variants and run timing phenotypes. This is particularly notable for the
interior stream-type lineage, which exhibits an earlier and more
constrained migration of fish than the other lineages and which are
exclusively premature when they enter freshwater. In both interior
stream-type and interior-ocean type Chinook salmon, heterozygotes of the
most strongly associated linkage groups are largely intermediate to
homozygotes in migration timing, and while we make no robust conclusions
about dominance, results indicate codominance or marginal partial
dominance of the early migrating allele. Our results lend support to the
cautious utilization of chromosome 28 variation in tracking and predicting
run timing in these Chinook salmon.