Genotype and phenotype data for Columbia River steelhead.

As life history diversity plays a critical role in supporting the
resilience of exploited populations, understanding the genetic basis of
those life history variations is important for conservation management.
However, effective application requires a robust understanding of the
strength and universality of genetic associations. Here, we examine
genetic variation of single nucleotide polymorphisms in genomic regions
previously associated with migration phenology and age-at-maturity in
steelhead (Oncorhynchus mykiss) from the Columbia River. We found
chromosome 28 markers (GREB1L, ROCK1 genes) explained significant variance
in migration timing in both coastal and inland steelhead. However,
strength of association was much greater in coastal than inland steelhead
(R2 0.51 vs 0.08), suggesting that genomic background and
challenging inland migration pathways may act to moderate effects of this
region. Further, we found that chromosome 25 candidate markers (SIX6 gene)
were significantly associated with age and size at first return migration
for inland steelhead, and this pattern was mediated by sex in a
predictable pattern (males R2 = 0.139-0.170; females
R2 = 0.096-0.111). While this encourages using these candidate
regions in predicting life history characteristics, we suggest that stock
specific associations and haplotype frequencies will be useful in guiding
implementation of genetic assays to inform management.