Whole genome resequencing reveals genomic regions associated with thermal adaptation in redband trout

Adaptation to local environments involves evolution of ecologically important traits and underlying physiological processes. Here, we used low coverage whole-genome resequencing (lcWGR) on individuals to identify genome regions involved in thermal adaptation in wild redband trout Oncorhynchus mykiss gairdneri, a subspecies of rainbow trout that inhabits ecosystems ranging from cold montane forests to high elevation deserts. This study includes allele frequency-based analyses for selective sweeps among populations, followed by multiple association tests for specific sets of phenotypes measured under thermal stress (acute and chronic survival/mortality; high or low cardiac performance groups). Depending on the groups in each set of analyses, sequencing reads covered 43%-75% of the genome at ≥15× and each analysis included millions of SNPs across the genome. In tests for selective sweeps among populations, a total of six chromosomal regions were significant. The further association tests for specific phenotypes revealed that the region on chromosome 4 was consistently the most significant and contains the cerk gene (ceramide kinase). This study provides insight into a potential genetic mechanism of local thermal adaptation and suggests cerk may be an important candidate gene. However, further validation of this cerk gene is necessary to determine if the association with cardiac performance results in a functional role to influence thermal performance when exposed to high water temperatures and hypoxic conditions.

Ecological and phenotypic differentiation among redband trout Oncorhynchus mykiss gairdneri populations. (a) Redband trout were sampled from ecologically divergent populations in Idaho, USA for population genomics and phenotypic trait association analyses following previous studies (Chen et al., 2018a; Narum et al., 2013). The heat map represents modelled 10 year average of August mean stream temperature for 2002–2011 (Isaak et al., 2016). (b) thermal stress experiment by exposing fish to diel temperature cycles (17°C–28°C). (c) response of pharmacologically-stimulated maximum heart rate (fH,max) to warming at the rate of 0.17°C/min. The fH,max is mass corrected to 1 g body mass using exponent of –0.1 (mean ± SEM) (d) proportion of fish showing cardiac arrhythmia during warming

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Molecular Ecology
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