Selection and simulated climate-warming effects on Brook Charr sperm DNA methylation
Directional selection in the domestication of fish species has resulted in rapid gains of growth, body size, and other production-relevant traits in relatively few generations. While there is clear evidence of genetic divergence contributing to selection-related phenotypic changes, emerging research suggests that intergenerational epigenetic inheritance may also be a relevant mechanism explaining rapid evolutionary change in domestic fish lines. Epigenetic changes have also been implicated in fish species' responses to warming associated with climate change. Domestic lines of Brook Charr (Salvelinus fontinalis) are the primary source of fish used for recreational fisheries stocking in many parts of Eastern North America and there are concerns about how these fish will fare when stocked into lakes in the coming decades. We jointly investigated the effects of directional selection for performance traits (i.e., absence of early sexual maturation and increased growth) and exposure to elevated temperatures on DNA methylation in sperm cells of two experimental lines (hereafter: Selected and Control lines) of Brook Charr . We used whole-genome bisulfite sequencing to characterize DNA methylation at over 17 million methylated sites and identified 393 selection-related differentially methylated regions (DMR). The putative functions of genes in proximity to these DMRs are consistent with well-characterized phenotypic differences between the lines, including lipid metabolism and precocial maturation, and support the hypothesis that rapid evolution of traits may be partially mediated by epigenetic inheritance. We subsequently detected 85 warming-related DMRs in the Control line and 302 DMRs in the Selected line. None of these regions were shared between the two lines, indicating that the directional selection regime significantly altered the environmentally sensitive epigenetic landscape. Overall design: Two lines of Brook Charr were maintained the ISMER for 5-6 generations. The selected line was directionally selected for low precocial maturation (immature at age 2) and then by growth (largest individuals were selected for line propagation). More details on line establishment and maintenance can be found in Bastien et al. (2011) [https://doi.org/10.1080/15222055.2011.544609]. During the period of final gamete maturation (Sept - Dec) each line was maintained in either ambient seasonal temperatures or in a simulated climate warming scenario that tracked the daily and seasonal fluctation, but with temperature consistently elevated by 2 degrees C. Gametes were collected during annual spawning activities and we used whole genome bisulfite sequencing of genomic DNA extracted from male milt (sperm). We compared effects of line (differential selection) and temperature on patterns of DNA methylation in this tissue.