Genetic variation drives seasonal onset of hibernation in the 13-lined ground squirrel

Abstract

Hibernation in sciurid rodents is a dynamic phenotype timed by a circannual clock. When housed in an animal facility, 13-lined ground squirrels exhibit variation in seasonal onset of hibernation, which is not explained by environmental or biological factors. We hypothesized that genetic factors instead drive variation in timing. After increasing genome contiguity, here, we employ a genotype-by-sequencing approach to characterize genetic variation in 153 ground squirrels. Combined with datalogger records (n = 72), we estimate high heritability (61–100%) for hibernation onset. Applying a genome-wide scan with 46,996 variants, we identify 2 loci significantly (p < 7.14 × 10−6), and 12 loci suggestively (p < 2.13 × 10−4), associated with onset. At the most significant locus, whole-genome resequencing reveals a putative causal variant in the promoter of FAM204A. Expression quantitative trait loci (eQTL) analyses further reveal gene associations for 8/14 loci. Our results highlight the power of applying genetic mapping to hibernation and present new insight into genetics driving its onset.

A unifying, eco‐physiological framework for animal dormancy

“…For example, in the insect literature, clines in clock gene allele frequency underlie evolved differences in diapause induction and initiation timing, and these alleles are under selection due to climate change (Bradshaw & Holzapfel, 2001; Pruisscher et al., 2018). Similar clines in timing also exist in other taxa (Figures 4 and 6), but we do not know the extent to which they share a common mechanism (see Box 2; Fenn et al., 2009; Grabek et al., 2019; Lane et al., 2011, 2019; Zervanos et al., 2010). The mammalian literature has shown that diet during preparation may influence the magnitude and duration of maintenance phase.…”

“…Mammal phylogeny from (Fritz et al, 2009) and insect phylogeny from (Wiens et al, 2015). Silhouettes and licenses are from phylo pic.org (Figures 4 and 6), but we do not know the extent to which they share a common mechanism (see Box 2; Fenn et al, 2009;Grabek et al, 2019;Lane et al, 2011Lane et al, , 2019Zervanos et al, 2010).…”

Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal

“…After aligning and scaffolding Chicago data, Dovetail HiC library sequences were aligned and scaffolded following the same method. We named this genome HiC_Itri_2, reflecting the assembly method and that this is the second super-assembly of SpeTri2.0 ( Grabek et al, 2019 ).…”

A Temporal Examination of Cytoplasmic Ca2 + Levels, Sarcoplasmic Reticulum Ca2 + Levels, and Ca2 + -Handling-Related Proteins in Different Skeletal Muscles of Hibernating Daurian Ground Squirrels

“…This may prompt the animals to arouse from torpor. In other words, the increase in cytoplasmic Ca 2+ during LT may be one of the factors resulting in interbout arousal following prolonged torpor (Grabek et al, 2019). Conversely, the reduction in cytoplasmic Ca 2+ during IBA and ET could represent a reduction in futile cycling meant to reduce energy expenditure.…”