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.
Highlights
Hibernation in sciurid rodents is a dynamic phenotype timed by a circannual clock
Consistent with being controlled by an endogenous circannual clock, we hypothesized that observed variation in the onset of torpor is due to underlying genetic variation between individuals
Long-range scaffolding of the draft genome assembly
Summary
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. When housed under standard laboratory conditions in an animal facility (Fig. 1b), 13-lined ground squirrels exhibit individual variation in the timing of their first bout of torpor This variation is not accounted for by the environmental signals of food withdrawal, shortened photoperiod, or falling ambient temperature, or by the biological factors of age, body mass, and sex. We employed a genotype-by-sequencing strategy to characterize genetic variation in 153 13-lined ground squirrels whose tissues were previously collected for use in biochemical, transcriptomic and proteomic studies[15,16,17] Many of these squirrels were surgically implanted with body temperature dataloggers, and from their records, we recorded the first day that torpor occurred in each individual (Fig. 1c). Our results present new insight into the genetics driving the transition from homeothermy to heterothermy in a mammal and illustrate the power of genetic analysis to attack questions of exceptional biological significance in a non-classical genetic model organism
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