Genetic and Behavioral Variation Underlying an Integrated Temporal Phenotype in an Admixed South American Population

Chronotype is a complex trait reflecting individual differences in the temporal organization of rest and activity, with important health implications. The Uruguayan population, characterized by a tri-hybrid origin (African, European, and Indigenous), exhibits a bias toward eveningness. The genetic variation in clock genes underlying chronotype in this population remains unexplored. To address this gap, we analyze healthy young adults from the extremes of the chronotype distribution (early, n = 37; late, n = 38; 63% female; 23.1 {+/-} 3.4 years), integrating self-reported measures, actigraphy, and low-pass whole-genome sequencing. Global ancestry is predominantly European, with Indigenous and African components, and does not differ between chronotypes. Variant density is highest in PER2. T-allele carriers of a PER2 variant previously associated with late chronotypes (rs35333999) differ from non-carriers in activity acrophase. Multidimensional scaling of variants across 19 canonical clock genes reveal differential representation of early and late chronotypes across genetic clusters. When examined by functional groups, the signal is restricted to genes involved in degradation of the circadian clock's repressor arm, with BTRC, a mediator of PER2 degradation, showing the same pattern when assessed individually. We derive a joint behavioral component capturing the variation in food intake, moderate-to-vigorous physical activity, light exposure, and sleep timing, which correlates with dim-light melatonin onset (DLMO), the gold-standard marker of circadian phase, and show differences among genetic clusters. Our integrative multilevel approach suggests a complex interplay between behavioral and genetic factors shaping chronotype in this cohort, highlighting the PER2BTRC axis as a candidate mechanism for future investigations.