Identification of Genomic Loci Associated with Cellular Rhythms in Diversity Outbred Mice

Inter-individual variation in human molecular and behavioral circadian rhythms motivates genetic dissection in model systems with human-like diversity. We quantified cellular clock phenotypes from primary skin fibroblasts of several hundred Diversity Outbred (DO) mice-each carrying a unique mosaic of eight founder genomes-by longitudinal bioluminescence recordings of a Bmal1-luciferase reporter (LumiCycle). Canonical rhythm parameters (period, phase, amplitude, damping) were extracted and exhibited broad variability (heritability ≈13–35%), exceeding the ranges of founder strains. We performed genome-wide QTL mapping with R/qtl2 (linear mixed models with sex and experimental group covariates, kinship control, permutation-based significance, 1.5-LOD support intervals). A suggestive QTL for amplitude localized to chromosome 12 (LOD 6.9; ∼7.5–12.0 Mb), with founder effects indicating higher amplitude for C57BL/6J and lower for PWK/PhJ. Among 21 protein-coding genes in this interval, Apob (apolipoprotein B), a clock-regulated determinant of lipoprotein assembly, emerged as a strong candidate for amplitude control. A phase QTL mapped to chromosome 1 (support interval ∼1.36 Mb) with divergent founder effects (C57BL/6J, NOD/ShiLtJ, WSB/EiJ: delayed; PWK/PhJ, CAST/EiJ: advanced) and prioritized candidates including Epha4 (an Eph receptor tyrosine kinase implicated in photic entrainment) and Acsl3 . Integrative analysis in GeneWeaver connected QTL gene sets to prior loci for voluntary alcohol consumption and circadian period on proximal chromosome 12, and highlighted overlaps with GWAS signals for adolescent idiopathic scoliosis and schizophrenia, suggesting shared pathways between circadian regulation, metabolism, and neurobehavioral traits. Together, these findings define reproducible genomic loci for cellular clock phenotypes in a highly recombinant population, nominate tractable candidate genes ( Apob, Epha4/Acsl3 ) for mechanistic follow-up, and illustrate how high-diversity mouse genetics bridges cellular circadian variation with complex disease biology.