Genome-wide epistatic interaction analysis reveals complex genetic determinants of circadian behavior in mice

Genetic heterogeneity underlies many phenotypic variations observed in circ adian rhythmicity. Continuous distributions in measures of circadian behavi or observed among multiple inbred strains of mice suggest that the inherent contributions to variability are polygenic in nature. To identify genetic loci that underlie this complex behavior, we have carried out a genome-wide complex trait analysis in 196 (C57BL/6J X BALB/cJ)F-2 hybrid mice. We have characterized variation in this panel of F-2 mice among five circadian phe notypes: free-running circadian period, phase angle of entrainment, amplitu de of the circadian rhythm, circadian activity level, and dissociation of r hythmicity. Our genetic analyses of these phenotypes have led to the identi fication of 14 loci having significant effects on this behavior, including significant main effect loci that contribute to three of these phenotypic m easures: period, phase, and amplitude. We describe an additional locus dete ction method, genome-wide generic interaction analysis, developed to identi fy locus pairs that may interact epistatically to significantly affect phen otype, Using this analysis, we identified two additional pairs of loci that have significant effects on dissociation and activity level; we also detec ted interaction effects in loci contributing to differences of period, phas e, and amplitude. Although single gene mutations can affect circadian rhyth ms, the analysis of interstrain variants demonstrates that significant gene tic complexity underlies this behavior. importantly, most of the loci that we have detected by these methods map to locations that differ from the nin e known clock genes, indicating the presence of additional clock-relevant g enes in the mammalian circadian system. These data demonstrate the analytic al value of both genome-wide complex trait and epistatic interaction analys es in further understanding complex phenotypes, and point to promising appr oaches for genetic analysis of such phenotypes in other mammals, including humans.