biostudies-literatureUnknown3Anwer MUDeutsche ForschungsgemeinschaftNatural selection of variants within the Arabidopsis thaliana circadian clock can be attributed to adaptation to varying environments. To define a basis for such variation, we examined clock speed in a reporter-modified Bay-0 x Shakdara recombinant inbred line and localized heritable variation. Extensive variation led us to identify EARLY FLOWERING3 (ELF3) as a major quantitative trait locus (QTL). The causal nucleotide polymorphism caused a short-period phenotype under light and severely dampened rhythm generation in darkness, and entrainment alterations resulted. We found that ELF3-Sha protein failed to properly localize to the nucleus, and its ability to accumulate in darkness was compromised. Evidence was provided that the ELF3-Sha allele originated in Central Asia. Collectively, we sheLifehttps://www.ebi.ac.uk/biostudies/studies/S-EPMC4071560biostudies-literatureNatural variation reveals that intracellular distribution of ELF3 protein is associated with function in the circadian clock.PMC4071560DA 1061/4-1SFB635SPP1530Davis SJHerrero EVelikkakam James GBoikoglou ENagy FDavis AMHallstein MAnwer MUfalseNatural variation reveals that intracellular distribution of ELF3 protein is associated with function in the circadian clock.Natural selection of variants within the Arabidopsis thaliana circadian clock can be attributed to adaptation to varying environments. To define a basis for such variation, we examined clock speed in a reporter-modified Bay-0 x Shakdara recombinant inbred line and localized heritable variation. Extensive variation led us to identify EARLY FLOWERING3 (ELF3) as a major quantitative trait locus (QTL). The causal nucleotide polymorphism caused a short-period phenotype under light and severely dampened rhythm generation in darkness, and entrainment alterations resulted. We found that ELF3-Sha protein failed to properly localize to the nucleus, and its ability to accumulate in darkness was compromised. Evidence was provided that the ELF3-Sha allele originated in Central Asia. Collectively, we sh2014-01-01T00:00:00Z2014 May2025-06-01T12:19:02.402Z2025-06-01T12:19:02.402ZS-EPMC40715602486721510.7554/eLife.02206