摘要:SummaryPhenotypic variation is the basis for trait adaptation via evolutionary selection. However, the driving forces behind quantitative trait variations remain unclear owing to their complexity at the molecular level. This study focused on the natural variation of the free-running period (FRP) of the circadian clock because FRP is a determining factor of the phase phenotype of clock-dependent physiology.Lemna aequinoctialisin Japan is a paddy field duckweed that exhibits a latitudinal cline of critical day length (CDL) for short-day flowering. We collected 72 strains ofL. aequinoctialisand found a significant correlation between FRPs and locally adaptive CDLs, confirming that variation in the FRP-dependent phase phenotype underlies photoperiodic adaptation. Diel transcriptome analysis revealed that the induction timing of anFTgene is key to connecting the clock phase to photoperiodism at the molecular level. This study highlights the importance of FRP as a variation resource for evolutionary adaptation.Graphical abstractDisplay OmittedHighlights•Natural variation of flowering/circadian traits in a paddy-field duckweed is studied.•Critical day length for flowering of the duckweed in Japan shows a latitudinal cline.•A negative correlation between critical day length and circadian period was found.•AnFTgene responding to lengthening of the dark period was isolated.Plant biology; Plant Biology; Plant genetics