Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature

Clock‐regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best‐understood clock output pathways in Arabidopsis , which control key regulators of flowering and elongation growth. In flowering, the model predicted regulatory links from the clock to CYCLING DOF FACTOR 1 ( CDF1 ) and FLAVIN‐BINDING, KELCH REPEAT, F‐BOX 1 ( FKF1 ) transcription. Physical interaction data support these links, which create threefold feed‐forward motifs from two clock components to the floral regulator FT . In hypocotyl growth, the model described clock‐regulated transcription of PHYTOCHROME‐INTERACTING FACTOR 4 and 5 ( PIF4 , PIF5 ), interacting with post‐translational regulation of PIF proteins by phytochrome B (phyB) and other light‐activated pathways. The model predicted bimodal and end‐of‐day PIF activity profiles that are observed across hundreds of PIF‐regulated target genes. In the response to temperature, warmth‐enhanced PIF4 activity explained the observed hypocotyl growth dynamics but additional, temperature‐dependent regulators were implicated in the flowering response. Integrating these two pathways with the clock model highlights the molecular mechanisms that coordinate plant development across changing conditions. Synopsis Crosstalk between the circadian clock and light/temperature signals controls seasonal plant development. Integrated mathematical models of the clock, flowering and elongation pathways identify new behaviours in light and temperature signalling. CCA1 negatively regulates FKF1 and CDF1 transcription. GI has an FKF1‐independent role in CDF1 protein stabilisation. PIF proteins function throughout light:dark cycles. Temperature regulates flowering time and hypocotyl elongation pathways at distinct times of day. Graphical Abstract Crosstalk between the circadian clock and light/temperature signals controls seasonal plant development. Integrated mathematical models of the clock, flowering and elongation pathways identify new behaviours in light and temperature signalling.