Differential Effects of Day/Night Cues and the Circadian Clock on the Barley Transcriptome

The circadian clock is a complex transcriptional network that regulates gene expression in anticipation of the day-night cycle and controls agronomic traits in plants. However, in crops, how the internal clock and day-night cues affect the transcriptome remains poorly understood. We analyzed the diel and circadian leaf transcriptomes in the barley (Hordeum vulgare) cultivar Bowman and derived introgression lines harboring mutations in EARLY FLOWERING 3 (ELF3), LUX ARRHYTHMO 1 (LUX1), and EARLY MATURITY 7 (EAM7). The elf3 and lux1 mutants exhibited abolished circadian transcriptome oscillations under constant conditions, whereas eam7 maintained oscillations of ≈30% of the circadian transcriptome. However, day-night cues fully restored transcript oscillations in all three mutants and thus compensated for a disrupted oscillator in the arrhythmic barley clock mutants elf3 and lux1. Nevertheless, elf3, but not lux1, affected the phase of the diel oscillating transcriptome and thus the integration of external cues into the clock. Using dynamical modeling, we predicted a structure of the barley circadian oscillator and interactions of its individual components with day-night cues. Our findings provide a valuable resource for exploring the function and output targets of the circadian clock and for further investigations into the diel and circadian control of the barley transcriptome.