Differential Effects of Day/Night Cues and the Circadian Clock on the Barley Transcriptome1[OPEN]

Based on diel and circadian leaf transcriptomes in barley wild-type and clock mutant lines we predicted a structure of the barley circadian oscillator and interactions of its individual components with day/night cues. 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 thedieland circadian leaf transcriptomes in the barley (Hordeum vulgare) cultivar 'Bowman' and derived introgression lines harboring mutations inEARLY FLOWERING3(ELF3),LUX ARRHYTHMO1(LUX1), andEARLY MATURITY7(EAM7). Theelf3andlux1mutants exhibited abolished circadian transcriptome oscillations under constant conditions, whereaseam7maintained oscillations of approximate to 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 mutantself3andlux1. Nevertheless,elf3, but notlux1, affected the phase of thedieloscillating 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 thedieland circadian control of the barley transcriptome.