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 FLOWERING3 (ELF3), LUX ARRHYTHMO1 (LUX1), and EARLY MATURITY7 (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.

昼夜节律钟是一个复杂的转录网络，可在昼夜周期中调节基因表达并控制植物的农艺性状。然而，在农作物中，内部时钟和昼夜提示如何影响转录组仍然知之甚少。我们分析了昼夜在大麦（和昼夜叶转录大麦）品种“鲍曼”和派生渐渗系中窝藏突变早期FLOWERING3（ELF3），LUX ARRHYTHMO1（LUX1），以及早期MATURITY7（EAM7）。该ELF3和LUX1突变体表现出在恒定条件下消除的生物钟转录组振荡，而eam7维持了生物钟转录组30％的振荡。然而，日/夜线索完全恢复在所有三个突变成绩单振荡，从而弥补了心律不齐大麦时钟突变体破坏的振荡器ELF3和LUX1。尽管如此，ELF3，但不LUX1，影响的相位昼夜转录组振荡，从而将外部提示整合到时钟中。使用动力学建模，我们预测了大麦昼夜节律振荡器的结构及其各个组成部分与昼夜提示的相互作用。我们的发现为探索昼夜节律的功能和输出目标以及进一步研究大麦转录组的diel和昼夜节律提供了宝贵的资源。