Abstract
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.
Highlights
The circadian clock is a time-keeping mechanism that reflects the day-night cycle through an endogenous transcriptional rhythm to anticipate dawn and dusk (McClung, 2006)
In the Arabidopsis circadian oscillator, two morning-expressed MYB transcription factors, CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), inhibit the expression of TIMING OF CAB EXPRESSION1/ PSEUDO-RESPONSE REGULATOR1 (TOC1/PRR1) that in turn represses the transcription of CCA1 and LHY in the night (Alabadí et al, 2001, Gendron et al, 2012; Huang et al, 2012b)
We sampled for 36 h in LL because barley circadian transcript oscillations rapidly dampen upon transfer to constant conditions, which results in a high signal-to-noise ratio of the rhythms which would have compromised the systems identification (Campoli et al, 2012, Hughes et al, 2017)
Summary
The circadian clock is a time-keeping mechanism that reflects the day-night cycle through an endogenous transcriptional rhythm to anticipate dawn and dusk (McClung, 2006). The Arabidopsis thaliana oscillator contains an interconnected regulatory network of transcriptional repressors and activators (Hsu et al, 2013; Fogelmark and Troein, 2014) These components are expressed sequentially to regulate output genes through regulatory elements present in target promoters (Harmer et al, 2000; Covington et al, 2008; Michael et al, 2008b). In the Arabidopsis circadian oscillator, two morning-expressed MYB transcription factors, CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), inhibit the expression of TIMING OF CAB EXPRESSION1/ PSEUDO-RESPONSE REGULATOR1 (TOC1/PRR1) that in turn represses the transcription of CCA1 and LHY in the night (Alabadí et al, 2001, Gendron et al, 2012; Huang et al, 2012b). The evening-expressed GIGANTEA (GI) protein was modeled as a negative regulator of the EC, which in turn inhibits TOC1 expression (Pokhilko et al, 2012, Huang et al, 2012)
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