Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis

Plants use the circadian clock to sense and respond to photoperiod length. Seasonal responses like flowering are triggered at a critical photoperiod when a light-sensitive clock output coincides with light or darkness. However, many metabolic processes, like starch turnover, and growth respond progressively to photoperiod duration. We first tested the photoperiod response of ten core clock genes and two output genes. qRT-PCR analyses of transcript abundance under 6, 8, 12 and 18 hour photoperiods revealed 1-4 hour earlier peak times under short photoperiods, and detailed changes like rising PRR7 expression before dawn. Clock models recapitulated most of these changes. We then explored the consequences for global gene expression by performing transcript profiling in 4, 6, 8, 12 and 18 hour photoperiods. There were major changes in transcript abundance at dawn, which were as large as those between dawn and dusk in a given photoperiod. Contributing factors included altered timing of the clock relative to dawn, and light-signaling and changes in carbon availability at night due to clock-dependent regulation of starch degradation. Their interaction facilitates coordinated transcriptional regulation of key processes like starch turnover, anthocyanin, flavonoid and glucosinolate biosynthesis and protein synthesis, and underpins the response of metabolism and growth to photoperiod. This article is protected by copyright. All rights reserved.