Wheels within wheels: the plant circadian system

•The circadian system is a complex regulatory network.•Multiple links exist between the clock and other cellular pathways and signaling networks.•Recent systems approaches have advanced our understanding of the clock system.•Insights into the Arabidopsis clock have been applied to several crop species.

Circadian clocks integrate environmental signals with internal cues to coordinate diverse physiological outputs so that they occur at the most appropriate season or time of day. Recent studies using systems approaches, primarily in Arabidopsis, have expanded our understanding of the molecular regulation of the central circadian oscillator and its connections to input and output pathways. Similar approaches have also begun to reveal the importance of the clock for key agricultural traits in crop species. In this review, we discuss recent developments in the field, including a new understanding of the molecular architecture underlying the plant clock; mechanistic links between clock components and input and output pathways; and our growing understanding of the importance of clock genes for agronomically important traits.