Rhythms of Transcription in Field-Grown Sugarcane Are Highly Organ Specific

Abstract We investigated whether different specialized organs in field-grown sugarcane follow the same temporal rhythms in transcription. We assayed the transcriptomes of three organs during the day: leaf, a source organ; internodes 1 and 2, sink organs focused on cell division and elongation; and internode 5, a sink organ focused on sucrose storage. The leaf had twice as many rhythmic transcripts (>68%) as internodes, and the rhythmic transcriptomes of the two internodes were more similar to each other than to those of the leaves. More transcripts were rhythmic under field conditions than under circadian conditions and most of their peaks were during the day. Among the transcripts that were considered expressed in all three organs, only 7.4% showed the same rhythmic time course pattern. The central oscillators of these three organs — the networks that generate circadian rhythms — had similar dynamics with different amplitudes. The differences between the rhythmic transcriptomes in circadian conditions and field conditions highlight the importance of field experiments to understand the plant circadian clock in natura . The highly specialized nature of the rhythmic transcriptomes in sugarcane organs probably arises from amplitude differences in tissue-specific circadian clocks and different sensitivities to environmental cues. One sentence summary The rhythmic transcriptome of field-grown sugarcane is highly organ-specific.