41We investigated whether different specialized organs in field-grown sugarcane follow 42 the same temporal rhythms in transcription. We assayed the transcriptomes of three 43 organs during the day: leaf, a source organ; internodes 1 and 2, sink organs focused 44 on cell division and elongation; and internode 5, a sink organ focused on sucrose 45 storage. The leaf had twice as many rhythmic transcripts (>68%) as internodes, and 46 the rhythmic transcriptomes of the two internodes were more similar to each other than 47 to those of the leaves. More transcripts were rhythmic under field conditions than under 48 circadian conditions and most of their peaks were during the day. Among the 49 transcripts that were considered expressed in all three organs, only 7.4% showed the 50 same rhythmic time course pattern. The central oscillators of these three organs -the 51 networks that generate circadian rhythms -had similar dynamics with different 52 amplitudes. The differences between the rhythmic transcriptomes in circadian 53 conditions and field conditions highlight the importance of field experiments to 54 understand the plant circadian clock in natura. The highly specialized nature of the 55 rhythmic transcriptomes in sugarcane organs probably arises from amplitude 56 differences in tissue-specific circadian clocks and different sensitivities to 57 environmental cues. 58 59 Introduction 60The circadian clock is an endogenous signaling network that allows organisms to adapt 61 to rhythmically changing environments. Plants with a circadian clock synchronized with 62 environmental rhythms accumulate more biomass and have better fitness than plants 63with defective or no circadian clocks 1,2 . In crops, changes in the circadian clock have 64 been indirectly selected through traditional breeding to change photoperiodic 65 responses, such as the transition to flowering. For example, the circadian clocks of 66 European tomatoes have longer periods than those of native American tomatoes, as 67 such periods allow these crops to adapt better to the long summer days occurring at 68 the high latitudes of much of Europe 3 . Similarly, some genotypes of Hordeum vulgare 69 L. (barley) and Triticum aestivum L. (wheat) carry mutations in their circadian clock 70 genes that reduce flowering induced by photoperiodic triggers, allowing cultivation in 71 higher latitudes in Europe 4,5 . 72The circadian clock is conceptually divided into three associated parts: the Input 73 Pathways, the Central Oscillator, and the Output Pathways. The Input Pathways detect 74 entraining cues that keep the circadian clock continuously synchronized to the 75 environment. In plants, these cues include light, temperature, and sugar levels [6][7][8] . The 76 Central Oscillator is a series of interlocking transcriptional-translational feedback loops 77 that can generate 24-h rhythms independently of the environment. In Arabidopsis 78 thaliana (L.) Heynh. (Arabidopsis), one loop, called the morning loop, starts with the 79 light induction of CIRCADIAN CLOCK ASSO...

Circadian clocks improve plant fitness in a rhythmic environment. As each cell has its own circadian clock, we hypothesized that sets of cells with different functions would have distinct rhythmic behaviour. To test this, we investigated whether different organs in field-grown sugarcane follow the same rhythms in transcription. We assayed the transcriptomes of three organs during a 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 internodes were more like each other than to those of the leaves. Among the transcripts expressed in all organs, only 7.4% showed the same rhythmic pattern. Surprisingly, the central oscillators of these organs -the networks that generate circadian rhythms -had similar dynamics, albeit with different amplitudes. The differences in rhythmic transcriptomes probably arise from amplitude differences in tissue-specific circadian clocks and different sensitivities to environmental cues, highlighted by the sampling under field conditions. The vast differences suggest that we must study tissue-specific circadian clocks in order to understand how the circadian clock increases the fitness of the whole plant.