Field microenvironments regulate crop diel transcript and metabolite rhythms.

Most research in plant chronobiology has been done in laboratory conditions. However, they usually fail to mimic natural conditions and their slight fluctuations, highlighting or obfuscating rhythmicity. High-density crops, such as sugarcane (Saccharum hybrid), generate field microenvironments with specific light and temperature due to mutual shading. We measured the metabolic and transcriptional rhythms in the leaves of 4-month-old (4 mo) and 9 mo sugarcane grown in the field. Most of the assayed rhythms in 9 mo sugarcane peaked >1 h later than in 4 mo sugarcane, including rhythms of the circadian clock gene, LATE ELONGATED HYPOCOTYL (LHY). We hypothesized that older sugarcane perceives dawn later than younger sugarcane due to self-shading. As a test, we measured LHY rhythms in plants on the east and the west side of a field. We also tested if a wooden wall built between lines of sugarcane changed their rhythms. The LHY peak was delayed in the plants in the west of the field or beyond the wall; both shaded at dawn. We conclude that plants in the same field may have different phases due to field microenvironments, impacting important agronomical traits, such as flowering time, stalk weight and number.