Field microenvironments regulate crop diel transcript and metabolite rhythms

Most research in plant chronobiology was done in laboratory conditions. However, they usually fail to mimic natural conditions and their nuanced fluctuations, highlighting or obfuscating rhythmicity. High-density crops, such as sugarcane (Saccharum hybrid), generate field microenvironments that have specific light and temperature, as they shade each other. Here, 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), but not TIMING OF CAB EXPRESSION (TOC1). 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 also changed their rhythms. In both experiments, the LHY peak was delayed in the plants shaded at dawn. We conclude that plants in the same field may have different phases due to field microenvironments, which may impact important agronomical traits, such as flowering time, stalk weight and number.