Time of day analysis over a field grown developmental time course in rice

Plants integrate time of day (TOD) information over an entire season to ensure optimal growth, flowering time, and grain fill. However, most TOD expression studies have focused on a limited number of combinations of daylength and temperature under laboratory conditions. Here we re-analyze an Oryza sativa (rice) expression study that followed TOD expression in the field over an entire growing season. We find that like Arabidopsis thaliana, almost all rice genes have a TOD specific expression over the developmental time course. As has been suggested in other grasses, thermocycles were a stronger cue for TOD expression than the photocycles over the growing season. All the core circadian clock genes display consistent TOD expression over the season with the interesting exception that the two grass paralogs of EARLY FLOWERING 3 (ELF3) display a distinct phasing based on the interaction between thermo- and photo-cycles. The dataset also revealed how specific pathways are modulated to distinct TOD over the season consistent with the changing biology. The data presented here provides a resource for researchers to study how TOD expression changes under natural conditions over a developmental time course, which will guide approaches to engineer more resilient and prolific crops.