Coincidence of the threshold temperature of seasonal switching for diel transcriptomic oscillations and growth

Predicting plant responses to global warming is essential for ecosystem management and crop yields. As many genes are controlled by the circadian clock, understanding the effects of temperature on transcriptomic rhythmicity under natural conditions is necessary. Here, we detected diel rhythmic genes (DRGs) in Arabidopsis halleri in four seasons. In winter, the expression of most DRGs showed low amplitude but kept at high levels, consistent with the high enrichment of cold response genes. We defined 204 core DRGs that were rhythmic over at least three seasons. Using machine learning, sampling time was successfully decoded by these 204 core DRGs across a year. In the three-dimensional principal component space for core DRGs, the diel transcriptomes appeared as four circular orbits with different diameters arranged in seasonal order, shaping a cone-like structure. Each transcriptome was mapped to the surface of the cone. The geometrical distance from the cone axis to the single-time-point transcriptome was defined as the amplitude of the transcriptomic clock. The amplitude showed seasonal switching with a sudden rhythm attenuation at 7°C and lower. Additionally, field monitoring of the plant size revealed growth arrest at similar temperatures. These results imply cooperation in the temperature-dependent regulations of circadian rhythmicity and growth, highlighting the importance of the circadian clock in predicting plant responses to climate change.