AbstractPhotosynthesis is involved in the essential process of transforming light energy into chemical energy. Although the interaction between photosynthesis and the circadian clock has been confirmed, the mechanism of how light intensity affects photosynthesis through the circadian clock remains unclear. Here, we propose a first computational model for circadian-clock-controlled photosynthesis, which consists of the light-sensitive protein P, the core oscillator, photosynthetic genes, and parameters involved in the process of photosynthesis. The model parameters were determined by minimizing the cost function (\documentclass[12pt]{minimal}
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}{}$\boldsymbol{\delta} =\mathbf{8.56}$\end{document}), which is defined by the errors of expression levels, periods, and phases of the clock genes (CCA1,PRR9,TOC1,ELF4,GI, andRVE8). The model recapitulates the expression pattern of the core oscillator under moderate light intensity (100 μmol m−2s−1). Further simulation validated the dynamic behaviors of the circadian clock and photosynthetic outputs under low (62.5 μmol m−2s−1) and normal (187.5 μmol m−2s−1) intensities. When exposed to low light intensity, the peak times of clock and photosynthetic genes were shifted backward by 1–2 hours, the period was elongated by approximately the same length, and the photosynthetic parameters attained low values and showed delayed peak times, which confirmed our model predictions. Our study reveals a potential mechanism underlying the circadian regulation of photosynthesis by the clock under different light intensities in tomato.