Light is the primary energy source and important signaling component for growth and development of plants. The effect of light transduction mechanisms on rice plants has not been studied well. Hence, a comprehensive understanding on how different light sources affect the growth, development and production of secondary metabolites both at metabolic and gene regulation levels will provide a significant insight towards improved rice varieties. To do so, we employed systems biology approach to study such light-driven metabolic and regulatory mechanism in rice. We initially reconstructed a fully compartmentalized genome-scale metabolic model of rice cells. Transcriptomics and metabolomics data were integrated with constraint-based modeling to find out different light-specific transcriptional signatures of rice metabolism. Specifically, effects of blue- and red-light signals on the primary and secondary metabolism identified the involvement of different phytohormones such as abscisic acid, ethylene, gibberellin and jasmonate. The subsequent analysis on the promoter region of relevant genes further identified several light-specific putative cis-elements and their associated transcription factors. Additionally, the analysis on the light-specific transcriptional regulation of the biosynthesis of carotenoids and phenolic compounds revealed the possible involvement of different phytohormones and key transcription factors such as bHLH, bZIP, MYB, WRKY, ZnF and ERF in response to blue light. Overall, the biological insights gained from the current study provide several potential applications for crop improvement.
