Integration of crop growth model and constraint-based metabolic model predicts metabolic changes over rice plant development under water-limited stress

Rice is a major staple food worldwide and understanding its metabolism is essential for improving crop yield and quality, especially in a changing climate. Constraint-based modelling is an established method for studying metabolism at a systems level, but one of its limitations is the difficulty in directly integrating certain environmental factors, such as water potential, to the model for predicting metabolic changes in response to environmental changes. Here, we developed a framework to integrate a crop growth model and an upgraded diel multi-organ genome-scale metabolic model of rice to predict the metabolism of rice growth under normal and water-limited conditions. Our model was able to predict distinct metabolic adaptations under water-limited stress compared to normal condition across multiple developmental stages. Our modelling results of dynamic changes in metabolism over the whole-plant growth period highlighted key features of rice metabolism under water-limited stress including early leaf senescence, reduction in photosynthesis and significant nitrogen assimilation during grain filling.