Effects of water deficit and flooding stress on rice’s intrinsic water-use efficiency (iWUE) and how iWUE variations are linked to stress-induced physiological changes are poorly understood. Here, we proposed a model-based approach to analyze iWUE across datasets and its relationship with physiological changes, using only leaf gas exchange data and plant hydraulic vulnerability parameters. We applied this approach to a leaf gas exchange dataset of rice, measured during the post-stress period of water deficit and flooding experiments. Results show that water deficit and flooding stress decreased rice’s photosynthetic capacity (Vcmax25) and water transport capacity (Kmax) during the post-stress period, and that these physiological changes altered the relationship between photosynthetic rate and stomatal conductance, leading to an increase in iWUE. Nevertheless, improved iWUE cannot avoid the yield reduction. Interestingly, the stress-induced decrease in Vcmax25 was significantly correlated with the decline in Kmax. The Vcmax25-Kmax relationship was significantly different between the water deficit and flooding treatments, with the slope of the latter being closer to 1:1. Model predicts that stress-induced disproportionate Vcmax25-Kmax co-reduction improved iWUE while maintaining a relatively high intercellular to atmosphere CO2 concentration ratio; this may represent optimal coordination between photosynthetic and hydraulic traits in response to stress. Our work has important implications for using leaf gas exchange data to diagnose variations in iWUE, and for improving our understanding of crop physiological responses to environmental stresses.
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