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Not AvailableBackground Rising food demand, slowing productivity growth, poor N-use efficiency in rice, and environmental degradation necessitate the development of more productive, environmentally-sound crop and soil management practices. The system of rice intensification (SRI) has been proposed as a methodology to address these trends. However, it is not known how its modified crop-soil-water management practices affect efficiency of inorganic nitrogen applications. Methods Field experiments investigated the impacts of SRI management practices with different N-application rates on grain yield, root growth and activity, uptake of N and its use-efficiency, leaf chlorophyll content, leaf Nconcentration, and photosynthetic rate in comparison with standard management practices for transplanted flooded rice (TFR). Results Overall, grain yield with SRI was 49 % higher than with TFR, with yield enhanced at every N application dose. N-uptake, use-efficiency, and partial factor productivity from applied N were significantly higher in SRI than TFR. Higher leaf nitrogen and chlorophyll contents during the ripening-stage in SRI plants reflected delayed leaf-senescence, extension of photosynthetic processes, and improved root-shoot activities contributing to increased grain yield. Conclusions Rice grown under SRI management used N fertilizer more efficiently due to profuse root development and improved physiological performance resulting in enhanced grain yield compared to traditional flooded rice.Not Availabl