Integrated Nutrient Management Enhances Root Growth, Nutrient Use Efficiency, and Ratooning Ability in Rice Under Acidic Paddy Soils

Ratoon rice is a unique cropping system that utilizes the regenerative capacity of rice tillers to achieve one sowing with two harvests in a single growing season, thus exhibiting great yield potential. However, the ratooning ability is often constrained by impaired root function after the first harvest. In this study, we established an integrated nutrient management (INM) strategy to enhance root growth and function, thereby improving nutrient use efficiency and yield. Compared with farmers’ conventional management (FCM), INM increased annual total yield by 7.8% and 13.9% and enhanced ratooning ability by 20.7% and 19.0% in 2024 and 2025, respectively. INM consistently maintained higher root biomass in both main and ratoon crops: by 26.9% and 54.0% in 2024, and by 44.8% and 26.0% in 2025. Root biomass was significantly and positively correlated with brown rice weight across both seasons, and was positively associated with ratooning ability. INM also promoted early root establishment after transplanting, increasing the white-root number by 105.7%, 175.0%, and 484.8% at 3, 5, and 14 days after transplanting (DAT), respectively. Meanwhile, the xylem sap exudation rate and root triphenyl tetrazolium chloride (TTC) reduction activity were increased by 37.4% and 64.5% relative to FCM. In the 2024 ratoon season, INM improved nutrient use efficiency, with partial factor productivity (PFP) of nitrogen (PFPN), phosphorus (PFPP), and potassium (PFPK) increased by 371.0%, 59.3%, and 91.1%, respectively. Gene Set Enrichment Analysis (GSEA) revealed significant enrichment of gene sets involved in root growth, development, nutrient acquisition, and assimilation under INM, providing molecular evidence for root-mediated nutrient synergy. In summary, INM enhances root growth and function, promotes nutrient uptake and utilization, and consequently improves yield. These results offer a practical management strategy supported by physiological and transcriptomic evidence for boosting ratoon rice production via root-mediated nutrient synergies.