Yield performance of rice with different root system architecture with combination of DRO1 and qSOR1 alleles under different fertilization regimes

Purpose Optimizing root system architecture (RSA) through genetic selection and targeted fertilization strategies can improve nutrient efficiency and crop productivity. We investigated the contrasting RSA determined by two major quantitative trait loci (QTLs), DRO1 and qSOR1 , which control root growth angle in rice, in the context of fertilization methods—broadcasting and local application—that differ markedly in nutrient distribution within the soil. Through this approach, we aimed to clarify how RSA related traits interact with fertilization strategies to enhance rice productivity in paddy field. Methods Field trials were conducted over two years (2022–2023) in Morioka and Takizawa, Japan, using lowland rice IR64 and its three introgression lines (ILs) differing in functional/unfunctional alleles of DRO1 and qSOR1 . Compared to IR64, the ILs exhibit three distinct RSA: shallow (SHALLOW), deep (DEEP), and shallow + deep (DIMORPHIC). Fertilization treatments included Mix (NPK broadcasted and mixed into the soil) and Local (NPK embedded 10-cm deep). Grain yield, mineral uptake and root distribution were measured. Results Over the two-year trial period, the DEEP and DIMORPHIC lines consistently exhibited superior yields compared with IR64 and SHALLOW across fertilization regimes and experimental sites. The root surface area in the deeper soil layer (10–20 cm below the soil surface) was strongly correlated with grain yield. Local fertilization consistently resulted in higher yields and enhanced mineral uptake relative to Mix fertilization. Moreover, root proliferation was observed at fertilized position under the Local regime across all lines. Conclusions DRO1 -mediated deep rooting enhanced mineral uptake and yield under flooded conditions. Local fertilization increased nutrient availability and stimulated root proliferation in nutrient-rich zones, thereby improving nutrient uptake. Together, these findings underscore the importance of integrating root architectural traits with fertilization strategies to maximize rice productivity and nutrient use efficiency, providing valuable insights for breeding resource-efficient varieties adapted to sustainable agricultural systems.