Identification of the key factors associated with yield reduction in rice genetic resources under low-nitrogen conditions

Rice is a staple cereal crop that plays a key role in global food security. However, the overuse of nitrogen fertilizers in rice cultivation has led to decreased nitrogen use efficiency (NUE), higher production costs, and significant environmental pollution. To address these challenges, we investigated the key factors contributing to yield reduction under low-nitrogen (LN) conditions using a rice core collection of 232 accessions. Field experiments were conducted over two years under normal-nitrogen (NN, 9.0 kg/10a) and LN (4.5 kg/10a) conditions. Agronomic and yield-related traits were analyzed using comprehensive statistical methods to identify the primary contributors to grain yield reduction. The number of panicles per plant (NPP) and number of spikelets per panicle (NSP) were the most influential traits linked to yield decline. Statistical analyses confirmed that NPP and NSP were significantly correlated with a grain yield per plant (GYP) ( r = 0.25–0.58, p < 0.05) across both nitrogen conditions and years. Path analysis revealed that NPP and NSP exerted the strongest direct effects on GYP, with standardized coefficients ranging from 0.47 to 0.77 across both nitrogen conditions and years, highlighting their critical role in yield determination. Multiple regression analysis demonstrated that NPP and NSP collectively explained up to 80 % of GYP variation under LN conditions in 2023. Cluster analysis identified genetic resources capable of maintaining stable yields under LN conditions, with the highest-yielding group exhibiting only a 24.1 % reduction in GYP. These findings suggest that NPP and NSP can serve as key phenotypic markers for selecting nitrogen-efficient rice varieties. This study offers critical insights into sustainable rice production by minimizing nitrogen input while maintaining grain yield. Identifying high-yielding, LN-adapted genetic resources provides essential breeding material for developing rice cultivars better suited to LN environments and climate resilience, thus supporting global food security in the face of climate change. • Low-nitrogen application reduces rice growth parameters and grain yield. • The key factors reducing rice yield under low-nitrogen conditions are decreased NPP and NSP. • NPP and NSP are key markers for selecting rice germplasms adapted to low-nitrogen conditions.