Multi-Omics Analysis Reveals the Regulatory and Metabolic Mechanisms Underlying Low-Nitrogen Tolerance at the Flowering Stage in Rice

Crop productivity depends on nitrogen fertilization, but plants take up only an average of 30–50% of the applied nitrogen. Developing rice cultivars with improved nitrogen use efficiency or low-nitrogen (LN) tolerance is critical for sustainable agriculture. In this study, a backcross introgression line (G9) with 15 introgressed regions from donor parent and its recurrent parent Shuhui 527 (G1), which are differentially responsive to LN stress, were used to investigate the mechanism mediating rice LN tolerance at the flowering stage based on metabolome and transcriptome profiles. Three genes (LOC_Os02g40010, LOC_Os11g25260 and LOC_Os11g47300) involved in purine metabolism, which are located in the introgressed regions, were detected with significantly higher expression levels in G9 than in G1 under LN stress, and the contents of two relative metabolites (uric acid and guanine) were significantly different between the two genotypes. Additionally, two genes (LOC_Os02g36880 and LOC_Os08g05830) located in the introgressed regions and relative metabolites (3-phosphoglyceric acid and sedoheptulose 7-phosphate) involved in glycosis and pentose phosphate pathway are differentially expressed between G9 and G1. In addition to the two nitrogen metabolism-related genes (OsLHT1 and OsACR9) located in the introgressed regions, 23 differentially expressed genes mainly involved in nitrogen metabolism were identified between genotypes or treatments. With the comprehensive analysis of transcriptomes and metabolomes, our results reveal that the active purine metabolism may be the main factor contributing to LN tolerance in rice at the flowering stage, and also provide five new candidate genes for improving LN tolerance during the molecular breeding of rice