Nitrogen (N) is an extremely important macronutrient for plant growth and development. It is the main limiting factor in most agricultural production. However, it is well known that the nitrogen use efficiency (NUE) of rice gradually decreases with the increase of the nitrogen application rate. In order to clarify the underlying metabolic and molecular mechanisms of this phenomenon, we performed an integrated analysis of the rice transcriptome and metabolome. Both differentially expressed genes (DEGs) and metabolite Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that carbon and nitrogen metabolism is significantly affected by nitrogen availability. Further analysis of carbon and nitrogen metabolism changes in rice under different nitrogen availability showed that high N inhibits nitrogen assimilation and aromatic metabolism pathways by regulating carbon metabolism pathways such as the tricarboxylic acid (TCA) cycle and the pentose phosphate pathway (PPP). Under low nitrogen, the TCA cycle is promoted to produce more energy and α-ketoglutarate, thereby enhancing nitrogen transport and assimilation. PPP is also inhibited by low N, which may be consistent with the lower NADPH demand under low nitrogen. Additionally, we performed a co-expression network analysis of genes and metabolites related to carbon and nitrogen metabolism. In total, 15 genes were identified as hub genes. In summary, this study reveals the influence of nitrogen levels on the regulation mechanisms for carbon and nitrogen metabolism in rice and provides new insights into coordinating carbon and nitrogen metabolism and improving nitrogen use efficiency in rice.

The japonica rice cultivar Jigeng 88 (14 leaves), Shennong 265 (15 leaves) and Shennong 1401 (16 leaves) with different main leaf ages were used to analyze the effects of different source-sink nitrogen fertilizer application models on agronomic traits, yield and nitrogen utilization characteristics of rice grown in the field-tube condition. Two kinds of fertilizer proportions (base fertilizer: panicle fertilizer was 6:4 and 8:2) were set under 225 kg hm^–2 of nitrogen application based on the light and simple fertilization model (basal fertilizer, tillering fertilizer, panicle fertilizer). The tillering fertilizer was applied at the stage of source construction, and panicle fertilizer was applied at stage of sink formation. The precise nitrogen application combined different nitrogen fertilizer modes for tillering and panicle fertilizers with different leaf ages. Number of differentiated spikelets, effective panicles, yield, and nitrogen use efficiency, were significantly higher by using the 6:4 fertilizer proportions than by using 8:2 under all nitrogen fertilizer application models in these cultivars. Under different nitrogen fertilizer regimes, the 8 leaves of Jigeng 88 (leaf age index was 57.1%), 9 leaves of Shennong 265 (leaf age index was 60.0%), and 10 leaves of Shennong 1401 (leaf age index was 62.55%) were the best stage to apply tillering fertilizer. It means that the leaf age index about 60% is better to protect the more panicle formation. The 11 leaves of Jigeng 88 (leaf age index was 78.6%), 12 leaves of Shennong 265 (leaf age index was 80.0%), 13 leaves of Shennong 1401 (leaf age index was 81.3%) were the best stage to apply panicle fertilizer. It means that leaf age index about 80% is better to promote spikelet differentiation. The yield, nitrogen accumulation, nitrogen uptake and utilization, agronomic efficiency, and partial productivity were significantly higher in 6:4 (8, 11) of Jigeng 88, 6:4 (9, 12) of Shennong 265, 6:4 (10, 13) of Shennong 1401 than in other treatments. Therefore, the delayed leaf age of tillering nitrogen fertilizer application (leaf age index was about 60%), ahead of applied the panicle fertilizer (leaf age index was about 80%), and increasing the ratio of nitrogen fertilizer application not only significantly increase nitrogen accumulation, nitrogen absorption and utilization, nitrogen agronomic utilization rate and partial productivity but also promote number of differentiated spikelets and the percentage of effective panicle number, achieving the dual role of protecting and promoting spikelets, and high yields.