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.

Nitrogen is an essential nutrient for plant growth and basic metabolic processes. Root systems play an important role in the ability of plants to obtain nutrients from the soil, and are closely related to the growth and development of above-ground plants. Root morphology analysis showed that root growth was induced under low-nitrogen conditions and inhibited under high-nitrogen conditions. To better understand the molecular mechanisms and metabolic basis underlying the rice root response to nitrogen availability, an integrated analysis of the rice root transcriptome and metabolome under three environmental conditions (low-, control, and high-nitrogen conditions) was conducted. A total of 262 and 262 differentially level metabolites were identified under low- and high-nitrogen conditions, respectively. A total of 696 and 808 differentially expressed genes were identified under low- and high-nitrogen conditions, respectively. For both the differentially expressed genes and metabolites, KEGG pathway analysis indicated that amino acid metabolism, carbon and nitrogen metabolism, phenylpropanoid metabolism, and phytohormones’ signal transduction were significantly affected by nitrogen availability. Additionally, variable levels of 65 transcription factors (TFs) were identified in rice leaves exposed to high and low nitrogen, covering 22 TF families. These results also indicate that there is a significant difference in the transcriptional regulation mechanisms of rice roots between low and high nitrogen. In summary, our study provides new information for a further understanding of the response of rice roots to low-nitrogen and high-nitrogen conditions.

Autophagy, a conserved pathway in eukaryotes, degrades and recycles cellular components, thus playing an important role in nitrogen (N) remobilization. N plays an important role in the growth and development of plants, which also affects plant yield and quality. In this research, it was found that the transcriptional level of a core autophagy gene of rice (Oryza sativa), OsATG8c, was increased during N starvation conditions. It was found that the overexpression of OsATG8c significantly enhanced the activity of autophagy and that the number of autophagosomes, dwarfed the plant height and increased the effective tillers’ number and yield. The nitrogen uptake efficiency (NUpE) and nitrogen use efficiency (NUE) significantly increased in the transgenic rice under both optimal and suboptimal N conditions. Based on our results, OsATG8c is considered to be a good candidate gene for increasing NUE, especially under suboptimal field conditions.

An understanding of the leaf and root traits associated with high nitrogen (N) absorption and utilization is very important in the development of N-efficient varieties in crop breeding programs. However, in rice, the relations between these traits and nitrogen use efficiencies (NUEs) have yet to be identified. Therefore, the responses of leaf and root traits and yields of the three main japonica rice cultivars in northern China were examined at a range of N application rates. The rice cultivars, Shennong 265 (SN265), Tiejing 11 (TJ11), and Fengjing (FJ), were grown in the field at six N rates (0, 60, 120, 180, 240, and 300 kg ha⁻¹) applied during two growing seasons (2018 and 2019). With the increase in N rate, the grain yield of SN265 and TJ11 increased, whereas the grain yield of FJ first increased and then decreased. The grain yield of FJ was higher than that of SN265 and TJ11 at lower N rates, whereas the grain yields of SN265 and TJ11 were higher than that of FJ at higher N rates. The NUEs decreased with the increase in N rates. At lower N rates, the ability of rice to obtain N was the main limitation on rice yield, but with the increase in N rates, the limitation on yield due to N absorption capacity gradually weakened. However, at higher N rates, rice yields were restricted by the ability to utilize N. Compared with TJ11 or FJ, SN265 had higher N utilization capacity primarily because of its higher Rubisco activity, NR activity, GS activity, and ROA. Compared with SN265 or TJ11, FJ had a higher N absorption capacity that was attributed to its larger root architecture, which might have also been one of the reasons for lower N utilization. Therefore, by improving N absorption and utilization-related leaf and root traits, high yields and NUEs can be achieved in rice production at different N application rates.