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.

Drought and low nitrogen are the most common abiotic stresses limiting rice productivity in the rainfed rice areas of Asia and Africa. Development and adoption of green super rice (GSR) varieties with greatly improved drought tolerance (DT) and low nitrogen tolerance (LNT) are the most efficient way to resolve this problem. In this study, using three sets of trait-specific introgression lines (ILs) in a Xian (indica) variety Huanghuazhan (HHZ) background, we identified nine DT-QTL and seven LNT-QTL by a segregation distortion approach and a genome-wide association study, respectively. Based on performances of DT and LNT and genotypes at the detected QTL, two ILs M79 and M387 with DT and LNT were selected for cross-making to validate the identified QTL and to develop DT and LNT rice lines by pyramiding two DT-QTL (qDT3.9 and qDT6.3) and two LNT-QTL (qGY1 and qSF8). Using four pairs of kompetitive allele specific PCR (KASP) SNP markers, we selected 66 F₂ individuals with different combinations of the target DT- and LNT-QTL favorable alleles and they showed expected improvement in DT and/or LNT, which were further validated by the significant improvement in DT and/or LNT of their F₃ progeny testing. Based on evaluation of pyramiding lines in F₃ lines under drought, low nitrogen (LN) and normal conditions, four promising pyramiding lines having different QTL favorable alleles were selected, which showed significantly improved tolerances to drought and/or LN than HHZ and their IL parents. Our results demonstrated that trait-specific ILs could effectively connect QTL mapping and QTL pyramiding breeding, and designed QTL pyramiding (DQP) using ILs could be more effective in molecular rice breeding for complex quantitative traits.

Japonica rice is widely planted in north-eastern China because of its superior food quality and stable grain yields. Nitrogen (N) is an essential element for rice growth, and development and its availability directly impacts on rice yields. The knowledge of N uptake and its utilization characteristics in japonica are thus important areas of research. Three japonica rice cultivars, SN265, SN1401, and SN9816, which are planted across large areas of north-eastern China, were used here to evaluate the uptake and utilization along the life cycle of both ammonium $\left(N{H}_4^{+}\right)$ and nitrate $\left(N{O}_3^{-}\right)$ in hydroponically grown plants. The plants were grown in one of three different solutions with varying $N{H}_4^{+}$:$N{O}_3^{-}$ ratios: 1:0, 0:1, and 1:1 (The total N content was 40 mg L⁻¹ for each treatment). At the tillering stage, when only $N{O}_3^{-}$ was provided, lower rates of N uptake and enzyme activities of three rice plants resulted in reduced tiller numbers. During the reproductive stage, the $N{H}_4^{+}$ and $\left(N{H}_4^{+}\right)$ uptake rates in SN1401 were consistently maintained at high levels, whereas the rates in SN265 and SN9816 were significantly lower, across all three treatments. At the booting stage, when only $N{O}_3^{-}$ was provided, SN1401 plants had significantly higher expression levels of OsNRT2.1 and OsNRT2.2, higher activity of nitrate reductase in the roots, and higher activity levels of glutamine synthetase and glutamate synthase in the leaves, compared with the SN265 and SN9816 plants. The higher enzyme activity was beneficial to the secondary assimilation of N, which ultimately promoted panicle development in SN1401. Consequently, the grain yield per plant of SN1401 was the highest with solutions of both $N{H}_4^{+}$ and $N{O}_3^{-}$. These results indicate that selecting a rice cultivar with higher utilization of $N{O}_3^{-}$ is beneficial for increasing the number of grains per panicle, grain yield, and N use efficiency.

Background: Food safety has become a major issue, with serious environmental pollution resulting from losses of nitrogen (N) fertilizers. N is a key element for plant growth and is often one of the most important yield-limiting nutrients in paddy soil. Urea-N immobilization is an important process for restoring the levels of soil nutrient depleted by rice production and sustaining productivity. The benefits of biochar application include improved soil fertility, altered N dynamics, and reduced nutrient leaching. However, due to high variability in the quality of biochar, the responses of N loss and rice productivity to biochar amendments, especially those prepared at different pyrolysis temperatures, are still unclear. The main objectives of the present study were to examine the effects of biochar prepared at different pyrolysis temperatures on fertilizer N immobilization in paddy soil and explore the underlying mechanisms. Methods: Two biochar samples were prepared by pyrolysis of maize straw at 400 °C (B400) and 700 °C (B700), respectively. The biochar was applied to paddy soil at three rates (0, 0.7, and 2.1%, w/w), with or without N fertilization (0, 168, and 210 kg N ha^–1). Pot experiments were performed to determine nitrous oxide (N₂O) emissions and ¹⁵N recovery from paddy soil using a ¹⁵N tracer across the rice growing season. Results: Compared with the non-biochar control, biochar significantly decreased soil bulk density while increasing soil porosity, irrespective of pyrolysis temperature and N fertilizer level. Under B400 and B700, a high biochar rate decreased N loss rate to 66.42 and 68.90%, whereas a high N level increased it to 77.21 and 76.99%, respectively. Biochar also markedly decreased N₂O emissions to 1.06 (B400) and 0.75 kg ha⁻¹ (B700); low-N treatment caused a decrease in N₂O emissions under B400, but this decrease was not observed under B700. An application rate of biochar of 2.1% plus 210 kg ha⁻¹ N fertilizer substantially decreased the N fertilizer-induced N₂O emission factor under B400, whereas under B700 no significant difference was observed. Biochar combined with N fertilizer treatment decreased rice biomass and grain yield by an average of 51.55 and 23.90 g pot^–1, respectively, but the yield reduction under B700 was lower than under B400. Conclusion: Irrespective of pyrolysis temperature, biochar had a positive effect on residual soil ¹⁵N content, while it negatively affected the ¹⁵N recovery of rice, N₂O emissions from soil, rice biomass, and grain yield in the first year. Generally, a high application rate of biochar prepared at high or low pyrolysis temperature reduced the N fertilizer-induced N₂O emission factor considerably. These biochar effects were dependent on N fertilizer level, biochar application rate, and their interactions.

The rolled leaf trait, long considered to be a key component of plant architecture, represents an important target trait for improving plant architecture at the population level. We therefore performed linkage mapping using a set of 262 highly variable RILs from two rice cultivars (Minghui 63 and 02428) with minor differences in leaf rolling index (LRI) in conjunction with GWAS mapping of a random subset of the 1127 germplasms from the 3K Rice Genomes Project (3K Rice). A total of seven main-effect loci were found to underlie the transgressive segregation of progenies from parents with minor differences in LRI. Five of these loci were previously identified and two (qRl7b and qRl9b) are newly reported with additional evidence from GWAS mapping for qRl7b. A total of 18 QTLs were identified by GWAS, including four newly identified QTLs. Six QTLs were confirmed by linkage mapping with the above RIL population, and 83.3% were found to be consistent with previously reported loci based on comparative mapping. We also performed allele mining with representative SNPs and identified the elite germplasms for the improvement of rolled leaf trait. Most favorable alleles at the detected loci were contributed by various 3K Rice germplasms. By a re-scanning of the candidate region with more saturated SNP markers, we dissected the region harboring gRl4-2 into three subregions, in which the average effect on LRI was 3.5% with a range from 2.4 to 4.1% in the third subregion, suggesting the presence of a new locus or loci within this region. The representative SNPs for favorable alleles in the reliable QTLs which were consistently identified in both bi-parental mapping and GWAS, such as qRl4, qRl5, qRl6, qRl7a, and qRl7b will be useful for future molecular breeding programs for ideal plant type in rice.