Arabidopsis CDF3 transcription factor increases carbon and nitrogen assimilation and yield in trans-grafted tomato plants

Grafting in tomato (Solanum lycopersicum L.) has mainly been used to prevent damage by soil-borne pathogens and the negative effects of abiotic stresses, although productivity and fruit quality can also be enhanced using high vigor rootstocks. In the context of a low nutrients input agriculture, the grafting of elite cultivars onto rootstocks displaying higher Nitrogen Use Efficiency (NUE) supports a direct strategy for yield maximization. In this study we assessed the use of plants overexpressing the Arabidopsis (AtCDF3) or tomato (SlCDF3) CDF3 genes, previously reported to increase NUE in tomato, as rootstocks to improve yield in the grafted scion under low N inputs. We found that the AtCDF3 gene induced greater production of sugars and amino acids, which allowed for greater biomass and fruit yield under both sufficient and limiting N supplies. Conversely, no positive impact was found with the SlCDF3 gene. Hormone analyses suggest that gibberellins (GA4), auxin and cytokinins (tZ) might be involved in the AtCDF3 responses to N. The differential responses triggered by the two genes could be related, at least in part, to the mobility of the AtCDF3 transcript through the phloem to the shoot. Consistently, a higher expression of the target genes of the transcription factor, such as glutamine synthase 2 (SlGS2) and GA oxidase 3 (SlGA3ox), involved in amino acid and gibberellin biosynthesis, respectively, was observed in the leaves of this graft combination. Altogether, our results provided further insights into the mode of action of CDF3 genes and their biotechnology potential for transgrafting approaches.

Natural variation in SSW1 coordinates seed growth and nitrogen use efficiency in Arabidopsis

Seed size is controlled not only by intrinsic genetic factors but also by external environmental signals. Here, we report a major quantitative trait locus (QTL) gene for seed size and weight on chromosome 1 (SSW1) in Arabidopsis, and we found SSW1 acts maternally to positively regulate seed size. Natural variation in SSW1 contains three types of alleles. The SSW1Cvi allele produces larger seeds with more amino acid and storage protein contents than the SSW1Ler allele. SSW1Cvi displays higher capacity for amino acid transport than SSW1Ler due to the differences in transport efficiency. Under low nitrogen supply, the SSW1Cvi allele exhibits increased seed yield and nitrogen use efficiency (NUE). Locations of natural variation alleles of SSW1 are associated with local soil nitrogen contents, suggesting that SSW1 might contribute to geographical adaptation in Arabidopsis. Thus, our findings reveal a mechanism that coordinates seed growth and NUE, suggesting a potential target for improving seed yield and NUE in crops.

Function of hormone signaling in regulating nitrogen-use efficiency in plants

Nitrogen (N) is one of the most important nutrients for crop plant performance, however, the excessive application of nitrogenous fertilizers in agriculture significantly increases production costs and causes severe environmental problems. Therefore, comprehensively understanding the molecular mechanisms of N-use efficiency (NUE) with the aim of developing new crop varieties that combine high yields with improved NUE is an urgent goal for achieving more sustainable agriculture. Plant NUE is a complex trait that is affected by multiple factors, of which hormones are known to play pivotal roles. In this review, we focus on the interaction between the biosynthesis and signaling pathways of plant hormones with N metabolism, and summarize recent studies on the interplay between hormones and N, including how N regulates multiple hormone biosynthesis, transport and signaling and how hormones modulate root system architecture (RSA) in response to external N sources. Finally, we explore potential strategies for promoting crop NUE by modulating hormone synthesis, transport and signaling. This provides insights for future breeding of N-efficient crop varieties and the advancement of sustainable agriculture.

Mitigating growth-stress tradeoffs via elevated TOR signaling in rice

Rice production accounts for approximately half of the freshwater resources utilized in agriculture, resulting in greenhouse gas emissions such as methane (CH4) from flooded paddy fields. To address this challenge, environmentally friendly and cost-effective water-saving techniques have become widely adopted in rice cultivation. However, the implementation of water-saving treatments (WSTs) in paddy-field rice has been associated with a substantial yield loss of up to 50% as well as a reduction in nitrogen use efficiency (NUE). In this study, we discovered that the target of rapamycin (TOR) signaling pathway is compromised in rice under WST. Polysome profiling-coupled transcriptome sequencing (polysome-seq) analysis unveiled a substantial reduction in global translation in response to WST associated with the downregulation of TOR activity. Molecular, biochemical, and genetic analyses revealed new insights into the impact of the positive TOR-S6K-RPS6 and negative TOR-MAF1 modules on translation repression under WST. Intriguingly, ammonium exhibited a greater ability to alleviate growth constraints under WST by enhancing TOR signaling, which simultaneously promoted uptake and utilization of ammonium and nitrogen allocation. We further demonstrated that TOR modulates the ammonium transporter AMT1;1 as well as the amino acid permease APP1 and dipeptide transporter NPF7.3 at the translational level through the 5' untranslated region. Collectively, these findings reveal that enhancing TOR signaling could mitigate rice yield penalty due to WST by regulating the processes involved in protein synthesis and NUE. Our study will contribute to the breeding of new rice varieties with increased water and fertilizer utilization efficiency.

Study on the effectiveness and mechanism of a sustainable dual slow-release model to improve N utilization efficiency and reduce N pollution in black soil

Long-term intensive cultivation has led to serious N loss and low N fertilizer utilization efficiency (NUE) in black soil areas. The lost N is not only a waste of resources but also a serious pollution threat to the environment, leading to the decline in water quality and food safety and the greenhouse effect. In the present study, a stable dual slow-release model, CPCS-Urea, was prepared by in situ polymerization using nitrapyrin, urea and melamine-formaldehyde resin as raw materials. The effect of the dual slow-release model was systematically evaluated using two consecutive years of field experiments. Five treatments were established in the field experiment: no N fertilizer (N0), urea (N180), 1 % CPEC-Urea, 0.5 % CPCS-Urea, and 1 % CPCS-Urea. The results showed that the new dual slow-release CPCS-Urea model outperformed both the use of urea and the traditional slow-release CPEC-Urea model in reducing N losses and improving NUE. The application of CPCS-Urea reduced nitrate (NO3-) leaching by 28.2 %-47.2 % and N2O emissions by 36.5 %-42.4 % and increased NUE by 20.7 %-28.5 % compared to urea application. The CPCS-Urea model modulated the activity of ammonia-oxidizing bacteria (AOB) and dissimilatory nitrate reduction to ammonium (DNRA) bacteria in soil, showing a significant decrease in AOB activity and an increase in DNRA activity. This results in a lower soil NO3--N yield and a 53.1 %-72.0 % increase in NH4+-N content, providing sufficient N for the entire growth and development cycle of maize. In short, the dual slow-release CPCS-Urea model has great application prospects for promoting agricultural development in black soil areas.

Integrated physiological, biochemical, and transcriptomics analyses reveal the underlying mechanisms of high nitrogen use efficiency of black sesame

Cultivating high nitrogen use efficient varieties is a sustainable solution to mitigating adverse effects on the environment caused by excessive nitrogen fertilizer application. However, in sesame, although immoderate nitrogen fertilizers are used to promote yield, the molecular basis of high nitrogen use efficiency (NUE) is largely unknown. Hence, this study aimed to identify high NUE black sesame variety and dissect the underlying physiological and molecular mechanisms. To achieve this, seventeen seedling traits of 30 black sesame varieties were evaluated under low nitrogen (LN) and high nitrogen (HN) conditions. Dry matter accumulation, root parameters, shoot nitrogen accumulation, and chlorophyll content are important factors for evaluating the NUE of sesame genotypes. The variety 17-156 was identified as the most efficient for N utilization. Comparative physiological and transcriptomics analyses revealed that 17-156 possesses a sophisticated nitrogen metabolizing machinery to uptake and assimilate higher quantities of inorganic nitrogen into amino acids and proteins, and simultaneously improving carbon metabolism and growth. Specifically, the total nitrogen and soluble protein contents significantly increased with the increase in nitrogen concentrations. Many important genes, including nitrate transporters (NPFs), amino acid metabolism-related (GS, GOGAT, GDH, etc.), phytohormone-related, and transcription factors, were significantly up-regulated in 17-156 under HN condition. In addition, 38 potential candidate genes were identified for future studies toward improving sesame's NUE. These findings offer valuable resources for deciphering the regulatory network of nitrogen metabolism and developing sesame cultivars with improved NUE.

OsCBL1 modulates rice nitrogen use efficiency via negative regulation of OsNRT2.2 by OsCCA1

BACKGROUND

For cereal crop breeding, it is meaningful to improve utilization efficiency (NUE) under low nitrogen (LN) levels while maintaining crop yield. OsCBL1-knockdown (OsCBL1-KD) plants exhibited increased nitrogen accumulation and NUE in the field of low N level.

RESULTS

OsCBL1-knockdown (OsCBL1-KD) in rice increased the expression of a nitrate transporter gene OsNRT2.2. In addition, the expression of OsNRT2.2, was suppressed by OsCCA1, a negative regulator, which could directly bind to the MYB-binding elements (EE) in the region of OsNRT2.2 promoter. The OsCCA1 expression was found to be down-regulated in OsCBL1-KD plants. At the low Nitrogen (N) level field, the OsCBL1-KD plants exhibited a substantial accumulation of content and higher NUE, and their actual biomass remained approximately as the same as that of the wild type.

CONCLUSION

These results indicated that down-regulation of OsCBL1 expression could upregulate the expression of OsNRT2.2 by suppressing the expression of OsCCA1and then increasing the NUE of OsCBL1-KD plants under low nitrogen availability.

Balanced nitrogen-iron sufficiency boosts grain yield and nitrogen use efficiency by promoting tillering

Crop yield plays a critical role in global food security. For optimal plant growth and maximal crop yields, nutrients must be balanced. However, the potential significance of balanced nitrogen-iron (N-Fe) for improving crop yield and nitrogen use efficiency (NUE) has not previously been addressed. Here, we show that balanced N-Fe sufficiency significantly increases tiller number and boosts yield and NUE in rice and wheat. NIN-like protein 4 (OsNLP4) plays a pivotal role in maintaining the N-Fe balance by coordinately regulating the expression of multiple genes involved in N and Fe metabolism and signaling. OsNLP4 also suppresses OsD3 expression and strigolactone (SL) signaling, thereby promoting tillering. Balanced N-Fe sufficiency promotes the nuclear localization of OsNLP4 by reducing H2O2 levels, reinforcing the functions of OsNLP4. Interestingly, we found that OsNLP4 upregulates the expression of a set of H2O2-scavenging genes to promote its own accumulation in the nucleus. Furthermore, we demonstrated that foliar spraying of balanced N-Fe fertilizer at the tillering stage can effectively increase tiller number, yield, and NUE of both rice and wheat in the field. Collectively, these findings reveal the previously unrecognized effects of N-Fe balance on grain yield and NUE as well as the molecular mechanism by which the OsNLP4-OsD3 module integrates N-Fe nutrient signals to downregulate SL signaling and thereby promote rice tillering. Our study sheds light on how N-Fe nutrient signals modulate rice tillering and provide potential innovative approaches that improve crop yield with reduced N fertilizer input for benefitting sustainable agriculture worldwide.

Rapid Visual Detection of High Nitrogen-Use Efficiency Gene OsGRF4 in Rice (Oryza sativa L.) Using Loop-Mediated Isothermal Amplification Method

The GROWTH-REGULATING FACTOR4 (OsGRF4) allele is an important target for the development of new high nitrogen-use efficiency (NUE) rice lines that would require less fertilizers. Detection of OsGRF4 through PCR (polymerase chain reaction)-based assay is cumbersome and needs advanced laboratory skills and facilities. Hence, a method for conveniently and rapidly detecting OsGRF4 on-field is a key requirement for further research and applications. In this study, we employed cleaved amplified polymorphic sequences (CAPs) and loop-mediated isothermal amplification (LAMP) techniques to develop a convenient visual detection method for high NUE gene OsGRF4NM73 (OsGRF4 from the rice line NM73). The TC→AA mutation at 1187-1188 bp loci was selected as the target sequence for the OsGRF4NM73 allele. We further employed this method of identification in 10 rice varieties that carried the OsGRF4 gene and results revealed that one variety (NM73) carries the target OsGRF4NM73 allele, while other varieties did not possess the osgrf4 genotype. The optimal LAMP reaction using hydroxynaphthol blue (HNB), a chromogenic indicator, was carried out at 65 °C for 60 min, and the presence of OsGRF4NM73 allele was confirmed by color changes from violet to sky blue. The results of this study showed that the LAMP method can be conveniently and accurately used to detect the OsGRF4NM73 gene in rice.

Nitrogen transport and assimilation in tea plant (Camellia sinensis): a review

Nitrogen is one of the most important nutrients for tea plants, as it contributes significantly to tea yield and serves as the component of amino acids, which in turn affects the quality of tea produced. To achieve higher yields, excessive amounts of N fertilizers mainly in the form of urea have been applied in tea plantations where N fertilizer is prone to convert to nitrate and be lost by leaching in the acid soils. This usually results in elevated costs and environmental pollution. A comprehensive understanding of N metabolism in tea plants and the underlying mechanisms is necessary to identify the key regulators, characterize the functional phenotypes, and finally improve nitrogen use efficiency (NUE). Tea plants absorb and utilize ammonium as the preferred N source, thus a large amount of nitrate remains activated in soils. The improvement of nitrate utilization by tea plants is going to be an alternative aspect for NUE with great potentiality. In the process of N assimilation, nitrate is reduced to ammonium and subsequently derived to the GS-GOGAT pathway, involving the participation of nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate synthase (GOGAT), and glutamate dehydrogenase (GDH). Additionally, theanine, a unique amino acid responsible for umami taste, is biosynthesized by the catalysis of theanine synthetase (TS). In this review, we summarize what is known about the regulation and functioning of the enzymes and transporters implicated in N acquisition and metabolism in tea plants and the current methods for assessing NUE in this species. The challenges and prospects to expand our knowledge on N metabolism and related molecular mechanisms in tea plants which could be a model for woody perennial plant used for vegetative harvest are also discussed to provide the theoretical basis for future research to assess NUE traits more precisely among the vast germplasm resources, thus achieving NUE improvement.

Identification of quantitative trait loci controlling nitrogen use efficiency-related traits in rice at the seedling stage under salt condition by genome-wide association study

Rice cultivation is facing both salt intrusion and overuse of nitrogen fertilizers. Hence, breeding new varieties aiming to improve nitrogen use efficiency (NUE), especially under salt conditions, is indispensable. We selected 2,391 rice accessions from the 3K Rice Genomes Project to evaluate the dry weight under two N concentrations [2.86 mM - standard N (SN), and 0.36 mM - low N (LN)] crossed with two NaCl concentrations [0 (0Na) and 60 mM (60Na)] at the seedling stage. Genome-wide association studies for shoot, root, and plant dry weight (DW) were carried out. A total of 55 QTLs - 32, 16, and 7 in the whole, indica, and japonica panel - associated with one of the tested traits were identified. Among these, 27 QTLs co-localized with previously identified QTLs for DW-related traits while the other 28 were newly detected; 24, 8, 11, and 4 QTLs were detected in SN-0Na, LN-0Na, SN-60Na, and LN-60Na, respectively, and the remaining 8 QTLs were for the relative plant DW between treatments. Three of the 11 QTLs in SN-60Na were close to the regions containing three QTLs detected in SN-0Na. Eleven candidate genes for eight important QTLs were identified. Only one of them was detected in both SN-0Na and SN-60Na, while 5, 0, 3, and 2 candidate genes were identified only once under SN-0Na, LN-0Na, SN-60Na, and LN-60Na, respectively. The identified QTLs and genes provide useful materials and genetic information for future functional characterization and genetic improvement of NUE in rice, especially under salt conditions.

Epigenetic Regulation of Nitrogen Signaling and Adaptation in Plants

Nitrogen (N) is a crucial nutrient that plays a significant role in enhancing crop yield. Its availability, including both supply and deficiency, serves as a crucial signal for plant development. However, excessive N use in agriculture leads to environmental and economic issues. Enhancing nitrogen use efficiency (NUE) is, therefore, essential to minimize negative impacts. Prior studies have investigated the genetic factors involved in N responses and the process of low-nitrogen (LN) adaptation. In this review, we discuss recent advances in understanding how epigenetic modifications, including DNA methylation, histone modification, and small RNA, participate in the regulation of N response and LN adaptation. We highlight the importance of decoding the epigenome at various levels to accelerate the functional study of how plants respond to N availability. Understanding the epigenetic control of N signaling and adaptation can lead to new strategies to improve NUE and enhance crop productivity sustainably.

Genome-wide association study using specific-locus amplified fragment sequencing identifies new genes influencing nitrogen use efficiency in rice landraces

Nitrogen is essential for crop production. It is a critical macronutrient for plant growth and development. However, excessive application of nitrogen fertilizer is not only a waste of resources but also pollutes the environment. An effective approach to solving this problem is to breed rice varieties with high nitrogen use efficiency (NUE). In this study, we performed a genome-wide association study (GWAS) on 419 rice landraces using 208,993 single nucleotide polymorphisms (SNPs). With the mixed linear model (MLM) in the Tassel software, we identified 834 SNPs associated with root surface area (RSA), root length (RL), root branch number (RBN), root number (RN), plant dry weight (PDW), plant height (PH), root volume (RL), plant fresh weight (PFW), root fractal dimension (RFD), number of root nodes (NRN), and average root diameter (ARD), with a significant level of p < 2.39×10^-7. In addition, we found 49 SNPs that were correlated with RL, RBN, RN, PDW, PH, PFW, RFD, and NRN using genome-wide efficient mixed-model association (GEMMA), with a significant level of p < 1×10^-6. Additionally, the final results for eight traits associated with 193 significant SNPs by using multi-locus random-SNP-effect mixed linear model (mrMLM) model and 272 significant SNPs associated with 11 traits by using IIIVmrMLM. Within the linkage intervals of significantly associated SNP, we identified eight known related genes to NUE in rice, namely, OsAMT2;3, OsGS1, OsNR2, OsNPF7.4, OsPTR9, OsNRT1.1B, OsNRT2.3, and OsNRT2.2. According to the linkage disequilibrium (LD) decay value of this population, there were 75 candidate genes within the 150-kb regions upstream and downstream of the most significantly associated SNP (Chr5_29804690, Chr5_29956584, and Chr10_17540654). These candidate genes included 22 transposon genes, 25 expressed genes, and 28 putative functional genes. The expression levels of these candidate genes were measured by real-time quantitative PCR (RT-qPCR), and the expression levels of LOC_Os05g51700 and LOC_Os05g51710 in C347 were significantly lower than that in C117; the expression levels of LOC_Os05g51740, LOC_Os05g51780, LOC_Os05g51960, LOC_Os05g51970, and LOC_Os10g33210 were significantly higher in C347 than C117. Among them, LOC_Os10g33210 encodes a peptide transporter, and LOC_Os05g51690 encodes a CCT domain protein and responds to NUE in rice. This study identified new loci related to NUE in rice, providing new genetic resources for the molecular breeding of rice landraces with high NUE.

Effects of physiological integration on nitrogen use efficiency of moso bamboo in homogeneous and heterogeneous environments

Introduction

Moso bamboo is one of the important clonal plants with complex underground rhizome-root system. Ramets connected by rhizome can translocate and share nitrogen (N), which may affect the nitrogen use efficiency (NUE) of moso bamboo. The aims of this study were to investigate the mechanisms of N physiological integration and its relationship with NUE of moso bamboo.

Methods

A pot experiment was conducted to trace the movement of ¹⁵N between the connected ramets of moso bamboo in both homogeneous and heterogeneous N environments.

Results

Results showed that N translocation within clonal fragments of moso bamboo was detected in both homogeneous and heterogeneous environments. The intensity of physiological integration (IPI) was significantly lower in homogeneous environments than that in heterogeneous environments. ¹⁵N translocation between the connected ramtes of moso bamboo was determined by the source-sink relationship in heterogeneous environments, and the ¹⁵N allocation of the fertilized ramet was higher than that of the connected unfertilized ramet. The NUE of connected treatment was significantly higher than that of severed treatment, which suggested that physiological integration significantly improved the NUE of moso bamboo. In addition, the NUE of moso bamboo was significantly higher in heterogeneous environments than that in homogeneous environments. The contribution rate of physiological integration (CPI) on NUE in heterogeneous environments was significantly higher than that in homogenous environments.

Discussion

These results will provide theoretical basis for precision fertilization in moso bamboo forests.

Grain nitrogen content and productivity of rice and maize under variable doses of fertilizer nitrogen

The rice-maize system is a dominant cropping system of south Asia and consumes a considerable amount of fertilizer. The indiscriminate use of fertilizer particularly nitrogen (N) is degrading the soil health and polluting the environment. Lower N-use efficiency is a major problem and needs to be improved for higher yield, lower cost of cultivation and better environment. The grain quality is also altered by the N-application as N is a major constituent of protein. Studies on the effect of N-application on grain N-content is still lacking. We hypothesised that optimization of N application would result in economising N dose, improving yield and NUE and improving grain quality. Under that context, a field experiment was conducted with different doses of fertilizer N for rice and maize. Fertilizer N was applied at the rate of 0, 40, 80, 120, 160, 200 and 240 kg ha^-1 (N0-N240). An increase in grain yield was observed up to 80 and 160 kg ha^-1 for rice and maize, respectively. The N content of grain increased with N rates and a significant increase was noted in N200 (1.42%) being at par with N240 (1.49%) but significantly higher than others by 13-32%. With an increase of each kilogram of N, the grain N content increased by 14 and 20 μg (microgram) for rice and maize, respectively. The leaf N content registered a decreasing trend with the progress of the crop growth for both rice and maize. The agronomic efficiency (AE) of N initially increased with an increase in the rate of fertilizer N followed by a decrease with higher doses of N. Unlike the AE, the partial factor productivity (PFP) of N decreased gradually with an increase in the rate of fertilizer N. The chlorophyll content of flag leaves also registered an increasing trend with an increasing rate of fertilizer N. On the surface soil (0-15 cm), the treatments which received lower (N0, N40) and higher (N240) fertilizer N recorded a comparatively higher total soil N than other treatments. The mean NUE was 0.42 and 0.75 for rice and maize, respectively. The study suggests an economic fertilizer N rate of 165 and 167 kg N ha^-1, for rice and maize, respectively. It also concludes that the grain N content can be altered by N-application rates though more research is needed.

Transcription factor OsSNAC1 positively regulates nitrate transporter gene expression in rice

Nitrogen (N) is a critical factor for crop growth and yield. Improving nitrogen use efficiency (NUE) in agricultural systems is crucial for sustainable food production. However, the underlying regulation of N uptake and utilization in crops is not well known. Here, we identified OsSNAC1 (stress-responsive NAC 1) as an upstream regulator of OsNRT2.1 (nitrate transporter 2.1) in rice (Oryza sativa) by yeast one-hybridization screening. OsSNAC1 was mainly expressed in roots and shoots and induced by N deficiency. We observed similar expression patterns of OsSNAC1, OsNRT2.1/2.2, and OsNRT1.1A/B in response to NO3- supply. Overexpression of OsSNAC1 resulted in increased concentrations of free NO3- in roots and shoots, as well as higher N uptake, higher NUE and nitrogen use index (NUI) in rice plants, which conferred increased plant biomass and grain yield. On the contrary, mutation of OsSNAC1 resulted in decreased N uptake and lower NUI, which inhibited plant growth and yield. OsSNAC1 overexpression significantly upregulated OsNRT2.1/2.2 and OsNRT1.1A/B expression, while the mutation of OsSNAC1 significantly downregulated OsNRT2.1/2.2 and OsNRT1.1A/B expression. Y1H, transient co-expression and ChIP assays showed OsSNAC1 directly binds to the upstream promoter region of OsNRT2.1/2.2 and OsNRT1.1A/1.1B. In conclusion, we identified a NAC transcription factor in rice, OsSNAC1, with a positive role in regulating NO3- uptake through directly binding to the upstream promoter region of OsNRT2.1/2.2 and OsNRT1.1A/1.1B and activating their expression. Our results provide a potential genetic approach for improving crop NUE in agriculture.

Influence of Variable Chloride/Sulfur Doses as Part of Potassium Fertilization on Nitrogen Use Efficiency by Coffee

Chloride (Cl-) is applied in coffee at rates as a "macronutrient" in the form of muriate of potash (MOP). Potassium (K+) is one of the most demanded nutrients by the coffee plant, and MOP is one of the most used fertilizers in coffee production. No scientific evidence shows how Cl- applied with MOP influences coffee growth, nutrient uptake, and nitrogen use efficiency (NUE). In order to address these questions, a greenhouse trial over two years and a field trial over four years were conducted. The trials were designed to test the influence of variable Cl-/S ratios on biomass accumulation, nutrient uptake, and NUE. A significant effect of the Cl- rates on growth was observed under greenhouse conditions but a non-significant effect on yield under field conditions. Cl- and S significantly influenced the NUE in coffee. The results allow us to conclude that Cl- rates need to be balanced with S rates, and that Cl- applied at macronutrient rates can improve the NUE in coffee between 7 and 21% in greenhouse conditions and between 9% and 14% in field conditions, as long as the rates do not exceed 180 mg L-1 Cl- and 80 mg·L-1 S in the greenhouse and 150 kg·ha-1·year-1 Cl- and 50 kg ha-1·year-1 S in the field. With the aim to improve the NUE in coffee, the Cl- content in leaves in coffee should be lower than 0.33% of dry matter, and in soil lower than 30 mg·L-1. In practical terms, coffee farmers need to balance K-based fertilizers to avoid the excessive Cl- applications that reduce the nutrient use efficiency, especially the NUE.

Assessing the impact of biochar and nitrogen application on yield, water-nitrogen use efficiency and quality of intercropped maize and soybean

Introduction

Biochar (BC) and nitrogen (N) application have the potential to increase grain yield and resource use efficiency in intercropping systems. However, the effects of different levels of BC and N application in these systems remain unclear. To address this gap, the study is intended to ascertain the impact of various combinations of BC and N fertilizer on the performance of maize-soybean intercropping and determine the optimum application of BC and N for maximizing the effect of the intercropping system.

Methods

A two-year (2021-2022) field experiment was conducted in Northeast China to assess the impact of BC (0, 15, and 30 t ha^-1) and N application (135, 180, and 225 kg ha^-1) on plant growth, yield, water use efficiency (WUE), N recovery efficiency (NRE) and quality in an intercropping system. Maize and soybean were selected as materials in the experiment, where every 2 rows of maize were intercropped with 2 rows of soybean.

Results and discussion

The results showed that the combination of BC and N significantly affected the yield, WUE, NRE and quality of intercropped maize and soybean. The treatment of 15 t ha^-1 BC and 180 kg ha^-1 N increased grain yield and WUE, while that of 15 t ha^-1 BC and 135 kg ha^-1 N enhanced NRE in both years. Nitrogen promoted the protein and oil content of intercropped maize, but decreased the protein and oil content of intercropped soybean. BC did not enhance the protein and oil content of intercropped maize, especially in the first year, but increased maize starch content. BC was found to have no positive impact on soybean protein, but it unexpectedly increased soybean oil content. The TOPSIS method revealed that the comprehensive assessment value first increased and then declined with increasing BC and N application. BC improved the performance of maize-soybean intercropping system in terms of yield, WUE, NRE, and quality while N fertilizer input was reduced. The highest grain yield in two years was achieved for BC of 17.1-23.0 t ha^-1 and N of 156-213 kg ha^-1 in 2021, and 12.0-18.8 t ha^-1 BC and 161-202 kg ha^-1 N in 2022. These findings provide a comprehensive understanding of the growth of maize-soybean intercropping system and its potential to enhance the production in northeast China.

A molecular framework underlying low-nitrogen-induced early leaf senescence in Arabidopsis thaliana

Nitrogen (N) deficiency causes early leaf senescence, resulting in accelerated whole-plant maturation and severely reduced crop yield. However, the molecular mechanisms underlying N-deficiency-induced early leaf senescence remain unclear, even in the model species Arabidopsis thaliana. In this study, we identified Growth, Development and Splicing 1 (GDS1), a previously reported transcription factor, as a new regulator of nitrate (NO₃^-) signaling by a yeast-one-hybrid screen using a NO₃^- enhancer fragment from the promoter of NRT2.1. We showed that GDS1 promotes NO₃^- signaling, absorption and assimilation by affecting the expression of multiple NO₃^- regulatory genes, including Nitrate Regulatory Gene2 (NRG2). Interestingly, we observed that gds1 mutants show early leaf senescence as well as reduced NO₃^- content and N uptake under N-deficient conditions. Further analyses indicated that GDS1 binds to the promoters of several senescence-related genes, including Phytochrome-Interacting Transcription Factors 4 and 5 (PIF4 and PIF5) and represses their expression. Interestingly, we found that N deficiency decreases GDS1 protein accumulation, and GDS1 could interact with Anaphase Promoting Complex Subunit 10 (APC10). Genetic and biochemical experiments demonstrated that Anaphase Promoting Complex or Cyclosome (APC/C) promotes the ubiquitination and degradation of GDS1 under N deficiency, resulting in loss of PIF4 and PIF5 repression and consequent early leaf senescence. Furthermore, we discovered that overexpression of GDS1 could delay leaf senescence and improve seed yield and N-use efficiency (NUE) in Arabidopsis. In summary, our study uncovers a molecular framework illustrating a new mechanism underlying low-N-induced early leaf senescence and provides potential targets for genetic improvement of crop varieties with increased yield and NUE.

Determining optimal nitrogen management to improve rice yield, quality and nitrogen use efficiency based on multi-index decision analysis method

BACKGROUND

Reasonable nitrogen (N) supply is critical for increasing rice yield while improving grain quality and nitrogen use efficiency (NUE). However, the trade-off relationship between yield, quality and NUE of rice under N management has not been well understood enough. In the present study, a 2-year field experiment was conducted to identify optimal N fertilizer management practices that resulted in high-yield, high-quality and high-NUE by using the technique for order preference by similarity to an ideal solution (TOPSIS) with entropy weight (EW) method.

RESULTS

All the parameters of rice yield, quality and efficiency were remarkably affected by fertilization treatments. Compared with farmer's fertilization practice (FFP), optimizing N fertilizer treatment (OPT) and substituting 20% of N fertilizer with pig manure based on OPT treatment (OPTM) increased grain yield (2.87-6.62%) by maintaining higher 1000-grain weight and filled grains rate. The agronomic NUE (AE) and N partial factor productivity (PFP) under OPT and OPTM treatment were also remarkably increased by 32.81-43.01% and 28.59-33.28% with respect to the value under FFP treatment, respectively. Meanwhile, OPT and OPTM significantly improved the milling quality of rice by increasing brown rice rate (0.71-1.17%) and head rice rate (1.34-2.31%). OPT and OPTM significantly improved appearance quality by decreasing chalkiness and eating quality by reducing amylose content in 2020. The TOPSIS with EW showed that rice comprehensive evaluation could be maintained at a high level under OPT and OPTM.

CONCLUSION

OPT and OPTM were nutrient management modes of high-yield, high-quality and high-efficiency, and promising practice to improve rice comprehensive productivity. This strategy is also highly-consistent with the United Nations Sustainable Development Goals. © 2023 Society of Chemical Industry.

The alleviation of ammonium toxicity in plants

Nitrogen (N) is an essential macronutrient for plants and profoundly affects crop yields and qualities. Ammonium (NH₄ ⁺ ) and nitrate (NO₃ ^- ) are major inorganic N forms absorbed by plants from the surrounding environments. Intriguingly, NH₄ ⁺ is usually toxic to plants when it serves as the sole or dominant N source. It is thus important for plants to coordinate the utilization of NH₄ ⁺ and the alleviation of NH₄ ⁺ toxicity. To fully decipher the molecular mechanisms underlying how plants minimize NH₄ ⁺ toxicity may broadly benefit agricultural practice. In the current minireview, we attempt to discuss recent discoveries in the strategies for mitigating NH₄ ⁺ toxicity in plants, which may provide potential solutions for improving the nitrogen use efficiency (NUE) and stress adaptions in crops.

Nitrogen assimilation and photorespiration become more efficient under chloride nutrition as a beneficial macronutrient

Chloride (Cl^-) and nitrate ( NO 3 - ) are closely related anions involved in plant growth. Their similar physical and chemical properties make them to interact in cellular processes like electrical balance and osmoregulation. Since both anions share transport mechanisms, Cl^- has been considered to antagonize NO 3 - uptake and accumulation in plants. However, we have recently demonstrated that Cl^- provided at beneficial macronutrient levels improves nitrogen (N) use efficiency (NUE). Biochemical mechanisms by which beneficial Cl^- nutrition improves NUE in plants are poorly understood. First, we determined that Cl^- nutrition at beneficial macronutrient levels did not impair the NO 3 - uptake efficiency, maintaining similar NO 3 - content in the root and in the xylem sap. Second, leaf NO 3 - content was significantly reduced by the treatment of 6 mM Cl^- in parallel with an increase in NO 3 - utilization and NUE. To verify whether Cl^- nutrition reduces leaf NO 3 - accumulation by inducing its assimilation, we analysed the content of N forms and the activity of different enzymes and genes involved in N metabolism. Chloride supply increased transcript accumulation and activity of most enzymes involved in NO 3 - assimilation into amino acids, along with a greater accumulation of organic N (mostly proteins). A reduced glycine/serine ratio and a greater ammonium accumulation pointed to a higher activity of the photorespiration pathway in leaves of Cl^--treated plants. Chloride, in turn, promoted higher transcript levels of genes encoding enzymes of the photorespiration pathway. Accordingly, microscopy observations suggested strong interactions between different cellular organelles involved in photorespiration. Therefore, in this work we demonstrate for the first time that the greater NO 3 - utilization and NUE induced by beneficial Cl^- nutrition is mainly due to the stimulation of NO 3 - assimilation and photorespiration, possibly favouring the production of ammonia, reductants and intermediates that optimize C-N re-utilization and plant growth. This work demonstrates new Cl^- functions and remarks on its relevance as a potential tool to manipulate NUE in plants.

Driving forces of nitrogen use efficiency in Chinese croplands on county scale

Nitrogen use efficiency (NUE, defined as the fraction of N input harvested as product) is an important indicator to understand nitrogen use and losses in croplands as an element of determining sustainable food production. China, as the country with the largest amount of nitrogen fertilizer use globally, research into NUE consistently finds it to be much lower than that in developed countries. Understanding the driving forces of the underlying causes of this low NUE is thus crucial to improve nitrogen use and reduce losses in China. Here we applied the CHANS model to estimate cropland NUE for over 2800 counties in China for the year 2017. Results showed that in most counties NUE ranged between 20% and 40%, while an NUE >50% was mainly found in Northeastern China, likely as a result of large-scale, modern agriculture operations. The source of N input and crop types significantly affected NUE in our assessment. Nitrogen deposition, straw recycling, and biological nitrogen fixation (BNF) could improve NUE, while chemical nitrogen fertilizer and manure inputs reduce NUE. Grain crops have a much higher NUE compared to vegetables, which are often over-fertilized. Moreover, NUE in Southern China is strongly influenced by natural factors such as temperature and precipitation. Specifically, NUE in the Yangtze River Delta (eastern coastal region of China) is associated with socio-economic factors including GDP and the degree of urbanization, while in North-central China, NUE is mainly determined by nitrogen input sources. These examples illustrate that approaches aiming at improving NUE need to be location-specific with consideration of multiple natural and socioeconomic factors.

Exogenous 24-epibrassinolide promoted growth and nitrogen absorption and assimilation efficiency of apple seedlings under salt stress

Introduction

High salinity significantly hampers global agricultural productivity. Plants typically undergo lower nitrogen utilization efficiency (NUE) under salt stress. As an active byproduct from brassinolide biosynthesis, 24-epibrassinolide (EBR) is involved in regulating the stress-treated plant N absorption and assimilation. However, the exogenous EBR application effects' on N absorption and assimilation in apple exposed to the salt-stressed condition remains unclear.

Methods

We sprayed exogenous EBR (0.2 mg L^-1) on apple dwarf rootstock (M9T337) seedlings (growing hydroponically) under salt (NaCl) stress in a growth chamber. We analyzed the seedling development, photosynthesis and its-mediated C fixation, N ( NO 3 - ) absorption and assimilation in reponse to exogenous EBR application under salt stress.

Results

The findings demonstrated that NaCl stress greatly hampered seedlings' root growth and that exogenous EBR application obviously alleviated this growth suppression. Exogenous EBR-treated plants under NaCl stress displayed the more ideal root morphology and root activity, stronger salt stress tolerance and photosynthetic capacity as well as higher C- and N-assimilation enzyme activities, NO 3 - ion flow rate and nitrate transporter gene expression level than did untreated plants. Furthermore, the results of isotope labeling noted that exogenous EBR application also enhanced ¹³C-photoassimilate transport from leaves to roots and ¹⁵ NO 3 - transport from roots to leaves under NaCl stress.

Conclusion

Our findings imply that exogenous EBR application, through strengthening photosynthesis, C- and N-assimilation enzyme activities, nitrate absorption and transport as well as synchronized optimizing the distribution of seedlings' C and N, has a fundamental role in improving NUE in apple rootstock seedlings under salt stress.

Nitrogen use efficiency-a key to enhance crop productivity under a changing climate

Nitrogen (N) is an essential element required for the growth and development of all plants. On a global scale, N is agriculture's most widely used fertilizer nutrient. Studies have shown that crops use only 50% of the applied N effectively, while the rest is lost through various pathways to the surrounding environment. Furthermore, lost N negatively impacts the farmer's return on investment and pollutes the water, soil, and air. Therefore, enhancing nitrogen use efficiency (NUE) is critical in crop improvement programs and agronomic management systems. The major processes responsible for low N use are the volatilization, surface runoff, leaching, and denitrification of N. Improving NUE through agronomic management practices and high-throughput technologies would reduce the need for intensive N application and minimize the negative impact of N on the environment. The harmonization of agronomic, genetic, and biotechnological tools will improve the efficiency of N assimilation in crops and align agricultural systems with global needs to protect environmental functions and resources. Therefore, this review summarizes the literature on nitrogen loss, factors affecting NUE, and agronomic and genetic approaches for improving NUE in various crops and proposes a pathway to bring together agronomic and environmental needs.

Breeding for Higher Yields of Wheat and Rice through Modifying Nitrogen Metabolism

Wheat and rice produce nutritious grains that provide 32% of the protein in the human diet globally. Here, we examine how genetic modifications to improve assimilation of the inorganic nitrogen forms ammonium and nitrate into protein influence grain yield of these crops. Successful breeding for modified nitrogen metabolism has focused on genes that coordinate nitrogen and carbon metabolism, including those that regulate tillering, heading date, and ammonium assimilation. Gaps in our current understanding include (1) species differences among candidate genes in nitrogen metabolism pathways, (2) the extent to which relative abundance of these nitrogen forms across natural soil environments shape crop responses, and (3) natural variation and genetic architecture of nitrogen-mediated yield improvement. Despite extensive research on the genetics of nitrogen metabolism since the rise of synthetic fertilizers, only a few projects targeting nitrogen pathways have resulted in development of cultivars with higher yields. To continue improving grain yield and quality, breeding strategies need to focus concurrently on both carbon and nitrogen assimilation and consider manipulating genes with smaller effects or that underlie regulatory networks as well as genes directly associated with nitrogen metabolism.

Role of Melatonin and Nitrogen Metabolism in Plants: Implications under Nitrogen-Excess or Nitrogen-Low

Melatonin is a new plant hormone involved in multiple physiological functions in plants such as germination, photosynthesis, plant growth, flowering, fruiting, and senescence, among others. Its protective role in different stress situations, both biotic and abiotic, has been widely demonstrated. Melatonin regulates several routes in primary and secondary plant metabolism through the up/down-regulation of many enzyme/factor genes. Many of the steps of nitrogen metabolism in plants are also regulated by melatonin and are presented in this review. In addition, the ability of melatonin to enhance nitrogen uptake under nitrogen-excess or nitrogen-low conditions is analyzed. A model that summarizes the distribution of nitrogen compounds, and the osmoregulation and redox network responses mediated by melatonin, are presented. The possibilities of using melatonin in crops for more efficient uptake, the assimilation and metabolization of nitrogen from soil, and the implications for Nitrogen Use Efficiency strategies to improve crop yield are also discussed.

The Critical Role of Arbuscular Mycorrhizal Fungi to Improve Drought Tolerance and Nitrogen Use Efficiency in Crops

Drought stress (DS) is a serious abiotic stress and a major concern across the globe as its intensity is continuously climbing. Therefore, it is direly needed to develop new management strategies to mitigate the adverse effects of DS to ensure better crop productivity and food security. The use of arbuscular mycorrhizal fungi (AMF) has emerged as an important approach in recent years to improve crop productivity under DS conditions. AMF establishes a relationship with 80% of land plants and it induces pronounced impacts on plant growth and provides protection to plants from abiotic stress. Drought stress significantly reduces plant growth and development by inducing oxidative stress, disturbing membrane integrity, plant water relations, nutrient uptake, photosynthetic activity, photosynthetic apparatus, and anti-oxidant activities. However, AMF can significantly improve the plant tolerance against DS. AMF maintains membrane integrity, improves plant water contents, nutrient and water uptake, and water use efficiency (WUE) therefore, improve the plant growth under DS. Moreover, AMF also protects the photosynthetic apparatus from drought-induced oxidative stress and improves photosynthetic efficiency, osmolytes, phenols and hormone accumulation, and reduces the accumulation of reactive oxygen species (ROS) by increasing anti-oxidant activities and gene expression which provide the tolerance to plants against DS. Therefore, it is imperative to understand the role of AMF in plants grown under DS. This review presented the different functions of AMF in different responses of plants under DS. We have provided a detailed picture of the different mechanisms mediated by AMF to induce drought tolerance in plants. Moreover, we also identified the potential research gaps that must be fulfilled for a promising future for AMF. Lastly, nitrogen (N) is an important nutrient needed for plant growth and development, however, the efficiency of applied N fertilizers is quite low. Therefore, we also present the information on how AMF improves N uptake and nitrogen use efficiency (NUE) in plants.

Nitrogen budgets for freshwater aquaculture and mariculture in a large tropical island - A case study for Hainan Island 1998-2018

Nitrogen is an essential nutrient in aquaculture. It is also an important factor in coastal and river eutrophication. We present an island-scale model to study the nitrogen flows in different aquaculture systems in Hainan Island during 1998-2018. The result indicated that nitrogen losses associated with pond sludge, wastewater discharge and gaseous emission increased by a factor of 1.4, 4.6 and 3.2, respectively. Sludge and wastewater account for 84% of the total losses to the environment. During the past 20 years, aquacultural yields and the nitrogen use efficiency (NUE) improved considerably in Hainan Island. Nevertheless, nitrogen losses to the environment increased significantly as well, with negative effects for local ecosystems. In the future, sustainable aquacultural practices are needed to improve NUE and to reduce nitrogen losses to the environment.

Controlled nitrogen transformation in chemo-amended urea improves nitrogen use efficiency and productivity of wheat grown on alkaline calcareous soil

Low wheat production is linked to soil degradation, low organic matter, temperature variation, and nutrient depletion in soils of semiarid regions. Nitrogen is mostly applied as urea to meet crop requirements; however, excessive N application may pollute the environment and contaminate groundwater. The current studies explored possible ways for decreasing N losses (NH₃ volatilization and NO₃ leaching) and improving N availability for wheat production in alkaline soil. The ZnO was coated on urea (1% Zn coating) to get zinc-coated urea (ZnU), and both urea and ZnU were incubated in laboratory at recommended rate (RR), i.e., 150 kg N ha^-1 and 80% (N of RR), after further coating with inhibitors [N-(n-butyl) thiophosphoric triamide (NBPT) at 1% of urea and 4-amino-1,2,4-triazole (ATC) at 2% of urea], thus creating six treatments. The results showed higher NH₃-N loss at day 4 and thereafter a decreasing trend reaching to minimum at day 14. The cumulative NH₃-N volatilization from urea alone was found higher (28.99%), except ATC treatments producing statistically similar losses due to restriction in nitrification process. In greenhouse, the treatments were tested in wheat cultivars (Faisalabad 2008 and Lasani) for crop growth, nutrient (N, P, K, and Zn) uptake, and yield parameters, where 80% of RR treatment, i.e., NBPT + ZnU₈₀, was found at par with full RR as commercial products, especially comparable to ZnU (at RR) that produced the highest chlorophyll (53.65unit value), net leaf photosynthetic rate (19.64 μmol CO₂ m^-2 s^-1), plant biomass (208.13 g/pot), grain yield (63.65 g/pot), and nutrient (NPK and Zn) accumulation in grain of Fsd-2008 cultivar. In field trial, NBPT + ZnU₈₀ also outperformed and produced the highest physiological efficiency (PE), agronomic efficiency (AE), and nitrogen recovery efficiency (REN); the treatment also found statistically similar with ZnU (at RR) that produced the maximum plant height (95.4 cm), plant biomass (11.58 t/ha), grain yield (4.69 t/ha), and 1000-grain weight (42.55 g). The relative NO₃ leaching was found lower in 80% N treatments, yet leaching was not significant from either treatment at the three stages of crop growth. Overall, current studies revealed the effectiveness of NBPT-amended urea (followed by ZnU) with 20% saving of N inputs through higher N availability for plant uptake that could benefit growers as well as conserve environment.

CRISPR/Cas9 gene editing and natural variation analysis demonstrate the potential for HvARE1 in improvement of nitrogen use efficiency in barley

Nitrogen is a major determinant of grain yield and quality. As excessive use of nitrogen fertilizer leads to environmental pollution and high production costs, improving nitrogen use efficiency (NUE) is fundamental for a sustainable agriculture. Here, we dissected the role of the barley abnormal cytokinin response1 repressor 1 (HvARE1) gene, a candidate for involvement in NUE previously identified in a genome-wide association study, through natural variation analysis and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated gene editing. HvARE1 was predominantly expressed in leaves and shoots, with very low expression in roots under low nitrogen conditions. Agrobacterium-mediated genetic transformation of immature embryos (cv. Golden Promise) with single guide RNAs targeting HvARE1 generated 22 T₀ plants, from which four T₁ lines harbored missense and/or frameshift mutations based on genotyping. Mutant are1 lines exhibited an increase in plant height, tiller number, grain protein content, and yield. Moreover, we observed a 1.5- to 2.8-fold increase in total chlorophyll content in the flag leaf at the grain filling stage. Delayed senescence by 10-14 d was also observed in mutant lines. Barley are1 mutants had high nitrogen content in shoots under low nitrogen conditions. These findings demonstrate the potential of ARE1 in NUE improvement in barley.

Biochar and slow-releasing nitrogen fertilizers improved growth, nitrogen use, yield, and fiber quality of cotton under arid climatic conditions

The efficiency of nitrogenous fertilizers in South Asia is on a declining trajectory due to increased losses. Biochar (BC) and slow-releasing nitrogen fertilizers (SRNF) have been found to improve nitrogen use efficiency (NUE) in certain cases. However, field-scale studies to explore the potential of BC and SRNF in south Asian arid climate are lacking. Here we conducted a field experiment in the arid environment to demonstrate the response of BC and SRNF on cotton growth and yield quality. The treatments were comprised of two factors, (A) nitrogen sources, (i) simple urea, (ii)neem-coated urea, (iii)sulfur-coated urea, (iv) bacterial coated urea, and cotton stalks biochar impregnated with simple urea, and (B) nitrogen application rates, N₁=160 kg ha^-1, N₂ = 120 kg ha^-1, and N₃ = 80 kg ha^-1. Different SRNF differentially affected cotton growth, morphological and physiological attributes, and seed cotton yield (SCY). The bacterial coated urea at the highest rate of N application (160 kg ha^-1) resulted in a higher net leaf photosynthetic rate (32.8 μmol m^-2 s^-1), leaf transpiration rate (8.10 mmol s^-1), and stomatal conductance (0.502 mol m^-2 s^-1), while leaf area index (LAI), crop growth rate (CGR), and seed cotton yield (4513 kg ha^-1) were increased by bacterial coated urea at 120 kg ha^-1 than simple urea. However, low rate N application (80 kg ha^-1) of bacterial coated urea showed higher nitrogen use efficiency (39.6 kg SCY kg^-1 N). The fiber quality (fiber length, fiber strength, ginning outturn, fiber index, and seed index) was also increased with the high N application rates than N2 and N3 application. To summarize, the bacterial coated urea with recommended N (160 kg ha^-1) and 75% of recommended N application (120 kg ha^-1) may be recommended for farmers in the arid climatic conditions of Punjab to enhance the seed cotton yield, thereby reducing nitrogen losses.

Validation of a high-confidence regulatory network for gene-to-NUE phenotype in field-grown rice

Nitrogen (N) and Water (W) - two resources critical for crop productivity - are becoming increasingly limited in soils globally. To address this issue, we aim to uncover the gene regulatory networks (GRNs) that regulate nitrogen use efficiency (NUE) - as a function of water availability - in Oryza sativa, a staple for 3.5 billion people. In this study, we infer and validate GRNs that correlate with rice NUE phenotypes affected by N-by-W availability in the field. We did this by exploiting RNA-seq and crop phenotype data from 19 rice varieties grown in a 2x2 N-by-W matrix in the field. First, to identify gene-to-NUE field phenotypes, we analyzed these datasets using weighted gene co-expression network analysis (WGCNA). This identified two network modules ("skyblue" & "grey60") highly correlated with NUE grain yield (NUEg). Next, we focused on 90 TFs contained in these two NUEg modules and predicted their genome-wide targets using the N-and/or-W response datasets using a random forest network inference approach (GENIE3). Next, to validate the GENIE3 TF→target gene predictions, we performed Precision/Recall Analysis (AUPR) using nine datasets for three TFs validated in planta. This analysis sets a precision threshold of 0.31, used to "prune" the GENIE3 network for high-confidence TF→target gene edges, comprising 88 TFs and 5,716 N-and/or-W response genes. Next, we ranked these 88 TFs based on their significant influence on NUEg target genes responsive to N and/or W signaling. This resulted in a list of 18 prioritized TFs that regulate 551 NUEg target genes responsive to N and/or W signals. We validated the direct regulated targets of two of these candidate NUEg TFs in a plant cell-based TF assay called TARGET, for which we also had in planta data for comparison. Gene ontology analysis revealed that 6/18 NUEg TFs - OsbZIP23 (LOC_Os02g52780), Oshox22 (LOC_Os04g45810), LOB39 (LOC_Os03g41330), Oshox13 (LOC_Os03g08960), LOC_Os11g38870, and LOC_Os06g14670 - regulate genes annotated for N and/or W signaling. Our results show that OsbZIP23 and Oshox22, known regulators of drought tolerance, also coordinate W-responses with NUEg. This validated network can aid in developing/breeding rice with improved yield on marginal, low N-input, drought-prone soils.

DMPP reduces nitrogen fertilizer application rate, improves fruit quality, and reduces environmental cost of intensive apple production in China

In China, excessive application of nitrogen (N) fertilizer is common in intensive apple production. To resolve issues of benefit reduction and environmental pollution caused by excessive N, a two-year trial was conducted in an apple orchard with a split-plot design, in which the main factor was the N level (500, 400, 300, and 200 kg N ha^-1 year^-1, expressed as TN, TN80%, TN60%, and TN40%, respectively) and the deputy factor was whether or not to add 3,4-dimethylpyrazole phosphate (DMPP, expressed as +D). The effects of N reduction combined with DMPP on soil N transformation, fruit quality, economic benefits, and environmental effects were investigated. The results showed that DMPP reduced the production of nitrate and its vertical migration by inhibiting the abundance of AOB amoA and decreased N₂O emission by reducing nirKC1 levels. Moreover, N reduction combined with DMPP improved N use efficiency (26.67-49.35%) and reduced N loss rate (15.25-38.76%). Compared with TN, TN60% + D increased the content of anthocyanin and soluble sugar by 21.15% and 13.09%, respectively, and decreased environmental costs caused by NH₃ volatilization and N₂O emission by 33.84%, while maintaining yield and N utilization rate at relatively high levels. Considering the agronomic, economic and environmental benefits, on the basis of traditional N application rate, 40% N reduction combined with DMPP (TN60% + D) could ensure target yield, corresponding quality and economic benefits, maintain soil N fertility, and reduce the risk of N losses to the environment. The present research could provide references for green, efficient, and sustainable development of apple production.

Meta-QTL Analysis in Rice and Cross-Genome Talk of the Genomic Regions Controlling Nitrogen Use Efficiency in Cereal Crops Revealing Phylogenetic Relationship

The phenomenal increase in the use of nitrogenous fertilizers coupled with poor nitrogen use efficiency is among the most important threats to the environment, economic, and social health. During the last 2 decades, a number of genomic regions associated with nitrogen use efficiency (NUE) and related traits have been reported by different research groups, but none of the stable and major effect QTL have been utilized in the marker-assisted introgression/pyramiding program. Compiling the data available in the literature could be very useful in identifying stable and major effect genomic regions associated with the root and NUE-related trait improving the rice grain yield. In the present study, we performed meta-QTL analysis on 1,330 QTL from 29 studies published in the past 2 decades. A total of 76 MQTL with a stable effect over different genetic backgrounds and environments were identified. The significant reduction in the confidence interval of the MQTL compared to the initial QTL resulted in the identification of annotated and putative candidate genes related to the traits considered in the present study. A hot spot region associated with correlated traits on chr 1, 4, and 8 and candidate genes associated with nitrate transporters, nitrogen content, and ammonium uptake on chromosomes 2, 4, 6, and 8 have been identified. The identified MQTL, putative candidate genes, and their orthologues were validated on our previous studies conducted on rice and wheat. The research-based interventions such as improving nitrogen use efficiency via identification of major genomic regions and candidate genes can be a plausible, simple, and low-cost solution to address the challenges of the crop improvement program.

Nitrogen use efficiency (NUE): elucidated mechanisms, mapped genes and gene networks in maize (Zea mays L.)

Nitrogen, the vital primary plant growth nutrient at deficit soil conditions, drastically affects the growth and yield of a crop. Over the years, excess use of inorganic nitrogenous fertilizers resulted in pollution, eutrophication and thereby demanding the reduction in the use of chemical fertilizers. Being a C₄ plant with fibrous root system and high NUE, maize can be deployed to be the best candidate for better N uptake and utilization in nitrogen deficient soils. The maize germplasm sources has enormous genetic variation for better nitrogen uptake contributing traits. Adoption of single cross maize hybrids as well as inherent property of high NUE has helped maize cultivars to achieve the highest growth rate among the cereals during last decade. Further, considering the high cost of nitrogenous fertilizers, adverse effects on soil health and environmental impact, maize improvement demands better utilization of existing genetic variation for NUE via introgression of novel allelic combinations in existing cultivars. Marker assisted breeding efforts need to be supplemented with introgression of genes/QTLs related to NUE in ruling varieties and thereby enhancing the overall productivity of maize in a sustainable manner. To achieve this, we need mapped genes and network of interacting genes and proteins to be elucidated. Identified genes may be used in screening ideal maize genotypes in terms of better physiological functionality exhibiting high NUE. Future genome editing may help in developing lines with increased productivity under low N conditions in an environment of optimum agronomic practices.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01113-z.

Using chlorate as an analogue to nitrate to identify candidate genes for nitrogen use efficiency in barley

Nitrogen (N) is one of the most important macronutrients for crop growth and development. Large amounts of N fertilizers are applied exogenously to improve grain yield and quality, which has led to environmental pollution and high cost of production. Therefore, improvement of N use efficiency (NUE) is a very important aspect for sustainable agriculture. Here, a pilot experiment was firstly conducted with a set of barley genotypes with confirmed NUE to validate the fast NUE screening, using chlorate as an analogue to nitrate. High NUE genotypes were susceptible to chlorate-induced toxicity whereas the low NUE genotypes were tolerant. A total of 180 barley RILs derived from four parents (Compass, GrangeR, Lockyer and La Trobe) were further screened for NUE. Leaf chlorosis induced by chlorate toxicity was the key parameter observed which was later related to low-N tolerance of the RILs. There was a distinct variation in chlorate susceptibility of the RILs with leaf chlorosis in the oldest leaf ranging from 10 to 80%. A genome-wide association study (GWAS) identified 9 significant marker-trait associations (MTAs) conferring high chlorate sensitivity on chromosomes 2H (2), 3H (1), 4H (4), 5H (1) and Un (1). Genes flanking with these markers were retrieved as potential targets for genetic improvement of NUE. Genes encoding Ferredoxin 3, leucine-rich receptor-like protein kinase family protein and receptor kinase are responsive to N stress. MTA4H5468 which exhibits concordance with high NUE phenotype can further be explored under different genetic backgrounds and successfully applied in marker-assisted selection.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01239-8.

Nitrogen Use Efficiency in Sorghum: Exploring Native Variability for Traits Under Variable N-Regimes

Exploring the natural genetic variability and its exploitation for improved Nitrogen Use Efficiency (NUE) in sorghum is one of the primary goals in the modern crop improvement programs. The integrated strategies include high-throughput phenotyping, next generation sequencing (NGS)-based genotyping technologies, and a priori selected candidate gene studies that help understand the detailed physiological and molecular mechanisms underpinning this complex trait. A set of sixty diverse sorghum genotypes was evaluated for different vegetative, reproductive, and yield traits related to NUE in the field (under three N regimes) for two seasons. Significant variations for different yield and related traits under 0 and 50% N confirmed the availability of native genetic variability in sorghum under low N regimes. Sorghum genotypes with distinct genetic background had interestingly similar NUE associated traits. The Genotyping-By-Sequencing based SNPs (>89 K) were used to study the population structure, and phylogenetic groupings identified three distinct groups. The information of grain N and stalk N content of the individuals covered on the phylogenetic groups indicated randomness in the distribution for adaptation under variable N regimes. This study identified promising sorghum genotypes with consistent performance under varying environments, with buffer capacity for yield under low N conditions. We also report better performing genotypes for varied production use-grain, stover, and dual-purpose sorghum having differential adaptation response to NUE traits. Expression profiling of NUE associated genes in shoot and root tissues of contrasting lines (PVK801 and HDW703) grown in varying N conditions revealed interesting outcomes. Root tissues of contrasting lines exhibited differential expression profiles for transporter genes [ammonium transporter (SbAMT), nitrate transporters (SbNRT)]; primary assimilatory (glutamine synthetase (SbGS), glutamate synthase (SbGOGAT[NADH], SbGOGAT[Fd]), assimilatory genes [nitrite reductase (SbNiR[NADH]3)]; and amino acid biosynthesis associated gene [glutamate dehydrogenase (SbGDH)]. Identification and expression profiling of contrasting sorghum genotypes in varying N dosages will provide new information to understand the response of NUE genes toward adaptation to the differential N regimes in sorghum. High NUE genotypes identified from this study could be potential candidates for in-depth molecular analysis and contribute toward the development of N efficient sorghum cultivars.

Rice Transcriptome Analysis Reveals Nitrogen Starvation Modulates Differential Alternative Splicing and Transcript Usage in Various Metabolism-Related Genes

Nitrogen (N) is crucial for plant growth and development; however, excessive use of N fertilizers cause many problems including environmental damage, degradation of soil fertility, and high cost to the farmers. Therefore, immediate implementation is required to develop N efficient crop varieties. Rice being low nitrogen use efficiency (NUE) and a high demand staple food across the world has become a favorite crop to study the NUE trait. In the current study, we used the publicly available transcriptome data generated from the root and shoot tissues of two rice genotypes IR-64 and Nagina-22 (N-22) under optimum N supply (N+) and chronic N-starvation (N-). A stringent pipeline was applied to detect differentially expressed genes (DEGs), alternatively spliced (DAS) genes, differentially expressed transcripts (DETs) and differential transcript usage (DTU) transcripts in both the varieties and tissues under N+ and N- conditions. The DAS genes and DTU transcripts identified in the study were found to be involved in several metabolic and biosynthesis processes. We suggest alternative splicing (AS) plays an important role in fine-tuning the regulation of metabolic pathways related genes in genotype, tissue, and condition-dependent manner. The current study will help in understanding the transcriptional dynamics of NUE traits in the future.

Nitrogen and Sulfur Fertilization Modulates the Yield, Essential Oil and Quality Traits of Wild Marigold (Tagetes minuta L.) in the Western Himalaya

Fertilization plays an irreplaceable role in raising crop yields; however, there are issues with unnecessary and blind use of chemical fertilizers, which raise the risk of contamination in the atmosphere. It is hypothesized that fertilization of nitrogen (N) and sulfur (S) will together improve the essential oil (EO) yield and composition of Tagetes minuta L. Thus, 2 years field experiment were carried out to evaluate the outcomes of N (0, 60, 90, and 120 kg ha^-1) and S levels (0, 20, 40, and 60 kg ha^-1) on T. minuta during 2018 and 2019. The growth, biomass, EO content and composition were influenced (P = 0.05) by N and S fertilization. N at 120 kg ha^-1 and S at 60 kg ha^-1 registered higher biomass (183.89 and 178.90 q ha^-1, respectively) and EO yield (102.09 and 88.60 kg ha^-1, respectively), than control. Stomatal density reduced significantly with increase of N and S levels, however, density of oil glands substantially increased with S at 40 and 60 kg ha^-1. The major component of EO (Z-β-ocimene) significantly increased with 120 kg N ha^-1 (42.59%) and 60 kg S ha^-1 (42.35%), respectively. Available nutrients in soil and plant tissues substantially increased with N and S fertilization upto 120 and 60 kg ha^-1, respectively. The highest nutrient use efficiency traits were recorded at 60 kg N ha^-1 and 20 kg S ha^-1. It was concluded that 120 kg N ha^-1 and 40 kg S ha^-1 can be proposed for T. minuta as a result of agronomic responses, which serves as a sustainable means of cropping.

Nitrogen use efficiency and critical leaf N concentration of Aloe vera in urea and diammonium phosphate amended soil

Aloe vera L. is widely cultivated in many countries due to its importance as an all-purpose herbal or medicinal plant. The growth and yield of this plant can be enhanced by application of fertilizer. It is expected that a higher and balanced nutrient supply will result in higher crop production maintaining soil health, which is possible when the applied fertilizers are done in way that is efficient. So, there is a need to understand the amount of applied and type of fertilizer that will give the best output for farmers and to formulate economical market products. This study was conducted to investigate the effect of N fertilizer on leaf yield, its uptake and requirement, critical concentration, use efficiency and economics of Aloe vera L. Plants were grown at six levels of N: 0, 40, 80, 100, 150 and 200 kg ha⁻¹ from urea and diammonium phosphate (DAP) following completely randomized design with three replicates under field condition. The highest values of yield and yield attributes and profit based on benefit cost ratio (3.81 for urea and 2.91 for DAP) were obtained with 150 kg N ha⁻¹ (urea) and 100 kg N ha⁻¹ (DAP). Leaf biomass yield increased by 18–128 % in urea-N and 30–139 % in DAP-N fertilized plant over control while DAP > urea by 7.59 %. Sucker production (mean number) was urea-N (4.95 Plant⁻¹) > DAP-N (2.28 Plant⁻¹). Both gel and leaf N concentration and uptake was highest at 200 kg ha⁻¹ for both sources. For 80 % leaf biomass yield, minimum requirement of N was ca 74.90 (urea) and 89.60 kg ha⁻¹ (DAP). Growth and yield parameters to N application exhibited significant and positive correlations. Critical leaf N concentration was ca 0.88% (DAP) and 0.90% (urea) while mean and maximum NUE was 34% and 64 % (urea) and 43% and 69% (DAP), respectively. Farmers can be advised to apply N at the rate of 150 kg ha⁻¹ from urea for producing economically higher yield and better-quality A. vera leaves.

Post-flowering biotic and abiotic stresses impact nitrogen use efficiency and seed filling in Arabidopsis thaliana

Nitrogen (N) is an essential nutrient that plants require for the synthesis of amino acids, proteins, and many other important metabolites. Plant metabolism and growth are consequently dependent on the amount of N that is assimilated and distributed from source leaves to developing sinks, such as fruits and seeds. The environmental stresses enhanced by climate change deeply influence seed yield and seed composition, and may disturb N use efficiency (NUE) in pants. We aimed to investigate plant responses to extreme climates with regard to NUE, N remobilization efficiency, and seed composition. By studying a collection of Arabidopsis genotypes showing a range of C:N ratios in seeds, we investigated the impact of different post-flowering growth conditions (control, heat, drought, low nitrate availability, induced senescence, and induced plant defense) on seed yield, N allocation in organs, NUE, and N remobilization efficiency. We analysed how post-flowering stresses could change seed filling and showed that post-flowering stresses change both the range of N and C concentrations and the C:N stoichiometry in seeds. Using a new trait, called delta seed composition, we measured the deviation in C:N stoichiometry of each genotype and revealed the genetic determinism of the C:N stoichiometry. Altogether, the results indicate that extreme climate impacts NUE dramatically in plants and generates different bottlenecks in N fluxes during seed filling.

Overexpression of the High-Affinity Nitrate Transporter OsNRT2.3b Driven by Different Promoters in Barley Improves Yield and Nutrient Uptake Balance

Improving nitrogen use efficiency (NUE) is very important for crops throughout the world. Rice mainly utilizes ammonium as an N source, but it also has four NRT2 genes involved in nitrate transport. The OsNRT2.3b transporter is important for maintaining cellular pH under mixed N supplies. Overexpression of this transporter driven by a ubiquitin promoter in rice greatly improved yield and NUE. This strategy for improving the NUE of crops may also be important for other cereals such as wheat and barley, which also face the challenges of nutrient uptake balance. To test this idea, we constructed transgenic barley lines overexpressing OsNRT2.3b. These transgenic barley lines overexpressing the rice transporter exhibited improved growth, yield, and NUE. We demonstrated that NRT2 family members and the partner protein HvNAR2.3 were also up-regulated by nitrate treatment (0.2 mM) in the transgenic lines. This suggests that the expression of OsNRT2.3b and other HvNRT2 family members were all up-regulated in the transgenic barley to increase the efficiency of N uptake and usage. We also compared the ubiquitin (Ubi) and a phloem-specific (RSs1) promoter-driven expression of OsNRT2.3b. The Ubi promoter failed to improve nutrient uptake balance, whereas the RSs1 promoter succeed in increasing the N, P, and Fe uptake balance. The nutrient uptake enhancement did not include Mn and Mg. Surprisingly, we found that the choice of promoter influenced the barley phenotype, not only increasing NUE and grain yield, but also improving nutrient uptake balance.

A wheat transcription factor positively sets seed vigour by regulating the grain nitrate signal

Seed vigour and early establishment are important factors determining the yield of crops. A wheat nitrate-inducible NAC transcription factor, TaNAC2, plays a critical role in promoting crop growth and nitrogen use efficiency (NUE), and now its role in seed vigour is revealed. A TaNAC2 regulated gene was identified that is a NRT2-type nitrate transporter TaNRT2.5 with a key role in seed vigour. Overexpressing TaNAC2-5A increases grain nitrate concentration and seed vigour by directly binding to the promoter of TaNRT2.5-3B and positively regulating its expression. TaNRT2.5 is expressed in developing grain, particularly the embryo and husk. In Xenopus oocyte assays TaNRT2.5 requires a partner protein TaNAR2.1 to give nitrate transport activity, and the transporter locates to the tonoplast in a tobacco leaf transient expression system. Furthermore, in the root TaNRT2.5 and TaNRT2.1 function in post-anthesis acquisition of soil nitrate. Overexpression of TaNRT2.5-3B increases seed vigour, grain nitrate concentration and yield, whereas RNA interference of TaNRT2.5 has the opposite effects. The TaNAC2-NRT2.5 module has a key role in regulating grain nitrate accumulation and seed vigour. Both genes can potentially be used to improve grain yield and NUE in wheat.

Effect of N dose, fertilisation duration and application of a nitrification inhibitor on GHG emissions from a peach orchard

Despite only occupying 5% of the worldwide arable area, fruit tree crops are of vital economic importance in many regions. Intensive cropping practices can lead to greenhouse gas (GHG) emissions. In order to reduce these emissions, numerous studies have been made on lowering N inputs or applying nitrification inhibitors (NIs) which tend to maintain or even increase yield while reducing N leaching and nitrogenous emissions to the atmosphere. However, very few studies have been conducted on potential GHG emissions from the peach crop. In this work, a three-year study was carried out in a commercial peach orchard with a split-plot design with three replicates, in which the main factor was N dose (25, 50 and 100 kg N ha^-1 year^-1, and 50 kg N ha^-1 year^-1 applied during a shorter period of time in 2015 and 2016; and only 70 kg N ha^-1 year^-1 in 2017). Subplots in the study were used to analyse the effect of the application of a NI (3,4-dimethylpyrazole phosphate; DMPP). The aim was to qualitatively compare the effect of these factors on N₂O, N₂O + N₂, CH₄ and CO₂ emissions from a peach orchard soil in order to recommend agricultural practices that minimise emissions without concurrent yield reductions. We show that N₂O and N₂O + N₂ emissions were linked to fertilisation and increased with N dose. The N₂O emissions were mitigated (up to 49%) by DMPP up to the 50 kg N ha^-1 dose (not significantly). It seems that between 70 and 100 kg N ha^-1 the application of DMPP loses effectiveness. Methane oxidation increased with N dose and decreased with DMPP application; CO₂ emissions increased with DMPP and were unaffected by N dose. The intermediate N dose (50 kg N ha^-1) applied during a shorter period of time increased yield (not significantly) and NUE without increasing GHG emissions.

Genetic Dissection of Nitrogen Use Efficiency in Tropical Maize Through Genome-Wide Association and Genomic Prediction

In sub-Saharan Africa, one of the major challenges to smallholder farmers is soil with low fertility and inability to apply nitrogen fertilizer externally due to the cost. Development of maize hybrids, which perform better in nitrogen depleted soils, is one of the promising solutions. However, breeding maize for nitrogen use efficiency (NUE) is hindered by expensive phenotypic evaluations and trait complexity under low N stress. Genome-wide association study (GWAS) and genomic prediction (GP) are promising tools to circumvent this interference. Here, we evaluated a mapping panel in diverse environments both under optimum and low N management. The objective of this study was to identify SNPs significantly associated with grain yield (GY) and other traits through GWAS and assess the potential of GP under low N and optimum conditions. Testcross progenies of 411 inbred lines were planted under optimum and low N conditions in several locations in Africa and Latin America. In all locations, low N fields were previously depleted over several seasons, and no N fertilizer was applied throughout the growing season. All inbred lines were genotyped with genotyping by sequencing. Genotypic and GxE interaction variances were significant, and heritability estimates were moderate to high for all traits under both optimum and low N conditions. Genome-wide LD decay at r ² = 0.2 and r ² = 0.34 were 0.24 and 0.19 Mbp, respectively. Chromosome-specific LD decays ranged from 0.13 to 0.34 Mbps with an average of 0.22 Mbp at r ² = 0.2. GWAS analyses revealed 38 and 45 significant SNPs under optimum and low N conditions, respectively. Out of these 83 significant SNPs, 3 SNPs on chromosomes 1, 2, and 6 were associated either with different traits or the same trait under different management conditions, suggesting pleiotropic effects of genes. A total of 136 putative candidate genes were associated with the significant SNPs, of which seven SNPs were linked with four known genes. Prediction accuracies were moderate to high for all traits under both optimum and low N conditions. These results can be used as useful resources for further applications to develop hybrids or lines with better performance under low N conditions.

Effects of Potassium Levels on Plant Growth, Accumulation and Distribution of Carbon, and Nitrate Metabolism in Apple Dwarf Rootstock Seedlings

Nitrogen (N) is one of the most required mineral elements for plant growth, and potassium (K) plays a vital role in nitrogen metabolism, both elements being widely applied as fertilizers in agricultural production. However, the exact relationship between K and nitrogen use efficiency (NUE) remains unclear. Apple dwarf rootstock seedlings (M9T337) were used to study the impacts of different K levels on plant growth, nitrogen metabolism, and carbon (C) assimilation in water culture experiments for 2 years. The results showed that both deficiency and excess K inhibited the growth and root development of M9T337 seedlings. When the K supply concentration was 0 mM and 12 mM, the biomass of each organ, root-shoot ratio, root activity and NO₃ ^- ion flow rate decreased significantly, net photosynthetic rate (P _n) and photochemical efficiency (F _v/F _m) being lower. Meanwhile, seedlings treated with 6 mM K⁺ had higher N and C metabolizing enzyme activities and higher nitrate transporter gene expression levels (NRT1.1; NRT2.1). ¹³C and ¹⁵N labeling results showed that deficiency and excess K could not only reduce ¹⁵N absorption and ¹³C assimilation accumulation of M9T337 seedlings, but also reduced the ¹⁵N distribution ratio in leaves and ¹³C distribution ratio in roots. These results suggest that appropriate K supply (6 mM) was optimal as it enhanced photoassimilate transport from leaves to roots and increased NUE by influencing photosynthesis, C and N metabolizing enzyme activities, nitrate assimilation gene activities, and nitrate transport.