Enhanced OsNLP4‐OsNiR cascade confers nitrogen use efficiency by promoting tiller number in rice

Increased use of nitrogen fertilizers has deleterious impact on the environment. Increase in yield potential at low nitrogen supply is regarded as a cereal breeding goal for future agricultural sustainability. Although natural variations of nitrogen transporters have been investigated, key genes associated with assimilation remain largely unexplored for nitrogen use efficiency (NUE) enhancement. Here, we identified a NIN‐like protein NLP4 associated with NUE through a GWAS in rice. We found that OsNLP4 transactivated OsNiR encoding nitrite reductase that was critical in nitrogen assimilation in rice. We further constructed quadrupling NREs (Nitrate‐responsive cis‐elements) in the promoter of OsNiR (p4xNRE:OsNiR) and enhanced nitrogen assimilation significantly. We demonstrated that OsNLP4‐OsNiR increased tiller number and yield through enhancing nitrogen assimilation and NUE. Our discovery highlights the genetic modulation of OsNLP4‐OsNiR signalling cascade as a strategy for high NUE and yield breeding in rice.     

Concurrent activation of OsAMT1;2 and OsGOGAT1 in rice leads to enhanced nitrogen use efficiency under nitrogen limitation

Nitrogen (N) is a major factor for plant development and productivity. However, the application of nitrogenous fertilizers generates environmental and economic problems. To cope with the increasing global food demand, the development of rice varieties with high nitrogen use efficiency (NUE) is indispensable for reducing environmental issues and achieving sustainable agriculture. Here, we report that the concomitant activation of the rice (Oryza sativa) Ammonium transporter 1;2 (OsAMT1;2) and Glutamate synthetase 1 (OsGOGAT1) genes leads to increased tolerance to nitrogen limitation and to better ammonium uptake and N remobilization at the whole plant level. We show that the double activation of OsAMT1;2 and OsGOGAT1 increases plant performance in agriculture, providing better N grain filling without yield penalty under paddy field conditions, as well as better grain yield and N content when plants are grown under N llimitations in field conditions. Combining OsAMT1;2 and OsGOGAT1 activation provides a good breeding strategy for improving plant growth, nitrogen use efficiency and grain productivity, especially under nitrogen limitation, through the enhancement of both nitrogen uptake and assimilation.     

Effect of Reaction-Finished Solution of Hydrochar (HRFS) Application on Rice Grain Yield and Nitrogen Use Efficiency in Saline Soil

We conducted a pot experiment to examine the feasibility of applying a reaction-finished solution of hydrochar (HRFS) to enhance rice production in a saline soil. With this purpose, HRFS was applied (0, 10, 20, 40, 60, 80 and 100 mL/pot) and rice yield and nitrogen (N) use efficiency (NUE) were determined. HRFS application significantly (P < 0.05) increased rice grain yield by 19.6%–30.0% compared to the control treatment (CKU, with N but without HRFS addition). Moreover, HRFS application promoted plant height and straw biomass of rice. Increases of rice yield were mainly achieved by increases in the number of panicles and grains per panicle. Compared with the CKU treatment, the NUE of HRFS amendments significantly (P < 0.05) increased by 56.3%–71.7%. This indicated that the improvement of NUE was one of the mechanisms to improve rice grain yield with HRFS amendment. The results of regression analysis showed that there was a positive relationship (R²=0.8332) between rice yield and HRFS application rate within an appropriate range. The highest rice yield was recorded with the HRFS application of 40 mL/pot, but a further increase in HRFS application rate appeared to reduce rice yield. Based on the results of this pot study, HRFS application can increase rice yield in a saline soil by regulating its yield components and enhancing NUE. However, impact of HRFS on these variables showed a “dose effect”.     

Development and field performance of nitrogen use efficient rice lines for Africa

Nitrogen (N) fertilizers are a major input cost in rice production, and its excess application leads to major environmental pollution. Development of rice varieties with improved nitrogen use efficiency (NUE) is essential for sustainable agriculture. Here, we report the results of field evaluations of marker‐free transgenic NERICA4 (New Rice for Africa 4) rice lines overexpressing barley alanine amino transferase (HvAlaAT) under the control of a rice stress‐inducible promoter (pOsAnt1). Field evaluations over three growing seasons and two rice growing ecologies (lowland and upland) revealed that grain yield of pOsAnt1:HvAlaAT transgenic events was significantly higher than sibling nulls and wild‐type controls under different N application rates. Our field results clearly demonstrated that this genetic modification can significantly increase the dry biomass and grain yield compared to controls under limited N supply. Increased yield in transgenic events was correlated with increased tiller and panicle number in the field, and evidence of early establishment of a vigorous root system in hydroponic growth. Our results suggest that expression of the HvAlaAT gene can improve NUE in rice without causing undesirable growth phenotypes. The NUE technology described in this article has the potential to significantly reduce the need for N fertilizer and simultaneously improve food security, augment farm economics and mitigate greenhouse gas emissions from the rice ecosystem.     

Enhanced‐efficiency fertilizers are not a panacea for resolving the nitrogen problem

Improving nitrogen (N) management for greater agricultural output while minimizing unintended environmental consequences is critical in the endeavor of feeding the growing population sustainably amid climate change. Enhanced‐efficiency fertilizers (EEFs) have been developed to better synchronize fertilizer N release with crop uptake, offering the potential for enhanced N use efficiency (NUE) and reduced losses. Can EEFs play a significant role in helping address the N management challenge? Here we present a comprehensive analysis of worldwide studies published in 1980–2016 evaluating four major types of EEFs (polymer‐coated fertilizers PCF, nitrification inhibitors NI, urease inhibitors UI, and double inhibitors DI, i.e. urease and nitrification inhibitors combined) regarding their effectiveness in increasing yield and NUE and reducing N losses. Overall productivity and environmental efficacy depended on the combination of EEF type and cropping systems, further affected by biophysical conditions. Best scenarios include: (i) DI used in grassland (n = 133), averaging 11% yield increase, 33% NUE improvement, and 47% decrease in aggregated N loss (sum of NO₃^‐, NH₃, and N₂O, totaling 84 kg N/ha); (ii) UI in rice‐paddy systems (n = 100), with 9% yield increase, 29% NUE improvement, and 41% N‐loss reduction (16 kg N/ha). EEF efficacies in wheat and maize systems were more complicated and generally less effective. In‐depth analysis indicated that the potential benefits of EEFs might be best achieved when a need is created, for example, by downward adjusting N application from conventional rate. We conclude that EEFs can play a significant role in sustainable agricultural production but their prudent use requires firstly eliminating any fertilizer mismanagement plus the implementation of knowledge‐based N management practices.     

Nitrogen assimilation in plants: current status and future prospects

Nitrogen(N) is the driving force for crop yields; however, excessive N application in agriculture not only increases production cost, but also causes severe environmental problems. Therefore, comprehensively understanding the molecular mechanisms of N use efficiency(NUE) and breeding crops with higher NUE is essential to tackle these problems. NUE of crops is determined by N uptake, transport, assimilation, and remobilization. In the process of N assimilation, nitrate reductase(NR), nitrite redu...     

Agronomic improvements through the genetic and physiological regulation of nitrogen uptake in wheat (Triticum aestivum L.)

Nitrogen (N) uptake is the first step in nitrate assimilation, and efficient N uptake is essential for plant growth, especially for protein biosynthesis and photosynthetic activities. In cereals, improved N uptake is closely coupled with an increase in nitrogen use efficiency (NUE) and yield improvements. Because wheat (Triticum aestivum L.) is a leading crop worldwide, a better understanding of N uptake regulation in wheat is vital to improving NUE and developing sustainable agricultural systems. However, detailed information regarding the biological mechanisms that are responsible for the more efficient uptake of ambient N by wheat is limited. This review presents recent developments in the biological mechanisms of N uptake in wheat, including plant growth regulations, fundamental roles of root systems, interactions between N species, and genetic controls. Specifically, this paper provides a number of potential strategies that can be used to increase wheat N uptake. The information provided here may guide N fertilizer management during wheat production and further elucidate the plant regulatory mechanisms that are involved in N uptake, which can thereby increase wheat NUE.     

Can genetic manipulation of plant nitrogen assimilation enzymes result in increased crop yield and greater N-use efficiency? An assessment

The literature on the relations between plant nitrogen (N) assimilation enzymes and plant/crop N assimilation, growth and yield is reviewed to assess if genetic manipulation of the activities of N assimilation enzymes can result in increased yield and/or increased N use efficiency. The available data indicate that (I) levels of N assimilation enzymes do not limit primary N assimilation and hence yield; (II) root or shoot nitrate assimilation can have advantages under specific environmental conditions; (III) for cereals, cytosolic glutamine synthetase (GS1) is a key enzyme in the mobilisation of N from senescing leaves and its activity in senescing leaves is positively related to yield; and (TV) for rice (Oryza sativd), NADH-glutamate synthase (NADH-GOGAT) is important in the utilisation of N in grain filling and its activity in developing grains is positively related to yield. In our opinion, selection of plants, from either a genetically manipulated population or genetic resources, with expression of nitrate reductase/nitrite reductase primarily in the root or shoot should increase plant/crop growth and hence yield under specific environmental conditions. In addition for cereals the selection of plants with high GS1 in senescing leaves and in some cases high NADH-GOGAT in developing grains could help maximise the retrieval of plant N in seeds.     

植物适应土壤氮素环境的基因选择:以水稻为例

在农业生产过程中,施用无机氮肥是提高作物产量的基础,但氮肥过量施加对生态系统和植物发育进程均会产生不利影响。因此,提高作物氮素利用效率是农业可持续发展的关键。目前,对重要粮食作物水稻(Oryza sativa)的氮高效研究取得了一系列重要进展,并克隆到多个调控氮素吸收、转运和代谢的关键基因。然而,在不断被人工选育的过程...     

不同氮效率水稻全生育期内对增硝营养的响应及其生理机制

通过添加硝化抑制剂（二氰胺,DCD）来控制硝化作用的水培试验方法,研究了氮高效水稻品种南光和氮低效水稻品种ELIO的籽粒产量对增硝营养（NH4＋∶NO3-比例为100∶0和75∶25）的响应,同时从产量构成、不同生育时期水稻生长、氮素吸收和同化4个方面研究了造成其产量差异的生理机制。结果表明：增NO3-营养可以显著促进氮高效水稻品种南光的生长,从而使其籽粒产量水平提高21%,而对氮低效水稻品种ELIO的籽粒产量没有显著影响。进一步分析表明：在增NO3-营养条件下,南光的穗粒数增加了25%,结实率增加了16%,而氮低效水稻品种ELIO的结实率和穗粒数在两种营养条件下没有显著变化;增NO3-营养可以促进南光对氮素的吸收,使其在苗期、分蘖盛期、齐穗期和成熟期对氮素的吸收量平均增加了36%,进而促进了其生长,干物质积累量在四个生育时期平均增加了30%;南光叶片硝酸还原酶和根系谷氨酰胺合成酶的活力在增硝营养条件下分别增加了100%和95%,说明增硝营养促进了南光对NH4＋和NO3-的同化利用。与氮低效水稻品种（ELIO）相比,氮高效水稻品种（南光）对增硝营养表现出较强的生理响应。     

Increased microbial functional diversity under long-term organic and integrated fertilization in a paddy soil

Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community and functional genes to long-term integrated fertilization (chemical combined with organic fertilization) remain unclear. Here, we used pyrosequencing and a microarray-based GeoChip to explore the shifts of microbial community and functional genes in a paddy soil which received over 21-year fertilization with various regimes, including control (no fertilizer), rice straw (R), rice straw plus chemical fertilizer nitrogen (NR), N and phosphorus (NPR), NP and potassium (NPKR), and reduced rice straw plus reduced NPK (L-NPKR). Significant shifts of the overall soil bacterial composition only occurred in the NPKR and L-NPKR treatments, with enrichment of certain groups including Bradyrhizobiaceae and Rhodospirillaceae families that benefit higher productivity. All fertilization treatments significantly altered the soil microbial functional structure with increased diversity and abundances of genes for carbon and nitrogen cycling, in which NPKR and L-NPKR exhibited the strongest effect, while R exhibited the least. Functional gene structure and abundance were significantly correlated with corresponding soil enzymatic activities and rice yield, respectively, suggesting that the structural shift of the microbial functional community under fertilization might promote soil nutrient turnover and thereby affect yield. Overall, this study indicates that the combined application of rice straw and balanced chemical fertilizers was more pronounced in shifting the bacterial composition and improving the functional diversity toward higher productivity, providing a microbial point of view on applying a cost-effective integrated fertilization regime with rice straw plus reduced chemical fertilizers for sustainable nutrient management.

     

Nitrogen Use Efficiency of Rice Cultivars (Oryza sativa L.) Under Salt Stress and Low Nitrogen Conditions

Improving nitrogen use efficiency (NUE) under salt stress has become crucial for rice as it is increasingly facing two major environmental constraints: excessive nitrogen fertilization and soil salinization. However, the interaction between salinity and N levels is very complex and has not yet been considered from the perspective of reduced nitrogen input. We conducted a hydroponic experiment at the early tillering stage on the Yoshida solution to evaluate the impact of rising NaCl and decreasing N application on NUE of four rice cultivars cultivated under three NaCl (0, 56, and 113 mM) and four N (2.86, 1.43, 0.72, and 0.36 mM) concentrations. After 4 weeks, physiological NUE (pNUE), absorption NUE (aNUE), agronomical NUE (agNUE), N transport efficiency (NTE), and physiological traits were evaluated. Significant interactions between N and NaCl-applied concentrations were found in all measured parameters. In all cultivars, increasing the NaCl-applied concentration markedly decreased aNUE and agNUE. For each NaCl treatment, lowering the N applied sharply increased aNUE and agNUE, and this effect was stronger when the NaCl applied was higher. The effect of N lowering on pNUE depended on the NaCl treatment: it enhanced pNUE in the absence of NaCl but had no influence under the highest NaCl-applied concentration. Cultivars largely differed in response to NaCl. The aNUE—but not pNUE—differed between salt-tolerant and salt-sensitive cultivars: aNUE markedly decreased with NaCl concentration in the most salt-sensitive cultivar, whereas it was the highest at the intermediate NaCl concentration in the most salt-tolerant cultivar, especially under low N levels. This finding suggests that under salt conditions, the use of salt-tolerant rice genotypes combined with reducing N level application is necessary to improve NUE. The study of NUE in rice should be focused on the improvement of aNUE with a strong emphasis on the salt tolerance of cultivars.

     

Association genetics of the parameters related to nitrogen use efficiency in Brassica juncea L.

Key message

Genome wide association studies allowed prediction of 17 candidate genes for association with nitrogen use efficiency. Novel information obtained may provide better understanding of genomic controls underlying germplasm variations for this trait in Indian mustard.

Abstract

Nitrogen use efficiency (NUE) of Indian mustard (Brassica juncea (L.) Czern & Coss.) is low and most breeding efforts to combine NUE with crop performance have not succeeded. Underlying genetics also remain unexplored. We tested 92 SNP-genotyped inbred lines for yield component traits, N uptake efficiency (NUPEFF), nitrogen utilization efficiency (NUTEFF), nitrogen harvest index (NHI) and NUE for two years at two nitrogen doses (N_o without added N and N₁₀₀ added @100 kg/ha). Genotypes IC-2489-88, M-633, MCP-632, HUJM 1080, GR-325 and DJ-65 recorded high NUE at low N. These also showed improved crop performance under high N. One determinate mustard genotype DJ-113 DT-3 revealed maximum NUTEFF. Genome wide association studies (GWAS) facilitated recognition of 17 quantitative trait loci (QTLs). Environment specificity was high. B-genome chromosomes (B02, B03, B05, B07 and B08) harbored many useful loci. We also used regional association mapping (RAM) to supplement results from GWAS. Annotation of the genomic regions around peak SNPs helped to predict several gene candidates for root architecture, N uptake, assimilation and remobilization. CAT9 (At1g05940) was consistently envisaged for both NUE and NUPEFF. Major N transporter genes, NRT1.8 and NRT3.1 were predicted for explaining variation for NUTEFF and NUPEFF, respectively. Most significant amino acid transporter gene, AAP1 appeared associated with NUE under limited N conditions. All these candidates were predicted in the regions of high linkage disequilibrium. Sequence information of the predicted candidate genes will permit development of molecular markers to aid breeding for high NUE.

     

A consortium of non‐rhizobial endophytic microbes from Typha angustifolia functions as probiotic in rice and improves nitrogen metabolism

• Endophytic microbes isolated from plants growing in nutrient‐deficient environments often possess properties that improve nutrition of agriculturally important plants. A consortium of non‐rhizobial endophytic microbes isolated from a macrophyte Typha angustifolia growing in the marginal wetlands associated with a Uranium mine was characterized for their beneficial effect on rice and the mechanisms of growth promotion were investigated.
• The microbes were identified and characterized for their potential plant growth promoting (PGP) properties. Effect of these microbes on nitrogen (N)‐metabolism of rice was tested as Typha endophytes were predominantly (N)‐fixing. Relative N‐use efficiency and expression of genes involved in N‐uptake and assimilation were investigated in treated plants.
• Evidence of horizontal gene transfer (HGT) of dinitrogen reductase gene was observed within the consortium from a Pseudomonas stutzeri strain. The consortium behaved as plant probiotic and showed substantial growth benefits to Typha, their natural host as well as to rice. Typha endophytes colonized rice endosphere significantly increasing biomass, shoot length and chlorophyll content in rice plants both under N‐sufficient and N‐deficient conditions. N‐uptake and assimilation genes were upregulated in plants treated with the endophytes even after three weeks post infection.
• Our results suggested, HGT of nitrogen‐fixation trait to be highly prevalent among endophytes isolated from nutrient‐poor habitats of the uranium mine. A long‐term nitrogen deficiency response in the treated plants was elicited by the consortium improving N‐uptake, assimilation and relative N‐use efficiency of rice plants. This appeared to be at least one of the main strategies of plant growth promotion.

     

Mining of Candidate Maize Genes for Nitrogen Use Efficiency by Integrating Gene Expression and QTL Data

Breeding maize varieties for high nitrogen (N) use efficiency (NUE) by marker-assisted selection using NUE quantitative trait locus (QTL) or by genetic transfer of NUE-associated genes is a viable approach for increasing grain yield in N-limited production areas. In this investigation, we evaluated a set of introgression line populations under N supply and N deficiency conditions. From 42 QTLs for grain yield and yield components, 23 were identified under N supply conditions and 33 from N limited conditions. Meta-analysis of published maize NUE QTLs revealed 37 “consensus” QTLs, of which, 18 was detected under low N conditions. In addition, 258 unique ESTs associated with low N stress response, N uptake, transport, and assimilation were aligned on the maize genome by in silico mapping. Integrating the EST map with the QTL map has resulted in the identification of candidate NUE-associated genes of the following functional categories: N uptake, transport, and assimilation; carbon (C) metabolism and assimilation; and cascades of stress response and signal transduction genes. Nine candidates that have been introgressed into Ye478 significantly altered grain yield/yield components. It is suggested that the dynamics of interactions between C and N metabolism are important for maize yield. A high NUE variety should have a highly efficient C assimilation per unit N and actively express CO₂ assimilation-related genes under N-limited conditions.