Improvement Of N Use Efficiency Research Articles

Identification of candidate genes and residues for improving nitrogen use efficiency in the N-sensitive medicinal plant Panax notoginseng

BackgroundNitrogen (N) metabolism-related key genes and conserved amino acid sites in key enzymes play a crucial role in improving N use efficiency (NUE) under N stress. However, it is not clearly known about the molecular mechanism of N deficiency-induced improvement of NUE in the N-sensitive rhizomatous medicinal plant Panax notoginseng (Burk.) F. H. Chen. To explore the potential regulatory mechanism, the transcriptome and proteome were analyzed and the three-dimensional (3D) information and molecular docking models of key genes were compared in the roots of P. notoginseng grown under N regimes.ResultsTotal N uptake and the proportion of N distribution to roots were significantly reduced, but the NUE, N use efficiency in biomass production (NUEb), the recovery of N fertilizer (RNF) and the proportion of N distribution to shoot were increased in the N0-treated (without N addition) plants. The expression of N uptake- and transport-related genes NPF1.2, NRT2.4, NPF8.1, NPF4.6, AVP, proteins AMT and NRT2 were obviously up-regulated in the N0-grown plants. Meanwhile, the expression of CIPK23, PLC2, NLP6, TCP20, and BT1 related to the nitrate signal-sensing and transduction were up-regulated under the N0 condition. Glutamine synthetase (GS) activity was decreased in the N-deficient plants, while the activity of glutamate dehydrogenase (GDH) increased. The expression of genes GS1-1 and GDH1, and proteins GDH1 and GDH2 were up-regulated in the N0-grown plants, there was a significantly positive correlation between the expression of protein GDH1 and of gene GDH1. Glu192, Glu199 and Glu400 in PnGS1 and PnGDH1were the key amino acid residues that affect the NUE and lead to the differences in GDH enzyme activity. The 3D structure, docking model, and residues of Solanum tuberosum and P. notoginseng was similar.ConclusionsN deficiency might promote the expression of key genes for N uptake (genes NPF8.1, NPF4.6, AMT, AVP and NRT2), transport (NPF1.2 and NRT2.4), assimilation (proteins GS1 and GDH1), signaling and transduction (genes CIPK23, PLC2, NLP6, TCP20, and BT1) to enhance NUE in the rhizomatous species. N deficiency might induce Glu192, Glu199 and Glu400 to improve the biological activity of GS1 and GDH, this has been hypothesized to be the main reason for the enhanced ability of N assimilation in N-deficient rhizomatous species. The key genes and residues involved in improving NUE provide excellent candidates for the breeding of medicinal plants.

Comparative physiological and transcriptome analysis of leaf nitrogen fluxes in stay-green maize during the vegetative stage

In maize, nitrogen (N) stored in leaves is an important internal source for supporting subsequent growth and development. However, the regulation of N fluxes and photosynthesis and the molecular and genotypic regulations that modify them are less clear in source leaves during the vegetative stage. This knowledge is crucial for improving N use efficiency (NUE). By using 15N labeling and transcriptome methods, an analysis of the physiological and molecular basis of leaf N import and export processes and photosynthetic N use efficiency (PNUE) was conducted in two maize hybrids (XY335 and XY696) with different stay-green characteristics during the vegetative stage. Leaf N import and export in XY696 were 45% and 33% greater than those in XY335. However, the PNUE in XY335 was 17% greater than that in XY696 due to the higher net photosynthetic rate (A) and lower SLN. Correspondingly, the chlorophyll content and photosynthesis-related enzyme (PEPc, PEPck, PPDK) activities increased by 18∼30% in XY335. Transcriptome analysis indicated that the expression levels of several N and carbon metabolism-related genes encoding Rubisco, PEPc, Nir, GS and AS were significantly increased or decreased in XY696 in parallel with enzyme activities. Moreover, there was a large difference in the expression abundance of genes encoding nitrate/nitrite transporters and transmembrane proteins. Our results suggest that two hybrids modulate leaf N fluxes and photosynthesis differently by altering gene expression and enzyme activities. Our study contributes to understanding leaf N fluxes and PNUE regulation and serves as a crucial reference for NUE improvement in maize breeding research.

Genetic dissection of N use efficiency using maize inbred lines and testcrosses

Although the use of heterosis in maize breeding has increased crop productivity, the genetic causes underlying heterosis for nitrogen (N) use efficiency (NUE) have been insufficiently investigated. In this study, five N-response traits and five low-N-tolerance traits were investigated using two inbred line populations (ILs) consisting of recombinant inbred lines (RIL) and advanced backcross (ABL) populations, derived from crossing Ye478 with Wu312. Both populations were crossed with P178 to construct two testcross populations. IL populations, their testcross populations, and the midparent heterosis (MPH) for NUE were investigated. Kernel weight, kernel number, and kernel number per row were sensitive to N level and ILs showed higher N response than did the testcross populations. Based on a high-density linkage map, 138 quantitative trait loci (QTL) were mapped, each explaining 5.6%–38.8% of genetic variation. There were 52, 34 and 52 QTL for IL populations, MPH, and testcross populations, respectively. The finding that 7.6% of QTL were common to the ILs and their testcross populations and that 11.7% were common to the MPH and testcross population indicated that heterosis for NUE traits was regulated by non-additive and non-dominant loci. A QTL on chromosome 5 explained 27% of genetic variation in all of the traits and Gln1-3 was identified as a candidate gene for this QTL. Genome-wide prediction of NUE traits in the testcross populations showed 14%–51% accuracy. Our results may be useful for clarifying the genetic basis of heterosis for NUE traits and the candidate gene may be used for genetic improvement of maize NUE.

Plant nitrogen availability and crosstalk with phytohormones signallings and their biotechnology breeding application in crops.

Nitrogen (N), one of the most important nutrients, limits plant growth and crop yields in sustainable agriculture system, in which phytohormones are known to play essential roles in N availability. Hence, it is not surprising that massive studies about the crosstalk between N and phytohormones have been constantly emerging. In this review, with the intellectual landscape of N and phytohormones crosstalk provided by the bibliometric analysis, we trace the research story of best-known crosstalk between N and various phytohormones over the last 20 years. Then, we discuss how N regulates various phytohormones biosynthesis and transport in plants. In reverse, we also summarize how phytohormones signallings modulate root system architecture (RSA) in response to N availability. Besides, we expand to outline how phytohormones signallings regulate uptake, transport, and assimilation of N in plants. Further, we conclude advanced biotechnology strategies, explain their application, and provide potential phytohormones-regulated N use efficiency (NUE) targets in crops. Collectively, this review provides not only a better understanding on the recent progress of crosstalk between N and phytohormones, but also targeted strategies for improvement of NUE to increase crop yields in future biotechnology breeding of crops.

Socioeconomic barriers of nitrogen management for agricultural and environmental sustainability

Synthetic nitrogen (N) fertilizers support global food production and feed over half of the global population. However, more than half of the N fertilizers applied to croplands are not absorbed by crops, but lost to the environment, leading to low N use efficiency (NUE) globally. Identifying and overcoming socioeconomic barriers to achieve an improvement of NUE and a reduction in N loss is thus key for N management and to attain agricultural and environmental sustainability. In this paper, we compiled the global cropland N budgets at a national scale (1961–2018) and developed robust econometric models to explore the relationship between cropland N use with socioeconomic factors. The results demonstrate that economic development and farm size are the key drivers to improve NUE for agricultural and environmental sustainability. In less developed countries, it is difficult for farmers to access chemical fertilizers, leading to croplands receiving too little N input and at a high NUE, but suffering from soil N depletion. As economic development progresses, more fertilizer is produced and applied, but smallholder farming typically leads to over-fertilization and consequently N losses to the environment. Large-scale farming improves NUE, reduces N loss and benefits agricultural production and environmental protection. Also, interactions between farm size and economic development, international trade, crop and livestock systems, and related policies are important causes for changes in the NUE of the whole agricultural system. Overcoming these socioeconomic barriers especially combining large-scale farming could effectively reduce excessive N inputs and sustain agricultural and environmental N management, while maintaining food production, resulting in a triple-win for food security, poverty alleviation, and environmental protection.

Rice NIN-LIKE PROTEIN 3 modulates nitrogen use efficiency and grain yield under nitrate-sufficient conditions.

Nitrogen (N) is an essential macronutrient for crop growth and yield. Improving the N use efficiency (NUE) of crops is important to agriculture. However, the molecular mechanisms underlying NUE regulation remain largely elusive. Here we report that the OsNLP3 (NIN-like protein 3) regulates NUE and grain yield in rice under N sufficient conditions. OsNLP3 transcript level is significantly induced by N starvation and its protein nucleocytosolic shuttling is specifically regulated by nitrate. Loss-of-function of OsNLP3 reduces plant growth, grain yield, and NUE under sufficient nitrate conditions, whereas under low nitrate or different ammonium conditions, osnlp3 mutants show no clear difference from the wild type. Importantly, under sufficient N conditions in the field, OsNLP3 overexpression lines display improved grain yield and NUE compared with the wild type. OsNLP3 orchestrates the expression of multiple N uptake and assimilation genes by directly binding to the nitrate-responsive cis-elements in their promoters. Overall, our study demonstrates that OsNLP3, together with OsNLP1 and OsNLP4, plays overlapping and differential roles in N acquisition and NUE, and modulates NUE and the grain yield increase promoted by N fertilizer. Therefore, OsNLP3 is a promising candidate gene for the genetic improvement of grain yield and NUE in rice.

Arabidopsis NLP7 improves nitrogen use efficiency and yield in cotton

BackgroundNitrogen (N) is a required macronutrient for cotton growth and productivity. Excessive N fertilizers are applied in agriculture for crop yield maximization, which also generates environmental pollution. Improving crop N use efficiency (NUE) is the most economical and desirable way of reducing fertilizer application and environmental pollution. NUE has been an important issue in cotton. So far there is no report on cotton NUE improvement via transgenic approach. Nin-like proteins (NLP) are transcription factors regulating NUE. We previously demonstrated that AtNLP7 improved NUE and biomass when overexpressed in Arabidopsis. However, it is not known whether AtNLP7 can be used to improve NUE in crops.ResultsTo test the feasibility, we expressed AtNLP7 in cotton and evaluated NUE and yield of the transgenic cotton in the field. Transgenic cotton showed improved NUE and yield under both low and high N conditions. In addition, plant biomass, amount of absorbed N, N contents, activities of N-assimilating enzymes, and the expression of N-related marker genes were significantly increased in transgenic cotton compared with the wild type control, suggesting that AtNLP7 enhances NUE in cotton.ConclusionTogether, our results demonstrate that AtNLP7 is a promising candidate to improve NUE and yield in cotton.

Spatiotemporal Variation Characteristics and Driving Factors of Nitrogen Use Efficiency of Wheat–Rice Rotation Systems in the Taihu Lake Region

During the past three decades, a large amount of nitrogen (N) fertilizers has been applied in the rice and wheat rotation system in the Taihu Lake region of southern China to achieve high yield, resulting in low N use efficiency (NUE). China is implementing the national strategy “fertilizer reduction with efficiency increase” to solve the serious ecological problems caused by excessive fertilization. However, the effects of N fertilizer reduction on soil fertility and their integrated effect on NUE of rice–wheat rotation systems in the Taihu Lake region are not fully understood. In this study, test fields with different soil-fertility qualities were selected in typical rice–wheat areas in the Taihu Lake region to perform a 2-year rice–wheat N fertilizer effect test to obtain the comprehensive quantitative relationship among the integrated fertility index (IFI), nitrogen application level (NA), and NUE. Through the investigation and spatial analysis of NA and IFI in the study area in 2003 and 2017, the spatial and temporal variation characteristics of NA and IFI in the study area in the past 15-year period were obtained, and this information was spatially coupled with the comprehensive quantitative relationship model of NUE to reveal the variation characteristics and driving factors of NUE in the study area. The result shows that the wheat and rice NA in the study area in 2017 increased by 35.5 and 8.4%, respectively, compared with 2003. Due to excessive fertilization, the soil nitrogen, phosphorus, and potassium content of cultivated land in the study area in 2017 was greater than that in 2003, especially soil-available phosphorus and potassium contents, whereas soil organic matter (SOM) content was reduced. The cultivated land IFI of the study area as a whole increased by 7.2% in the 15-year period. The NUE of rice and wheat rotation increased by 5.8% in 2017 compared with that of 2003 due to the improvement in crop varieties and N fertilizer yield benefits. The increases of NA and IFI both have negative correlations with the NUE improvement, and the NA increase has a greater impact. In addition, the terrain, soil type, texture, and parent material also affect the soil nutrient-preserving capability and, thus, affect the spatial variation of IFI and NUE improvement. These factors have greater influence on NUE improvement of wheat than rice. This study provides a novel and effective method for analyzing the spatial-temporal variation characteristics of NUE in the rice–wheat system and is conducive to guide precise fertilization and N fertilizer reduction based on the spatial analysis of NA with IFI and NUE.

Long-Term Fertilization and Lime-Induced Soil pH Changes Affect Nitrogen Use Efficiency and Grain Yields in Acidic Soil under Wheat-Maize Rotation

Liming (L) is a common practice to mitigate soil acidification and enhance soil quality and crop productivity. However, in acidic soil, it is not clear how long-term application of lime and nitrogen (N)-based fertilizer affects soil chemical properties, the wheat and maize grain yields (GY), and N-use efficiency (NUE). Thus, to investigate the effects of N-based fertilizations without L (−L) and with L (+L) on wheat and maize GY and NUE through their effects on soil chemical properties, we analyzed a 28-year field experiment in acidic soil under a wheat-maize system in South China. The analysis was carried out between 1991 and 2010 (before L) and between 2011 and 2018 (after L). We categorized the treatments into (1) no fertilizer (C); nitrogen (N); N and phosphorus (NP); N and potassium (NK); N, P and K (NPK); and NPKCR, NPK and crops residue (CR) applications (NPKCR), before L; and (2) C; N−L; N+L; NP−L; NP+L; NK−L; NK+L; NPK−L; NPK+L; NPKCR−L and NPKCR+L, after L. The effects of long-term fertilization resulted in lower soil pH by 15%, soil available K (AK) by 19%, POlsen by 6%, NO3−-N by 15%, soil organic matter (SOM) by 16%, total N by 16%, and C:N ratio by 13% in −L soil than in +L soil. However, the accumulation of NH4+-N was higher by 40% in −L soil than in +L soil. Wheat and maize GY, N recovery efficiency (REN), and N partial factor productivity (PEPN) were more adversely affected by 8-year fertilizations in −L compared with fertilizations before L and in +L primarily because of the significantly decreased soil pH. Conversely, improvements in wheat and maize yields, REN, and PFPN by 8-year fertilizations in +L were related to increasing soil pH, exchangeable base cations such as Ca2+, Mg2+, and the alleviated toxicity of Al3+. Overall, improvement of GY and NUE from the acidified soil in South China requires the long-term integrated use of fertilizer (NPK), retention of CR, and the +L (i.e., NPKCR+L).

SLAF-Based Linkage Map Construction and QTL Mapping of Nitrogen Use Efficiency in Rice (Oryza sativa L.)

Rice production relies on large amounts of synthetic nitrogen fertilizer to meet crop nutritional demands. However, the current fertilizer use efficiency is poor, with an average of 30–50% of total applied nitrogen (N) recovered in grains. Consequently, optimizing N availability and N use efficiency (NUE) has become a major target for rice yield improvement, and looking for quantitative trait loci (QTL) associated with NUE can provide useful information for developing nitrogen efficient rice genotypes. The present study aims to identify QTLs associated with NUE and its two components, agronomic NUE (agNUE) and grain nitrogen increase rate (GIR). A recombinant inbred line population (RIL) derived from a cross between Nipponbare and OM052, consisting of 159 F3 individuals was developed and cultivated in low-N (8 kg N/0.67 ha, N8) and high-N (18 kg N/0.67 ha, N18) conditions. Specific length amplified fragment sequencing (SLAF) was used to genotype the RILs and construct a high-density linkage map spanning 1587.70 cM, consisting 2707 SLAF markers with an average interval of 0.59 cM between adjacent marker loci. QTL analysis confirmed four significant QTLs distributed among chromosome 1, 6, and 11, with the proportion of phenotypic variance explained by each QTL ranging from 2.96 to 11.11% and LOD scores from 1.67 to 3.75. Functional annotation of genes located within the QTL intervals revealed NUE putative candidate genes. Overall, the QTLs identified in this study contribute information that could be useful for NUE improvement in rice.

The food nitrogen footprint for African countries under fertilized and unfertilized farms

Although nitrogen (N) is a limiting factor for food production (FP) in Africa, and African food security is seriously threatened by the phenomenon of soil N depletion, there is a dearth of information that shows the points to focus on throughout the chain of FP and food consumption (FC) in all African countries to minimize N loss while securing food N supply. Food N footprint (NF) is an indicator for tracing the losses of reactive N (Nr) with regard to the FP and FC chain. This is the first study to calculate the food NF for all African countries under fertilized and unfertilized farms, by calculating two sets of virtual N factors (VNFs; kg Nr released to the environment kg−1 N in consumed product): one for unfertilized farms (the unfertilized scenario) and one for fertilized farms (the fertilized scenario). The fertilized and unfertilized VNFs were utilized to calculate a weighted average set of VNFs (the combined scenario). From the percentage of farms that utilize N fertilizer, and the N percentage in production that comes from soil depletion, the proportion used for the combined scenario was determined. Soil N depletion factors (SNDFs; kg N taken from the unfertilized soil kg−1 N in food consumed) were also computed to identify the quantity of N extracted from the soil for food production. We have also provided the changes in N inputs, N outputs, and N use efficiency (NUE) for North Africa and Sub-Saharan Africa (SSA) during the last 57 years. The average total N input to croplands increased from 24 and 19 kg N ha−1 yr−1 in 1961–1965 to 100 and 42 kg N ha−1 yr−1 in 2010–2017 for North Africa and SSA, respectively. The NUE declined from 109% and 67% (1961–1965) to 47% and 63% (2010–2017) for North Africa and SSA, respectively. The total average per-capita food NF was 11 and 5.8 kg N cap−1 yr−1 in unfertilized farms; 21 and 14 kg N cap−1 yr−1 in fertilized farms; and 19 and 7.5 kg N cap−1 yr−1 under the combined scenario for North Africa and SSA, respectively. Vegetable-fruit and beef have the highest SDNFs in Africa. FP in Africa contributes approximately 70% of the total food NF. Therefore, if possible, the best way for Africans to reduce soil N depletion and N emissions is to encourage the production and consumption of livestock and crops products with less VNF and SNDF. However, African people do not have this luxury of choice because of poverty and ignorance. Therefore, African policy-makers must adopt integrated approaches that provide effective tools to control the production of animals and crops in conjunction with the improvement of NUE. Trying to completely change the African agricultural system is impossible, but strategies must be developed to reduce soil depletion in a gradual way, as well as a shift towards low-VNF foods.

Dynamic transcriptome analysis indicates extensive and discrepant transcriptomic reprogramming of two rapeseed genotypes with contrasting NUE in response to nitrogen deficiency

Oilseed rape (Brassica napus L.) has high nitrogen (N) requirement for its optimal growth and yield. However, little is known about the transcriptomic reprogramming of rapeseed in response to N deficiency. Two rapeseed genotypes with contrasting N use efficiency (NUE) were used to perform whole-transcriptome sequencing on the shoots and roots supplied with or without N in a time-course experiment. A total of 24,435 differentially expressed genes (DEGs) were identified. Among them, 8811 genes were differentially expressed between two N treatments and between the two genotypes. Coexpression networks reveal central N-deficiency-response modules with diverse expression patterns between the two genotypes. Major expression hubs involved in phytohormone signaling were identified and showed strong association with DEGs in each module. Genes involved in N uptake and assimilation, carbohydrate catabolism, amino acid metabolism, and fatty acid biosynthesis were enriched between the two genotypes under N deprivation. In addition, photosynthesis and carbon assimilation declined under prolonged N stress, but starch biosynthesis was enhanced by N deprivation. Our results revealed N-responsive genes and gene networks and expanded the knowledge of regulatory hubs in N-deprived rapeseed. The detailed gene information might assist the genetic improvement of NUE in B. napus.

Rice NIN-LIKE PROTEIN 4 plays a pivotal role in nitrogen use efficiency.

SummaryNitrogen (N) is one of the key essential macronutrients that affects rice growth and yield. Inorganic N fertilizers are excessively used to boost yield and generate serious collateral environmental pollution. Therefore, improving crop N use efficiency (NUE) is highly desirable and has been a major endeavour in crop improvement. However, only a few regulators have been identified that can be used to improve NUE in rice to date. Here we show that the rice NIN‐like protein 4 (OsNLP4) significantly improves the rice NUE and yield. Field trials consistently showed that loss‐of‐OsNLP4 dramatically reduced yield and NUE compared with wild type under different N regimes. In contrast, the OsNLP4 overexpression lines remarkably increased yield by 30% and NUE by 47% under moderate N level compared with wild type. Transcriptomic analyses revealed that OsNLP4 orchestrates the expression of a majority of known N uptake, assimilation and signalling genes by directly binding to the nitrate‐responsive cis‐element in their promoters to regulate their expression. Moreover, overexpression of OsNLP4 can recover the phenotype of Arabidopsis nlp7 mutant and enhance its biomass. Our results demonstrate that OsNLP4 plays a pivotal role in rice NUE and sheds light on crop NUE improvement.

Environmental losses and driving forces of nitrogen flow in two agricultural towns of Hebei province during 1997–2017

Excessive nitrogen (N) losses from food production and consumption have resulted in noticeable environmental impacts, e.g., air pollution and climate change, saturation of soil N, and water eutrophication. In the present study, a rural-scale N flow model was constructed in Quzhou county, Hebei province to investigate the characteristics of the N flux, N use efficiency (NUE), and N loss and their driving factors in the food production and consumption system during 1997–2017. Our results show that the N fluxes of the crop-production subsystem (CPS), the livestock-breeding subsystem (LBS), and the household-consumption subsystem (HCS) all followed an upward trend. During 1997–2017, the N losses from the system were high (51.38%), and the CPS was a major source. When the N fertilizer application level was optimal (403–475 kg N ha−1), the NUE in the CPS (NUEc) decreased sharply, resulting in a higher N cost than that observed at larger scales. For the LBS, the NUE of animal feed (NUEa) was high (46.37%); however, the waste utilization rate of the HCS was below 30%. The chemical fertilizer application level, feed input, animal-food demand, and livestock manure application level were closely related to the environmental N losses. Due to the lack of reasonable N treatment and utilization methods, the increasing N losses are expected to have a large future impact on environmental issues such as haze, soil acidification, and frequent algal blooms. Therefore, adjusting N management in the processes of food production and consumption is of great significance to the improvement of global NUE and reduction of environmental pollution.

Proteolysis and nitrogen: emerging insights.

Nitrogen (N) is a core component of fertilizers used in modern agriculture to increase yields and thus to help feed a growing global population. However, this comes at a cost to the environment, through run-off of excess N as a result of poor N-use efficiency (NUE) by crops. An obvious remedy to this problem would therefore be the improvement of NUE, which requires advancing our understanding on N homeostasis, sensing, and uptake. Proteolytic pathways are linked to N homeostasis as they recycle proteins that contain N and carbon; however, emerging data suggest that their functions extend beyond this simple recycling. Here, we highlight roles of proteolytic pathways in non-symbiotic and symbiotic N uptake and in systemic N sensing. We also offer a novel view in which we suggest that proteolytic pathways have roles in N homeostasis that differ from their accepted function in recycling.

Integrated physiologic, genomic and transcriptomic strategies involving the adaptation of allotetraploid rapeseed to nitrogen limitation

BackgroundNitrogen (N) is a macronutrient that is essential for optimal plant growth and seed yield. Allotetraploid rapeseed (AnAnCnCn, 2n = 4x = 38) has a higher requirement for N fertilizers whereas exhibiting a lower N use efficiency (NUE) than cereal crops. N limitation adaptation (NLA) is pivotal for enhancing crop NUE and reducing N fertilizer use in yield production. Therefore, revealing the genetic and molecular mechanisms underlying NLA is urgent for the genetic improvement of NUE in rapeseed and other crop species with complex genomes.ResultsIn this study, we integrated physiologic, genomic and transcriptomic analyses to comprehensively characterize the adaptive strategies of oilseed rape to N limitation stresses. Under N limitations, we detected accumulated anthocyanin, reduced nitrate (NO3−) and total N concentrations, and enhanced glutamine synthetase activity in the N-starved rapeseed plants. High-throughput transcriptomics revealed that the pathways associated with N metabolism and carbon fixation were highly over-represented. The expression of the genes that were involved in efficient N uptake, translocation, remobilization and assimilation was significantly altered. Genome-wide identification and molecular characterization of the microR827-NLA1-NRT1.7 regulatory circuit indicated the crucial role of the ubiquitin-mediated post-translational pathway in the regulation of rapeseed NLA. Transcriptional analysis of the module genes revealed their significant functional divergence in response to N limitations between allotetraploid rapeseed and the model Arabidopsis. Association analysis in a rapeseed panel comprising 102 genotypes revealed that BnaC5.NLA1 expression was closely correlated with the rapeseed low-N tolerance.ConclusionsWe identified the physiologic and genome-wide transcriptional responses of oilseed rape to N limitation stresses, and characterized the global members of the BnamiR827-BnaNLA1s-BnaNRT1.7s regulatory circuit. The transcriptomics-assisted gene co-expression network analysis accelerates the rapid identification of central members within large gene families of plant species with complex genomes. These findings would enhance our comprehensive understanding of the physiologic responses, genomic adaptation and transcriptomic alterations of oilseed rape to N limitations and provide central gene resources for the genetic improvement of crop NLA and NUE.

Integrated genomic and transcriptomic insights into the two-component high-affinity nitrate transporters in allotetraploid rapeseed

The two-component high-affinity nitrate (NO3-) transport system (THATS) proteins (NRT2/NAR2) play key roles in the efficient nitrogen (N) uptake and transport under N limitations. We aimed at uncovering the core THATS gene(s) regulating N use efficiency (NUE) in allotetraploid rapeseed (Brassica napus L.). Genomic information, high-throughput transcriptome sequencing and gene co-expression network were integrated to identify and characterize the core THATS genes. We identified 17 BnaNRT2 and eight BnaNAR2.1 homologs spanning across the rapeseed genome. Copy number and gene presence/absence variations of BnaNRT2s/BnaNAR2.1 s, undergoing strong purifying selection, occurred. The over-representation of Dof, MYB and WRKY cis-regulatory elements and the enrichment of CpG islands, and protein phosphorylation sites indicated the importance of transcriptional and epigenetic regulation in the BnaNRT2 activities, respectively. qRT-PCR assays and high-throughput RNA-seq revealed that both BnaNRT2s and BnaNAR2.1 s were expressed preferentially in the roots; and they showed significantly differential expression under different N forms or different levels of NO3- supply. A gene co-expression network identified BnaC8.NRT2.1a and BnaC2.NAR2.1 as the core THATS genes. The core THATS members can serve as elite gene resources for crop NUE improvement. The transcriptomics-assisted gene co-expression network analysis provides novel insights regarding the rapid identification of central members within large gene families of plant species with complex genomes.

Rapid Generation of Barley Mutant Lines With High Nitrogen Uptake Efficiency by Microspore Mutagenesis and Field Screening.

In vitro mutagenesis via isolated microspore culture provides an efficient way to produce numerous double haploid (DH) lines with mutation introduction and homozygosity stabilization, which can be used for screening directly. In this study, 356 DH lines were produced from the malt barley (Hordeum vulgare L.) cultivar Hua-30 via microspore mutagenic treatment with ethyl methane sulfonate or pingyangmycin during in vitro culture. The lines were subjected to field screening under high nitrogen (HN) and low nitrogen (LN) conditions, and the number of productive tillers was used as the main screening index. Five mutant lines (A1-28, A1-84, A1-226, A16-11, and A9-29) with high numbers of productive tillers were obtained over three consecutive years of screening. In the fifth year, components related to N-use efficiency (NUE), including N accumulation, utilization, and translocation, were characterized for these lines based on N uptake efficiency (NUpE), N utilization efficiency (NUtE), and N translocation efficiency (NTE). The results show that the NUpE of four mutant lines (A1-84, A1-226, A9-29, and A16-11) improved significantly under HN, whereas that of two lines (A1-84 and A9-29) improved under LN. As a result, their NUE improved greatly. No improvement in NUtE was observed in any of the five mutant lines. A1-84 and A9-29 were selected as an enhanced genotype in N uptake, and A1-28 showed improved NTE at the grain-filling stage. Our results imply that high-NUpE mutants can be produced through microspore mutagenesis and field screening, and that improvement of NUE in barley depends on enhancement of N uptake.

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 N2 O, totaling 84kg N/ha); (ii) UI in rice-paddy systems (n=100), with 9% yield increase, 29% NUE improvement, and 41% N-loss reduction (16kg 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.

Identification of QTL Associated with Nitrogen Uptake and Nitrogen Use Efficiency Using High Throughput Genotyped CSSLs in Rice (Oryza sativa L.).

Nitrogen (N) availability is a major factor limiting crop growth and development. Identification of quantitative trait loci (QTL) for N uptake (NUP) and N use efficiency (NUE) can provide useful information regarding the genetic basis of these traits and their associated effects on yield production. In this study, a set of high throughput genotyped chromosome segment substitution lines (CSSLs) derived from a cross between recipient 9311 and donor Nipponbare were used to identify QTL for rice NUP and NUE. Using high throughput sequencing, each CSSL were genotyped and an ultra-high-quality physical map was constructed. A total of 13 QTL, seven for NUP and six for NUE, were identified in plants under hydroponic culture with all nutrients supplied in sufficient quantities. The proportion of phenotypic variation explained by these QTL for NUP and NUE ranged from 3.16–13.99% and 3.76–12.34%, respectively. We also identified several QTL for biomass yield (BY) and grain yield (GY), which were responsible for 3.21–45.54% and 6.28–7.31%, respectively, of observed phenotypic variation. GY were significantly positively correlated with NUP and NUE, with NUP more closely correlated than NUE. Our results contribute information to NUP and NUE improvement in rice.