The challenge of improving nitrogen use efficiency in crop plants: towards a more central role for genetic variability and quantitative genetics within integrated approaches

Raising yield potential of wheat. III. Optimizing partitioning to grain while maintaining lodging resistance

A substantial increase in grain yield potential is required, along with better use of water and fertilizer, to ensure food security and environmental protection in future decades. For improvements in photosynthetic capacity to result in additional wheat yield, extra assimilates must be partitioned to developing spikes and grains and/or potential grain weight increased to accommodate the extra assimilates. At the same time, improvement in dry matter partitioning to spikes should ensure that it does not increase stem or root lodging. It is therefore crucial that improvements in structural and reproductive aspects of growth accompany increases in photosynthesis to enhance the net agronomic benefits of genetic modifications. In this article, six complementary approaches are proposed, namely: (i) optimizing developmental pattern to maximize spike fertility and grain number, (ii) optimizing spike growth to maximize grain number and dry matter harvest index, (iii) improving spike fertility through desensitizing floret abortion to environmental cues, (iv) improving potential grain size and grain filling, and (v) improving lodging resistance. Since many of the traits tackled in these approaches interact strongly, an integrative modelling approach is also proposed, to (vi) identify any trade-offs between key traits, hence to define target ideotypes in quantitative terms. The potential for genetic dissection of key traits via quantitative trait loci analysis is discussed for the efficient deployment of existing variation in breeding programmes. These proposals should maximize returns in food production from investments in increased crop biomass by increasing spike fertility, grain number per unit area and harvest index whilst optimizing the trade-offs with potential grain weight and lodging resistance.

Loci controlling nitrate reductase activity in maize: ultraviolet-B signaling in aerial tissues increases nitrate reductase activity in leaf and root when responsive alleles are present

Environmental factors, such as ultraviolet-B (UV-B) irradiation, have the ability to affect pathways such as nitrogen metabolism. As fixed nitrogen is the keystone mineral nutrient that controls grain crop yield, any alteration in this cycle can be detrimental to plant productivity. Nitrate reductase enzyme activity is responsible for the reduction of nitrate to nitrite, and nitrate is the major form of nitrogen assimilated in plants. In maize (Zea mays L.) production, nitrate assimilation kinetics are important for both high- and low-input agricultural systems. Nitrate reductase protein activity is controlled by phosphatases and kinases. Nitrate reductase activity is responsive to environmental signals such as light-dark cycles and UV-B radiation, although the regulatory controls are not yet fully understood. We have determined the location of maize genetic factors that control nitrate reductase activity and the extent of contribution of each of these factors, both locally in the leaf tissue and via long-distance signaling loci that affect root nitrate reductase activity upon leaf UV irradiation. In the IBM94 recombinant inbred mapping population, the loci controlling regulation of nitrate reductase activity under UV-B map to different positions than the loci controlling nitrate reductase activity in unexposed plants.

Analysis of amino acid metabolism in the ear of maize mutants deficient in two cytosolic glutamine synthetase isoenzymes highlights the importance of asparagine for nitrogen translocation within sink organs

Nitrogen (N) metabolism was characterized in the developing ear of glutamine synthetase deficient mutants (gln1-3, gln1-4 and gln1-3/gln1-4) of maize exhibiting a reduction in kernel yield. During the grain-filling period, the metabolite contents, enzyme activities and steady-state levels of transcripts for marker genes of amino acid synthesis and interconversion were monitored in the cob and kernels. The ear of gln1-3 and gln1-3/gln1-4 had a higher free amino acid content and a lower C/N ratio, when compared to the wild type. The free ammonium concentrations were also much higher in gln1-3/gln1-4, and Asn accumulation was higher in gln1-3 and gln1-3/gln1-4. The level of transcripts of ZmAS3 and ZmAS4, two genes encoding asparagine synthetase, increased in the 'aborted kernels' of gln1-3 and gln1-3/gln1-4. The results show that N metabolism is clearly different in developing and 'aborted kernels'. The data support the hypothesis that N accumulated in 'aborted kernels' is remobilized via the cob to developing kernels using Asn as a transport molecule. The two genes ZmAS3 and ZmAS4 are likely to play an important role during this process.

Altered xylem-phloem transfer of amino acids affects metabolism and leads to increased seed yield and oil content in Arabidopsis

Seed development and nitrogen (N) storage depend on delivery of amino acids to seed sinks. For efficient translocation to seeds, amino acids are loaded into the phloem in source leaves and along the long distance transport pathway through xylem-phloem transfer. We demonstrate that Arabidopsis thaliana AMINO ACID PERMEASE2 (AAP2) localizes to the phloem throughout the plant. AAP2 T-DNA insertion lines showed changes in source-sink translocation of amino acids and a decrease in the amount of seed total N and storage proteins, supporting AAP2 function in phloem loading and amino acid distribution to the embryo. Interestingly, in aap2 seeds, total carbon (C) levels were unchanged, while fatty acid levels were elevated. Moreover, branch and silique numbers per plant and seed yield were strongly increased. This suggests changes in N and C delivery to sinks and subsequent modulations of sink development and seed metabolism. This is supported by tracer experiments, expression studies of genes of N/C transport and metabolism in source and sink, and by phenotypic and metabolite analyses of aap2 plants. Thus, AAP2 is key for xylem to phloem transfer and sink N and C supply; moreover, modifications of N allocation can positively affect C assimilation and source-sink transport and benefit sink development and oil yield.

Optimizing root system architecture in biofuel crops for sustainable energy production and soil carbon sequestration

Root system architecture (RSA) describes the dynamic spatial configuration of different types and ages of roots in a plant, which allows adaptation to different environments. Modifications in RSA enhance agronomic traits in crops and have been implicated in soil organic carbon content. Together, these fundamental properties of RSA contribute to the net carbon balance and overall sustainability of biofuels. In this article, we will review recent data supporting carbon sequestration by biofuel crops, highlight current progress in studying RSA, and discuss future opportunities for optimizing RSA for biofuel production and soil carbon sequestration.

Unraveling new genes associated with seed development and metabolism in Bixa orellana L. by expressed sequence tag (EST) analysis

The tropical tree Bixa orellana L. produces a range of secondary metabolites which biochemical and molecular biosynthesis basis are not well understood. In this work we have characterized a set of ESTs from a non-normalized cDNA library of B. orellana seeds to obtain information about the main developmental and metabolic processes taking place in developing seeds and their associated genes. After sequencing a set of randomly selected clones, most of the sequences were assigned with putative functions based on similarity, GO annotations and protein domains. The most abundant transcripts encoded proteins associated with cell wall (prolyl 4-hydroxylase), fatty acid (acyl carrier protein), and hormone/flavonoid (2OG-Fe oxygenase) synthesis, germination (MADS FLC-like protein) and embryo development (AP2/ERF transcription factor) regulation, photosynthesis (chlorophyll a-b binding protein), cell elongation (MAP65-1a), and stress responses (metallothionein- and thaumatin-like proteins). Enzymes were assigned to 16 different metabolic pathways related to both primary and secondary metabolisms. Characterization of two candidate genes of the bixin biosynthetic pathway, BoCCD and BoOMT, showed that they belong, respectively, to the carotenoid-cleavage dioxygenase 4 (CCD4) and caffeic acid O-methyltransferase (COMT) families, and are up-regulated during seed development. It indicates their involvement in the synthesis of this commercially important carotenoid pigment in seeds of B. orellana. Most of the genes identified here are the first representatives of their gene families in B. orellana.

Nitrogen uptake, assimilation and remobilization in plants: challenges for sustainable and productive agriculture

BACKGROUND

Productive agriculture needs a large amount of expensive nitrogenous fertilizers. Improving nitrogen use efficiency (NUE) of crop plants is thus of key importance. NUE definitions differ depending on whether plants are cultivated to produce biomass or grain yields. However, for most plant species, NUE mainly depends on how plants extract inorganic nitrogen from the soil, assimilate nitrate and ammonium, and recycle organic nitrogen. Efforts have been made to study the genetic basis as well as the biochemical and enzymatic mechanisms involved in nitrogen uptake, assimilation, and remobilization in crops and model plants. The detection of the limiting factors that could be manipulated to increase NUE is the major goal of such research.

SCOPE

An overall examination of the physiological, metabolic, and genetic aspects of nitrogen uptake, assimilation and remobilization is presented in this review. The enzymes and regulatory processes manipulated to improve NUE components are presented. Results obtained from natural variation and quantitative trait loci studies are also discussed.

CONCLUSIONS

This review presents the complexity of NUE and supports the idea that the integration of the numerous data coming from transcriptome studies, functional genomics, quantitative genetics, ecophysiology and soil science into explanatory models of whole-plant behaviour will be promising.

Nitrogen use efficiencies of spring barley grown under varying nitrogen conditions in the field and growth chamber

BACKGROUND AND AIMS

Nitrogen-use efficiency (NUE) of cereals needs to be improved by nitrogen (N) management, traditional plant breeding methods and/or biotechnology, while maintaining or, optimally, increasing crop yields. The aims of this study were to compare spring-barley genotypes grown on different nitrogen levels in field and growth-chamber conditions to determine the effects on N uptake (NUpE) and N utilization efficiency (NUtE) and ultimately, NUE.

METHODS

Morphological characteristics, seed yield and metabolite levels of 12 spring barley (Hordeum vulgare) genotypes were compared when grown at high and low nitrogen levels in field conditions during the 2007 and 2008 Canadian growing seasons, and in potted and hydroponic growth-chamber conditions. Genotypic NUpE, NUtE and NUE were calculated and compared between field and growth-chamber environments.

KEY RESULTS

Growth chamber and field tests generally showed consistent NUE characteristics. In the field, Vivar, Excel and Ponoka, showed high NUE phenotypes across years and N levels. Vivar also had high NUE in growth-chamber trials, showing NUE across complex to simplistic growth environments. With the high NUE genotypes grown at low N in the field, NUtE predominates over NUpE. N metabolism-associated amino acid levels were different between roots (elevated glutamine) and shoots (elevated glutamate and alanine) of hydroponically grown genotypes. In field trials, metabolite levels were different between Kasota grown at high N (elevated glutamine) and Kasota at low N plus Vivar at either N condition.

CONCLUSIONS

Determining which trait(s) or gene(s) to target to improve barley NUE is important and can be facilitated using simplified growth approaches to help determine the NUE phenotype of various genotypes. The genotypes studied showed similar growth and NUE characteristics across field and growth-chamber tests demonstrating that simplified, low-variable growth environments can help pinpoint genetic targets for improving spring barley NUE.

Plant nutrition for sustainable development and global health

BACKGROUND

Plants require at least 14 mineral elements for their nutrition. These include the macronutrients nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg) and sulphur (S) and the micronutrients chlorine (Cl), boron (B), iron (Fe), manganese (Mn), copper (Cu), zinc (Zn), nickel (Ni) and molybdenum (Mo). These are generally obtained from the soil. Crop production is often limited by low phytoavailability of essential mineral elements and/or the presence of excessive concentrations of potentially toxic mineral elements, such as sodium (Na), Cl, B, Fe, Mn and aluminium (Al), in the soil solution.

SCOPE

This article provides the context for a Special Issue of the Annals of Botany on 'Plant Nutrition for Sustainable Development and Global Health'. It provides an introduction to plant mineral nutrition and explains how mineral elements are taken up by roots and distributed within plants. It introduces the concept of the ionome (the elemental composition of a subcellular structure, cell, tissue or organism), and observes that the activities of key transport proteins determine species-specific, tissue and cellular ionomes. It then describes how current research is addressing the problems of mineral toxicities in agricultural soils to provide food security and the optimization of fertilizer applications for economic and environmental sustainability. It concludes with a perspective on how agriculture can produce edible crops that contribute sufficient mineral elements for adequate animal and human nutrition.

Differences in the triticale (X Triticosecale Wittmack) flag leaf 2-DE protein profile between varieties and nitrogen fertilization levels

Nitrogen nutrition is one of the major factors limiting the growth and production of crop plants. Limited information on proteome changes occurring in response to nitrogen amount have been available up to now. We used 2-DE to investigate proteome differences between two triticale varieties and the changes caused by nitrogen nutrition deficit in the flag leaf tissue. Some physiological features, such as the number of tillers per plant, SPAD index, dry weight, and protein content were measured previous to the proteomic analysis. Statistical analysis identified 29 differential protein spots in the selected pairwise comparisons of experimental conditions and correlated with the expression cluster revealed by the principal component analysis. The 29 protein spots were subjected to matrix-assisted laser desorption ionization time of flight (MALDI-TOF) to deduce their possible functions. Many of these changes referred to enzymes involved in photosynthesis, metabolic pathways implicated in the balance of the energy, and redox status of the cell. This work provides a first characterization of the proteome changes that occur in response to nitrogen deficit in flag leaves of triticale plants.

Natural variation of nitrate uptake and nitrogen use efficiency in Arabidopsis thaliana cultivated with limiting and ample nitrogen supply

Eighteen accessions of Arabidopsis thaliana were grown with low (N-) and high (N+) nitrogen supply. N uptake was monitored by feeding plants with 15N-enriched nutritive solution over 24 h. Biomass [fresh matter (FM) and dry matter (DM)], N concentration (N%), and 15N content were monitored and computed to determine the nitrogen use efficiency (NUE) and nitrogen uptake efficiency (NupE). NUE has been estimated as the ratio between biomass and N concentration (DM/N%) and NupE as the concentration of 15N in plants [microg (g(-1) DM)]. Accession traits were analysed to detect common and individual genotype features. The genetic variation in NUE at high N input was mainly explained by variation in N uptake. Even though plants managed N uptake and N metabolism differently under N+ and N-, NUE was similar in these two conditions, showing that NUE was exclusively genetically determined. Hierarchical classification revealed that the physiological classes arising were similar under N- and N+. Both wasteful and efficient genotypes were detected. Three extreme genotypes, Col-0, Bur-0, and Tsu-0, were noted. Bur-0 and Tsu-0 exhibited high NUE and large biomass. Col-0 showed the reverse: low NUE and low biomass. Bur-0 appeared poorly tolerant of a high N supply. The present data will facilitate the choice of Arabidopsis accessions as parents of recombinant inbred line populations suitable for the mapping of quantitiative trait loci related to NUE, NupE, and N storage capacity.

Barriers and paths to market for genetically engineered crops

Each year, billions of dollars are invested in efforts to improve crops through genetic engineering (GE). These activities have resulted in a surge of publications and patents on technologies and genes: a momentum in basic research that, unfortunately, is not sustained throughout the subsequent phases of product development. After more than two decades of intensive research, the market for transgenic crops is still dominated by applications of just a handful of methods and genes. This discrepancy between research and development reflects difficulties in understanding and overcoming seven main barriers-to-entry: (1) trait efficacy in the field, (2) critical product concepts, (3) freedom-to-operate, (4) industry support, (5) identity preservation and stewardship, (6) regulatory approval and (7) retail and consumer acceptance. In this review, I describe the various roadblocks to market for transgenic crops and also discuss methods and approaches on how to overcome these, especially in the United States.

[Cultivation and environmental impacts of GMO crops]

Transgenic plant varieties are grown since 1996 on surfaces increasing each year. They covered 114 million hectares worldwide in 2007, which shows their success among the farmers in developed as well as developing countries, despite the propaganda campaigns of the environmental movements and advocates of decline. The first transgenic crops (soybean, corn, coton and rapeseed) offer benefits in terms of health, economy and environment. Europe and especially France, which reject this technology, sentence their research to death and penalize their agriculture.

Metabolism and long-distance translocation of cytokinins

During plant development, distantly-located organs must communicate in order to adapt morphological and physiological features in response to environmental inputs. Among the recognized signaling molecules, a class of phytohormones known as the cytokinins functions as both local and long-distance regulatory signals for the coordination of plant development. This cytokinin-dependent communication system consists of orchestrated regulation of the metabolism, translocation, and signal transduction of this phytohormone class. Here, to gain insight into this elaborate signaling system, we summarize current models of biosynthesis, trans-membrane transport, and long-distance translocation of cytokinins in higher plants.

Genetic engineering for modern agriculture: challenges and perspectives

Abiotic stress conditions such as drought, heat, or salinity cause extensive losses to agricultural production worldwide. Progress in generating transgenic crops with enhanced tolerance to abiotic stresses has nevertheless been slow. The complex field environment with its heterogenic conditions, abiotic stress combinations, and global climatic changes are but a few of the challenges facing modern agriculture. A combination of approaches will likely be needed to significantly improve the abiotic stress tolerance of crops in the field. These will include mechanistic understanding and subsequent utilization of stress response and stress acclimation networks, with careful attention to field growth conditions, extensive testing in the laboratory, greenhouse, and the field; the use of innovative approaches that take into consideration the genetic background and physiology of different crops; the use of enzymes and proteins from other organisms; and the integration of QTL mapping and other genetic and breeding tools.

Metabolic profiling of maize mutants deficient for two glutamine synthetase isoenzymes using 1H-NMR-based metabolomics

INTRODUCTION

Maize mutants deficient for the expression of two genes encoding cytosolic glutamine synthetase (GS) isoenzymes GS1.3 and GS1.4 displayed reduced kernel number and kernel size, respectively, the effect of the mutation being cumulative in the double mutant. However, at maturity, shoot biomass production was not modified in all the mutants, indicating that the reaction catalysed by the enzyme is specifically involved in the control of grain yield.

OBJECTIVE

To examine the physiological impact of the GS mutations on the leaf metabolic profile during the kernel filling period, during which nitrogen is remobilized from the shoots to be further exported to the kernels.

METHODOLOGY

An (1)H-NMR spectroscopy metabolomic was applied to the investigation of metabolic change of the gln1.3, gln1.4 and gln1.3/1.4 double mutant.

RESULTS

In the three GS mutants, an increase in the amount of several N-containing metabolites such as asparagine, alanine, threonine and phophatidylcholine was observed whatever the level of nitrogen fertilisation. In addition, we found an accumulation of phenylalanine and tyrosine, two metabolites involved the primary steps of the phenylpropanoid pathway.

CONCLUSION

Changes in the metabolic profile of the GS mutants suggest that, when cytosolic GS activity is strongly reduced, either alternative metabolic pathways participate in the reassimilation of ammonium released during leaf protein remobilization or that premature leaf senescence is induced when kernel set and kernel filling are affected. The accumulation of phenylalanine and tyrosine in the mutant plants indicates that lignin biosynthesis is altered, thus possibly affecting ear development.

Increased nitrogen-use efficiency in transgenic rice plants over-expressing a nitrogen-responsive early nodulin gene identified from rice expression profiling

Development of genetic varieties with improved nitrogen-use efficiency (NUE) is essential for sustainable agriculture. In this study, we developed a growth system for rice wherein N was the growth-limiting factor, and identified N-responsive genes by a whole genome transcriptional profiling approach. Some genes were selected to test their functionality in NUE by a transgenic approach. One such example with positive effects on NUE is an early nodulin gene OsENOD93-1. This OsENOD93-1 gene responded significantly to both N induction and N reduction. Transgenic rice plants over-expressing the OsENOD93-1 gene had increased shoot dry biomass and seed yield. This OsENOD93-1 gene was expressed at high levels in roots of wild-type (WT) plants, and its protein product was localized in mitochondria. Transgenic plants accumulated higher concentrations of total amino acids and total N in roots. A higher concentration of amino acids in xylem sap was detected in transgenic plants, especially under N stress. In situ hybridization revealed that OsENOD93-1 is expressed in vascular bundles, as well as in epidermis and endodermis. This work demonstrates that transcriptional profiling, coupled with a transgenic validation approach, is an effective strategy for gene discovery. The knowledge gained from this study could be applied to other important crops.

Cytokinin-induced changes of nitrogen remobilization and chloroplast ultrastructure in wheat (Triticum aestivum)

Nitrogen (N) remobilization in wheat (Triticum aestivum) plants is crucial because it determines the grain protein concentration and the baking quality of flour. In order to evaluate the influence of cytokinins on N remobilization during N starvation, we analyzed various N remobilization parameters in wheat plants that were watered with 6-benzylaminopurine (BAP) either with or without KNO(3). Besides, the effects of BAP on protein synthesis were evaluated, and the size and ultrastructure of chloroplasts of BAP-treated plants were studied. BAP supply inhibited N remobilization of plants independently of N supply as shown by the increase in protein, Rubisco, chlorophyll, sugar and starch concentrations in the older leaves, the decrease in amino acid and sugar export to the phloem, and the decrease in protein, Rubisco and chlorophyll concentrations in the younger leaves. Besides, BAP supply increased nitrate reductase activity and decreased nitrate concentration, thus suggesting an increased assimilatory capacity. The increase in protein concentration could be explained mainly by a significant decrease in protein degradation and, to a lesser extent, by an increase in protein synthesis. Finally, an increase both in the size of the chloroplast and in the plastoglobuli and starch contents in BAP-supplied plants was observed. We propose that cytokinins retain the sink activity of the older leaves by inhibiting amino acid and sugar export to the phloem and stimulating assimilate accumulation in the chloroplasts of the older leaves. Besides, BAP may increase protein concentration of the older leaves both by decreasing protein degradation and maintaining protein synthesis even under stress conditions.

Nitrogen metabolism in the developing ear of maize (Zea mays): analysis of two lines contrasting in their mode of nitrogen management

*The main steps of nitrogen (N) metabolism were characterized in the developing ear of the two maize (Zea mays) lines F2 and Io, which were previously used to investigate the genetic basis of nitrogen use efficiency (NUE) in relation to yield. *During the grain-filling period, we monitored changes in metabolite content, enzyme activities and steady-state levels of transcripts for marker genes of amino acid synthesis and interconversion in the cob and the kernels. *Under low N fertilization conditions, line Io accumulated glutamine, asparagine and alanine preferentially in the developing kernels, whereas in line F2, glutamine and proline were the predominant amino acids. Quantification of the mRNA-encoding enzymes involved in asparagine, alanine and proline biosynthesis confirmed that the differences observed between the two lines at the physiological level are likely to be attributable to enhanced expression of the cognate genes. *Integrative analysis of physiological and gene expression data indicated that the developing ear of line Io had higher N use and transport capacities than line F2. Thus, in maize there is genetic and environmental control of N metabolism not only in vegetative source organs but also in reproductive sink organs.

Natural variation in Arabidopsis adaptation to growth at low nitrogen conditions

Improving nutrient use efficiency of crop plants, especially at low input, is essential to ensure sustainable food production in the future. In order to address the genetic basis of nutrient use efficiency in a model system, growth of Arabidopsis ecotypes at normal and low nitrogen (N) supply was compared. The ecotypes differed significantly in the extent of growth reduction in limiting conditions. The fresh weight of Shahdara and Ws grown at 1mM nitrate was reduced by 30% compared to control, whereas Col-0 and Ga-0 were almost unaffected. Total N content was reduced in all ecotypes by 10-30%. The capacity to store nitrate correlated with the tolerance to low N; in Shahdara and Ws, but not in Col-0 and Ga-0, nitrate content on low N was significantly reduced compared to control nutrition. The mRNA levels for genes of nitrate uptake and assimilation were only moderately affected by the treatment. The transcript levels of nitrate reductase NIA1 and nitrite reductase were higher in the ecotypes tolerant to low N (Col-0 and Ga-0) with normal N nutrition but on low N they were reduced to a much higher extent than the sensitive ecotypes (Shahdara and Ws). It seems that a higher capacity to keep nitrate reserves at low N, perhaps due to the ability to turn down nitrate reduction rate, is responsible for a better tolerance of Col-0 and Ga-0 to low N supply.

Root based approaches to improving nitrogen use efficiency in plants

In the majority of agricultural growing regions, crop production is highly dependent on the supply of exogenous nitrogen (N) fertilizers. Traditionally, this dependency and the use of N-fertilizers to restore N depleted soils has been rewarded with increased plant health and yields. In recent years, increased competition for non-renewable fossil fuel reserves has directly elevated prices of N-fertilizers and the cost of agricultural production worldwide. Furthermore, N-fertilizer based pollution is becoming a serious issue for many regions where agriculture is highly concentrated. To help minimize the N footprint associated with agricultural production there is significant interest at the plant level to develop technologies which can allow economically viable production while using less applied N. To complement recent reviews examining N utilization efficiency in agricultural plants, this review will explore those strategies operating specifically at the root level, which may directly contribute to improved N use efficiencies in agricultural crops such as cereals, where the majority of N-fertilizers are used and lost to the environment. Root specific phenotypes that will be addressed in the context of improvements to N acquisition and assimilation efficiencies include: root morphology; root to shoot ratios; root vigour, root length density; and root N transport and metabolism.

A quantitative genetic study for elucidating the contribution of glutamine synthetase, glutamate dehydrogenase and other nitrogen-related physiological traits to the agronomic performance of common wheat

To better understand the genetic variability for nitrogen use efficiency in winter wheat is a necessity in the frame of the present economic and ecological context. The objective of this work was to investigate the role of the enzymes glutamine synthetase (GS) and glutamate dehydrogenase (GDH), and other nitrogen (N)-related physiological traits in the control of agronomic performance in wheat. A quantitative genetics approach was developed using the Arche x Récital population of doubled haploid lines grown for 3 years in the field. GS and GDH activities, ammonium, amino acid and protein contents were measured at different stages of plant development in different organs after flowering. Significant genotypic effects were observed for all measured physiological and agronomical traits. Heading date was negatively correlated with ammonium, amino acid, protein contents and GS activity in the flag leaf lamina. Grain protein content was positively correlated with both ammonium and amino acid content, and to a lesser extent with soluble protein content and GS activity. A total of 148 quantitative trait loci (QTLs) were detected, 104 QTLs for physiological traits and 44 QTLs for agronomic traits. Twenty-six QTLs were detected for GDH activity spread over 13 chromosomes and 25 QTLs for GS activity spread over 12 chromosomes. We found only a co-localization between a QTL for GS activity and GSe, a structural gene encoding cytosolic GS on chromosome 4B. A coincidence between a QTL for GDH activity and a gene encoding GDH was also found on chromosome 2B. QTL regions combining both physiological and agronomical QTLs were mainly identified on linkage groups 2A, 2B, 2D, 5A, 5B and 5D. This approach allowed us to propose possible functions of physiological traits to explain the variation observed for agronomic traits including yield and its components.

Transcriptome analysis of nitrogen-efficient rice over-expressing alanine aminotransferase

Crop plants require nitrogen for key macromolecules, such as DNA, proteins and metabolites, yet they are generally inefficient at acquiring nitrogen from the soil. Crop producers compensate for this low nitrogen utilization efficiency by applying nitrogen fertilizers. However, much of this nitrogen is unavailable to the plants as a result of microbial uptake and environmental loss of nitrogen, causing air, water and soil pollution. We engineered rice over-expressing alanine aminotransferase (AlaAT) under the control of a tissue-specific promoter that showed a strong nitrogen use efficiency phenotype. In this study, we examined the transcriptome response in roots and shoots to the over-expression of AlaAT to provide insights into the nitrogen-use-efficient phenotype of these plants. Transgenic and control rice plants were grown hydroponically and the root and shoot gene expression profiles were analysed using Affymetrix Rice GeneChip microarrays. Transcriptome analysis revealed that there was little impact on the transgenic transcriptome compared with controls, with 0.11% and 0.07% differentially regulated genes in roots and shoots, respectively. The most up-regulated transcripts, a glycine-rich cell wall (GRP) gene and a gene encoding a hypothetical protein (Os8823), were expressed in roots. Another transgenic root-specific up-regulated gene was leucine rich repeat (LRR). Genes induced in the transgenic shoots included GRP, LRR, acireductone dioxygenase (OsARD), SNF2 ATP-translocase and a putative leucine zipper transcription factor. This study provides a genome-wide view of the response to AlaAT over-expression, and elucidates some of the genes that may play a role in the nitrogen-use-efficient phenotype.

Phospholipase D epsilon and phosphatidic acid enhance Arabidopsis nitrogen signaling and growth

Activation of phospholipase D (PLD) produces phosphatidic acid (PA), a lipid messenger implicated in cell growth and proliferation, but direct evidence for PLD and PA promotion of growth at the organism level is lacking. Here we characterize a new PLD gene, PLD epsilon, and show that it plays a role in promoting Arabidopsis growth. PLD epsilon is mainly associated with the plasma membrane, and is the most permissive of all PLDs tested with respect to its activity requirements. Knockout (KO) of PLD epsilon decreases root growth and biomass accumulation, whereas over-expression (OE) of PLD epsilon enhances root growth and biomass accumulation. The level of PA was higher in OE plants, but lower in KO plants than in wild-type plants, and suppression of PLD-mediated PA formation by alcohol alleviated the growth-promoting effect of PLD epsilon. OE and KO of PLD epsilon had opposite effects on lateral root elongation in response to nitrogen. Increased expression of PLD epsilon also promoted root hair elongation and primary root growth under severe nitrogen deprivation. The results suggest that PLD epsilon and PA promote organism growth and play a role in nitrogen signaling. The lipid-signaling process may play a role in connecting membrane sensing of nutrient status to increased plant growth and biomass production.

Regulation of glutamine synthetase 1 and amino acids transport in the phloem of young wheat plants

The possible regulation of amino acid remobilization via the phloem in wheat (Triticum aestivum L.) by the primary enzyme in nitrogen (N) assimilation and re-assimilation, glutamine synthetase (GS, E.C. 6.3.1.2) was studied using two conditions known to alter N phloem transport, N deficiency and cytokinins. The plants were grown for 15 days in controlled conditions with optimum N supply and then N was depleted from and/or 6-benzylaminopurine was added to the nutrient solution. Both treatments generated an induction of GS1, monitored at the level of gene expression, protein accumulation and enzyme activity, and a decrease in the exudation of amino acids to the phloem, obtained with EDTA technique, which correlated negatively. GS inhibition by metionine sulfoximide (MSX) produced an increase of amino acids exudation and the inhibitor successfully reversed the effect of N deficiency and cytokinin addition over phloem exudation. Our results point to an important physiological role for GS1 in the modulation of amino acids export levels in wheat plants.

Overexpressed glutamine synthetase gene modifies nitrogen metabolism and abiotic stress responses in rice

Glutamine synthetase (GS; EC 6.3.1.2) is a key enzyme in nitrogen metabolism; it catalyzes the critical incorporation of inorganic ammonium into glutamine. Two full-length cDNAs that encode the rice (Oryza sativa) cytosolic glutamine synthetase1 genes (OsGS1;1 and OsGS1;2) were isolated from a Minghui 63 normalized cDNA library, and glnA encoding GS in Escherichia coli was isolated by PCR amplification. Transformants for GS gene (GS1;1, GS1;2, and glnA) in rice were produced by an Agrobacterium tumefaciens-mediated transformation method, and transcripts of GS gene accumulated at higher levels in the primary transgenic plants. Our results indicated an increased metabolic level in GS-overexpressed plants, which showed higher total GS activities and soluble protein concentrations in leaves and higher total amino acids and total nitrogen content in the whole plant. Decreases in both grain yield production and total amino acids were observed in seeds of GS-overexpressed plants compared with wild-type plants. In addition, GS1;2-overexpressed plants exhibited resistance to Basta selection and higher sensitivity to salt, drought, and cold stress conditions, whereas the other two types of GS-overexpressed plants failed to show any significant changes for these stress conditions compared with wild-type plants.

Adjustment of growth and central metabolism to a mild but sustained nitrogen-limitation in Arabidopsis

We have established a simple soil-based experimental system that allows a small and sustained restriction of growth of Arabidopsis by low nitrogen (N). Plants were grown in a large volume of a peat-vermiculite mix that contained very low levels of inorganic N. As a control, inorganic N was added in solid form to the peat-vermiculite mix, or plants were grown in conventional nutrient-rich solids. The low N growth regime led to a sustained 20% decrease of the relative growth rate over a period of 2 weeks, resulting in a two- to threefold decrease in biomass in 35- to 40-day-old plants. Plants in the low N regime contained lower levels of nitrate, lower nitrate reductase activity, lower levels of malate, fumarate and other organic acids and slightly higher levels of starch, as expected from published studies of N-limited plants. However, their rosette protein content was unaltered, and total and many individual amino acid levels increased compared with N-replete plants. This metabolic phenotype reveals that Arabidopsis responds adaptively to low N by decreasing the rate of growth, while maintaining the overall protein content, and maintaining or even increasing the levels of many amino acids.

Water and nitrogen conditions affect the relationships of Delta13C and Delta18O to gas exchange and growth in durum wheat

Whereas the effects of water and nitrogen (N) on plant Delta(13)C have been reported previously, these factors have scarcely been studied for Delta(18)O. Here the combined effect of different water and N regimes on Delta(13)C, Delta(18)O, gas exchange, water-use efficiency (WUE), and growth of four genotypes of durum wheat [Triticum turgidum L. ssp. durum (Desf.) Husn.] cultured in pots was studied. Water and N supply significantly increased plant growth. However, a reduction in water supply did not lead to a significant decrease in gas exchange parameters, and consequently Delta(13)C was only slightly modified by water input. Conversely, N fertilizer significantly decreased Delta(13)C. On the other hand, water supply decreased Delta(18)O values, whereas N did not affect this parameter. Delta(18)O variation was mainly determined by the amount of transpired water throughout plant growth (T(cum)), whereas Delta(13)C variation was explained in part by a combination of leaf N and stomatal conductance (g(s)). Even though the four genotypes showed significant differences in cumulative transpiration rates and biomass, this was not translated into significant differences in Delta(18)O(s). However, genotypic differences in Delta(13)C were observed. Moreover, approximately 80% of the variation in biomass across growing conditions and genotypes was explained by a combination of both isotopes, with Delta(18)O alone accounting for approximately 50%. This illustrates the usefulness of combining Delta(18)O and Delta(13)C in order to assess differences in plant growth and total transpiration, and also to provide a time-integrated record of the photosynthetic and evaporative performance of the plant during the course of crop growth.

Analysing nitrogen responses of cereals to prioritize routes to the improvement of nitrogen use efficiency

The efficient use of fertilizer nitrogen (N) is crucial to sustainable human nutrition. All crops receive significant amounts of additional N in temperate environments, through fixation or fertilizer use. This paper reviews progress towards the efficient use of fertilizer N by winter wheat (Triticum aesitivum L.) and spring barley (Hordeum vulgare L.) in the UK, acknowledging that on-farm this is governed by economics. Recent multi-site N response experiments on old and modern varieties show that yield improvements since the 1980s have been accompanied by increases in economic optimum N amounts for wheat but not for spring barley. On-farm N use efficiency (NUE) has increased for barley because increased yields with optimum N were associated with compensatory decreases in grain N concentration, whereas on-farm NUE has not increased for wheat because grain N concentration has not changed and improvements in N capture were insufficient to make up for the increased yield. Genetic effects on NUE are shown to differ markedly depending on whether they are determined at a single N rate, as in variety trials, or with optimum N amounts. It is suggested that, in order to elicit faster improvement in NUE on farms, breeding and variety testing should be conducted at some sites with more than one level of applied N, and that grain N%, N harvest index, and perhaps canopy N ratio (kg N ha(-1) green area) should be measured more widely. It is also suggested that, instead of using empirical functions, N responses might be analysed more effectively using functions based on explanations of yield determination for which the parameters have some physiological meaning.

Is it good noise? The role of developmental instability in the shaping of a root system

Root architecture plays a major part in determining a root system's ability to function effectively and efficiently in its essential roles of anchorage and the capture of soil resources. The characteristics of root development that are conventionally considered to be the main determinants of root architecture are the rate, angle, and duration of root growth and the pattern of root branching. In this review, the case is made that there is an additional trait that has been largely ignored but which has a significant influence on root architecture, namely the degree to which stochasticity (or 'developmental instability') affects the developmental process. Although the intrinsic variability in the development and growth of lateral roots has been recognized for some time, in almost every study of root development this remarkable facet of root behaviour tends to be hidden beneath the veil of statistical averaging. Progress in other fields is providing intriguing insights into the phenomenon of developmental instability, how it is generated at the molecular and cellular levels and the genetic mechanisms by which it is buffered. This review will consider the existence of developmental instability in roots, its underlying causes, its effects on root architecture, and the evidence that it is under genetic control. The hypothesis will be advanced that developmental instability in roots is an adaptive trait, and its potential relevance to root function will be discussed in both an ecological and an agronomic context.

The importance of cytosolic glutamine synthetase in nitrogen assimilation and recycling

Glutamine synthetase assimilates ammonium into amino acids, thus it is a key enzyme for nitrogen metabolism. The cytosolic isoenzymes of glutamine synthetase assimilate ammonium derived from primary nitrogen uptake and from various internal nitrogen recycling pathways. In this way, cytosolic glutamine synthetase is crucial for the remobilization of protein-derived nitrogen. Cytosolic glutamine synthetase is encoded by a small family of genes that are well conserved across plant species. Members of the cytosolic glutamine synthetase gene family are regulated in response to plant nitrogen status, as well as to environmental cues, such as nitrogen availability and biotic/abiotic stresses. The complex regulation of cytosolic glutamine synthetase at the transcriptional to post-translational levels is key to the establishment of a specific physiological role for each isoenzyme. The diverse physiological roles of cytosolic glutamine synthetase isoenzymes are important in relation to current agricultural and ecological issues.

Effects of an alfalfa protein hydrolysate on the gene expression and activity of enzymes of the tricarboxylic acid (TCA) cycle and nitrogen metabolism in Zea mays L

The effects through which an alfalfa protein hydrolysate (EM) possessing gibberellin- and auxin-like activity may promote plant nitrogen (N) nutrition have been investigated in Zea mays L. Treatment with 0.01 or 0.1 mg L(-1) EM for 48 h resulted in enhanced plant growth and leaf sugar accumulation. Concomitantly, the level of nitrates decreased, whereas total N percentage was unchanged. The activity of a number of enzymes involved in carbon (C) metabolism (malate dehydrogenase, MDH; isocitrate dehydrogenase, IDH; citrate synthase, CS) and N reduction and assimilation (nitrate reductase, NR; nitrite reductase, NiR; glutamine synthetase, GS; glutamate synthase, GOGAT; aspartate aminotransferase, AspAT) was significantly induced by EM supply to plants, and the transcription pattern of MDH, IDH, CS, and NR strongly correlated with data of enzyme activity. The transcript accumulation of asparagine synthetase (AS) was also induced by EM in the roots. The results suggest that EM might promote nitrogen assimilation in plants through a coordinate regulation of C and N metabolic pathways and open the way for further research on protein hydrolysates as a valid tool to improve N use efficiency and, as a consequence, to reduce the intensive use of inorganic N fertilizers in agriculture.

Leaf senescence and nutrient remobilisation in barley and wheat

Extensive studies have been undertaken on senescence processes in barley and wheat and their importance for the nitrogen use efficiency of these crop plants. During the senescence processes, proteins are degraded and nutrients are re-mobilised from senescing leaves to other organs, especially the developing grain. Most of the proteins degraded reside in the chloroplasts, with Rubisco constituting the most dominant protein fraction. Despite intensive studies, the proteases responsible for Rubisco degradation have not yet been identified. Evidence for degradation of stromal proteins outside of chloroplasts is summarised. Rubisco is thought to be released from chloroplasts into vesicles containing stroma material (RCB = Rubisco-containing bodies). These vesicles may then take different routes for their degradation. Transcriptome analyses on barley and wheat senescence have identified genes involved in degradative, metabolic and regulatory processes that could be used in future strategies aimed at modifying the senescence process. The breeding of crops for characters related to senescence processes, e.g. higher yields and better nutrient use efficiency, is complex. Such breeding has to cope with the dilemma that delayed senescence, which could lead to higher yields, is correlated with a decrease in nutrient use efficiency. Pinpointing regulatory genes involved in senescence might lead to tools that could effectively overcome this dilemma.

Leaf senescence and nutrient remobilisation in barley and wheat

Extensive studies have been undertaken on senescence processes in barley and wheat and their importance for the nitrogen use efficiency of these crop plants. During the senescence processes, proteins are degraded and nutrients are re-mobilised from senescing leaves to other organs, especially the developing grain. Most of the proteins degraded reside in the chloroplasts, with Rubisco constituting the most dominant protein fraction. Despite intensive studies, the proteases responsible for Rubisco degradation have not yet been identified. Evidence for degradation of stromal proteins outside of chloroplasts is summarised. Rubisco is thought to be released from chloroplasts into vesicles containing stroma material (RCB = Rubisco-containing bodies). These vesicles may then take different routes for their degradation. Transcriptome analyses on barley and wheat senescence have identified genes involved in degradative, metabolic and regulatory processes that could be used in future strategies aimed at modifying the senescence process. The breeding of crops for characters related to senescence processes, e.g. higher yields and better nutrient use efficiency, is complex. Such breeding has to cope with the dilemma that delayed senescence, which could lead to higher yields, is correlated with a decrease in nutrient use efficiency. Pinpointing regulatory genes involved in senescence might lead to tools that could effectively overcome this dilemma.

Genetic engineering of improved nitrogen use efficiency in rice by the tissue-specific expression of alanine aminotransferase

Summary Nitrogen is quantitatively the most essential nutrient for plants and a major factor limiting crop productivity. One of the critical steps limiting the efficient use of nitrogen is the ability of plants to acquire it from applied fertilizer. Therefore, the development of crop plants that absorb and use nitrogen more efficiently has been a long-term goal of agricultural research. In an attempt to develop nitrogen-efficient plants, rice (Oryza sativa L.) was genetically engineered by introducing a barley AlaAT (alanine aminotransferase) cDNA driven by a rice tissue-specific promoter (OsAnt1). This modification increased the biomass and grain yield significantly in comparison with control plants when plants were well supplied with nitrogen. Compared with controls, transgenic rice plants also demonstrated significant changes in key metabolites and total nitrogen content, indicating increased nitrogen uptake efficiency. The development of crop plants that take up and assimilate nitrogen more efficiently would not only improve the use of nitrogen fertilizers, resulting in lower production costs, but would also have significant environmental benefits. These results are discussed in terms of their relevance to the development of strategies to engineer enhanced nitrogen use efficiency in crop plants.

Genetic variation for N-remobilization and postsilking N-uptake in a set of maize recombinant inbred lines. 3. QTL detection and coincidences

The objective of this study was to map and characterize QTLs for traits related to nitrogen utilization efficiency (NUE), grain N yield, N-remobilization and post-silking N-uptake. Furthermore, to examine whether QTLs detected with recombinant inbred lines (RILs) crossed to a tester are common to those detected with line per se evaluation, both types of evaluations were developed from the same set of RILs. The material was studied over two years at high N-input, and one year at low N-input. We used (15)N-labelling to evaluate with accuracy the proportion of N remobilized from stover to kernels and the proportion of postsilking N-uptake allocated to kernels. With 59 traits studied in three environments, 608 QTLs were detected. Using a method of QTL clustering, 72 clusters were identified, with few QTLs being specific to one environment or to the type of plant material (lines or testcross families). However, considering each trait separately, few QTLs were common to both line per se and testcross evaluation. This shows that genetic variability is expressed differently according to the type of progeny. Studies of coincidences among QTLs within the clusters showed an antagonism between N-remobilization and N-uptake in several QTL-clusters. QTLs for N-uptake, root system architecture and leaf greenness coincided positively in eight clusters. QTLs for remobilization mainly coincided in clusters with QTLs for leaf senescence. On the whole, sign of coincidences between QTLs underlined the role of a "stay-green" phenotype in favouring N-uptake capacity, and thus grain yield and N grain yield.

Enzymatic and metabolic diagnostic of nitrogen deficiency in Arabidopsis thaliana Wassileskija accession

Adaptation to steady-state low-nutrient availability was investigated by comparing the Wassileskija (WS) accession of Arabidopsis thaliana grown on 2 or 10 mM nitrate. Low nitrogen conditions led to a limited rosette biomass and seed yield. The latter was mainly due to reduced seed number, while seed weight was less affected. However, harvest index was lower in high nitrate compared with limited nitrate conditions. Under nitrogen-limiting conditions, nitrate reductase activity was decreased while glutamine synthetase activity was increased due to a higher accumulation of the cytosolic enzyme. The level of nitrogen remobilization to the seeds was higher under low nitrogen, and the vegetative parts of the plants remaining after seed production stored very low residual nitrogen. Through promoting nitrogen remobilization and recycling pathways, nitrogen limitation modified plant and seed compositions. Rosette leaves contained more sugars and less free amino acids when grown under nitrogen-limiting conditions. Compared with high nitrogen, the levels of proline, asparagine and glutamine were decreased. The seed amino acid composition reflected that of the rosette leaves, thus suggesting that phloem loading for seed filling was poorly selective. The major finding of this report was that together with decreasing biomass and yield, nitrogen limitation triggers large modifications in vegetative products and seed quality.

The Arabidopsis halophytic relative Thellungiella halophila tolerates nitrogen-limiting conditions by maintaining growth, nitrogen uptake, and assimilation

A comprehensive knowledge of mechanisms regulating nitrogen (N) use efficiency is required to reduce excessive input of N fertilizers while maintaining acceptable crop yields under limited N supply. Studying plant species that are naturally adapted to low N conditions could facilitate the identification of novel regulatory genes conferring better N use efficiency. Here, we show that Thellungiella halophila, a halophytic relative of Arabidopsis (Arabidopsis thaliana), grows better than Arabidopsis under moderate (1 mm nitrate) and severe (0.4 mm nitrate) N-limiting conditions. Thellungiella exhibited a lower carbon to N ratio than Arabidopsis under N limitation, which was due to Thellungiella plants possessing higher N content, total amino acids, total soluble protein, and lower starch content compared with Arabidopsis. Furthermore, Thellungiella had higher amounts of several metabolites, such as soluble sugars and organic acids, under N-sufficient conditions (4 mm nitrate). Nitrate reductase activity and NR2 gene expression in Thellungiella displayed less of a reduction in response to N limitation than in Arabidopsis. Thellungiella shoot GS1 expression was more induced by low N than in Arabidopsis, while in roots, Thellungiella GS2 expression was maintained under N limitation but was decreased in Arabidopsis. Up-regulation of NRT2.1 and NRT3.1 expression was higher and repression of NRT1.1 was lower in Thellungiella roots under N-limiting conditions compared with Arabidopsis. Differential transporter gene expression was correlated with higher nitrate influx in Thellungiella at low (15)NO(3)(-) supply. Taken together, our results suggest that Thellungiella is tolerant to N-limited conditions and could act as a model system to unravel the mechanisms for low N tolerance.

Gene expression, cellular localisation and function of glutamine synthetase isozymes in wheat (Triticum aestivum L.)

We present the first cloning and study of glutamine synthetase (GS) genes in wheat (Triticum aestivum L.). Based on sequence analysis, phylogenetic studies and mapping data, ten GS sequences were classified into four sub-families: GS2 (a, b and c), GS1 (a, b and c), GSr (1 and 2) and GSe (1 and 2). Phylogenetic analysis showed that the wheat GS sub-families together with the GS genes from other monocotyledonous species form four distinct clades. Immunolocalisation studies in leaves, stems and rachis in plants at flowering showed GS protein to be present in parenchyma, phloem companion and perifascicular sheath cells. In situ localisation confirmed that GS1 transcripts were present in the perifascicular sheath cells whilst those for GSr were confined to the vascular cells. Studies of the expression and protein profiles showed that all GS sub-families were differentially expressed in the leaves, peduncle, glumes and roots. Expression of GS genes in leaves was developmentally regulated, with both GS2 and GS1 assimilating or recycling ammonia in leaves during the period of grain development and filling. During leaf senescence the cytosolic isozymes, GS1 and GSr, were the predominant forms, suggesting major roles in assimilating ammonia during the critical phases of remobilisation of nitrogen to the grain. A preliminary analysis of three different wheat genotypes showed that the ratio of leaf GS2 protein to GS1 protein was variable. Use of this genetic variation should inform future efforts to modulate this enzyme for pre-breeding efforts to improve nitrogen use in wheat.

Sugarcane genotypes differ in internal nitrogen use efficiency

The large amounts of nitrogen (N) fertiliser applied to most cropping systems support high yields but cause N pollution. More efficient use of N in cropping systems can be achieved through improved N management practices combined with genetic improvement of the crop. The magnitude of genetic variation in sugarcane (Saccharum officinarum L.) for internal nitrogen use efficiency (iNUE, biomass produced per unit tissue N) was investigated as this could provide a basis for breeding varieties with reduced N demand. Genotypes of a mapping population were examined for biomass production and physiological variables under low or high N supply in controlled conditions. Key findings were: (i) genotypic variation for biomass production and iNUE was up to 3-fold greater under low than high N supply, (ii) elite parent Q165 was among the best performing genotypes for biomass and iNUE at high N but not at low N supply, and (iii) several genotypes had high iNUE at both N supplies. While glutamine synthetase (GS; EC 6.3.1.2) activity has been linked with grain yield in other crops, no direct relationship was observed between whole tissue GS activity and vegetative biomass or iNUE in sugarcane genotypes. Soluble protein content was negatively correlated with iNUE and biomass production. This study demonstrates that there is considerable genetic variation for iNUE in sugarcane, which can be exploited for breeding. It is proposed that breeding programs should assess genotypes not only at high N, but also at low N supply rates to select genotypes that produce high biomass with low and high N supply.