Mapping of QTLs associated with cytosolic glutamine synthetase and NADH-glutamate synthase in rice (Oryza sativa L.)

Wheat glutamine synthetase TaGSr-4B is a candidate gene for a QTL of thousand grain weight on chromosome 4B

KEY MESSAGE

Glutamine synthetase TaGSr-4B is a candidate gene for a QTL of thousand grain weight on 4B, and the gene marker is ready for wheat breeding. A QTL for thousand grain weight (TGW) in wheat was previously mapped on chromosome 4B in a DH population of Westonia × Kauz. For identifying the candidate genes of the QTL, wheat 90 K SNP array was used to saturate the existing linkage map, and four field trials plus one glasshouse experiment over five locations were conducted to refine the QTL. Three nitrogen levels were applied to two of those field trials, resulting in a TGW phenotype data set from nine environments. A robust TGW QTL cluster including 773 genes was detected in six environments with the highest LOD value of 13.4. Based on differentiate gene expression within the QTL cluster in an RNAseq data of Westonia and Kauz during grain filling, a glutamine synthesis gene (GS: TaGSr-4B) was selected as a potential candidate gene for the QTL. A SNP on the promoter region between Westonia and Kauz was used to develop a cleaved amplified polymorphic marker for TaGSr-4B gene mapping and QTL reanalysing. As results, TGW QTL appeared in seven environments, and in four out of seven environments, the TGW QTL were localized on the TaGSr-4B locus and showed significant contributions to the phenotype. Based on the marker, two allele groups of Westonia and Kauz formed showed significant differences on TGW in eight environments. In agreement with the roles of GS genes on nitrogen and carbon remobilizations, TaGSr-4B is likely the candidate gene of the TGW QTL on 4B and the TaGSr-4B gene marker is ready for wheat breeding.

KNOX II transcription factor HOS59 functions in regulating rice grain size

Plant Knotted1-like homeobox (KNOX) genes encode homeodomain-containing transcription factors. In rice (Oryza sativa L.), little is known about the downstream target genes of KNOX Class II subfamily proteins. Here we generated chromatin immunoprecipitation (ChIP)-sequencing datasets for HOS59, a member of the rice KNOX Class II subfamily, and characterized the genome-wide binding sites of HOS59. We conducted trait ontology (TO) analysis of 9705 identified downstream target genes, and found that multiple TO terms are related to plant structure morphology and stress traits. ChIP-quantitative PCR (qPCR) was conducted to validate some key target genes. Meanwhile, our IP-MS datasets showed that HOS59 was closely associated with BELL family proteins, some grain size regulators (OsSPL13, OsSPL16, OsSPL18, SLG, etc.), and some epigenetic modification factors such as OsAGO4α and OsAGO4β, proteins involved in small interfering RNA-mediated gene silencing. Furthermore, we employed CRISPR/Cas9 editing and transgenic approaches to generate hos59 mutants and overexpression lines, respectively. Compared with wild-type plants, the hos59 mutants have longer grains and increased glume cell length, a loose plant architecture, and drooping leaves, while the overexpression lines showed smaller grain size, erect leaves, and lower plant height. The qRT-PCR results showed that mutation of the HOS59 gene led to upregulation of some grain size-related genes such as OsSPL13, OsSPL18, and PGL2. In summary, our results indicate that HOS59 may be a repressor of the downstream target genes, negatively regulating glume cell length, rice grain size, plant architecture, etc. The identified downstream target genes and possible interaction proteins of HOS59 improve our understanding of the KNOX regulatory networks.

Cytosolic Glutamine Synthetase GS1;3 Is Involved in Rice Grain Ripening and Germination

Ammonium is combined with glutamate to form glutamine. This reaction is catalyzed by glutamine synthetase (GS or GLN). Plants harbor several isoforms of cytosolic GS (GS1). Rice GS1;3 is highly expressed in seeds during grain filling and germination, suggesting a unique role in these processes. This study aimed to investigate the role of GS1;3 for rice growth and yield. Tos17 insertion lines for GS1;3 were isolated, and the nitrogen (N), amino acid, and ammonium contents of GS1;3 mutant grains were compared to wild-type grains. The spatiotemporal expression of GS1;3 and the growth and yield of rice plants were evaluated in hydroponic culture and the paddy field. Additionally, the stable isotope of N was used to trace the foliar N flux during grain filling. Results showed that the loss of GS1;3 retarded seed germination. Seeds of GS1;3 mutants accumulated glutamate but did not show a marked change in the level of phytohormones. The expression of GS1;3 was detected at the beginning of germination, with limited promoter activity in seeds. GS1;3 mutants showed a considerably decreased ripening ratio and decreased N efflux in the 12th leaf blade under N deficient conditions. The β-glucuronidase gene expression under control of the GS1;3 promoter was detected in the vascular tissue and aleurone cell layer of developing grains. These data suggest unique physiological roles of GS1;3 in the early stage of seed germination and grain filling under N deficient conditions in rice.

Morphological study of different varieties of rice traits influencing nitrogen and water uptake efficiency

This research aimed at establishing the morphology of the root and sizes under various irrigation cultures. The comparison was made for root to shoot ratio under the traditional culture of flooding. We hypothesize that, due to limited root system development under aerobic conditions, rice is poorly adapted to different environments. In the meantime, there has to be an increase in demand for grain and output per area, as newly planted areas are scarce. This study discusses the latest theoretical physiological, metabolic and genetic factors affecting nitrogen intake and use in different N processes. It covers the root system's position and nitrate- ammonium assimilation and its relationship with Nitrogen Use Efficiency (NUE) and Water Use Efficiency (WUE), were discussed. Phenotyping and molecular breeding techniques concerning N and water regimes and genetic diversity were also evaluated and simulated.

Cisgenic overexpression of cytosolic glutamine synthetase improves nitrogen utilization efficiency in barley and prevents grain protein decline under elevated CO2

Cytosolic glutamine synthetase (GS1) plays a central role in nitrogen (N) metabolism. The importance of GS1 in N remobilization during reproductive growth has been reported in cereal species but attempts to improve N utilization efficiency (NUE) by overexpressing GS1 have yielded inconsistent results. Here, we demonstrate that transformation of barley (Hordeum vulgare L.) plants using a cisgenic strategy to express an extra copy of native HvGS1-1 lead to increased HvGS1.1 expression and GS1 enzyme activity. GS1 overexpressing lines exhibited higher grain yields and NUE than wild-type plants when grown under three different N supplies and two levels of atmospheric CO₂ . In contrast with the wild-type, the grain protein concentration in the GS1 overexpressing lines did not decline when plants were exposed to elevated (800-900 μL/L) atmospheric CO₂ . We conclude that an increase in GS1 activity obtained through cisgenic overexpression of HvGS1-1 can improve grain yield and NUE in barley. The extra capacity for N assimilation obtained by GS1 overexpression may also provide a means to prevent declining grain protein levels under elevated atmospheric CO₂ .

Concurrent Overexpression of OsGS1;1 and OsGS2 Genes in Transgenic Rice (Oryza sativa L.): Impact on Tolerance to Abiotic Stresses

Glutamine synthetase (GS) is a key enzyme involved in the nitrogen metabolism of higher plants. Abiotic stresses have adverse effects on crop production and pose a serious threat to global food security. GS activity and expression is known to be significantly modulated by various abiotic stresses. However, very few transgenic overexpression studies of GS have studied its impact on abiotic stress tolerance. GS is also the target enzyme of the broad spectrum herbicide Glufosinate (active ingredient: phosphinothricin). In this study, we investigated the effect of concurrent overexpression of the rice cytosolic GS1 (OsGS1;1) and chloroplastic GS2 (OsGS2) genes in transgenic rice on its tolerance to abiotic stresses and the herbicide Glufosinate. Our results demonstrate that the co-overexpression of OsGS1;1 and OsGS2 isoforms in transgenic rice plants enhanced its tolerance to osmotic and salinity stress at the seedling stage. The transgenic lines maintained significantly higher fresh weight, chlorophyll content, and relative water content than wild type (wt) and null segregant (ns) controls, under both osmotic and salinity stress. The OsGS1;1/OsGS2 co-overexpressing transgenic plants accumulated higher levels of proline but showed lower electrolyte leakage and had lower malondialdehyde (MDA) content under the stress treatments. The transgenic lines showed considerably enhanced photosynthetic and agronomic performance under drought and salinity stress imposed during the reproductive stage, as compared to wt and ns control plants. The grain filling rates of the transgenic rice plants under reproductive stage drought stress (64.6 ± 4.7%) and salinity stress (58.2 ± 4.5%) were significantly higher than control plants, thereby leading to higher yields under these abiotic stress conditions. Preliminary analysis also revealed that the transgenic lines had improved tolerance to methyl viologen induced photo-oxidative stress. Taken together, our results demonstrate that the concurrent overexpression of OsGS1;1 and OsGS2 isoforms in rice enhanced physiological tolerance and agronomic performance under adverse abiotic stress conditions, apparently acting through multiple mechanistic routes. The transgenic rice plants also showed limited tolerance to the herbicide Glufosinate. The advantages and limitations of glutamine synthetase overexpression in crop plants, along with future strategies to overcome these limitations for utilization in crop improvement have also been discussed briefly.

A temporal and spatial contribution of asparaginase to asparagine catabolism during development of rice grains

BACKGROUND

Asparagine is one of the most dominant organic nitrogen compounds in phloem and xylem sap in a wide range of plant species. Asparaginase (ASNase; EC, 3.5.1.1) catabolizes asparagine into aspartate and ammonium; therefore, it is suggested to play a key role in asparagine metabolism within legume sink organs. However, the metabolic fate of asparagine in source and sink organs during rice seed production remains to be elucidated. Therefore, the main objective of this study is to investigate the asparagine metabolism in a temporal and spatial manner during rice seed production.

RESULTS

For this purpose, the expression of genes involved in asparagine catabolism, such as asparaginase1 (OsASNase1) and 2 (OsASNase2), were quantitatively measured, and contents of asparagine, aspartate and ammonium ions were determined in sink and source organs during spikelet ripening. Quantitative real-time PCR and in situ localization studies determined that OsASNase2 is expressed in the dorsal vascular bundles and nucellar projection of developing grains, as well as in mesophyll and phloem companion cells of senescent flag leaves. Amino acid measurements revealed that the aspartate concentration is higher than asparagine in both source and sink organs.

CONCLUSION

This work suggests that asparaginase dependent asparagine catabolism occurred not only in sink but also in source organs.

Genetic approaches to enhancing nitrogen-use efficiency (NUE) in cereals: challenges and future directions

Over 100million tonnes of nitrogen (N) fertiliser are applied globally each year to maintain high yields in agricultural crops. The rising price of N fertilisers has made them a major cost for farmers. Inefficient use of N fertiliser leads to substantial environmental problems through contamination of air and water resources and can be a significant economic cost. Consequently, there is considerable need to improve the way N fertiliser is used in farming systems. The efficiency with which crops use applied N fertiliser - the nitrogen-use efficiency (NUE) - is currently quite low for cereals. This is the case in both high yielding environments and lower yielding environments characteristic of cereal growing regions of Australia. Multiple studies have attempted to identify the genetic basis of NUE, but the utility of the results is limited because of the complex nature of the trait and the magnitude of genotype by environment interaction. Transgenic approaches have been applied to improve plant NUE but with limited success, due, in part, to a combination of the complexity of the trait but also due to lack of accurate phenotyping methods. This review documents these two approaches and suggests future directions in improving cereal NUE with a focus on the Australian cereal industry.

The Genetics of Nitrogen Use Efficiency in Crop Plants

In the past 50 years, the application of synthetic nitrogen (N) fertilizer to farmland resulted in a dramatic increase in crop yields but with considerable negative impacts on the environment. New solutions are therefore needed to simultaneously increase yields while maintaining, or preferably decreasing, applied N to maximize the nitrogen use efficiency (NUE) of crops. In this review, we outline the definition of NUE, the selection and development of NUE crops, and the factors that interact with NUE. In particular, we emphasize the challenges of developing crop plants with enhanced NUE, using more classical genetic approaches based on utilizing existing allelic variation for NUE traits. The challenges of phenotyping, mapping quantitative trait loci (QTLs), and selecting candidate genes for NUE improvement are described. In addition, we highlight the importance of different factors that lead to changes in the NUE components of nitrogen uptake efficiency (NUpE) and nitrogen utilization efficiency (NUtE).

An integrated "omics" approach to the characterization of maize (Zea mays L.) mutants deficient in the expression of two genes encoding cytosolic glutamine synthetase

Background

To identify the key elements controlling grain production in maize, it is essential to have an integrated view of the responses to alterations in the main steps of nitrogen assimilation by modification of gene expression. Two maize mutant lines (gln1.3 and gln1.4), deficient in two genes encoding cytosolic glutamine synthetase, a key enzyme involved in nitrogen assimilation, were previously characterized by a reduction of kernel size in the gln1.4 mutant and by a reduction of kernel number in the gln1.3 mutant. In this work, the differences in leaf gene transcripts, proteins and metabolite accumulation in gln1.3 and gln1.4 mutants were studied at two key stages of plant development, in order to identify putative candidate genes, proteins and metabolic pathways contributing on one hand to the control of plant development and on the other to grain production.

Results

The most interesting finding in this study is that a number of key plant processes were altered in the gln1.3 and gln1.4 mutants, including a number of major biological processes such as carbon metabolism and transport, cell wall metabolism, and several metabolic pathways and stress responsive and regulatory elements. We also found that the two mutants share common or specific characteristics across at least two or even three of the “omics” considered at the vegetative stage of plant development, or during the grain filling period.

Conclusions

This is the first comprehensive molecular and physiological characterization of two cytosolic glutamine synthetase maize mutants using a combined transcriptomic, proteomic and metabolomic approach. We find that the integration of the three “omics” procedures is not straight forward, since developmental and mutant-specific levels of regulation seem to occur from gene expression to metabolite accumulation. However, their potential use is discussed with a view to improving our understanding of nitrogen assimilation and partitioning and its impact on grain production.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1005) contains supplementary material, which is available to authorized users.

Senescence, nutrient remobilization, and yield in wheat and barley

Cereals including wheat and barley are of primary importance to ensure food security for the 21st century. A combination of lab- and field-based approaches has led to a considerably improved understanding of the importance of organ and particularly of whole-plant (monocarpic) senescence for wheat and barley yield and quality. A delicate balance between senescence timing, grain nutrient content, nutrient-use efficiency, and yield needs to be considered to (further) improve cereal varieties for a given environment and end use. The recent characterization of the Gpc-1 (NAM-1) genes in wheat and barley demonstrates the interdependence of these traits. Lines or varieties with functional Gpc-1 genes demonstrate earlier senescence and enhanced grain protein and micronutrient content but, depending on the environment, somewhat reduced yields. A major effort is needed to dissect regulatory networks centred on additional wheat and barley transcription factors and signalling pathways influencing the senescence process. Similarly, while important molecular details of nutrient (particularly nitrogen) remobilization from senescing organs to developing grains have been identified, important knowledge gaps remain. The genes coding for the major proteases involved in senescence-associated plastidial protein degradation are largely unknown. Membrane transport proteins involved in the different transport steps occurring between senescing organ (such as leaf mesophyll) cells and protein bodies in the endosperm of developing grains remain to be identified or further characterized. Existing data suggest that an improved understanding of all these steps will reveal additional, important targets for continued cereal improvement.

Engineering nitrogen use efficient crop plants: the current status

In the last 40 years the amount of synthetic nitrogen (N) applied to crops has risen drastically, resulting in significant increases in yield but with considerable impacts on the environment. A requirement for crops that require decreased N fertilizer levels has been recognized in the call for a 'Second Green Revolution' and research in the field of nitrogen use efficiency (NUE) has continued to grow. This has prompted a search to identify genes that improve the NUE of crop plants, with candidate NUE genes existing in pathways relating to N uptake, assimilation, amino acid biosynthesis, C/N storage and metabolism, signalling and regulation of N metabolism and translocation, remobilization and senescence. Herein is a review of the approaches taken to determine possible NUE candidate genes, an overview of experimental study of these genes as effectors of NUE in both cereal and non-cereal plants and the processes of commercialization of enhanced NUE crop plants. Patents issued regarding increased NUE in plants as well as gene pyramiding studies are also discussed as well as future directions of NUE research.

Approaches towards nitrogen- and phosphorus-efficient rice

BACKGROUND AND AIMS

Food production has to increase to meet the demand of a growing population. In light of the high energy costs and increasingly scarce resources, future agricultural systems have to be more productive and more efficient in terms of inputs such as fertilizer and water. The development of rice varieties with high yield under low-nutrient conditions has therefore become a breeding priority. The rapid progress made in sequencing and molecular-marker technology is now beginning to change the way breeding is done, providing new opportunities.

SCOPE

Nitrogen (N) and phosphorus (P) are applied to agricultural systems in large quantities and a deficiency of either nutrient leads to yield losses and triggers complex molecular and physiological responses. The underlying genes are now being identified and studied in detail, and an increasing number of quantitative trait loci (QTLs) related to N and P uptake and utilization are being reported. Here, we provide an overview of the different aspects related to N and P in rice production systems, and apply a breeder's perspective on the potential of relevant genes and pathways for breeding applications.

MAIN POINTS

For the development of nutrient-efficient rice, a holistic approach should be followed combining optimized fertilizer management with enhanced nutrient uptake via a vigorous root system, leading to increased grain filling and yield. Despite an increasing number of N- and P-related genes and QTLs being reported, very few are actively used in molecular breeding programmes. The complex regulation of N- and P-related pathways challenges breeders and the research community to identify large-effect genes/QTLs. For this it will be important to focus more on the analysis of tolerant genotypes rather than model plants, since tolerance pathways may employ a different set of genes.

Disruption of a Novel NADH-Glutamate Synthase2 Gene Caused Marked Reduction in Spikelet Number of Rice

Inorganic ammonium ions are assimilated by a coupled reaction of glutamine synthetase and glutamate synthase (GOGAT). In rice, three genes encoding either ferredoxin (Fd)-GOGAT, NADH-GOGAT1, or NADH-GOGAT2, have been identified. OsNADH-GOGAT2, a newly identified gene, was expressed mainly in fully expanded leaf blades and leaf sheaths. Although the distinct expression profile to OsNADH-GOGAT1, which is mainly detected in root tips, developing leaf blades, and grains, was shown in our previous studies, physiological role of NADH-GOGAT2 is not yet known. Here, we isolated retrotransposon mediated-knockout mutants lacking OsNADH-GOGAT2. In rice grown under paddy field conditions, disruption of the OsNADH-GOGAT2 gene caused a remarkable decrease in spikelet number per panicle associated with a reductions in yield and whole plant biomass, when compared with wild-type (WT) plants. The total nitrogen contents in the senescing leaf blade of the mutants were approximately a half of the WT plants. Expression of this gene was mainly detected in phloem companion cells and phloem parenchyma cells associated with large vascular bundles in fully expanded leaf blades, when the promoter region fused with a β-glucuronidase gene was introduced into the WT rice. These results suggest that the NADH-GOGAT2 is important in the process of glutamine generation in senescing leaves for the remobilization of leaf nitrogen through phloem to the panicle during natural senescence. These results also indicate that other GOGATs, i.e., NADH-GOGAT1 and ferredoxin-GOGAT are not able to compensate the function of NADH-GOGAT2.

Reappraisal of nitrogen use efficiency in rice overexpressing glutamine synthetase1

Cytosolic glutamine synthetase (GS1) is responsible for the primary assimilation of ammonia, and a role in nitrogen (N) remobilization is implicated from its vascular localization and enhanced expression during senescence. This paper tested the hypothesis that overexpression (OX) of GS1 in rice improves utilization N use efficiency (UtE = spikelet yield/shoot N content). Three GS1 OX lines were identified using activity assays and quantitative polymerase chain reaction. Physiological analysis of the OX lines, as well as azygous and wild-type (Wt) controls, was conducted with mature plants after growth under varying nitrate conditions (non-limiting N, limiting N, transfer from non-limiting N to limiting N at panicle emergence) and growth environments (growth chamber vs greenhouse). Overall, OX lines did not differ from azygous controls in vegetative yield or shoot N content. In two of the three growth trials (i.e. the growth chamber trials) harvest index, N harvest index (spikelet N content/shoot N content) and UtE were generally enhanced in the OX lines relative to their azygous controls. These characteristics were highly correlated with percent spikelets filled and spikelet number. Thus, N partitioning in rice during grain filling could be altered by GS1 OX, resulting in improved UtE. Unfortunately, GS OX did not result in more efficient use of N under limiting N than under non-limiting N, and is therefore unlikely to result in the use of less N under field conditions. Transformation effects significantly hindered the productivity of the OX lines, but backcrossing to the Wt should overcome this.

Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution

Monitoring nitrogen use efficiency (NUE) in plants is becoming essential to maintain yield while reducing fertilizer usage. Optimized NUE application in major crops is essential for long-term sustainability of agriculture production. Here, we report the precise identification of 11 major chromosomal regions controlling NUE in wheat that co-localise with key developmental genes such as Ppd (photoperiod sensitivity), Vrn (vernalization requirement), Rht (reduced height) and can be considered as robust markers from a molecular breeding perspective. Physical mapping, sequencing, annotation and candidate gene validation of an NUE metaQTL on wheat chromosome 3B allowed us to propose that a glutamate synthase (GoGAT) gene that is conserved structurally and functionally at orthologous positions in rice, sorghum and maize genomes may contribute to NUE in wheat and other cereals. We propose an evolutionary model for the NUE locus in cereals from a common ancestral region, involving species specific shuffling events such as gene deletion, inversion, transposition and the invasion of repetitive elements.

New perspectives on glutamine synthetase in grasses

Members of the glutamine synthetase (GS) gene family have now been characterized in many crop species such as wheat, rice, and maize. Studies have shown that cytosolic GS isoforms are involved in nitrogen remobilization during leaf senescence and emphasized a role in seed production particularly in small grain crop species. Data from the sequencing of genomes for model crops and expressed sequence tag (EST) libraries from non-model species have strengthened the idea that the cytosolic GS genes are organized in three functionally and phylogenetically conserved subfamilies. Using a bioinformatic approach, the considerable publicly available information on high throughput gene expression was mined to search for genes having patterns of expression similar to GS. Interesting new hypotheses have emerged from searching for co-expressed genes across multiple unfiltered experimental data sets in rice. This approach should inform new experimental designs and studies to explore the regulation of the GS gene family further. It is expected that understanding the regulation of GS under varied climatic conditions will emerge as an important new area considering the results from recent studies that have shown nitrogen assimilation to be critical to plant acclimation to high CO(2) concentrations.

Haplotype analysis of the genes encoding glutamine synthetase plastic isoforms and their association with nitrogen-use- and yield-related traits in bread wheat

Glutamine synthetase (GS) plays a key role in the growth, nitrogen (N) use and yield potential of cereal crops. Investigating the haplotype variation of GS genes and its association with agronomic traits may provide useful information for improving wheat N-use efficiency and yield. We isolated the promoter and coding region sequences of the plastic glutamine synthetase isoform (GS2) genes located on chromosomes 2A, 2B and 2D in bread wheat. By analyzing nucleotide sequence variations of the coding region, two, six and two haplotypes were distinguished for TaGS2-A1 (a and b), TaGS2-B1 (a-f) and TaGS2-D1 (a and b), respectively. By analyzing the frequency data of different haplotypes and their association with N use and agronomic traits, four major and favorable TaGS2 haplotypes (A1b, B1a, B1b, D1a) were revealed. These favorable haplotypes may confer better seedling growth, better agronomic performance, and improved N uptake during vegetative growth or grain N concentration. Our data suggest that certain TaGS2 haplotypes may be valuable in breeding wheat varieties with improved agronomic performance and N-use efficiency.

Fine-mapping of qRL6.1, a major QTL for root length of rice seedlings grown under a wide range of NH4(+) concentrations in hydroponic conditions

Root system development is an important target for improving yield in cereal crops. Active root systems that can take up nutrients more efficiently are essential for enhancing grain yield. In this study, we attempted to identify quantitative trait loci (QTL) involved in root system development by measuring root length of rice seedlings grown in hydroponic culture. Reliable growth conditions for estimating the root length were first established to renew nutrient solutions daily and supply NH4(+) as a single nitrogen source. Thirty-eight chromosome segment substitution lines derived from a cross between 'Koshihikari', a japonica variety, and 'Kasalath', an indica variety, were used to detect QTL for seminal root length of seedlings grown in 5 or 500 microM NH4(+). Eight chromosomal regions were found to be involved in root elongation. Among them, the most effective QTL was detected on a 'Kasalath' segment of SL-218, which was localized to the long-arm of chromosome 6. The 'Kasalath' allele at this QTL, qRL6.1, greatly promoted root elongation under all NH4(+) concentrations tested. The genetic effect of this QTL was confirmed by analysis of the near-isogenic line (NIL) qRL6.1. The seminal root length of the NIL was 13.5-21.1% longer than that of 'Koshihikari' under different NH4(+) concentrations. Toward our goal of applying qRL6.1 in a molecular breeding program to enhance rice yield, a candidate genomic region of qRL6.1 was delimited within a 337 kb region in the 'Nipponbare' genome by means of progeny testing of F2 plants/F3 lines derived from a cross between SL-218 and 'Koshihikari'.

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.

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.

Cellular distribution of ACT domain repeat protein 9, a nuclear localizing protein, in rice (Oryza sativa)

Regulatory ACT domains serve as amino acid-binding sites in certain amino acid metabolic enzymes and transcriptional regulators in bacteria. The ACT domain repeat protein (ACR) family in plants is primarily composed of four copies of the domain homologous to those of the bacteria Gln sensor GLND. In the current study, to evaluate the possible involvement of the protein OsACR9 in the Gln-sensing system related to nitrogen (N) metabolism in rice (Oryza sativa L.), subcellular localization of OsACR9 and its accumulation and cellular distribution in various rice organs were examined by transient expression analysis and immunological methods using a monospecific antibody, respectively. Transient expression analysis of OsACR9 fused with a synthetic green fluorescent protein in cultured rice cells suggested nuclear localization of OsACR9. In rice roots, OsACR9 protein was distributed in epidermis, exodermis, sclerenchyma and vascular parenchyma cells, and its accumulation markedly increased after supply of NH(+)(4). In rice leaf samples, OsACR9 protein was abundant in the vascular parenchyma and mestome-sheath cells of young leaf blades at the early stage of development and in the vascular parenchyma and phloem-companion cells of mature leaf sheaths. OsACR9 protein also showed a high level of accumulation in vascular parenchyma cells of dorsal vascular bundles and aleurone cells in young rice grains at the early stage of ripening. The possibility of the nuclear protein OsACR9 acting as a Gln sensor in rice is subsequently discussed through comparison of its spatiotemporal expression with that of Gln-responsive N-assimilatory genes.

Combined agronomic and physiological aspects of nitrogen management in wheat highlight a central role for glutamine synthetase

In wheat the period of grain filling is characterized by a transition for all vegetative organs from sink to source status. To study this transition, the progression of physiological markers and enzyme activities representative of nitrogen metabolism was monitored from the vegetative stage to maturity in different leaf stages and stem sections of two wheat (Triticum aestivum) cultivars grown at high and low levels of N fertilization. In the two cultivars examined, we found a general decrease of the metabolic and enzyme markers occurred during leaf ageing, and that this decrease was enhanced when plants were N-limited. Both correlation studies and principal components analysis (PCA) showed that there was a strong relationship among total N, chlorophyll, soluble protein, ammonium, amino acids and glutamine synthetase (GS) activity. The use of a marker such as GS activity to predict the N status of wheat, as a function of both plant development and N availability, is discussed with the aim of selecting wheat genotypes with better N-use efficiency.

QTLs for low nitrogen tolerance at seedling stage identified using a recombinant inbred line population derived from an elite rice hybrid

Tolerance to low nitrogen conditions is a highly desired characteristic for sustainable crop production. In this study, we analyzed the genetic components associated with low N tolerance in rice at seedling stage, including main effects, epistatic effects of the quantitative trait locus (QTLs), and QTL by environment interactions (QEs), using a population of 239 recombinant inbred lines (RILs) from a cross between Zhenshan 97 and Minghui 63, the parents of an elite hybrid. A genetic linkage map with 253 DNA maker loci was constructed. Seedlings of RILs were cultivated in low N and normal N solutions. Root, shoot and plant weight in the two N treatments were measured and the relative weight of the two treatments for each trait was considered as measurements for low N tolerance. Four to eight QTLs with main effects were detected for each of the nine traits. Very few QTLs were detected in both low and normal N conditions, and most QTLs for the relative measurements were different from those for traits under the two N treatments, indicating very little commonality in the genetic basis of the traits and their relative performance under low and normal N conditions. A total of 103 digenic interactions were detected for the nine traits. While the epistatic effects collectively accounted for large proportions of the variation for several traits, the effects of QEs appeared to be trivial. It was concluded that low N tolerance of rice seedling had complex genetic basis that requires extensive studies for full characterization.

Can less yield more? Is reducing nutrient input into the environment compatible with maintaining crop production?

Plant scientists have long recognized the need to develop crops that absorb and use nutrients more efficiently. Two approaches have been used to increase nutrient use efficiency (NUE) in crop plants. The first involves both traditional breeding and marker-assisted selection in an attempt to identify the genes involved. The second uses novel gene constructs designed to improve specific aspects of NUE. Here, we discuss some recent developments in the genetic manipulation of NUE in crop plants and argue that an improved understanding of the transition between nitrogen assimilation and nitrogen recycling will be important in applying this technology to increasing crop yields. Moreover, we emphasize the need to combine genetic and transgenic approaches to make significant improvements in NUE.

Improved growth in a field trial of transgenic hybrid poplar overexpressing glutamine synthetase

•  In the present work the performance of transgenic poplars expressing a pine glutamine synthetase (GS) transgene was studied in natural conditions. •  A field study of eight independent transgenic lines and control plants was carried out for 3 yr in the province of Granada (Spain). •  Transgenic poplars reached average heights that were 21, 36 and 41% greater than control plants after the first, second and third year of growth, respectively. Transgene expression affected plant features with time resulting in increased protein, total GS and ferredoxin-dependent glutamate synthase (Fd-GOGAT) in leaves. However, neither differences in the large subunit of Rubisco (LSU) abundance nor water content were detected between lines. Furthermore, no significant differences were found in total polysaccharide and lignin content in tree trunks. •  The analyses of stem diameter, and protein contents in the bark suggest that higher levels of nitrogen reserves accumulated in the stem of transgenics. Our results suggest that modification of GS1 expression may be a useful strategy to complement traditional tree breeding in short rotation plantations.

New insights towards the function of glutamate dehydrogenase revealed during source-sink transition of tobacco (Nicotiana tabacum) plants grown under different nitrogen regimes

The metabolic, biochemical and molecular events occurring in the different leaf stages along the main axis of tobacco (Nicotiana tabacum) plants grown either on a nitrogen-rich medium, on a medium containing ammonium as sole nitrogen source or on a nitrogen-depleted medium, are presented. This study shows that the highest induction of cytosolic glutamine synthetase (GS1) protein and transcript occurs when nitrogen remobilization is maximal as the result of nitrogen starvation, whereas both glutamate dehydrogenase (GDH) transcript and activity remain at a very low level. In contrast, GDH is highly induced when plants are grown on ammonium as sole nitrogen source, a physiological situation during which leaf protein nitrogen remobilization is limited. It is therefore concluded that GDH does not play a direct role during the process of nitrogen remobilization but is rather induced following a built up of ammonium provided externally or released as the result of protein hydrolysis during natural leaf senescence.

Variation in nitrate uptake and assimilation between two ecotypes of Lotus japonicus and their recombinant inbred lines

A large genetic variability was observed in the shoot NO(3) (-) content of recombinant inbred lines (RILs) of Lotus japonicus. To determine the cause of this variability, we have studied some aspects of nitrate uptake and assimilation in the two parental ecotypes (Gifu and Funakura) and four representatives of the RILs population differing both in their shoot biomass and shoot NO(3) (-) content. Higher shoot NO(3) (-)content was mainly due to an increase in the uptake of the ion regardless of the plant biomass production. The positive correlation observed between the shoot NO(3) (-) content and the steady state level of mRNA encoding high affinity NO(3) (-) transporters suggests that the higher NO(3) (-) influx is due to enhanced expression of the transporters. In contrast, neither the level of nitrate reductase mRNA, nor the potential enzyme activity in vivo in the different lines was correlated with the shoot NO(3) (-) content. This indicates that NO(3) (-) transport in Lotus is one of the main checkpoints controlling shoot NO(3) (-) accumulation. In addition, this study shows that at least in Lotus, it is possible, through breeding strategies, to lower the NO(3) (-) content without affecting biomass production.

Mapping of quantitative trait loci associated with ultraviolet-B resistance in rice (Oryza sativa L.)

The detection of quantitative trait loci (QTLs) associated with UV-B resistance in rice should allow their practical application in breeding for such a complex trait, and may lead to the identification of gene characteristics and functions. Considerable variation in UV-B resistance exists within cultivated rice (Oryza sativa L.), but its detailed genetic control mechanism has not been well elucidated. We detected putative QTLs associated with the resistance to enhanced UV-B radiation in rice, using 98 BC(1)F(5) (backcross inbred lines; BILs) derived from a cross between Nipponbare (a resistant japonica rice variety) and Kasalath (a sensitive indica rice variety). We used 245 RFLP markers to construct a framework linkage map. BILs and both parents were grown under visible light with or without supplemental UV-B radiation in a growth chamber. In order to evaluate UV-B resistance, we used the relative fresh weight of aerial parts (RFW) and the relative chlorophyll content of leaf blades (RCC). The BIL population exhibited a wide range of variation in RFW and RCC. Using composite interval mapping with a LOD threshold of 2.9, three putative QTLs associated with both RFW and RCC were detected on chromosomes 1, 3 and 10. Nipponbare alleles at the QTLs on chromosome 1 and 10 increased the RFW and RCC, while the Kasalath allele at the QTL on chromosome 3 increased both traits. Furthermore, the existence of both QTLs on chromosomes 1 and 10 for UV-B resistance was confirmed using chromosome segment substitution lines. Plants with Kasalath alleles at the QTL on chromosome 10 were more sensitive to UV-B radiation than plants with them on chromosome 1. These results also provide the information not only for the improvement of UV-B resistance in rice though marker-associated selection, but also for the identification of UV-B resistance mechanisms by using near-isogenic lines.