Over-expression of OsPTR6 in rice increased plant growth at different nitrogen supplies but decreased nitrogen use efficiency at high ammonium supply

Mitigating growth-stress tradeoffs via elevated TOR signaling in rice

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

The Arabidopsis eIF4E1 regulates NRT1.1-mediated nitrate signaling at both translational and transcriptional levels

Identifying new nitrate regulatory genes and illustrating their mechanisms in modulating nitrate signaling are of great significance for achieving the high yield and nitrogen use efficiency (NUE) of crops. Here, we screened a mutant with defects in nitrate response and mapped the mutation to the gene eIF4E1 in Arabidopsis. Our results showed that eIF4E1 regulated nitrate signaling and metabolism. Ribo-seq and polysome profiling analysis revealed that eIF4E1 modulated the amount of some nitrogen (N)-related mRNAs being translated, especially the mRNA of NRT1.1 was reduced in the eif4e1 mutant. RNA-Seq results enriched some N-related genes, supporting that eIF4E1 is involved in nitrate regulation. The genetic analysis indicated that eIF4E1 worked upstream of NRT1.1 in nitrate signaling. In addition, an eIF4E1-interacting protein GEMIN2 was identified and found to be involved in nitrate signaling. Further investigation showed that overexpression of eIF4E1 promoted plant growth and enhanced yield and NUE. These results demonstrate that eIF4E1 regulates nitrate signaling by modulating NRT1.1 at both translational and transcriptional levels, laying the foundation for future research on the regulation of mineral nutrition at the translational level.

Transcriptome and Co-Expression Network Analysis Reveals the Molecular Mechanism of Rice Root Systems in Response to Low-Nitrogen Conditions

Nitrogen is an important nutrient for plant growth and essential metabolic processes. Roots integrally obtain nutrients from soil and are closely related to the growth and development of plants. In this study, the morphological analysis of rice root tissues collected at different time points under low-nitrogen and normal nitrogen conditions demonstrated that, compared with normal nitrogen treatment, the root growth and nitrogen use efficiency (NUE) of rice under low-nitrogen treatment were significantly improved. To better understand the molecular mechanisms of the rice root system’s response to low-nitrogen conditions, a comprehensive transcriptome analysis of rice seedling roots under low-nitrogen and control conditions was conducted in this study. As a result, 3171 differentially expressed genes (DEGs) were identified. Rice seedling roots enhance NUE and promote root development by regulating the genes related to nitrogen absorption and utilization, carbon metabolism, root growth and development, and phytohormones, thereby adapting to low-nitrogen conditions. A total of 25,377 genes were divided into 14 modules using weighted gene co-expression network analysis (WGCNA). Two modules were significantly associated with nitrogen absorption and utilization. A total of 8 core genes and 43 co-expression candidates related to nitrogen absorption and utilization were obtained in these two modules. Further studies on these genes will contribute to the understanding of low-nitrogen adaptation and nitrogen utilization mechanisms in rice.

Bioengineering Techniques to Improve Nitrogen Transformation and Utilization: Implications for Nitrogen Use Efficiency and Future Sustainable Crop Production

Nitrogen (N) is crucial for plant growth and development, especially in physiological and biochemical processes such as component of different proteins, enzymes, nucleic acids, and plant growth regulators. Six categories, such as transporters, nitrate absorption, signal molecules, amino acid biosynthesis, transcription factors, and miscellaneous genes, broadly encompass the genes regulating NUE in various cereal crops. Herein, we outline detailed research on bioengineering modifications of N metabolism to improve the different crop yields and biomass. We emphasize effective and precise molecular approaches and technologies, including N transporters, transgenics, omics, etc., which are opening up fascinating opportunities for a complete analysis of the molecular elements that contribute to NUE. Moreover, the detection of various types of N compounds and associated signaling pathways within plant organs have been discussed. Finally, we highlight the broader impacts of increasing NUE in crops, crucial for better agricultural yield and in the greater context of global climate change.

Unlocking the potentials of nitrate transporters at improving plant nitrogen use efficiency

Nitrate ( NO 3 - ) transporters have been identified as the primary targets involved in plant nitrogen (N) uptake, transport, assimilation, and remobilization, all of which are key determinants of nitrogen use efficiency (NUE). However, less attention has been directed toward the influence of plant nutrients and environmental cues on the expression and activities of NO 3 - transporters. To better understand how these transporters function in improving plant NUE, this review critically examined the roles of NO 3 - transporters in N uptake, transport, and distribution processes. It also described their influence on crop productivity and NUE, especially when co-expressed with other transcription factors, and discussed these transporters' functional roles in helping plants cope with adverse environmental conditions. We equally established the possible impacts of NO 3 - transporters on the uptake and utilization efficiency of other plant nutrients while suggesting possible strategic approaches to improving NUE in plants. Understanding the specificity of these determinants is crucial to achieving better N utilization efficiency in crops within a given environment.

Overexpression of Nitrate Transporter 1/Peptide Gene OsNPF7.6 Increases Rice Yield and Nitrogen Use Efficiency

Overuse of nitrogen fertilizer in fields has raised production costs, and caused environmental problems. Improving nitrogen use efficiency (NUE) of rice is essential for sustainable agriculture. Here we report the cloning, characterization and roles for rice of OsNPF7.6, a member of the nitrate transporter 1/peptide transporter family (NPF). The OsNPF7.6 protein is located in the plasma membrane, expressed in each tissue at all stages and is significantly regulated by nitrate in rice. Our study shows that the overexpression of OsNPF7.6 can increase the nitrate uptake rate of rice. Additionally, field experiments showed that OsNPF7.6 overexpression increased the total tiller number per plant and the grain weight per panicle, thereby improving grain yield and agronomic NUE in rice. Thus, OsNPF7.6 can be applied to be a novel target gene for breeding rice varieties with high NUE, and provide a reference for breeding higher yielding rice.

Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings

Nitrogen is not only a macronutrient essential for crop growth and development, but also one of the most critical nutrients in farmland ecosystem. Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and eco-environment damage. Therefore, mining low-nitrogen tolerant rice genes and improving nitrogen use efficiency are of great significance to the sustainable development of agriculture. This study was conducted by Genome-wide association study on a basis of two root morphological traits (root length and root diameter) and 788,396 SNPs of a natural population of 295 rice varieties. The transcriptome of low-nitrogen tolerant variety (Longjing 31) and low-nitrogen sensitive variety (Songjing 10) were sequenced between low and high nitrogen treatments. A total of 35 QTLs containing 493 genes were mapped. 3085 differential expressed genes were identified. Among these 493 genes, 174 genes showed different haplotype patterns. There were significant phenotype differences among different haplotypes of 58 genes with haplotype differences. These 58 genes were hypothesized as candidate genes for low nitrogen tolerance related to root morphology. Finally, six genes (Os07g0471300, Os11g0230400, Os11g0229300, Os11g0229400, Os11g0618300 and Os11g0229333) which expressed differentially in Longjing 31 were defined as more valuable candidate genes for low-nitrogen tolerance. The results revealed the response characteristics of rice to low-nitrogen, and provided insights into regulatory mechanisms of rice to nitrogen deficiency.

Superior Haplotypes for Early Root Vigor Traits in Rice Under Dry Direct Seeded Low Nitrogen Condition Through Genome Wide Association Mapping

Water and land resources have been aggressively exploited in the recent decades to meet the growing demands for food. The changing climate has prompted rice scientists and farmers of the tropics and subtropics to adopt the direct seeded rice (DSR) system. DSR system of rice cultivation significantly reduces freshwater consumption and labor requirements, while increasing system productivity, resource use efficiency, and reducing greenhouse gas emissions. Early root vigor is an essential trait required in an ideal DSR system of rice cultivation to ensure a good crop stand, adequate uptake of water, nutrients and compete with weeds. The aus subpopulation which is adapted for DSR was evaluated to understand the biology of early root growth under limited nitrogen conditions over two seasons under two-time points (14 and 28 days). The correlation study identified a positive association between shoot dry weight and root dry weight. The genome-wide association study was conducted on root traits of 14 and 28 days with 2 million single-nucleotide polymorphisms (SNPs) using an efficient mixed model. QTLs over a significant threshold of p < 0.0001 and a 10% false discovery rate were selected to identify genes involved in root growth related to root architecture and nutrient acquisition from 97 QTLs. Candidate genes under these QTLs were explored. On chromosome 4, around 30 Mbp are two important peptide transporters (PTR5 and PTR6) involved in mobilizing nitrogen in the root during the early vegetative stage. In addition, several P transporters and expansin genes with superior haplotypes are discussed. A novel QTL from 21.12 to 21.46 Mb on chromosome 7 with two linkage disequilibrium (LD) blocks governing root length at 14 days were identified. The QTLs/candidate genes with superior haplotype for early root vigor reported here could be explored further to develop genotypes for DSR conditions.

The importance of utilizing nitrate (NO3-) over ammonium (NH4+) as nitrogen source during detoxification of exogenous thiocyanate (SCN-) in Oryza sativa

Thiocyanate (SCN^-) is a nitrogen-containing pollutant, which can be involved in the nitrogen (N) cycle and interferes with plant growth. The current study highlights a new insight into the N (nitrate [NO₃^-] and ammonium [NH₄⁺]) utilization ways in rice seedlings under SCN^- exposure to clarify the interactive effect on uptake and assimilation between these N-containing chemicals. Phenotypically, relative growth rates (RGR) of NO₃^--fed seedlings were significantly higher than NH₄⁺-fed rice seedlings at the same SCN^- concentration. Both N fertilizations have no significant influence on SCN^- content and its assimilation in rice seedlings. However, significant accumulation of NO₃^- and NH₄⁺ were detected in shoots prior to roots under SCN^- stress. Enzymatic assay and mRNA analysis showed that the carbonyl sulfide (COS) pathway of SCN^- degradation occurred in both roots and shoots of NO₃^--fed seedlings but only evident in roots of NH₄⁺-fed seedlings. Moreover, the effect of SCN^- on the activity of nitrate reductase (NR), glutamine synthetase (GS), and glutamate synthase (GOGAT) was negligible in NO₃^--fed seedlings, while GOGAT activity was significantly inhibited in shoots of NH₄⁺-fed seedlings. Nitrogen use efficiency (NUE) estimation provided positive evidence in utilizing NO₃^- over NH₄⁺ as the main N source to support rice seedling growth during detoxification of exogenous SCN^-. Overall, SCN^- pollution has unexpectedly changed the rice preference for N source which shifted from NH₄⁺ to NO₃^-, suggesting that the interactions of SCN^- with different N sources in terms of uptake and assimilation in rice plants should not be overlooked, especially at the plant N nutritional level.

Comparative Transcriptomic Analyses of Nitrate-Response in Rice Genotypes With Contrasting Nitrogen Use Efficiency Reveals Common and Genotype-Specific Processes, Molecular Targets and Nitrogen Use Efficiency-Candidates

The genetic basis for nitrogen (N)-response and N use efficiency (NUE) must be found in N-responsive gene expression or protein regulation. Our transcriptomic analysis of nitrate response in two contrasting rice genotypes of Oryza sativa ssp. Indica (Nidhi with low NUE and Panvel1 with high NUE) revealed the processes/functions underlying differential N-response/NUE. The microarray analysis of low nitrate response (1.5 mM) relative to normal nitrate control (15 mM) used potted 21-days old whole plants. It revealed 1,327 differentially expressed genes (DEGs) exclusive to Nidhi and 666 exclusive to Panvel1, apart from 70 common DEGs, of which 10 were either oppositely expressed or regulated to different extents. Gene ontology analyses revealed that photosynthetic processes were among the very few processes common to both the genotypes in low N response. Those unique to Nidhi include cell division, nitrogen utilization, cytoskeleton, etc. in low N-response, whereas those unique to Panvel1 include signal transduction, protein import into the nucleus, and mitochondria. This trend of a few common but mostly unique categories was also true for transporters, transcription factors, microRNAs, and post-translational modifications, indicating their differential involvement in Nidhi and Panvel1. Protein-protein interaction networks constructed using DEG-associated experimentally validated interactors revealed subnetworks involved in cytoskeleton organization, cell wall, etc. in Nidhi, whereas in Panvel1, it was chloroplast development. NUE genes were identified by selecting yield-related genes from N-responsive DEGs and their co-localization on NUE-QTLs revealed the differential distribution of NUE-genes between genotypes but on the same chromosomes 1 and 3. Such hotspots are important for NUE breeders.

The Role of Membrane Transporters in Plant Growth and Development, and Abiotic Stress Tolerance

The proteins of membrane transporters (MTs) are embedded within membrane-bounded organelles and are the prime targets for improvements in the efficiency of water and nutrient transportation. Their function is to maintain cellular homeostasis by controlling ionic movements across cellular channels from roots to upper plant parts, xylem loading and remobilization of sugar molecules from photosynthesis tissues in the leaf (source) to roots, stem and seeds (sink) via phloem loading. The plant's entire source-to-sink relationship is regulated by multiple transporting proteins in a highly sophisticated manner and driven based on different stages of plant growth and development (PG&D) and environmental changes. The MTs play a pivotal role in PG&D in terms of increased plant height, branches/tiller numbers, enhanced numbers, length and filled panicles per plant, seed yield and grain quality. Dynamic climatic changes disturbed ionic balance (salt, drought and heavy metals) and sugar supply (cold and heat stress) in plants. Due to poor selectivity, some of the MTs also uptake toxic elements in roots negatively impact PG&D and are later on also exported to upper parts where they deteriorate grain quality. As an adaptive strategy, in response to salt and heavy metals, plants activate plasma membranes and vacuolar membrane-localized MTs that export toxic elements into vacuole and also translocate in the root's tips and shoot. However, in case of drought, cold and heat stresses, MTs increased water and sugar supplies to all organs. In this review, we mainly review recent literature from Arabidopsis, halophytes and major field crops such as rice, wheat, maize and oilseed rape in order to argue the global role of MTs in PG&D, and abiotic stress tolerance. We also discussed gene expression level changes and genomic variations within a species as well as within a family in response to developmental and environmental cues.

Genetic Engineering and Genome Editing for Improving Nitrogen Use Efficiency in Plants

Low nitrogen availability is one of the main limiting factors for plant growth and development, and high doses of N fertilizers are necessary to achieve high yields in agriculture. However, most N is not used by plants and pollutes the environment. This situation can be improved by enhancing the nitrogen use efficiency (NUE) in plants. NUE is a complex trait driven by multiple interactions between genetic and environmental factors, and its improvement requires a fundamental understanding of the key steps in plant N metabolism—uptake, assimilation, and remobilization. This review summarizes two decades of research into bioengineering modification of N metabolism to increase the biomass accumulation and yield in crops. The expression of structural and regulatory genes was most often altered using overexpression strategies, although RNAi and genome editing techniques were also used. Particular attention was paid to woody plants, which have great economic importance, play a crucial role in the ecosystems and have fundamental differences from herbaceous species. The review also considers the issue of unintended effects of transgenic plants with modified N metabolism, e.g., early flowering—a research topic which is currently receiving little attention. The future prospects of improving NUE in crops, essential for the development of sustainable agriculture, using various approaches and in the context of global climate change, are discussed.

Strategies for engineering improved nitrogen use efficiency in crop plants via redistribution and recycling of organic nitrogen

Global use of nitrogen (N) fertilizers has increased sevenfold from 1960 to 1995 but much of the N applied is lost to the environment. Modifying the temporal and spatial distribution of organic N within the plant can lead to improved grain yield and/or grain protein content for the same or reduced N fertilizer inputs. Biotechnological approaches to modify whole plant distribution of amino acids and ureides has proven successful in several crop species. Manipulating selective autophagy pathways in crops has also improved N remobilization efficiency to sink tissues whilst the contribution of ribophagy, RNA and purine catabolism to N recycling in crops is still too early to foretell. Improved recycling and remobilization of N must exploit N-stress responsive transcriptional regulators, N-sensing or phloem-localized promotors and genetic variation for N-responsive traits.

Transporters and transcription factors gene families involved in improving nitrogen use efficiency (NUE) and assimilation in rice (Oryza sativa L.)

Nitrogen (N) as a macronutrient is an important determinant of plant growth. The excessive usage of chemical fertilizers is increasing environmental pollution; hence, the improvement of crop's nitrogen use efficiency (NUE) is imperative for sustainable agriculture. N uptake, transportation, assimilation, and remobilization are four important determinants of plant NUE. Oryza sativa L. (rice) is a staple food for approximately half of the human population, around the globe and improvement in rice yield is pivotal for rice breeders. The N transporters, enzymes indulged in N assimilation, and several transcription factors affect the rice NUE and subsequent yield. Although, a couple of improvements have been made regarding rice NUE, the knowledge about regulatory mechanisms operating NUE is scarce. The current review provides a precise knowledge of how rice plants detect soil N and how this detection is translated into the language of responses that regulate the growth. Additionally, the transcription factors that control N-associated genes in rice are discussed in detail. This mechanistic insight will help the researchers to improve rice yield with minimized use of chemical fertilizers.

Genetic basis and network underlying synergistic roots and shoots biomass accumulation revealed by genome-wide association studies in rice

Genetic basis and network studies underlying synergistic biomass accumulation of roots and shoots (SBA) are conducive for rational design of high-biomass rice breeding. In this study, association signals for root weight, shoot weight, and the ratio of root-to-shoot mass (R/S) were identified using 666 rice accessions by genome-wide association study, together with their sub-traits, root length, root thickness and shoot length. Most association signals for root weight and shoot weight did not show association with their sub-traits. Based on the results, we proposed a top-to-bottom model for SBA, i.e. root weight, shoot weight and R/S were determined by their highest priority in contributing to biomass in the regulatory pathway, followed by a lower priority pathway for their sub-traits. Owing to 37 enriched clusters with more than two association signals identified, the relationship among the six traits could be also involved in linkage and pleiotropy. Furthermore, a discrimination of pleiotropy and LD at sequencing level using the known gene OsPTR9 for root weight, R/S and root length was provided. The results of given moderate correlation between traits and their corresponding sub-traits, and moderate additive effects between a trait and the accumulation of excellent alleles corresponding to its sub-traits supported a bottom-to-top regulation model for SBA. This model depicted each lowest-order trait (root length, root thickness and shoot length) was determined by its own regulation loci, and competition among different traits, as well as the pleiotropy and LD. All above ensure the coordinated development of each trait and the accumulation of the total biomass, although the predominant genetic basis of SBA is still indistinguishable. The presentation of the above two models and evidence of this study shed light on dissecting the genetic architecture of SBA.

Novel plant breeding techniques to advance nitrogen use efficiency in rice: A review

Recently, there has been a remarkable increase in rice production owing to genetic improvement and increase in application of synthetic fertilizers. For sustainable agriculture, there is dire need to maintain a balance between profitability and input cost. To meet the steady growing demands of the farming community, researchers are utilizing all available resources to identify nutrient use efficient germplasm, but with very little success. Therefore, it is essential to understand the underlying genetic mechanism controlling nutrients efficiency, with the nitrogen use efficiency (NUE) being the most important trait. Information regarding genetic factors controlling nitrogen (N) transporters, assimilators, and remobilizers can help to identify candidate germplasms via high-throughput technologies. Large-scale field trials have provided morphological, physiological, and biochemical trait data for the detection of genomic regions controlling NUE. The functional aspects of these attributes are time-consuming, costly, labor-intensive, and less accurate. Therefore, the application of novel plant breeding techniques (NPBTs) with context to genome engineering has opened new avenues of research for crop improvement programs. Most recently, genome editing technologies (GETs) have undergone enormous development with various versions from Cas9, Cpf1, base, and prime editing. These GETs have been vigorously adapted in plant sciences for novel trait development to insure food quantity and quality. Base editing has been successfully applied to improve NUE in rice, demonstrating the potential of GETs to develop germplasms with improved resource use efficiency. NPBTs continue to face regulatory setbacks in some countries due to genome editing being categorized in the same category as genetically modified (GM) crops. Therefore, it is essential to involve all stakeholders in a detailed discussion on NPBTs and to formulate uniform policies tackling biosafety, social, ethical, and environmental concerns. In the current review, we have discussed the genetic mechanism of NUE and NPBTs for crop improvement programs with proof of concepts, transgenic and GET application for the development of NUE germplasms, and regulatory aspects of genome edited crops with future directions considering NUE.

Genetic regulation of the traits contributing to wheat nitrogen use efficiency

High nitrogen application aimed at increasing crop yield is offset by higher production costs and negative environmental consequences. For wheat, only one third of the applied nitrogen is utilized, which indicates there is scope for increasing Nitrogen Use Efficiency (NUE). However, achieving greater NUE is challenged by the complexity of the trait, which comprises processes associated with nitrogen uptake, transport, reduction, assimilation, translocation and remobilization. Thus, knowledge of the genetic regulation of these processes is critical in increasing NUE. Although primary nitrogen uptake and metabolism-related genes have been well studied, the relative influence of each towards NUE is not fully understood. Recent attention has focused on engineering transcription factors and identification of miRNAs acting on expression of specific genes related to NUE. Knowledge obtained from model species needs to be translated into wheat using recently-released whole genome sequences, and by exploring genetic variations of NUE-related traits in wild relatives and ancient germplasm. Recent findings indicate the genetic basis of NUE is complex. Pyramiding various genes will be the most effective approach to achieve a satisfactory level of NUE in the field.

Genome-wide identification of the peptide transporter family in rice and analysis of the PTR expression modulation in two near-isogenic lines with different nitrogen use efficiency

BACKGROUND

Nitrogen (N) is a major nutrient element for crop growth. In plants, the members of the peptide transporter (PTR) gene family may involve in nitrate uptake and transport. Here, we identified PTR gene family in rice and analyzed their expression profile in near-isogenic lines.

RESULTS

We identified 96, 85 and 78 PTR genes in Nipponbare, R498 and Oryza glaberrima, and the phylogenetic trees were similar in Asian cultivated rice and African cultivated rice. The number of PTR genes was higher in peanut (125) and soybean (127). The 521 PTR genes in rice, maize, sorghum, peanut, soybean and Arabidopsis could be classified into 4 groups, and their distribution was different between monocots and dicots. In Nipponbare genome, the 25 PTR genes were distributed in 5 segmental duplication regions on chromosome 1, 2, 3, 4, 5, 7, 8, 9, and 10. The PTR genes in rice have 0-11 introns and 1-12 exons, and 16 of them have the NPF (NRT1/PTR family) domain. The results of RNA-seq showed that the number of differentially expressed genes (DEGs) between NIL15 and NIL19 at three stages were 928, 1467, and 1586, respectively. Under low N conditions, the number of differentially expressed PTR genes increased significantly. The RNA-seq data was analyzed using WGCNA to predict the potential interaction between genes. We classified the genes with similar expression pattern into one module, and obtained 25 target modules. Among these modules, three modules may be involved in rice N uptake and utilization, especially the brown module, in which hub genes were annotated as protein kinase that may regulate rice N metabolism.

CONCLUSIONS

In this study, we comprehensively analyzed the PTR gene family in rice. 96 PTR genes were identified in Nippobare genome and 25 of them were located on five large segmental duplication regions. The Ka/Ks ratio indicated that many PTR genes had undergone positive selection. The RNA-seq results showed that many PTR genes were involved in rice nitrogen use efficiency (NUE), and protein kinases might play an important role in this process. These results provide a fundamental basis to improve the rice NUE via molecular breeding.

Genomic Breeding of Green Super Rice Varieties and Their Deployment in Asia and Africa

KEY MESSAGE

The "Green Super Rice" (GSR) project aims to fundamentally transform crop production techniques and promote the development of green agriculture based on functional genomics and breeding of GSR varieties by whole-genome breeding platforms. Rice (Oryza sativa L.) is one of the leading food crops of the world, and the safe production of rice plays a central role in ensuring food security. However, the conflicts between rice production and environmental resources are becoming increasingly acute. For this reason, scientists in China have proposed the concept of Green Super Rice for promoting resource-saving and environment-friendly rice production, while still achieving a yield increase and quality improvement. GSR is becoming one of the major goals for agricultural research and crop improvement worldwide, which aims to mine and use vital genes associated with superior agronomic traits such as high yield, good quality, nutrient efficiency, and resistance against insects and stresses; establish genomic breeding platforms to breed and apply GSR; and set up resource-saving and environment-friendly cultivation management systems. GSR has been introduced into eight African and eight Asian countries and has contributed significantly to rice cultivation and food security in these countries. This article mainly describes the GSR concept and recent research progress, as well as the significant achievements in GSR breeding and its application.

Improvement of nutrient use efficiency in rice: current toolbox and future perspectives

Modern agriculture relies heavily on chemical fertilizers, especially in terms of cereal production. The excess application of fertilizers not only increases production cost, but also causes severe environmental problems. As one of the major cereal crops, rice (Oryza sativa L.) provides the staple food for nearly half of population worldwide, especially in developing countries. Therefore, improving rice yield is always the priority for rice breeding. Macronutrients, especially nitrogen (N) and phosphorus (P), are two most important players for the grain yield of rice. However, with economic development and improved living standard, improving nutritional quality such as micronutrient contents in grains has become a new goal in order to solve the "hidden hunger." Micronutrients, such as iron (Fe), zinc (Zn), and selenium (Se), are critical nutritional elements for human health. Therefore, breeding the rice varieties with improved nutrient use efficiency (NUE) is thought to be one of the most feasible ways to increase both grain yield and nutritional quality with limited fertilizer input. In this review, we summarized the progresses in molecular dissection of genes for NUE by reverse genetics on macronutrients (N and P) and micronutrients (Fe, Zn, and Se), exploring natural variations for improving NUE in rice; and also, the current genetic toolbox and future perspectives for improving rice NUE are discussed.

Overexpression of OsMYB305 in Rice Enhances the Nitrogen Uptake Under Low-Nitrogen Condition

Excessive nitrogen fertilizer application causes severe environmental degradation and drives up agricultural production costs. Thus, improving crop nitrogen use efficiency (NUE) is essential for the development of sustainable agriculture. Here, we characterized the roles of the MYB transcription factor OsMYB305 in nitrogen uptake and assimilation in rice. OsMYB305 encoded a transcriptional activator and its expression was induced by N deficiency in rice root. Under low-N condition, OsMYB305 overexpression significantly increased the tiller number, shoot dry weight and total N concentration. In the roots of OsMYB305-OE rice lines, the expression of OsNRT2.1, OsNRT2.2, OsNAR2.1, and OsNiR2 was up-regulated and 15NO3 - influx was significantly increased. In contrast, the expression of lignocellulose biosynthesis-related genes was repressed so that cellulose content decreased, and soluble sugar concentration increased. Certain intermediates in the glycolytic pathway and the tricarboxylic acid cycle were significantly altered and NADH-GOGAT, Pyr-K, and G6PDH were markedly elevated in the roots of OsMYB305-OE rice lines grown under low-N condition. Our results revealed that OsMYB305 overexpression suppressed cellulose biosynthesis under low-nitrogen condition, thereby freeing up carbohydrate for nitrate uptake and assimilation and enhancing rice growth. OsMYB305 is a potential molecular target for increasing NUE in rice.

Internal ammonium excess induces ROS-mediated reactions and causes carbon scarcity in rice

BACKGROUND

Overuse of nitrogen fertilizers is often a major practice to ensure sufficient nitrogen demand of high-yielding rice, leading to persistent NH4+ excess in the plant. However, this excessive portion of nitrogen nutrient does not correspond to further increase in grain yields. For finding out the main constraints related to this phenomenon, the performance of NH4+ excess in rice plant needs to be clearly addressed beyond the well-defined root growth adjustment. The present work isolates an acute NH4+ excess condition in rice plant from causing any measurable growth change and analyses the initial performance of such internal NH4+ excess.

RESULTS

We demonstrate that the acute internal NH4+ excess in rice plant accompanies readily with a burst of reactive oxygen species (ROS) and initiates the downstream reactions. At the headstream of carbon production, photon caption genes and the activity of primary CO2 fixation enzymes (Rubisco) are evidently suppressed, indicating a reduction in photosynthetic carbon income. Next, the vigorous induction of glutathione transferase (GST) genes and enzyme activities along with the rise of glutathione (GSH) production suggest the activation of GSH cycling for ROS cleavage. Third, as indicated by strong induction of glycolysis / glycogen breakdown related genes in shoots, carbohydrate metabolisms are redirected to enhance the production of energy and carbon skeletons for the cost of ROS scavenging. As the result of the development of these defensive reactions, a carbon scarcity would accumulatively occur and lead to a growth inhibition. Finally, a sucrose feeding cancels the ROS burst, restores the activity of Rubisco and alleviates the demand for the activation of GSH cycling.

CONCLUSION

Our results demonstrate that acute NH4+ excess accompanies with a spontaneous ROS burst and causes carbon scarcity in rice plant. Therefore, under overuse of N fertilizers carbon scarcity is probably a major constraint in rice plant that limits the performance of nitrogen.

Nitrogen Use Efficiency Phenotype and Associated Genes: Roles of Germination, Flowering, Root/Shoot Length and Biomass

Crop improvement for Nitrogen Use Efficiency (NUE) requires a well-defined phenotype and genotype, especially for different N-forms. As N-supply enhances growth, we comprehensively evaluated 25 commonly measured phenotypic parameters for N response using 4 N treatments in six indica rice genotypes. For this, 32 replicate potted plants were grown in the green-house on nutrient-depleted sand. They were fertilized to saturation with media containing either nitrate or urea as the sole N source at normal (15 mM N) or low level (1.5 mM N). The variation in N-response among genotypes differed by N form/dose and increased developmentally from vegetative to reproductive parameters. This indicates survival adaptation by reinforcing variation in every generation. Principal component analysis segregated vegetative parameters from reproduction and germination. Analysis of variance revealed that relative to low level, normal N facilitated germination, flowering and vegetative growth but limited yield and NUE. Network analysis for the most connected parameters, their correlation with yield and NUE, ranking by Feature selection and validation by Partial least square discriminant analysis enabled shortlisting of eight parameters for NUE phenotype. It constitutes germination and flowering, shoot/root length and biomass parameters, six of which were common to nitrate and urea. Field-validation confirmed the NUE differences between two genotypes chosen phenotypically. The correspondence between multiple approaches in shortlisting parameters for NUE makes it a novel and robust phenotyping methodology of relevance to other plants, nutrients or other complex traits. Thirty-Four N-responsive genes associated with the phenotype have also been identified for genotypic characterization of NUE.

Altered expression of OsNPF7.1 and OsNPF7.4 differentially regulates tillering and grain yield in rice

The rice nitrate and di/tripeptide transporter (NPF) gene family plays an indispensable role in nitrogen transport and plant growth. In this study, 18 alternatively spliced OsNPF genes with 36 different forms of mRNAs were identified, and two of these, namely OsNPF7.1 and OsNPF7.4, showed opposite expression patterns in axillary buds under different nitrogen concentrations. Our results indicate that the expression levels of OsNPF7.1 and OsNPF7.4 determine the axillary bud outgrowth, especially for the second bud, and subsequently influence the tiller number in rice. The overexpression of either of the variants of OsNPF7.1 or the knockout of OsNPF7.4 increased the seedling biomass as well as the tiller number, filled grain number, and grain yield in rice. However, the RNAi-mediated silencing of OsNPF7.1 or the overexpression of either of the variants of OsNPF7.4 had an opposite effect. The overexpression of OsNPF7.1 or OsNPF7.4 could improve the uptake of nitrate, but the OsNPF7.4-overexpressing plants had lower biomass. It is possible that excessive nitrate in the OsNPF7.4-overexpressing plants led to the accumulation of amino acids in the leaf sheath, which inhibited seedling biomass. In addition, the reduced reutilization of nitrate in the seedlings also limited the plant biomass. However, the moderate increase in nitrate and amino acid concentrations in the OsNPF7.1-overexpressing plants could promote seedling biomass and enhance grain yield. In conclusion, our data suggest that different members in the NPF family have different roles in rice, and this study suggests an alternative way to modify rice architecture and enhance grain yield by regulating the expression of OsNPF7.1 and OsNPF7.4.

Target genes for plant productivity improvement

The use of chemical fertilizers and pesticides, as well as the development of high-yielding varieties enabled substantial increase in crop productivity during the 20th century. However, the increase in yield over the last two decades has been slower. It is thought that further improvement in productivity of the major crop species using traditional cultivation methods is limited. Therefore, the use of genetic engineering seems to be a promising approach. There is ongoing research concerning genes that have an impact on plant growth, development and yield. The proteins and miRNAs encoded by these genes participate in a variety of processes, such as growth regulation, assimilate transport and partitioning as well as macronutrient uptake and metabolism. This paper presents the major directions in research concerning genes that may be targets of genetic engineering aimed to improve plant productivity.

Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions

A robust (long and thick) root system is characteristic of upland japonica rice adapted to drought conditions. Using deep sequencing and large scale phenotyping data of 795 rice accessions and an integrated strategy combining results from high resolution mapping by GWAS and linkage mapping, comprehensive analyses of genomic, transcriptomic and haplotype data, we identified large numbers of QTLs affecting rice root length and thickness (RL and RT) and shortlisted relatively few candidate genes for many of the identified small-effect QTLs. Forty four and 97 QTL candidate genes for RL and RT were identified, and five of the RL QTL candidates were validated by T-DNA insertional mutation; all have diverse functions and are involved in root development. This work demonstrated a powerful strategy for highly efficient cloning of moderate- and small-effect QTLs that is difficult using the classical map-based cloning approach. Population analyses of the 795 accessions, 202 additional upland landraces, and 446 wild rice accessions based on random SNPs and SNPs within robust loci suggested that there could be much less diversity in robust-root candidate genes among upland japonica accessions than in other ecotypes. Further analysis of nucleotide diversity and allele frequency in the robust loci among different ecotypes and wild rice accessions showed that almost all alleles could be detected in wild rice, and pyramiding of robust-root alleles could be an important genetic characteristic of upland japonica. Given that geographical distribution of upland landraces, we suggest that during domestication of upland japonica, the strongest pyramiding of robust-root alleles makes it a unique ecotype adapted to aerobic conditions.

Asian cultivated rice is well-known for its rich-within-species diversity with two major subspecies, indica and japonica and subpopulation differentiation. A robust (long and thick) root system that is characteristic of upland japonica rice represents a predominant ecotype grown under aerobic and rain-fed conditions. In this study, we identified candidate genes for root length and root thickness, and validated five root length candidates by T-DNA insertional mutations. Further analyses of an Asian cultivated and wild rice population were performed based on random SNPs and SNPs within robust loci. The findings hold promise for application in improving drought resistance and also reveal the adaptive domestication history of upland rice as a unique Asian cultivated rice ecotype.

Molecular Genetics and Breeding for Nutrient Use Efficiency in Rice

In the coming decades, rice production needs to be carried out sustainably to keep the balance between profitability margins and essential resource input costs. Many fertilizers, such as N, depend primarily on fossil fuels, whereas P comes from rock phosphates. How long these reserves will last and sustain agriculture remains to be seen. Therefore, current agricultural food production under such conditions remains an enormous and colossal challenge. Researchers have been trying to identify nutrient use-efficient varieties over the past few decades with limited success. The concept of nutrient use efficiency is being revisited to understand the molecular genetic basis, while much of it is not entirely understood yet. However, significant achievements have recently been observed at the molecular level in nitrogen and phosphorus use efficiency. Breeding teams are trying to incorporate these valuable QTLs and genes into their rice breeding programs. In this review, we seek to identify the achievements and the progress made so far in the fields of genetics, molecular breeding and biotechnology, especially for nutrient use efficiency in rice.

Nitrate Transport, Signaling, and Use Efficiency

Nitrogen accounts for approximately 60% of the fertilizer consumed each year; thus, it represents one of the major input costs for most nonlegume crops. Nitrate is one of the two major forms of nitrogen that plants acquire from the soil. Mechanistic insights into nitrate transport and signaling have enabled new strategies for enhancing nitrogen utilization efficiency, for lowering input costs for farming, and, more importantly, for alleviating environmental impacts (e.g., eutrophication and production of the greenhouse gas N₂O). Over the past decade, significant progress has been made in understanding how nitrate is acquired from the surroundings, how it is efficiently distributed into different plant tissues in response to environmental changes, how nitrate signaling is perceived and transmitted, and how shoot and root nitrogen status is communicated. Several key components of these processes have proven to be novel tools for enhancing nitrate- and nitrogen-use efficiency. In this review, we focus on the roles of NRT1 and NRT2 in nitrate uptake and nitrate allocation among different tissues; we describe the functions of the transceptor NRT1.1, transcription factors, and small signaling peptides in nitrate signaling and tissue communication; and we compile the new strategies for improving nitrogen-use efficiency.

Effect of Functionalised and Non-Functionalised Carbon Nanotubes-Urea Fertilizer on the Growth of Paddy

The roles of multi-walled carbon nanotubes (MWNTs) and functionalised multiwalled carbon nanotubes (fMWNTs) in enhancing the efficacy of urea fertilizer (UF) as plant nutrition for local MR219 paddy variety was investigated. The MWNTs and fMWNTs were grafted onto UF to produce UF-MWNTs fertilizer with three different conditions, coded as FMU1 (0.6 wt. % fMWNTs), FMU2 (0.1 wt. % fMWNTs) and MU (0.6 wt. % MWNTs. The batches of MR219 paddy were systematically grown in accordance to the general practice performed by the Malaysian Agricultural Research and Development Institute (MARDI). The procedure was conducted using a pot under exposure to natural light at three different fertilization times; after a certain number of days of sowing (DAS) at 14, 35 and 55 days. Interestingly, it was found that the crop growth of plants treated with FMU1 and FMU2 significantly increased by 22.6% and 38.5% compared to plants with MU addition. Also, paddy treated with FMU1 produced 21.4% higher number of panicles and 35% more grain yield than MU while paddy treated with FMU2 gave 28.6% more number of panicles and 36% higher grain yield than MU, which implies the advantage of fMWNTs over MWNTs to be combined with UF as plant nutrition. The chemical composition and morphology of UF-MWNTs fertilizers which is further characterised by FTiR and FESEM confirmed the successful and homogeneous grafting of UF onto the fMWNTs.

Rice Functional Genomics Research: Past Decade and Future

Rice (Oryza sativa) is a major staple food crop for more than 3.5 billion people worldwide. Understanding the regulatory mechanisms of complex agronomic traits in rice is critical for global food security. Rice is also a model plant for genomics research of monocotyledons. Thanks to the rapid development of functional genomic technologies, over 2000 genes controlling important agronomic traits have been cloned, and their molecular biological mechanisms have also been partially characterized. Here, we briefly review the advances in rice functional genomics research during the past 10 years, including a summary of functional genomics platforms, genes and molecular regulatory networks that regulate important agronomic traits, and newly developed tools for gene identification. These achievements made in functional genomics research will greatly facilitate the development of green super rice. We also discuss future challenges and prospects of rice functional genomics research.

Rice nitrate transporter OsNPF7.2 positively regulates tiller number and grain yield

BACKGROUND

Rice tiller number is one of the most important factors that determine grain yield, while nitrogen is essential for the crop growth and development, especially for tiller formation. Genes involved in nitrogen use efficiency processes have been identified in the previous studies, however, only a small number of these genes have been found to improve grain yield by promoting tillering.

RESULTS

We constructed over-expression (OX) lines and RNA-interference (Ri) lines, and selected a mutant of OsNPF7.2, a low-affinity nitrate transporter. Our analyses showed that rice tiller number and grain yield were significantly increased in OX lines, whereas Ri lines and mutant osnpf7.2 had fewer tiller number and lower grain yield. Under different nitrate concentrations, tiller buds grew faster in OX lines than in WT, but they grew slower in Ri lines and mutant osnpf7.2. These results indicated that altered expression of OsNPF7.2 plays a significant role in the control of tiller bud growth and regulation of tillering. Elevated expression of OsNPF7.2 also improved root length, root number, fresh weight, and dry weight. However, reduced expression of OsNPF7.2 had the opposite result on these characters. OsNPF7.2 OX lines showed more significantly enhanced influx of nitrate and had a higher nitrate concentration than WT. The levels of gene transcripts related to cytokinin pathway and cell cycle in tiller bud, and cytokinins concentration in tiller basal portion were higher in OX lines than that in WT, suggesting that altered expression of OsNPF7.2 controlled tiller bud growth and root development by regulating cytokinins content and cell cycle in plant cells. Altered expression of OsNPF7.2 also was responsible for the change in expression of the genes involved in strigolactone pathway, such as D27, D17, D10, Os900, Os1400, D14, D3, and OsFC1.

CONCLUSION

Our results suggested that OsNPF7.2 is a positive regulator of nitrate influx and concentration, and that it also regulates cell division in tiller bud and alters expression of genes involved in cytokinin and strigolactone pathways, resulting in the control over rice tiller number. Since elevated expression of OsNPF7.2 is capable of improving rice grain yield, this gene might be applied to high-yield rice breeding.

Genome Mining of Plant NPFs Reveals Varying Conservation of Signature Motifs Associated With the Mechanism of Transport

Nitrogen is essential for all living species and may be taken up from the environment in different forms like nitrate or peptides. In plants, members of a transporter family named NPFs transport nitrate and peptides across biological membranes. NPFs are phylogenetically related to a family of peptide transporters (PTRs) or proton-coupled oligopeptide transporters (POTs) that are evolutionarily conserved in all organisms except in Archaea. POTs are present in low numbers in bacteria, algae and animals. NPFs have expanded in plants and evolved to transport a wide range of substrates including phytohormones and glucosinolates. Functional studies have shown that most NPFs, like POTs, operate as symporters with simultaneous inwardly directed movement of protons. Here we focus on four structural features of NPFs/POTs/PTRs that have been shown by structural and functional studies to be essential to proton-coupled symport transport. The first two features are implicated in proton binding and transport: a conserved motif named ExxER/K, located in the first transmembrane helix (TMH1) and a D/E residue in TMH7 that has been observed in some bacterial and algal transporters. The third and fourth features are two inter-helical salt bridges between residues on TMH1 and TMH7 or TMH4 and TMH10. To understand if the mechanism of transport is conserved in NPFs with the expansion to novel substrates, we collected NPFs sequences from 42 plant genomes. Sequence alignment revealed that the ExxER/K motif is not strictly conserved and its conservation level is different in the NPF subfamilies. The proton binding site on TMH7 is missing in all NPFs with the exception of two NPFs from moss. The two moss NPFs also have a positively charged amino acid on TMH1 that can form the salt bridge with the TMH7 negative residue. None of the other NPFs we examined harbor residues that can form the TMH1-TMH7 salt bridge. In contrast, the amino acids required to form the TMH4-TMH10 salt bridge are highly conserved in NPFs, with some exceptions. These results support the need for further biochemical and structural studies of individual NPFs for a better understanding of the transport mechanism in this family of transporters.

Two Splicing Variants of OsNPF7.7 Regulate Shoot Branching and Nitrogen Utilization Efficiency in Rice

Rice includes 93 nitrate and peptide transporters family (NPF) members that facilitate the soil uptake and internal reallocation of nitrogen for growth and development. This study demonstrated that OsNPF7.7 had two splicing variants, and altered expression of each variant could regulate shoot branching and nitrogen utilization efficiency (NUtE) in rice. The expression of both variants was down-regulated in the buds by increased nitrogen level in the Japonica rice variety ZH11. The expression level of long-variant OsNPF7.7-1 was higher in panicles at reproductive stage, however, the expression level of short-variant OsNPF7.7-2 was higher in buds and leaves at vegetative stage compared to each other in ZH11. OsNPF7.7-1 was localized in the plasma membrane, whereas OsNPF7.7-2 was localized in the vacuole membrane. Furthermore, the results indicated that the expression level of each variant for OsNPF7.7 determined axillary bud outgrowth, and then influenced the rice tiller number. Overexpression of OsNPF7.7-1 could promote nitrate influx and concentration in root, whereas overexpression of OsNPF7.7-2 could improve ammonium influx and concentration in root. RNAi and osnpf7.7 lines of OsNPF7.7 showed an increased amount of amino acids in leaf sheaths, but a decreased amount in leaf blades, which affected nitrogen allocation and plant growth. The elevated expression of each variant for OsNPF7.7 in ZH11 enhanced NUtE using certain fertilization regimes under paddy field conditions. Moreover, overexpression of each variant for OsNPF7.7 in KY131 increased significantly the filled grain number per plant. Thus, increased each variant of OsNPF7.7 has the potential to improve grain yield and NUtE in rice.

Source and sink mechanisms of nitrogen transport and use

Contents Summary 35 I. Introduction 35 II. Nitrogen acquisition and assimilation 36 III. Root-to-shoot transport of nitrogen 38 IV. Nitrogen storage pools in vegetative tissues 39 V. Nitrogen transport from source leaf to sink 40 VI. Nitrogen import into sinks 42 VII. Relationship between source and sink nitrogen transport processes and metabolism 43 VIII. Regulation of nitrogen transport 43 IX. Strategies for crop improvement 44 X. Conclusions 46 Acknowledgements 47 References 47 SUMMARY: Nitrogen is an essential nutrient for plant growth. World-wide, large quantities of nitrogenous fertilizer are applied to ensure maximum crop productivity. However, nitrogen fertilizer application is expensive and negatively affects the environment, and subsequently human health. A strategy to address this problem is the development of crops that are efficient in acquiring and using nitrogen and that can achieve high seed yields with reduced nitrogen input. This review integrates the current knowledge regarding inorganic and organic nitrogen management at the whole-plant level, spanning from nitrogen uptake to remobilization and utilization in source and sink organs. Plant partitioning and transient storage of inorganic and organic nitrogen forms are evaluated, as is how they affect nitrogen availability, metabolism and mobilization. Essential functions of nitrogen transporters in source and sink organs and their importance in regulating nitrogen movement in support of metabolism, and vegetative and reproductive growth are assessed. Finally, we discuss recent advances in plant engineering, demonstrating that nitrogen transporters are effective targets to improve crop productivity and nitrogen use efficiency. While inorganic and organic nitrogen transporters were examined separately in these studies, they provide valuable clues about how to successfully combine approaches for future crop engineering.

Engineering crop nutrient efficiency for sustainable agriculture

Increasing crop yields can provide food, animal feed, bioenergy feedstocks and biomaterials to meet increasing global demand; however, the methods used to increase yield can negatively affect sustainability. For example, application of excess fertilizer can generate and maintain high yields but also increases input costs and contributes to environmental damage through eutrophication, soil acidification and air pollution. Improving crop nutrient efficiency can improve agricultural sustainability by increasing yield while decreasing input costs and harmful environmental effects. Here, we review the mechanisms of nutrient efficiency (primarily for nitrogen, phosphorus, potassium and iron) and breeding strategies for improving this trait, along with the role of regulation of gene expression in enhancing crop nutrient efficiency to increase yields. We focus on the importance of root system architecture to improve nutrient acquisition efficiency, as well as the contributions of mineral translocation, remobilization and metabolic efficiency to nutrient utilization efficiency.

OsPTR7 (OsNPF8.1), a Putative Peptide Transporter in Rice, is Involved in Dimethylarsenate Accumulation in Rice Grain

Rice (Oryza sativa) is a major dietary source of arsenic (As) for the population consuming rice as their staple food. Rice grain contains both inorganic As and methylated As species, especially dimethyarsinate (DMA). DMA is highly mobile in long-distance translocation in plants, but the underlying mechanism remains unknown. In the present study, we showed that OsPTR7 (OsNPF8.1), a putative peptide transporter in rice, was permeable to DMA in Xenopus laevis oocytes. Transient expression of the OsPTR7-green fluorescent protein (GFP) in tobacco protoplasts showed that OsPTR7 was localized in the cell plasma membrane. Quantitative real-time PCR analysis showed that OsPTR7 was more highly expressed in the shoots than in the roots at the seedling stage. At the flowering and grain-filling stage, the OsPTR7 transcript was abundant in the leaves, node I and roots. Knockout or knockdown mutants of OsPTR7 had significantly decreased root to shoot translocation of DMA compared with wild-type plants and accumulated less As in the brown rice. In field-grown plants, DMA accounted for 35% of the total As in the brown rice of wild-type plants but was undetectable in the knockout mutant. Our study demonstrates that OsPTR7 is involved in the long-distance translocation of DMA and contributes to the accumulation of DMA in rice grain.

Spatio-temporal dynamics in global rice gene expression (Oryza sativa L.) in response to high ammonium stress

Ammonium (NH₄⁺) is the predominant nitrogen (N) source in many natural and agricultural ecosystems, including flooded rice fields. While rice is known as an NH₄⁺-tolerant species, it nevertheless suffers NH₄⁺ toxicity at elevated soil concentrations. NH₄⁺ excess rapidly leads to the disturbance of various physiological processes that ultimately inhibit shoot and root growth. However, the global transcriptomic response to NH₄⁺ stress in rice has not been examined. In this study, we mapped the spatio-temporal specificity of gene expression profiles in rice under excess NH₄⁺ and the changes in gene expression in root and shoot at various time points by RNA-Seq (Quantification) using Illumina HiSeqTM 2000. By comparative analysis, 307 and 675 genes were found to be up-regulated after 4h and 12h of NH₄⁺ exposure in the root, respectively. In the shoot, 167 genes were up-regulated at 4h, compared with 320 at 12h. According to KEGG analysis, up-regulated DEGs mainly participate in phenylpropanoid (such as flavonoid) and amino acid (such as proline, cysteine, and methionine) metabolism, which is believed to improve NH₄⁺ stress tolerance through adjustment of energy metabolism in the shoot, while defense and signaling pathways, guiding whole-plant acclimation, play the leading role in the root. We furthermore critically assessed the roles of key phytohormones, and found abscisic acid (ABA) and ethylene (ET) to be the major regulatory molecules responding to excess NH₄⁺ and activating the MAPK (mitogen-activated protein kinase) signal-transduction pathway. Moreover, we found up-regulated hormone-associated genes are involved in regulating flavonoid biosynthesis and are regulated by tissue flavonoid accumulation.

Nitrogen use efficiency in crops: lessons from Arabidopsis and rice

Application of chemical fertilizers, especially nitrogen (N), to crops has increased dramatically in the last half century and therefore developing crop varieties with improved N use efficiency (NUE) is urgent for sustainable agriculture. N utilization procedures generally can be divided into uptake, transport, and assimilation. Transporters for nitrate or ammonium acquisition and enzymes for assimilation are among the essential components determining NUE, and many transcription factors also play a pivotal role in regulating N use-associated genes, thereby contributing to NUE. Although some efforts in improving NUE have been made in various plants, the regulatory mechanisms underlying NUE are still elusive, and NUE improvement in crop breeding is very limited. In this review, the crucial components involved in N utilization and the candidates with the potential for NUE improvement in dicot Arabidopsis and monocot rice are summarized. In addition, strategies based on new techniques which can be used for dissecting regulatory mechanisms of NUE and also the possible ways in which NUE can be improved in crops are discussed.

The Rice Peptide Transporter OsNPF7.3 Is Induced by Organic Nitrogen, and Contributes to Nitrogen Allocation and Grain Yield

Nitrogen use efficiency is important for the development of sustainable agriculture. Plants have different transporters to facilitate nitrogen uptake and internal distribution. This study demonstrates that the peptide transporter OsNPF7.3 enhances nitrogen allocation and increases grain yield in rice. OsNPF7.3 is a member of the nitrate transporter 1/peptide transporter family (NPF) and is localized in the vacuolar membrane. Its expression is higher in the lateral roots and stems. Its transcripts concentrate in the vascular bundle and significantly regulated by organic nitrogen sources. The RNAi lines of OsNPF7.3 affect plant growth and cause amino acids to accumulate in leaf sheaths and decrease in the leaf blades. At later stages of reproductive growth, nitrogen degradation accelerates in the leaves of plants over-expressing OsNPF7.3 and the nitrogen is translocated to grains. The tiller numbers, panicles per plant, filled grain numbers per panicle, and grain nitrogen content of the OsNPF7.3 over-expressing plant were more than that of wide type. The elevated gene expression in OsNPF7.3 could enhance nitrogen utilization efficiency in rice paddy.

Organic amendments enhance Pb tolerance and accumulation during micropropagation of Daphne jasminea

The study investigated the effects of organic amendments: pineapple pulp (PP) and agar hydrolyzate (AH), on micropropagation and Pb bioaccumulation and tolerance in a woody shrub Daphne jasminea cultured in vitro. The amendments were analyzed for their content of carbohydrates, phenolic acids, and phytohormones and added at a dose of 10 mL L^-1 to the medium containing 1.0 mM lead nitrate. Micropropagation coefficient increased by 10.2-16.6 % in PP and AH variants, respectively. Growth tolerance index increased by 22.9-31.8 % for the shoots and by 60.1-82.4 % for the roots. In the absence of Pb, the additives inhibited multiplication and growth of microplantlets. PP and AH facilitated Pb accumulation in plant organs, especially in the roots. PP enhanced bioconcentration factor and AH improved Pb translocation to the shoots. Adaptation to Pb was associated with increased accumulation of phenolics and higher radical scavenging activity. Medium supplementation, particularly with AH, enhanced antiradical activity of Pb-adapted lines but reduced the content of phenolic compounds. The study results indicated that supplementation with organic amendments may be beneficial in in vitro selection against lead toxicity.

Overexpression of Arabidopsis NLP7 improves plant growth under both nitrogen-limiting and -sufficient conditions by enhancing nitrogen and carbon assimilation

Nitrogen is essential for plant survival and growth. Excessive application of nitrogenous fertilizer has generated serious environment pollution and increased production cost in agriculture. To deal with this problem, tremendous efforts have been invested worldwide to increase the nitrogen use ability of crops. However, only limited success has been achieved to date. Here we report that NLP7 (NIN-LIKE PROTEIN 7) is a potential candidate to improve plant nitrogen use ability. When overexpressed in Arabidopsis, NLP7 increases plant biomass under both nitrogen-poor and -rich conditions with better-developed root system and reduced shoot/root ratio. NLP7-overexpressing plants show a significant increase in key nitrogen metabolites, nitrogen uptake, total nitrogen content, and expression levels of genes involved in nitrogen assimilation and signalling. More importantly, overexpression of NLP7 also enhances photosynthesis rate and carbon assimilation, whereas knockout of NLP7 impaired both nitrogen and carbon assimilation. In addition, NLP7 improves plant growth and nitrogen use in transgenic tobacco (Nicotiana tabacum). Our results demonstrate that NLP7 significantly improves plant growth under both nitrogen-poor and -rich conditions by coordinately enhancing nitrogen and carbon assimilation and sheds light on crop improvement.

Advances in Agrobacterium tumefaciens-mediated genetic transformation of graminaceous crops

Steady increase in global population poses several challenges to plant science research, including demand for increased crop productivity, grain yield, nutritional quality and improved tolerance to different environmental factors. Transgene-based approaches are promising to address these challenges by transferring potential candidate genes to host organisms through different strategies. Agrobacterium-mediated gene transfer is one such strategy which is well known for enabling efficient gene transfer in both monocot and dicots. Due to its versatility, this technique underwent several advancements including development of improved in vitro plant regeneration system, co-cultivation and selection methods, and use of hyper-virulent strains of Agrobacterium tumefaciens harbouring super-binary vectors. The efficiency of this method has also been enhanced by the use of acetosyringone to induce the activity of vir genes, silver nitrate to reduce the Agrobacterium-induced necrosis and cysteine to avoid callus browning during co-cultivation. In the last two decades, extensive efforts have been invested towards achieving efficient Agrobacterium-mediated transformation in cereals. Though high-efficiency transformation systems have been developed for rice and maize, comparatively lesser progress has been reported in other graminaceous crops. In this context, the present review discusses the progress made in Agrobacterium-mediated transformation system in rice, maize, wheat, barley, sorghum, sugarcane, Brachypodium, millets, bioenergy and forage and turf grasses. In addition, it also provides an overview of the genes that have been recently transferred to these graminaceous crops using Agrobacterium, bottlenecks in this technique and future possibilities for crop improvement.

Restricting the above ground sink corrects the root/shoot ratio and substantially boosts the yield potential per panicle in field-grown rice (Oryza sativa L.)

Rice has shallow, weak roots, but it is unknown how much increase in yield potential could be achieved if the root/shoot ratio is corrected. Removing all tillers except the main one, in a japonica (Sakha 101) and an indica (IR64) rice cultivar, instantly increased the root/shoot ratio from 0.21 to 1.16 in Sakha 101 and from 0.16 to 1.46 in IR64. Over 30 days after detillering, the root/shoot ratios of the detillered plants decreased to 0.49 in Sakha 101 and 0.46 in IR64 but remained significantly higher than in the controls. The detillered plants showed two- or fourfold increase in the main tiller fresh weight, as a consequence of more positive midday leaf relative water content (RWC), and consistently higher rates of stomatal conductance and photosynthesis, but not transpiration, compared with the controls. The enhanced photosynthesis in Sakha 101 after detillering resulted from both improved water status and higher Rubisco contents whereas in IR64, increasing the Rubisco content did not contribute to improving photosynthesis. Detillering did not increase the carbohydrate contents of leaves but prevented starch depletion at the end of grain filling. The leaf protein content during vegetative and reproductive stages, the grain filling rate, the number of filled grains per panicle were greatly improved, bringing about 38.3 and 35.9% increase in the harvested grain dry weight per panicle in Sakha 101 and IR64, respectively. We provide evidence that improving the root performance by increasing the root/shoot ratio would eliminate the current limitations to photosynthesis and growth in rice.

Identification of Nitrogen Use Efficiency Genes in Barley: Searching for QTLs Controlling Complex Physiological Traits

Over the past half century, the use of nitrogen (N) fertilizers has markedly increased crop yields, but with considerable negative effects on the environment and human health. Consequently, there has been a strong push to reduce the amount of N fertilizer used by maximizing the nitrogen use efficiency (NUE) of crops. One approach would be to use classical genetics to improve the NUE of a crop plant. This involves both conventional breeding and quantitative trait loci (QTL) mapping in combination with marker-assisted selection (MAS) to track key regions of the chromosome that segregate for NUE. To achieve this goal, one of initial steps is to characterize the NUE-associated genes, then use the profiles of specific genes to combine plant physiology and genetics to improve plant performance. In this study, on the basis of genetic homology and expression analysis, barley candidate genes from a variety of families that exhibited potential roles in enhancing NUE were identified and mapped. We then performed an analysis of QTLs associated with NUE in field trials and further analyzed their map-location data to narrow the search for these candidate genes. These results provide a novel insight on the identification of NUE genes and for the future prospects, will lead to a more thorough understanding of physiological significances of the diverse gene families that may be associated with NUE in barley.

Application of Response Surface Methodology for Optimization of Urea Grafted Multiwalled Carbon Nanotubes in Enhancing Nitrogen Use Efficiency and Nitrogen Uptake by Paddy Plants

Efficient use of urea fertilizer (UF) as important nitrogen (N) source in the world’s rice production has been a concern. Carbon-based materials developed to improve UF performance still represent a great challenge to be formulated for plant nutrition. Advanced N nanocarrier is developed based on functionalized multiwall carbon nanotubes (f-MWCNTs) grafted with UF to produce urea-multiwall carbon nanotubes (UF-MWCNTs) for enhancing the nitrogen uptake (NU) and use efficiency (NUE). The grafted N can be absorbed and utilized by rice efficiently to overcome the N loss from soil-plant systems. The individual and interaction effect between the specified factors of f-MWCNTs amount (0.10–0.60 wt%) and functionalization reflux time (12–24 hrs) with the corresponding responses (NUE, NU) were structured via the Response Surface Methodology (RSM) based on five-level CCD. The UF-MWCNTs with optimized 0.5 wt% f-MWCNTs treated at 21 hrs reflux time achieve tremendous NUE up to 96% and NU at 1180 mg/pot. Significant model terms (pvalue < 0.05) for NUE and NU responses were confirmed by the ANOVA. Homogeneous dispersion of UF-MWCNTs was observed via FESEM and TEM. The chemical changes were monitored by FT-IR and Raman spectroscopy. Hence, this UF-MWCNTs’ approach provides a promising strategy in enhancing plant nutrition for rice.

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.

Rice nitrate transporter OsNPF2.4 functions in low-affinity acquisition and long-distance transport

Plant proteins belonging to the NPF (formerly NRT1/PTR) family are well represented in every genome and function in transporting a wide variety of substrates. In this study, we showed that rice OsNPF2.4 is located in the plasma membrane and is expressed mainly in the epidermis, xylem parenchyma, and phloem companion cells. Functional analysis in oocytes showed that OsNPF2.4 is a pH-dependent, low-affinity NO₃⁻ transporter. Short-term (¹⁵NO₃⁻) influx rate, long-term NO₃⁻ acquisition by root, and upward transfer from root to shoot were decreased by disruption of OsNPF2.4 and increased by OsNPF2.4 overexpression under high NO₃⁻ supply. Moreover, the redistribution of NO₃⁻ in the mutants in comparison with the wild type from the oldest leaf to other organs, particularly to N-starved roots, was dramatically changed. Knockout of OsNPF2.4 decreased rice growth and potassium (K) concentration in xylem sap, root, culm, and sheath, but increased the shoot:root ratio of tissue K under higher NO₃⁻. We conclude that OsNPF2.4 functions in acquisition and long-distance transport of NO₃⁻ , and that altering its expression has an indirect effect on K recycling between the root and shoot.