Rice Ferredoxin-Dependent Glutamate Synthase Regulates Nitrogen-Carbon Metabolomes and Is Genetically Differentiated between japonica and indica Subspecies

Enhancing quality traits in staple crops: current advances and future perspectives

Staple crops such as rice, wheat and maize are crucial for global food security; however, improving their quality remains a significant challenge. This review summarizes recent advances in enhancing crop quality, focusing on key areas such as the molecular mechanisms underlying endosperm filling initiation, starch granule synthesis, protein body formation, and the interactions between carbon and nitrogen metabolism. It also highlights ten unresolved questions related to starch-protein spatial distribution, epigenetic regulation, and the environmental impacts on quality traits. The integration of multi-omics approaches, and rational design strategies presents opportunities to develop high-yield "super-crop" varieties with enhanced nutritional value, better processing characteristics, and attributes preferred by consumers. Addressing these challenges is crucial to promote sustainable agriculture and achieve the dual objectives of food security and environmental conservation.

Suppressed OsPsbS1 expression triggers rice leaf senescence mediated by reactive oxygen species

Premature leaf senescence is an important factor affecting rice growth, development, and fitness. Although rice photosystem II subunit S (OsPsbS1) is a major gene controlling nonphotochemical quenching capacity (NPQ) in the photoprotective process, the role it plays in rice leaf senescence has not been explored yet. In this study, we use CRISPR/Cas9 technology to edit the OsPsbS1 gene, resulting in stable homozygous lines with premature leaf senescence. The Ospsbs1 mutant lines have pale-yellow leaves, reduced chlorophyll content, and show accelerated chloroplast degradation. Reactive oxygen species, malondialdehyde, superoxide dismutase, and peroxidase activity were significantly increased in the mutants, whereas ascorbate peroxidase and catalase activity, as well as chlorophyll content and photosynthetic rate, were markedly decreased. Furthermore, they showed increased expression of genes involved in senescence, ROS, and chlorophyll degradation. The Ospsbs1 mutant plants were found to have severe DNA degradation and programmed cell death through TUNEL and staining, suggesting that excess ROS may cause leaf senescence. RNA sequencing analysis revealed that OsPsbS1 is involved in the regulation of multiple biological processes, such as glutathione (GSH), starch and sucrose, and nitrogen metabolism pathways. Our results demonstrate that disruption of OsPsbS1 can accelerate leaf senescence as a result of over-accumulation of ROS. The discovery of OsPsbS1's function in controlling leaf aging in rice provides further genetic insights for understanding the molecular pathways that govern premature leaf senescence.

Positional variations of rice protein compositions accumulation within a panicle during the grain filling

Grain protein is a critical quality attribute of rice that influences consumer preferences. However, the spatial variation in protein accumulation within a rice panicle remains poorly understood. This study investigated the dynamics of protein accumulation, including protein components and protein synthesis-related enzymes and genes, among grains located at the top, middle, and bottom primary rachises of a rice panicle during the grain filling. The results revealed significant variations in protein compositions across different rachis positions. The contents of albumin, globulin, prolamin, glutelin, and total protein contents exhibited fluctuations during grain filling. Notably, the grain position had a significant effect on glutelin content, with grains at the bottom primary rachis consistently having higher glutelin level than those at the top and middle rachises, except 17 days after flowering (DAF). A similar trend was observed for total protein content. Grains at the bottom rachis demonstrated dominance in the rate of protein accumulation, initiating rapid accumulation 2.0 d later and 2.2 d earlier than grains at the top and middle rachises, respectively. Furthermore, the duration of active protein accumulation was 1.9 d and 3.4 d shorter for grains at the bottom rachis compared to those at the top and middle rachises, respectively. This phenomenon was attributed to alterations in enzymatic activities. Specifically, the activities of glutamine synthetase (GS), glutamate synthase (GOGAT), glutamate pyruvate transaminase (GPT), and glutamic oxalo-acetic transaminase (GOT) in grains located at the basal rachis exhibited a marked increase from 8 DAF to 17 DAF. These activities were significantly elevated compared to those observed in grains at the top and middle rachis, although they experienced a subsequent sharp decline. The glutelin content and enzymatic activities demonstrated a strong correlation, either positive or negative, at 11 DAF and 20 DAF. These findings suggest that the positional changes of grain protein were closely associated with nitrogen assimilation and glutelin accumulation during the rice grain filling process.

Genetic Foundation of Leaf Senescence: Insights from Natural and Cultivated Plant Diversity

Leaf senescence, the final stage of leaf development, is crucial for plant fitness as it enhances nutrient reutilization, supporting reproductive success and overall plant adaptation. Understanding its molecular and genetic regulation is essential to improve crop resilience and productivity, particularly in the face of global climate change. This review explores the significant contributions of natural genetic diversity to our understanding of leaf senescence, focusing on insights from model plants and major crops. We discuss the physiological and adaptive significance of senescence in plant development, environmental adaptation, and agricultural productivity. The review emphasizes the importance of natural genetic variation, including studies on natural accessions, landraces, cultivars, and artificial recombinant lines to unravel the genetic basis of senescence. Various approaches, from quantitative trait loci mapping to genome-wide association analysis and in planta functional analysis, have advanced our knowledge of senescence regulation. Current studies focusing on key regulatory genes and pathways underlying natural senescence, identified from natural or recombinant accession and cultivar populations, are highlighted. We also address the adaptive implications of abiotic and biotic stress factors triggering senescence and the genetic mechanisms underlying these responses. Finally, we discuss the challenges in translating these genetic insights into crop improvement. We propose future research directions, such as expanding studies on under-researched crops, investigating multiple stress combinations, and utilizing advanced technologies, including multiomics and gene editing, to harness natural genetic diversity for crop resilience.

The OsAGO2-OsNAC300-OsNAP module regulates leaf senescence in rice

Leaves play a crucial role in the growth and development of rice (Oryza sativa) as sites for the production of photosynthesis. Early leaf senescence leads to substantial drops in rice yields. Whether and how DNA methylation regulates gene expression and affects leaf senescence remains elusive. Here, we demonstrate that mutations in rice ARGONAUTE 2 (OsAGO2) lead to premature leaf senescence, with chloroplasts in Osago2 having lower chlorophyll content and an abnormal thylakoid structure compared with those from wild-type plants. We show that OsAGO2 associates with a 24-nt microRNA and binds to the promoter region of OsNAC300, which causes DNA methylation and suppressed expression of OsNAC300. Overexpressing OsNAC300 causes the similar premature leaf senescence as Osago2 mutants and knocking out OsNAC300 in the Osago2 mutant background suppresses the early senescence of Osago2 mutants. Based on yeast one-hybrid, dual-luciferase, and electrophoresis mobility shift assays, we propose that OsNAC300 directly regulates transcription of the key rice aging gene NAC-like, activated by APETALA3/PISTILLATA (OsNAP) to control leaf senescence. Our results unravel a previously unknown epigenetic regulatory mechanism underlying leaf senescence in which OsAGO2-OsNAC300-OsNAP acts as a key regulatory module of leaf senescence to maintain leaf function.

The poetry of nitrogen and carbon metabolic shifts: The role of C/N in pitaya phase change

Pitaya, a desert plant, has an underexplored flowering mechanism due to a lack of functional validation assays. This study reveals that the transition from vegetative to generative growth in pitaya is regulated by significant metabolic shift, underscoring the importance of understanding and address the challenging issue pitaya's phase change. Lateral buds from 6-years-old 'Guanhuahong' pitaya (Hylocereus monacanthus) plants were collected on April 8th, 18th, and 28th 2023, representing early, middle, and late stages of phase transition, respectively. Results showed diminished nitrogen levels concurrent with increased carbon levels and carbon-to-nitrogen (C/N) ratios during pitaya phase transition. Transcriptomic analysis identified batches of differentially expressed genes (DEGs) involved in downregulating nitrogen metabolism and upregulating carbon metabolism. These batches of genes play a central role in the metabolic shifts that predominantly regulate the transition to the generative phase in pitaya. This study unveils the intricate regulatory network involving 6 sugar synthesis and transport, 11 photoperiod (e.g., PHY, CRY, PIF) and 6 vernalization (e.g., VIN3) pathways, alongside 11 structural flowering genes (FCA, FLK, LFY, AGL) out of a vast array of potential candidates in pitaya phase change. These findings provide insights into the metabolic pathways involved in pitaya's phase transition, offering a theoretical framework for managing flowering, guiding breeding strategies to optimize flowering timing and improve crop yields under varied nitrogen conditions.

Effects of nitrogen forms on Cd uptake and tolerance in wheat seedlings

Hydroponic experiment was conducted to explore the effects of two nitrogen (N) levels with five nitrate nitrogen (NO3--N) and ammonium nitrogen (NH4+-N) ratios on the growth status and Cd migration patterns of wheat seedlings under Cd5 and Cd30 level. Results showed that higher Cd were detrimental to the growth, absorption of K and Ca, expression of genes mediating NO3--N and NH4+-N transport, which also increased the content of malondialdehyde (MDA) and hydrogen peroxide (H2O2) in shoots and roots of wheat seedlings. Higher N treatment alleviated the inhibitory effects of Cd stress on the biomass, root development, photosynthesis and increased the tolerance index of wheat seedlings. The ratio of NO3--N and NH4+-N was the main factor driving Cd accumulation in wheat seedlings, the combined application of NH4+-N and NO3--N was more conducive for the growth, nitrogen assimilation and Cd tolerance to the Cd stressed wheat seedlings. Increased NO3--N application rates significantly up-regulated the expression levels of TaNPF2.12, TaNRT2.2, increased NH4+-N application rates significantly up-regulated the expression levels of TaAMT1.1. The high proportion of NO3--N promoted the absorption of K, Ca and Cd in the shoots and roots of wheat seedlings, while NH4+-N was the opposite. Under low Cd conditions, the NO3--N to NH4+-N ratio of 1:1 was more conducive to the growth of wheat seedlings, under high Cd stress, the optimal of NO3--N to NH4+-N was 1:2 for inhibiting the accumulation of Cd in wheat seedlings. The results indicated that increasing NH4+-N ratio appropriately could inhibit wheat Cd uptake by increasing NH4+, K+ and Ca2+ for K and Ca channels, and promote wheat growth by promoting N assimilation process.

Application of slow-controlled release fertilizer coordinates the carbon flow in carbon-nitrogen metabolism to effect rice quality

Slow-controlled release fertilizers are experiencing a popularity in rice cultivation due to their effectiveness in yield and quality with low environmental costs. However, the underlying mechanism by which these fertilizers regulate grain quality remains inadequately understood. This study investigated the effects of five fertilizer management practices on rice yield and quality in a two-year field experiment: CK, conventional fertilization, and four applications of slow-controlled release fertilizer (UF, urea formaldehyde; SCU, sulfur-coated urea; PCU, polymer-coated urea; BBF, controlled-release bulk blending fertilizer). In 2020 and 2021, the yields of UF and SCU groups showed significant decreases when compared to conventional fertilization, accompanied by a decline in nutritional quality. Additionally, PCU group exhibited poorer cooking and eating qualities. However, BBF group achieved increases in both yield (10.8 t hm-2 and 11.0 t hm-2) and grain quality reaching the level of CK group. The adequate nitrogen supply in PCU group during the grain-filling stage led to a greater capacity for the accumulation of proteins and amino acids in the PCU group compared to starch accumulation. Intriguingly, BBF group showed better carbon-nitrogen metabolism than that of PCU group. The optimal nitrogen supply present in BBF group suitable boosted the synthesis of amino acids involved in the glycolysis/ tricarboxylic acid cycle, thereby effectively coordinating carbon-nitrogen metabolism. The application of the new slow-controlled release fertilizer, BBF, is advantageous in regulating the carbon flow in the carbon-nitrogen metabolism to enhance rice quality.

Exploring Genetic Diversity within aus Rice Germplasm: Insights into the Variations in Agro-morphological Traits

The aus (Oryza sativa L.) varietal group comprises of aus, boro, ashina and rayada seasonal and/or field ecotypes, and exhibits unique stress tolerance traits, making it valuable for rice breeding. Despite its importance, the agro-morphological diversity and genetic control of yield traits in aus rice remain poorly understood. To address this knowledge gap, we investigated the genetic structure of 181 aus accessions using 399,115 SNP markers and evaluated them for 11 morpho-agronomic traits. Through genome-wide association studies (GWAS), we aimed to identify key loci controlling yield and plant architectural traits.Our population genetic analysis unveiled six subpopulations with strong geographical patterns. Subpopulation-specific differences were observed in most phenotypic traits. Principal component analysis (PCA) of agronomic traits showed that principal component 1 (PC1) was primarily associated with panicle traits, plant height, and heading date, while PC2 and PC3 were linked to primary grain yield traits. GWAS using PC1 identified OsSAC1 on Chromosome 7 as a significant gene influencing multiple agronomic traits. PC2-based GWAS highlighted the importance of OsGLT1 and OsPUP4/ Big Grain 3 in determining grain yield. Haplotype analysis of these genes in the 3,000 Rice Genome Panel revealed distinct genetic variations in aus rice.In summary, this study offers valuable insights into the genetic structure and phenotypic diversity of aus rice accessions. We have identified significant loci associated with essential agronomic traits, with GLT1, PUP4, and SAC1 genes emerging as key players in yield determination.

Spermidine or spermine pretreatment regulates organic metabolites and ions homeostasis in favor of white clover seed germination against salt toxicity

White clover is widely cultivated as a leguminous forage or ground cover plant worldwide. However, soil salinization decreases its yield and quality. Aims of the present experiment were to elucidate the impact of seed pretreatment with spermidine (Spd) or spermine (Spm) on amylolysis, Na+/K+ accumulation, and metabolic homeostasis during germination. Seed was soaked in distilled water (control), Spd or Spm solution and then germinated under optimal or salt stress conditions for 7 days. Results showed that germination vigor, germination percentage, or seed vigour index of seeds pretreatment with Spd increased by 7%, 11%, or 70% when compared with water-pretreated seeds under salt stress, respectively. Germination percentage or seed vigour index of seeds pretreatment with Spm increased by 17% or 78% than water-pretreated seeds under saline condition, respectively. In response to salt stress, accelerated amylolysis via activation of β-amylase activity was induced by Spd or Spm pretreatment. Spd or Spm pretreatment also significantly enhanced accumulation of diverse amino acids, organic acids, sugars, and other metabolites (putrescine, myo-inositol, sorbitol, daidzein etc.) associated with enhanced osmotic adjustment, antioxidant capacity, and energy supply during germination under salt stress. In addition, Spd or Spm pretreatment not only significantly reduced salt-induced K+ loss and overaccumulation of Na+, but also improved the ratio of K+ to Na+, contributing to Na+ and K+ balance in seedlings. In response to salt stress, seeds pretreatment with Spd or Spm up-regulated transcription level of NHX2 related to enhancement in compartmentation of Na+ from cytoplasm to vacuole, thus reducing Na+ toxicity in cytoplasm. Spm priming also uniquely up-regulated transcription levels of SKOR, HKT1, and HAL2 associated with K+ and Na + homeostasis and decline in cytotoxicity under salt stress.

Glutamine Metabolism, Sensing and Signaling in Plants

Glutamine (Gln) is the first amino acid synthesized in nitrogen (N) assimilation in plants. Gln synthetase (GS), converting glutamate (Glu) and NH4+ into Gln at the expense of ATP, is one of the oldest enzymes in all life domains. Plants have multiple GS isoenzymes that work individually or cooperatively to ensure that the Gln supply is sufficient for plant growth and development under various conditions. Gln is a building block for protein synthesis and an N-donor for the biosynthesis of amino acids, nucleic acids, amino sugars and vitamin B coenzymes. Most reactions using Gln as an N-donor are catalyzed by Gln amidotransferase (GAT) that hydrolyzes Gln to Glu and transfers the amido group of Gln to an acceptor substrate. Several GAT domain-containing proteins of unknown function in the reference plant Arabidopsis thaliana suggest that some metabolic fates of Gln have yet to be identified in plants. In addition to metabolism, Gln signaling has emerged in recent years. The N regulatory protein PII senses Gln to regulate arginine biosynthesis in plants. Gln promotes somatic embryogenesis and shoot organogenesis with unknown mechanisms. Exogenous Gln has been implicated in activating stress and defense responses in plants. Likely, Gln signaling is responsible for some of the new Gln functions in plants.

The Role of Glutamine Synthetase (GS) and Glutamate Synthase (GOGAT) in the Improvement of Nitrogen Use Efficiency in Cereals

Cereals are the most broadly produced crops and represent the primary source of food worldwide. Nitrogen (N) is a critical mineral nutrient for plant growth and high yield, and the quality of cereal crops greatly depends on a suitable N supply. In the last decades, a massive use of N fertilizers has been achieved in the desire to have high yields of cereal crops, leading to damaging effects for the environment, ecosystems, and human health. To ensure agricultural sustainability and the required food source, many attempts have been made towards developing cereal crops with a more effective nitrogen use efficiency (NUE). NUE depends on N uptake, utilization, and lastly, combining the capability to assimilate N into carbon skeletons and remobilize the N assimilated. The glutamine synthetase (GS)/glutamate synthase (GOGAT) cycle represents a crucial metabolic step of N assimilation, regulating crop yield. In this review, the physiological and genetic studies on GS and GOGAT of the main cereal crops will be examined, giving emphasis on their implications in NUE.

Improving rice eating and cooking quality by enhancing endogenous expression of a nitrogen-dependent floral regulator

Improving rice eating and cooking quality (ECQ) is one of the primary tasks in rice production to meet the rising demands of consumers. However, improving grain ECQ without compromising yield faces a great challenge under varied nitrogen (N) supplies. Here, we report the approach to upgrade rice ECQ by native promoter-controlled high expression of a key N-dependent floral and circadian clock regulator Nhd1. The amplification of endogenous Nhd1 abundance alters rice heading date but does not affect the entire length of growth duration, N use efficiency and grain yield under both low and sufficient N conditions. Enhanced expression of Nhd1 reduces amylose content, pasting temperature and protein content while increasing gel consistence in grains. Metabolome and transcriptome analyses revealed that increased expression of Nhd1 mainly regulates the metabolism of carbohydrates and amino acids in the grain filling stage. Moreover, expression level of Nhd1 shows a positive relationship with grain ECQ in some local main cultivars. Thus, intensifying endogenous abundance of Nhd1 is a promising strategy to upgrade grain ECQ in rice production.

Linking glucose signaling to nitrogen utilization by the OsHXK7-ARE4 complex in rice

How reciprocal regulation of carbon and nitrogen metabolism works is a long-standing question. In plants, glucose and nitrate are proposed to act as signaling molecules, regulating carbon and nitrogen metabolism via largely unknown mechanisms. Here, we show that the MYB-related transcription factor ARE4 coordinates glucose signaling and nitrogen utilization in rice. ARE4 is retained in the cytosol in complexing with the glucose sensor OsHXK7. Upon sensing a glucose signal, ARE4 is released, is translocated into the nucleus, and activates the expression of a subset of high-affinity nitrate transporter genes, thereby boosting nitrate uptake and accumulation. This regulatory scheme displays a diurnal pattern in response to circadian changes of soluble sugars. The are4 mutations compromise in nitrate utilization and plant growth, whereas overexpression of ARE4 increases grain size. We propose that the OsHXK7-ARE4 complex links glucose to the transcriptional regulation of nitrogen utilization, thereby coordinating carbon and nitrogen metabolism.

Acclimation of sugar beet in morphological, physiological and BvAMT1.2 expression under low and high nitrogen supply

Understanding the response and tolerance mechanisms of nitrogen (N) stress is essential for the taproot plant of sugar beet. Hence, in this study, low (0.5 and 3 mmol/L; N0.5 and N3), moderate (5 mmol/L; N5; control) and high (10 and 12 mmol/L; N10 and N12) N were imposed to sugar beet to comparatively investigate the growth and physiological changes, and expression pattern of the gene involving ammonia transporting at different seedling stages. The results showed that, different from N5 which could induce maximum biomass of beet seedlings, low N was more likely to inhibit the growth of beet seedlings than high N treatments. Morphological differences and adverse factors increased significantly with extension of stress time, but sugar beet seedlings displayed a variety of physical responses to different N concentrations to adapt to N abnormal. At 14 d, the chlorophyll content, leaf and root surface area, total dry weight and nitrogen content of seedlings treated with N0.5 decreased 15.83%, 53.65%, 73.94%, 78.08% and 24.88% respectively, compared with N12; however, the root shoot ratio increased significantly as well as superoxide dismutase (SOD), peroxidase (POD), glutamine synthetase (GS) activity and malondialdehyde (MDA) and proline content, especially in root. The expression of BvAMT1.2 was also regulated in an N concentration-dependent manner, and was mainly involved in the tolerance of beet leaves to N stress, which significantly positively correlated to GS activity on the basis of its high affinity to N. It can be deduced that the stored nutrients under low N could only maintain relatively stable root growth, and faced difficulty in being transported to the shoots. Sugar beet was relatively resilient to N0.5 stress according to the mean affiliation function analysis. These results provide a theoretical basis for the extensive cultivation of sugar beet in N-stressed soil.

Effects of tebuconazole application at different growth stages on rice grain quality of rice-based untargeted metabolomics

Tebuconazole (TEB) is a pesticide widely used in crops and has a strong control effect on fungal pathogens. TEB abuse has caused many food safety problems. In this study, the TEB residue in rice and the effect of TEB on white rice quality were investigated. The results showed that under two spraying concentrations, the TEB residue in rice was 11.21-19.05 μg/kg and 24.45-31.12 μg/kg, and there was no food safety risk of pesticide residue. When applying TEB according to the instructions, no significant effect was found. However, when 3 times the recommended TEB concentration was used at the filling stage, the protein content of white rice decreased significantly from 106.52 mg/g to 80.72 mg/g. At the jointing，heading and filling stage, the amylose content of white rice decreased to 53.95 mg/g, 48.77 mg/g and 49.04 mg/g from the blank control group. Plant metabolic analysis using LC-QTOF/MS revealed that the amino acid-related metabolic pathways in white rice were significantly affected by TEB. This is closely related to the decrease in protein accumulation in white rice and the stress response of rice plants. The increase in pantothenic acid content in white rice indicated that the glycolysis pathway of white rice plants was affected, and the consumption of starch and sucrose increased, leading to the inhibition of amylose accumulation in white rice. The increase in soluble sugar content and decrease in phosphocholine content in white rice suggested that rice plants were affected by TEB exposure, which produced similar effects under drought stress.

Methylation and Expression of Rice NLR Genes after Low Temperature Stress

Nucleotide-binding leucine-rich repeat receptors (NLRs) are included in most plant disease resistance proteins. Some NLR proteins have been revealed to be induced by the invasion of plant pathogens. DNA methylation is required for adaption to adversity and proper regulation of gene expression in plants. Low temperature stress (LTS) is a restriction factor in rice growth, development and production. Here, we report the methylation and expression of NLR genes in two rice cultivars, i.e., 9311 (an indica rice cultivar sensitive to LTS), and P427 (a japonica cultivar, tolerant to LTS), after LTS. We found that the rice NLR genes were heavily methylated within CG sites at room temperature and low temperature in 9311 and P427, and many rice NLR genes showed DNA methylation alteration after LTS. A great number of rice NLR genes were observed to be responsive to LTS at the transcriptional level. Our observation suggests that the alteration of expression of rice NLR genes was similar but their change in DNA methylation was dynamic between the two rice cultivars after LTS. We identified that more P427 NLR genes reacted to LTS than those of 9311 at the methylation and transcriptional level. The results in this study will be useful for further understanding the transcriptional regulation and potential functions of rice NLR genes.

Improving Crop Nitrogen Use Efficiency Toward Sustainable Green Revolution

The Green Revolution of the 1960s improved crop yields in part through the widespread cultivation of semidwarf plant varieties, which resist lodging but require a high-nitrogen (N) fertilizer input. Because environmentally degrading synthetic fertilizer use underlies current worldwide cereal yields, future agricultural sustainability demands enhanced N use efficiency (NUE). Here, we summarize the current understanding of how plants sense, uptake, and respond to N availability in the model plants that can be used to improve sustainable productivity in agriculture. Recent progress in unlocking the genetic basis of NUE within the broader context of plant systems biology has provided insights into the coordination of plant growth and nutrient assimilation and inspired the implementation of a new breeding strategy to cut fertilizer use in high-yield cereal crops. We conclude that identifying fresh targets for N sensing and response in crops would simultaneously enable improved grain productivity and NUE to launch a new Green Revolution and promote future food security.

Genetic Diversity in Nitrogen Fertiliser Responses and N Gas Emission in Modern Wheat

Crops assimilate nitrogen (N) as ammonium via the glutamine synthetase/glutamate synthase (GS/GOGAT) pathway which is of central importance for N uptake and potentially represents a bottle neck for N fertiliser-use efficiency. The aim of this study was to assess whether genetic diversity for N-assimilation capacity exists in wheat and could be exploited for breeding. Wheat plants rapidly, within 6 h, responded to N application with an increase in GS activity. This was not accompanied by an increase in GS gene transcript abundance and a comparison of GS1 and GS2 protein models revealed a high degree of sequence conservation. N responsiveness amongst ten wheat varieties was assessed by measuring GS enzyme activity, leaf tissue ammonium, and by a leaf-disc assay as a proxy for apoplastic ammonia. Based on these data, a high-GS group showing an overall positive response to N could be distinguished from an inefficient, low-GS group. Subsequent gas emission measurements confirmed plant ammonia emission in response to N application and also revealed emission of N2O when N was provided as nitrate, which is in agreement with our current understanding that N2O is a by-product of nitrate reduction. Taken together, the data suggest that there is scope for improving N assimilation capacity in wheat and that further investigations into the regulation and role of GS-GOGAT in NH3 emission is justified. Likewise, emission of the climate gas N2O needs to be reduced, and future research should focus on assessing the nitrate reductase pathway in wheat and explore fertiliser management options.

Glutamate: A multifunctional amino acid in plants

Glutamate (Glu) is a versatile metabolite and a signaling molecule in plants. Glu biosynthesis is associated with the primary nitrogen assimilation pathway. The conversion between Glu and 2-oxoglutarate connects Glu metabolism to the tricarboxylic acid cycle, carbon metabolism, and energy production. Glu is the predominant amino donor for transamination reactions in the cell. In addition to protein synthesis, Glu is a building block for tetrapyrroles, glutathione, and folate. Glu is the precursor of γ-aminobutyric acid that plays an important role in balancing carbon/nitrogen metabolism and various cellular processes. Glu can conjugate to the major auxin indole 3-acetic acid (IAA), and IAA-Glu is destined for oxidative degradation. Glu also conjugates with isochorismate for the production of salicylic acid. Accumulating evidence indicates that Glu functions as a signaling molecule to regulate plant growth, development, and defense responses. The ligand-gated Glu receptor-like proteins (GLRs) mediate some of these responses. However, many of the Glu signaling events are GLR-independent. The receptor perceiving extracellular Glu as a danger signal is still unknown. In addition to GLRs, Glu may act on receptor-like kinases or receptor-like proteins to trigger immune responses. Glu metabolism and Glu signaling may entwine to regulate growth, development, and defense responses in plants.

Genetic dissection of seed yield and yield-related traits in Brassica napus grown with contrasting nitrogen supplies

Oilseed rape (B. napus) is the main oil crop in China as well as in the world. Nitrogen (N) deficiency significantly reduces the seed yield of B. napus. However, a very few studies involved in the genetic mechanism of seed yield and SY-related traits of B. napus in response to N deficiency. In this study, plant height (PH), branch number per plant (BN), pod number per plant (PN), seed number per pod (SN), 1000-seed weight (SW), and seed yield per plant (SY) were investigated using a B. napus double haploid (BnaTNDH) population derived from a cross between cultivars "Tapidor" and "Ningyou7" grown at an optimal N (ON) and a low N (LN) supplies in three-year field trials. Great variations of SY and related traits were observed in BnaTNDH population under contrasting N supplies. A total of 106 and 110 significant quantitative trait loci (QTLs) were detected for six traits at ON and LN in three field trials, respectively. All of these significant QTLs for the same trait identified in two or three trials were integrated into 20 stable QTLs. A total of 50 consensus QTLs and 53 unique QTLs were obtained from 172 significant QTLs and 20 stable QTLs, including 35 ON-specific QTLs, 29 LN-specific QTLs and 39 constitutive QTLs detected at both ON and LN. cqA3l was integrated from four QTLs for PN, PH, SN, SY at LN, cqC9c was integrated from QTLs for BN, SY, PN at ON and LN. Both cqA3l and cqC9c were detected in three trials. In addition, a total of 194 epistatic interactions, inculding 15 pleiotropic epistatic interactions, were identified. Eight of the 15 pleiotropic epistatic interactions were detected to affect SY. This result may help to better understand the genetic mechanism of yield traits in response to low N and promote the breeding of N-efficient varieties.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01281-0.

Nitrogen assimilation in plants: current status and future prospects

Nitrogen (N) is the driving force for crop yields, however, excessive N application in agriculture not only increases production cost, but also causes severe environmental problems. Therefore, comprehensively understanding the molecular mechanisms of N use efficiency (NUE) and breeding crops with higher NUE is essential to tackle these problems. NUE of crops is determined by N uptake, transport, assimilation, and remobilization. In the process of N assimilation, nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), and glutamine-2-oxoglutarate aminotransferase (GOGAT, also known as glutamate synthase) are the major enzymes. NR and NiR mediate the initiation of inorganic N utilization, and GS/GOGAT cycle converts inorganic N to organic N, playing a vital role in N assimilation and the final NUE of crops. Besides, asparagine synthetase (ASN), glutamate dehydrogenase (GDH), and carbamoylphosphate synthetase (CPSase) are also involved. In this review, we summarize the function and regulation of these enzymes reported in three major crops, rice, maize, wheat, also in the model plant Arabidopsis, and we highlight their application in improving NUE of crops via manipulating N assimilation. Anticipated challenges and prospects toward fully understanding the function of N assimilation and further exploring the potential for NUE improvement are discussed.

Five OsS40 Family Members Are Identified as Senescence-Related Genes in Rice by Reverse Genetics Approach

A total of 16 OsS40 genes of Oryza sativa were identified in our previous work, but their functions remain unclear. In this study, 13 OsS40 members were knocked out using the CRISPR/cas9 gene-editing technology. After screening phenotype characterization of CRISPR/Cas9 mutants compared to WT, five oss40s mutants exhibited a stay-green phenotype at 30 days after heading. Moreover, increased grain size and grain weight occurred in the oss40-1, oss40-12, and oss40-14 lines, while declined grain weight appeared in the oss40-7 and oss40-13 mutants. The transcript levels of several senescence-associated genes (SAGs), chlorophyll degradation-related genes (CDGs), as well as WRKY members were differentially decreased in the five stay-green oss40s mutants compared to WT. Five oss40 mutants also exhibited a stay-green phenotype when the detached leaves were incubated under darkness for 4 days. OsSWEET4 and OsSWEET1b were significantly upregulated, while OsSWEET1a and OsSWEET13 were significantly downregulated in both oss40-7 and oss40-14 compared to WT. Furthermore, these five OsS40 displayed strong transcriptional activation activity and were located in the nucleus. Most of the OsS40 genes were downregulated in the oss40-1, oss40-7, and oss40-12 mutants, but upregulated in the oss40-13 and oss40-14 mutants, indicating coordinated regulation among OsS40 members. These results suggest that OsS40-1, OsS40-7, OsS40-12, OsS40-13, and OsS40-14 are senescence-associated genes, involved in the senescence and carbon allocation network by modulating other OsS40 members, SWEET member genes, and senescence-related gene expression.

Rice Ferredoxins localize to chloroplasts/plastids and may function in different tissues

Ferredoxins (Fds) play a unique and important role in photosynthetic electron transport. Recently, we characterized the function of Fd1 in rice (Oryza sativa L.), showing that Fd1 is the primary photosynthetic electron transport protein and that Fd1 participates in carbon assimilation. However, the subcellular localization and specific functions of other Fds in rice are not yet fully understood. Here, our subcellular localization analysis of the seven Fds in rice showed that they are located in the chloroplasts of photosynthetic tissues and the plastids of non-photosynthetic tissues. Moreover, qRT-PCR indicated that Fd1 transcript levels were highest in photosynthetic tissues, while Fd4 transcript levels were highest in non-photosynthetic tissues. Collectively, our results suggest that rice Fds are located in chloroplasts/plastids, but may function in different tissues, and Fd4 may be a non-photosynthetic type Fd.

Increasing yield potential through manipulating of an ARE1 ortholog related to nitrogen use efficiency in wheat by CRISPR/Cas9

Wheat (Triticum aestivum L.) is a staple food crop consumed by more than 30% of world population. Nitrogen (N) fertilizer has been applied broadly in agriculture practice to improve wheat yield to meet the growing demands for food production. However, undue N fertilizer application and the low N use efficiency (NUE) of modern wheat varieties are aggravating environmental pollution and ecological deterioration. Under nitrogen-limiting conditions, the rice (Oryza sativa) abnormal cytokinin response1 repressor1 (are1) mutant exhibits increased NUE, delayed senescence and consequently, increased grain yield. However, the function of ARE1 ortholog in wheat remains unknown. Here, we isolated and characterized three TaARE1 homoeologs from the elite Chinese winter wheat cultivar ZhengMai 7698. We then used CRISPR/Cas9-mediated targeted mutagenesis to generate a series of transgene-free mutant lines either with partial or triple-null taare1 alleles. All transgene-free mutant lines showed enhanced tolerance to N starvation, and showed delayed senescence and increased grain yield in field conditions. In particular, the AABBdd and aabbDD mutant lines exhibited delayed senescence and significantly increased grain yield without growth defects compared to the wild-type control. Together, our results underscore the potential to manipulate ARE1 orthologs through gene editing for breeding of high-yield wheat as well as other cereal crops with improved NUE.

Integrative Transcriptomic and Proteomic Analysis Reveals an Alternative Molecular Network of Glutamine Synthetase 2 Corresponding to Nitrogen Deficiency in Rice (Oryza sativa L.)

Nitrogen (N) is an essential nutrient for plant growth and development. The root system architecture is a highly regulated morphological system, which is sensitive to the availability of nutrients, such as N. Phenotypic characterization of roots from LY9348 (a rice variety with high nitrogen use efficiency (NUE)) treated with 0.725 mM NH₄NO₃ (1/4N) was remarkable, especially primary root (PR) elongation, which was the highest. A comprehensive analysis was performed for transcriptome and proteome profiling of LY9348 roots between 1/4N and 2.9 mM NH₄NO₃ (1N) treatments. The results indicated 3908 differential expression genes (DEGs; 2569 upregulated and 1339 downregulated) and 411 differential abundance proteins (DAPs; 192 upregulated and 219 downregulated). Among all DAPs in the proteome, glutamine synthetase (GS2), a chloroplastic ammonium assimilation protein, was the most upregulated protein identified. The unexpected concentration of GS2 from the shoot to the root in the 1/4N treatment indicated that the presence of an alternative pathway of N assimilation regulated by GS2 in LY9348 corresponded to the low N signal, which was supported by GS enzyme activity and glutamine/glutamate (Gln/Glu) contents analysis. In addition, N transporters (NRT2.1, NRT2.2, NRT2.3, NRT2.4, NAR2.1, AMT1.3, AMT1.2, and putative AMT3.3) and N assimilators (NR2, GS1;1, GS1;2, GS1;3, NADH-GOGAT2, and AS2) were significantly induced during the long-term N-deficiency response at the transcription level (14 days). Moreover, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that phenylpropanoid biosynthesis and glutathione metabolism were significantly modulated by N deficiency. Notably, many transcription factors and plant hormones were found to participate in root morphological adaptation. In conclusion, our study provides valuable information to further understand the response of rice roots to N-deficiency stress.

The Ghd7 transcription factor represses ARE1 expression to enhance nitrogen utilization and grain yield in rice

The genetic improvement of nitrogen use efficiency (NUE) of crops is vital for grain productivity and sustainable agriculture. However, the regulatory mechanism of NUE remains largely elusive. Here, we report that the rice Grain number, plant height, and heading date7 (Ghd7) gene genetically acts upstream of ABC1 REPRESSOR1 (ARE1), a negative regulator of NUE, to positively regulate nitrogen utilization. As a transcriptional repressor, Ghd7 directly binds to two Evening Element-like motifs in the promoter and intron 1 of ARE1, likely in a cooperative manner, to repress its expression. Ghd7 and ARE1 display diurnal expression patterns in an inverse oscillation manner, mirroring a regulatory scheme based on these two loci. Analysis of a panel of 2656 rice varieties suggests that the elite alleles of Ghd7 and ARE1 have undergone diversifying selection during breeding. Moreover, the allelic distribution of Ghd7 and ARE1 is associated with the soil nitrogen deposition rate in East Asia and South Asia. Remarkably, the combination of the Ghd7 and ARE1 elite alleles substantially improves NUE and yield performance under nitrogen-limiting conditions. Collectively, these results define a Ghd7-ARE1-based regulatory mechanism of nitrogen utilization, providing useful targets for genetic improvement of rice NUE.

Current Understanding of Leaf Senescence in Rice

Leaf senescence, which is the last developmental phase of plant growth, is controlled by multiple genetic and environmental factors. Leaf yellowing is a visual indicator of senescence due to the loss of the green pigment chlorophyll. During senescence, the methodical disassembly of macromolecules occurs, facilitating nutrient recycling and translocation from the sink to the source organs, which is critical for plant fitness and productivity. Leaf senescence is a complex and tightly regulated process, with coordinated actions of multiple pathways, responding to a sophisticated integration of leaf age and various environmental signals. Many studies have been carried out to understand the leaf senescence-associated molecular mechanisms including the chlorophyll breakdown, phytohormonal and transcriptional regulation, interaction with environmental signals, and associated metabolic changes. The metabolic reprogramming and nutrient recycling occurring during leaf senescence highlight the fundamental role of this developmental stage for the nutrient economy at the whole plant level. The strong impact of the senescence-associated nutrient remobilization on cereal productivity and grain quality is of interest in many breeding programs. This review summarizes our current knowledge in rice on (i) the actors of chlorophyll degradation, (ii) the identification of stay-green genotypes, (iii) the identification of transcription factors involved in the regulation of leaf senescence, (iv) the roles of leaf-senescence-associated nitrogen enzymes on plant performance, and (v) stress-induced senescence. Compiling the different advances obtained on rice leaf senescence will provide a framework for future rice breeding strategies to improve grain yield.

Targeting Nitrogen Metabolism and Transport Processes to Improve Plant Nitrogen Use Efficiency

In agricultural cropping systems, relatively large amounts of nitrogen (N) are applied for plant growth and development, and to achieve high yields. However, with increasing N application, plant N use efficiency generally decreases, which results in losses of N into the environment and subsequently detrimental consequences for both ecosystems and human health. A strategy for reducing N input and environmental losses while maintaining or increasing plant performance is the development of crops that effectively obtain, distribute, and utilize the available N. Generally, N is acquired from the soil in the inorganic forms of nitrate or ammonium and assimilated in roots or leaves as amino acids. The amino acids may be used within the source organs, but they are also the principal N compounds transported from source to sink in support of metabolism and growth. N uptake, synthesis of amino acids, and their partitioning within sources and toward sinks, as well as N utilization within sinks represent potential bottlenecks in the effective use of N for vegetative and reproductive growth. This review addresses recent discoveries in N metabolism and transport and their relevance for improving N use efficiency under high and low N conditions.

Adaptation Mechanism of Roots to Low and High Nitrogen Revealed by Proteomic Analysis

BACKGROUND

Nitrogen-based nutrients are the main factors affecting rice growth and development. Root systems play an important role in helping plants to obtain nutrients from the soil. Root morphology and physiology are often closely related to above-ground plant organs performance. Therefore, it is important to understand the regulatory effects of nitrogen (N) on rice root growth to improve nitrogen use efficiency.

RESULTS

In this study, changes in the rice root traits under low N (13.33 ppm), normal N (40 ppm) and high N (120 ppm) conditions were performed through root morphology analysis. These results show that, compared with normal N conditions, root growth is promoted under low N conditions, and inhibited under high N conditions. To understand the molecular mechanism underlying the rice root response to low and high N conditions, comparative proteomics analysis was performed using a tandem mass tag (TMT)-based approach, and differentially abundant proteins (DAPs) were further characterized. Compared with normal N conditions, a total of 291 and 211 DAPs were identified under low and high N conditions, respectively. The abundance of proteins involved in cell differentiation, cell wall modification, phenylpropanoid biosynthesis, and protein synthesis was differentially altered, which was an important reason for changes in root morphology. Furthermore, although both low and high N can cause nitrogen stress, rice roots revealed obvious differences in adaptation to low and high N.

CONCLUSIONS

These results provide insights into global changes in the response of rice roots to nitrogen availability and may facilitate the development of rice cultivars with high nitrogen use efficiency through root-based genetic improvements.

Nitrogen Mediates Flowering Time and Nitrogen Use Efficiency via Floral Regulators in Rice

High nitrogen (N) fertilization for maximizing crop yield commonly leads to postponed flowering time (heading date in rice) and ripening, thus affecting resources use efficiency and followed planting time. We found that N-mediated heading date-1 (Nhd1) can directly activate florigen gene OsHd3a in rice. Inactivation of either Nhd1 or OsHd3a results in delay and insensitivity to N supply of flowering time. Knockout of Nhd1 increases N uptake and utilization efficiency at low-to-moderate N level under both short- and long-day field conditions. Increasing glutamine, the product of N assimilation, can upregulate expression of Nhd1, which in turn downregulates OsFd-GOGAT expression and OsFd-GOGAT activity, displaying a Nhd1-controlled negative feedback regulatory pathway of N assimilation. Moreover, N fertilization effect on rice flowering time shows genetically controlled diversity, and single-nucleotide polymorphism in Nhd1 promoter may relate to different responses of flowering time to N application. Nhd1 thus balances flowering time and N use efficiency in addition to photoperiod in rice.

A study of leaf-senescence genes in rice based on a combination of genomics, proteomics and bioinformatics

Leaf senescence is a highly complex, genetically regulated and well-ordered process with multiple layers and pathways. Delaying leaf senescence would help increase grain yields in rice. Over the past 15 years, more than 100 rice leaf-senescence genes have been cloned, greatly improving the understanding of leaf senescence in rice. Systematically elucidating the molecular mechanisms underlying leaf senescence will provide breeders with new tools/options for improving many important agronomic traits. In this study, we summarized recent reports on 125 rice leaf-senescence genes, providing an overview of the research progress in this field by analyzing the subcellular localizations, molecular functions and the relationship of them. These data showed that chlorophyll synthesis and degradation, chloroplast development, abscisic acid pathway, jasmonic acid pathway, nitrogen assimilation and ROS play an important role in regulating the leaf senescence in rice. Furthermore, we predicted and analyzed the proteins that interact with leaf-senescence proteins and achieved a more profound understanding of the molecular principles underlying the regulatory mechanisms by which leaf senescence occurs, thus providing new insights for future investigations of leaf senescence in rice.

Natural variation in the OsbZIP18 promoter contributes to branched-chain amino acid levels in rice

Branched-chain amino acids (BCAAs) are essential amino acids that must be obtained from the diet for humans and animals, and they play important roles in various aspects of plant growth and development. Although BCAA biosynthetic pathways in higher plants have been uncovered, knowledge of their genetic control is still limited, and no positive regulators have been identified to date. Here, we showed that variation in BCAA levels in rice is attributable to differential transcription of OsbZIP18, a basic leucine zipper (bZIP) transcription factor, due to polymorphisms in its promoter. Functional analysis revealed that OsbZIP18 positively regulates BCAA synthesis by binding directly to the ACE and C-box cis-elements in the promoters of the biosynthetic genes branched-chain aminotransferase1 (OsBCAT1) and OsBCAT2. We further demonstrated that OsbZIP18 is strongly induced by nitrogen (N) deficiency and that N starvation results in enhanced BCAA levels in an OsbZIP18-dependent manner. Overall, we identified OsbZIP18, a positive regulator of BCAA biosynthesis, which contributed to natural variation in BCAA levels and mediated BCAA accumulation through de novo synthesis by directly modulating the key biosynthetic genes OsBCAT1 and OsBCAT2.

Glutamate synthase 1 is involved in iron-deficiency response and long-distance transportation in Arabidopsis

Iron is an essential microelement for plant growth. After uptake from the soil, iron is chelated by ligands and translocated from roots to shoots for subsequent utilization. However, the number of ligands involved in iron chelation is unclear. In this study, we identified and demonstrated that GLU1, which encodes a ferredoxin-dependent glutamate synthase, was involved in iron homeostasis. First, the expression of GLU1 was strongly induced by iron deficiency condition. Second, lesion of GLU1 results in reduced transcription of many iron-deficiency-responsive genes in roots and shoots. The mutant plants revealed a decreased iron concentration in the shoots, and displayed severe leaf chlorosis under the condition of Fe limitation, compared to wild-type. Third, the product of GLU1, glutamate, could chelate iron in vivo and promote iron transportation. Last, we also found that supplementation of glutamate in the medium can alleviate cadmium toxicity in plants. Overall, our results provide evidence that GLU1 is involved in iron homeostasis through affecting glutamate synthesis under iron deficiency conditions in Arabidopsis.

Improving coordination of plant growth and nitrogen metabolism for sustainable agriculture

The agricultural green revolution of the 1960s boosted cereal crop yield was in part due to cultivation of semi-dwarf green revolution varieties. The semi-dwarf plants resist lodging and require high nitrogen (N) fertilizer inputs to maximize yield. To produce higher grain yield, inorganic fertilizer has been overused by Chinese farmers in intensive crop production. With the ongoing increase in the food demand of global population and the environmental pollution, improving crop productivity with reduced N supply is a pressing challenge. Despite a great deal of research efforts, to date only a few genes that improve N use efficiency (NUE) have been identified. The molecular mechanisms underlying the coordination of plant growth, carbon (C) and N assimilation is still not fully understood, thus preventing significant improvement. Recent advances have shed light on how explore NUE within an overall plant biology system that considered the co-regulation of plant growth, C and N metabolisms as a whole, rather than focusing specifically on N uptake and assimilation. There are several potential approaches to improve NUE discussed in this review. Increasing knowledge of how plants sense and respond to changes in N availability, as well as identifying new targets for breeding strategies to simultaneously improve NUE and grain yield, could usher in a new green revolution.

Primary leaf-type ferredoxin 1 participates in photosynthetic electron transport and carbon assimilation in rice

Ferredoxins (Fds) play a crucial role in photosynthesis by regulating the distribution of electrons to downstream enzymes. Multiple Fd genes have been annotated in the Oryza sativa L. (rice) genome; however, their specific functions are not well understood. Here, we report the functional characterization of rice Fd1. Sequence alignment, phylogenetic analysis of seven rice Fd proteins and quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that rice Fd1 is a primary leaf-type Fd. Electron transfer assays involving NADP⁺ and cytochrome c indicated that Fd1 can donate electrons from photosystem I (PSI) to ferredoxin-NADP⁺ reductase. Loss-of-function fd1 mutants showed chlorosis and seedling lethality at the three-leaf stage. The deficiency of Fd1 impaired photosynthetic electron transport, which affected carbon assimilation. Exogenous glucose treatment partially restored the mutant phenotype, suggesting that Fd1 plays an important role in photosynthetic electron transport in rice. In addition, the transcript levels of Fd-dependent genes were affected in fd1 mutants, and the trend was similar to that observed in fdc2 plants. Together, these results suggest that OsFd1 is the primary Fd in photosynthetic electron transport and carbon assimilation in rice.

Rice EARLY SENESCENCE 2, encoding an inositol polyphosphate kinase, is involved in leaf senescence

BACKGROUND

Early leaf senescence influences yield and yield quality by affecting plant growth and development. A series of leaf senescence-associated molecular mechanisms have been reported in rice. However, the complex genetic regulatory networks that control leaf senescence need to be elucidated.

RESULTS

In this study, an early senescence 2 (es2) mutant was obtained from ethyl methanesulfonate mutagenesis (EMS)-induced mutational library for the Japonica rice cultivar Wuyugeng 7 (WYG7). Leaves of es2 showed early senescence at the seedling stage and became severe at the tillering stage. The contents of reactive oxygen species (ROS) significantly increased, while chlorophyll content, photosynthetic rate, catalase (CAT) activity significantly decreased in the es2 mutant. Moreover, genes which related to senescence, ROS and chlorophyll degradation were up-regulated, while those associated with photosynthesis and chlorophyll synthesis were down-regulated in es2 mutant compared to WYG7. The ES2 gene, which encodes an inositol polyphosphate kinase (OsIPK2), was fine mapped to a 116.73-kb region on chromosome 2. DNA sequencing of ES2 in the mutant revealed a missense mutation, ES2 was localized to nucleus and plasma membrane of cells, and expressed in various tissues of rice. Complementation test and overexpression experiment confirmed that ES2 completely restored the normal phenotype, with chlorophyll contents and photosynthetic rate increased comparable with the wild type. These results reveal the new role of OsIPK2 in regulating leaf senescence in rice and therefore will provide additional genetic evidence on the molecular mechanisms controlling early leaf senescence.

CONCLUSIONS

The ES2 gene, encoding an inositol polyphosphate kinase localized in the nucleus and plasma membrane of cells, is essential for leaf senescence in rice. Further study of ES2 will facilitate the dissection of the genetic mechanisms underlying early leaf senescence and plant growth.

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.

Systems Metabolic Alteration in a Semi-Dwarf Rice Mutant Induced by OsCYP96B4 Gene Mutation

Dwarfism and semi-dwarfism are among the most valuable agronomic traits in crop breeding, which were adopted by the “Green Revolution”. Previously, we reported a novel semi-dwarf rice mutant (oscyp96b4) derived from the insertion of a single copy of Dissociator (Ds) transposon into the gene OsCYP96B4. However, the systems metabolic effect of the mutation is not well understood, which is important for understanding the gene function and developing new semi-dwarf mutants. Here, the metabolic phenotypes in the semi-dwarf mutant (M) and ectopic expression (ECE) rice line were compared to the wild-type (WT) rice, by using nuclear magnetic resonance (NMR) metabolomics and quantitative real-time polymerase chain reaction (qRT-PCR). Compared with WT, ECE of the OsCYP96B4 gene resulted in significant increase of γ-aminobutyrate (GABA), glutamine, and alanine, but significant decrease of glutamate, aromatic and branched-chain amino acids, and some other amino acids. The ECE caused significant increase of monosaccharides (glucose, fructose), but significant decrease of disaccharide (sucrose); induced significant changes of metabolites involved in choline metabolism (phosphocholine, ethanolamine) and nucleotide metabolism (adenosine, adenosine monophosphate, uridine). These metabolic profile alterations were accompanied with changes in the gene expression levels of some related enzymes, involved in GABA shunt, glutamate and glutamine metabolism, choline metabolism, sucrose metabolism, glycolysis/gluconeogenesis pathway, tricarboxylic acid (TCA) cycle, nucleotide metabolism, and shikimate-mediated secondary metabolism. The semi-dwarf mutant showed corresponding but less pronounced changes, especially in the gene expression levels. It indicates that OsCYP96B4 gene mutation in rice causes significant alteration in amino acid metabolism, carbohydrate metabolism, nucleotide metabolism, and shikimate-mediated secondary metabolism. The present study will provide essential information for the OsCYP96B4 gene function analysis and may serve as valuable reference data for the development of new semi-dwarf mutants.

Comparative population genomics dissects the genetic basis of seven domestication traits in jujube

Jujube (Ziziphus jujuba Mill.) is an important perennial fruit tree with a range of interesting horticultural traits. It was domesticated from wild jujube (Ziziphus acidojujuba), but the genomic variation dynamics and genetic changes underlying its horticultural traits during domestication are poorly understood. Here, we report a comprehensive genome variation map based on the resequencing of 350 accessions, including wild, semi-wild and cultivated jujube plants, at a >15× depth. Using the combination of a genome-wide association study (GWAS) and selective sweep analysis, we identified several candidate genes potentially involved in regulating seven domestication traits in jujube. For fruit shape and kernel shape, we integrated the GWAS approach with transcriptome profiling data, expression analysis and the transgenic validation of a candidate gene to identify a causal gene, ZjFS3, which encodes an ethylene-responsive transcription factor. Similarly, we identified a candidate gene for bearing-shoot length and the number of leaves per bearing shoot and two candidate genes for the seed-setting rate using GWAS. In the selective sweep analysis, we also discovered several putative genes for the presence of prickles on bearing shoots and the postharvest shelf life of fleshy fruits. This study outlines the genetic basis of jujube domestication and evolution and provides a rich genomic resource for mining other horticulturally important genes in jujube.

Integrated Analysis of the Transcriptome and Metabolome Revealed the Molecular Mechanisms Underlying the Enhanced Salt Tolerance of Rice Due to the Application of Exogenous Melatonin

High salinity is one of the major abiotic stresses limiting rice production. Melatonin has been implicated in the salt tolerance of rice. However, the molecular basis of melatonin-mediated salt tolerance in rice remains unclear. In the present study, we performed an integrated transcriptome and metabolome profiling of rice seedlings treated with salt, melatonin, or salt + melatonin. The application of exogenous melatonin increased the salt tolerance of rice plants by decreasing the sodium content to maintain Na⁺/K⁺ homeostasis, alleviating membrane lipid oxidation, and enhancing chlorophyll contention. A comparative transcriptome analysis revealed that complex molecular pathways contribute to melatonin-mediated salt tolerance. More specifically, the AP2/EREBP-HB-WRKY transcriptional cascade and phytohormone (e.g., auxin and abscisic acid) signaling pathways were activated by an exogenous melatonin treatment. On the basis of metabolome profiles, 64 metabolites, such as amino acids, organic acids, nucleotides, and secondary metabolites, were identified with increased abundances only in plants treated with salt + melatonin. Several of these metabolites including endogenous melatonin and its intermediates (5-hydroxy-L-tryptophan, N ¹-acetyl-N ²-formyl-5-methoxykynuramine), gallic acid, diosmetin, and cyanidin 3-O-galactoside had antioxidant functions, suggesting melatonin activates multiple antioxidant pathways to alleviate the detrimental effects of salt stress. Combined transcriptome and metabolome analyses revealed a few gene-metabolite networks related to various pathways, including linoleic acid metabolism and amino acid metabolism that are important for melatonin-mediated salt tolerance. The data presented herein may be useful for further elucidating the multiple regulatory roles of melatonin in plant responses to abiotic stresses.

Transcriptomic and Co-Expression Network Profiling of Shoot Apical Meristem Reveal Contrasting Response to Nitrogen Rate between Indica and Japonica Rice Subspecies

Reducing nitrogen (N) input is a key measure to achieve a sustainable rice production in China, especially in Jiangsu Province. Tiller is the basis for achieving panicle number that plays as a major factor in the yield determination. In actual production, excessive N is often applied in order to produce enough tillers in the early stages. Understanding how N regulates tillering in rice plants is critical to generate an integrative management to reduce N use and reaching tiller number target. Aiming at this objective, we utilized RNA sequencing and weighted gene co-expression network analysis (WGCNA) to compare the transcriptomes surrounding the shoot apical meristem of indica (Yangdao6, YD6) and japonica (Nipponbare, NPB) rice subspecies. Our results showed that N rate influenced tiller number in a different pattern between the two varieties, with NPB being more sensitive to N enrichment, and YD6 being more tolerant to high N rate. Tiller number was positively related to N content in leaf, culm and root tissue, but negatively related to the soluble carbohydrate content, regardless of variety. Transcriptomic comparisons revealed that for YD6 when N rate enrichment from low (LN) to medium (MN), it caused 115 DEGs (LN vs. MN), from MN to high level (HN) triggered 162 DEGs (MN vs. HN), but direct comparison of low with high N rate showed a 511 DEGs (LN vs. HN). These numbers of DEG in NPB were 87 (LN vs. MN), 40 (MN vs. HN), and 148 (LN vs. HN). These differences indicate that continual N enrichment led to a bumpy change at the transcription level. For the reported sixty-five genes which affect tillering, thirty-six showed decent expression in SAM at tiller starting phase, among them only nineteen being significantly influenced by N level, and two genes showed significant interaction between N rate and variety. Gene ontology analysis revealed that the majority of the common DEGs are involved in general stress responses, stimulus responses, and hormonal signaling process. WGCNA network identified twenty-two co-expressing gene modules and ten candidate hubgenes for each module. Several genes associated with tillering and N rate fall on the related modules. These indicate that there are more genes participating in tillering regulation in response to N enrichment.

Genome-wide alternative polyadenylation dynamics in response to biotic and abiotic stresses in rice

Alternative polyadenylation (APA) is an important way to regulate gene expression at the post-transcriptional level, and is extensively involved in plant stress responses. However, the systematic roles of APA regulation in response to abiotic and biotic stresses in rice at the genome scale remain unknown. To take advantage of available RNA-seq datasets, using a novel tool APAtrap, we identified thousands of genes with significantly differential usage of polyadenylation [poly(A)] sites in response to the abiotic stress (drought, heat shock, and cadmium) and biotic stress [bacterial blight (BB), rice blast, and rice stripe virus (RSV)]. Genes with stress-responsive APA dynamics commonly exhibited higher expression levels when their isoforms with short 3' untranslated region (3' UTR) were more abundant. The stress-responsive APA events were widely involved in crucial stress-responsive genes and pathways: e.g. APA acted as a negative regulator in heat stress tolerance; APA events were involved in DNA repair and cell wall formation under Cd stress; APA regulated chlorophyll metabolism, being associated with the pathogenesis of leaf diseases under RSV and BB challenges. Furthermore, APA events were found to be involved in glutathione metabolism and MAPK signaling pathways, mediating a crosstalk among the abiotic and biotic stress-responsive regulatory networks in rice. Analysis of large-scale datasets revealed that APA may regulate abiotic and biotic stress-responsive processes in rice. Such post-transcriptome diversities contribute to rice adaption to various environmental challenges. Our study would supply useful resource for further molecular assisted breeding of multiple stress-tolerant cultivars for rice.

Differential Uptake and Utilization of Two Forms of Nitrogen in Japonica Rice Cultivars From North-Eastern China

Japonica rice is widely planted in north-eastern China because of its superior food quality and stable grain yields. Nitrogen (N) is an essential element for rice growth, and development and its availability directly impacts on rice yields. The knowledge of N uptake and its utilization characteristics in japonica are thus important areas of research. Three japonica rice cultivars, SN265, SN1401, and SN9816, which are planted across large areas of north-eastern China, were used here to evaluate the uptake and utilization along the life cycle of both ammonium( N H 4 + ) and nitrate( N O 3 - ) in hydroponically grown plants. The plants were grown in one of three different solutions with varying N H 4 + : N O 3 - ratios: 1:0, 0:1, and 1:1 (The total N content was 40 mg L-1 for each treatment). At the tillering stage, when only N O 3 - was provided, lower rates of N uptake and enzyme activities of three rice plants resulted in reduced tiller numbers. During the reproductive stage, the N H 4 + and( N H 4 + ) uptake rates in SN1401 were consistently maintained at high levels, whereas the rates in SN265 and SN9816 were significantly lower, across all three treatments. At the booting stage, when only N O 3 - was provided, SN1401 plants had significantly higher expression levels of OsNRT2.1 and OsNRT2.2, higher activity of nitrate reductase in the roots, and higher activity levels of glutamine synthetase and glutamate synthase in the leaves, compared with the SN265 and SN9816 plants. The higher enzyme activity was beneficial to the secondary assimilation of N, which ultimately promoted panicle development in SN1401. Consequently, the grain yield per plant of SN1401 was the highest with solutions of both N H 4 + and N O 3 - . These results indicate that selecting a rice cultivar with higher utilization of N O 3 - is beneficial for increasing the number of grains per panicle, grain yield, and N use efficiency.

Reducing expression of a nitrate-responsive bZIP transcription factor increases grain yield and N use in wheat

Nitrogen (N) plays critical role in plant growth; manipulating N assimilation could be a target to increase grain yield and N use. Here, we show that ABRE-binding factor (ABF)-like leucine zipper transcription factor TabZIP60 mediates N use and growth in wheat. The expression of TabZIP60 is repressed when the N-deprived wheat plants is exposed to nitrate. Knock down of TabZIP60 through RNA interference (RNAi) increases NADH-dependent glutamate synthase (NADH-GOGAT) activity, lateral root branching, N uptake and spike number, and improves grain yield more than 25% under field conditions, while overexpression of TabZIP60-6D had the opposite effects. Further investigation shows TabZIP60 binds to ABRE-containing fragment in the promoter of TaNADH-GOGAT-3B and negatively regulates its expression. Genetic analysis reveals that TaNADH-GOGAT-3B overexpression overcomes the spike number and yield reduction caused by overexpressing TabZIP60-6D. As such, TabZIP60-mediated wheat growth and N use is associated with its negative regulation on TaNADH-GOGAT expression. These findings indicate that TabZIP60 and TaNADH-GOGAT interaction plays important roles in mediating N use and wheat growth, and provides valuable information for engineering N use efficiency and yield in wheat.

Effect of Imidacloprid Uptake from Contaminated Soils on Vegetable Growth

In the present study, the effect of imidacloprid uptake from contaminated soils on the growth of leaf vegetable Shanghaiqing was investigated. The result showed that during 35-day exposure, the concentration of imidacloprid (IMI) was in the order of vegetable shoots > vegetable roots > soil, indicating that IMI was more readily concentrated in vegetable shoots than in roots. Moreover, the biomass of IMI-treated vegetable shoots was comparable to that of the controls with early exposure, but was higher than that of the controls after 7-day exposure, showing that the test concentration of IMI could stimulate vegetable growth. The plant metabolic analysis of vegetable shoots using LC-QTOF/MS revealed that IMI may cause oxidative stress to the plant shoots with early exposure; however, the stressful situation of IMI seems to be relieved with the increase of some substances (such as spermidine and phenylalanine) with late exposure. Moreover, the upregulation of N-rich amino acids (glutamine, aspartate, and arginine) suggested that the process of fixing inorganic nitrogen in the plant should be enhanced, possibly contributing to enhanced growth rates. Additionally, four IMI's metabolites were identified by using MS-FINDER software, and the distribution of three metabolites in vegetable tissues was compared.

An Integrated Analysis of the Rice Transcriptome and Metabolome Reveals Differential Regulation of Carbon and Nitrogen Metabolism in Response to Nitrogen Availability

Nitrogen (N) is an extremely important macronutrient for plant growth and development. It is the main limiting factor in most agricultural production. However, it is well known that the nitrogen use efficiency (NUE) of rice gradually decreases with the increase of the nitrogen application rate. In order to clarify the underlying metabolic and molecular mechanisms of this phenomenon, we performed an integrated analysis of the rice transcriptome and metabolome. Both differentially expressed genes (DEGs) and metabolite Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that carbon and nitrogen metabolism is significantly affected by nitrogen availability. Further analysis of carbon and nitrogen metabolism changes in rice under different nitrogen availability showed that high N inhibits nitrogen assimilation and aromatic metabolism pathways by regulating carbon metabolism pathways such as the tricarboxylic acid (TCA) cycle and the pentose phosphate pathway (PPP). Under low nitrogen, the TCA cycle is promoted to produce more energy and α-ketoglutarate, thereby enhancing nitrogen transport and assimilation. PPP is also inhibited by low N, which may be consistent with the lower NADPH demand under low nitrogen. Additionally, we performed a co-expression network analysis of genes and metabolites related to carbon and nitrogen metabolism. In total, 15 genes were identified as hub genes. In summary, this study reveals the influence of nitrogen levels on the regulation mechanisms for carbon and nitrogen metabolism in rice and provides new insights into coordinating carbon and nitrogen metabolism and improving nitrogen use efficiency in rice.

A 3-bp deletion of WLS5 gene leads to weak growth and early leaf senescence in rice

BACKGROUND

In rice (Oryza sativa) and other grains, weak growth (dwarfism, short panicle length, and low seed-setting rate) and early senescence lead to reduced yield. The molecular mechanisms behind these processes have been widely studied; however, the complex genetic regulatory networks controlling growth and senescence require further elucidation.

RESULTS

We isolated a mutant exhibiting weak growth throughout development and early senescence of leaf tips, and designated this mutant weakness and leaf senescence5 (wls5). Histological analysis showed that the poor growth of wls5 plants involved a reduction in cell length and number. Physiological analysis and transmission electron microscopy revealed that the wls5 cells had abnormal chloroplasts, and the mutants underwent chlorophyll degradation triggered by accumulation of reactive oxygen species. Consistent with this, RNA sequencing revealed changes in senescence-related gene expression in wls5 plants. The wls5 mutants also exhibited significantly higher stomatal density and altered phytohormone contents compared with wild-type plants. Fine mapping delimited WLS5 to a 29-kb region on chromosome 5. DNA sequencing of wls5 identified a 3-bp deletion in the first exon of LOC_Os05g04900, resulting in a deletion of a lysine in the predicted protein. Knockout of LOC_Os05g04900 in Nipponbare plants caused leaf senescence, confirming this locus as the causal gene for WLS5.

CONCLUSIONS

We identified a novel mutant (wls5) that affects plant development and leaf senescence in rice. LOC_Os05g04900, encoding a protein of unknown function, is the causal gene for wls5. Further molecular study of WLS5 will uncover the roles of this gene in plant growth and leaf senescence.