The ferredoxin-dependent glutamate synthase (OsFd-GOGAT) participates in leaf senescence and the nitrogen remobilization in rice

Identification of Wheat Glutamate Synthetase Gene Family and Expression Analysis under Nitrogen Stress

Nitrogen (N), as the main component of biological macromolecules, maintains the basic process of plant growth and development. GOGAT, as a key enzyme in the N assimilation process, catalyzes α-ketoglutaric acid and glutamine to form glutamate. In this study, six GOGAT genes in wheat (Triticum aestivum L.) were identified and classified into two subfamilies, Fd-GOGAT (TaGOGAT2s) and NADH-GOGAT (TaGOGAT3s), according to the type of electron donor. Subcellular localization prediction showed that TaGOGAT3-D was localized in mitochondria and that the other five TaGOGATs were localized in chloroplasts. Via the analysis of promoter elements, many binding sites related to growth and development, hormone regulation and plant stress resistance regulations were found on the TaGOGAT promoters. The tissue-specificity expression analysis showed that TaGOGAT2s were mainly expressed in wheat leaves and flag leaves, while TaGOGAT3s were highly expressed in roots and leaves. The expression level of TaGOGATs and the enzyme activity of TaGOGAT3s in the leaves and roots of wheat seedlings were influenced by the treatment of N deficiency. This study conducted a systematic analysis of wheat GOGAT genes, providing a theoretical basis not only for the functional analysis of TaGOGATs, but also for the study of wheat nitrogen use efficiency (NUE).

Integrated proteome and physiological traits reveal interactive mechanisms of new leaf growth and storage protein degradation with mature leaves of evergreen citrus trees

The growth of fruit trees depends on the nitrogen (N) remobilization in mature tissues and N acquisition from the soil. However, in evergreen mature citrus (Citrus reticulata Blanco) leaves, proteins with N storage functions and hub molecules involved in driving N remobilization remain largely unknown. Here, we combined proteome and physiological analyses to characterize the spatiotemporal mechanisms of growth of new leaves and storage protein degradation in mature leaves of citrus trees exposed to low-N and high-N fertilization in the field. Results show that the growth of new leaves is driven by remobilization of stored reserves, rather than N uptake by the roots. In this context, proline and arginine in mature leaves acted as N sources supporting the growth of new leaves in spring. Time-series analyses with gel electrophoresis and proteome analysis indicated that the mature autumn shoot leaves are probably the sites of storage protein synthesis, while the aspartic endopeptidase protein is related to the degradation of storage proteins in mature citrus leaves. Furthermore, bioinformatic analysis based on protein-protein interactions indicated that glutamate synthetase and ATP-citrate synthetase are hub proteins in N remobilization from mature citrus leaves. These results provide strong physiological data for seasonal optimization of N fertilizer application in citrus orchards.

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.

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.

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.

Millet-inspired systems metabolic engineering of NUE in crops

The use of nitrogen (N) fertilizers in agriculture has a great ability to increase crop productivity. However, their excessive use has detrimental effects on the environment. Therefore, it is necessary to develop crop varieties with improved nitrogen use efficiency (NUE) that require less N but have substantial yields. Orphan crops such as millets are cultivated in limited regions and are well adapted to lower input conditions. Therefore, they serve as a rich source of beneficial traits that can be transferred into major crops to improve their NUE. This review highlights the tremendous potential of systems biology to unravel the enzymes and pathways involved in the N metabolism of millets, which can open new possibilities to generate transgenic crops with improved NUE.

Molecular basis of nitrogen starvation-induced leaf senescence

Nitrogen (N), a macronutrient, is often a limiting factor in plant growth, development, and productivity. To adapt to N-deficient environments, plants have developed elaborate N starvation responses. Under N-deficient conditions, older leaves exhibit yellowing, owing to the degradation of proteins and chlorophyll pigments in chloroplasts and subsequent N remobilization from older leaves to younger leaves and developing organs to sustain plant growth and productivity. In recent years, numerous studies have been conducted on N starvation-induced leaf senescence as one of the representative plant responses to N deficiency, revealing that leaf senescence induced by N deficiency is highly complex and intricately regulated at different levels, including transcriptional, post-transcriptional, post-translational and metabolic levels, by multiple genes and proteins. This review summarizes the current knowledge of the molecular mechanisms associated with N starvation-induced leaf senescence.

Integrated physiological, proteome and gene expression analyses provide new insights into nitrogen remobilization in citrus trees

Nitrogen (N) remobilization is an important physiological process that supports the growth and development of trees. However, in evergreen broad-leaved tree species, such as citrus, the mechanisms of N remobilization are not completely understood. Therefore, we quantified the potential of N remobilization from senescing leaves of spring shoots to mature leaves of autumn shoots of citrus trees under different soil N availabilities and further explored the underlying N metabolism characteristics by physiological, proteome and gene expression analyses. Citrus exposed to low N had an approximately 38% N remobilization efficiency (NRE), whereas citrus exposed to high N had an NRE efficiency of only 4.8%. Integrated physiological, proteomic and gene expression analyses showed that photosynthesis, N and carbohydrate metabolism interact with N remobilization. The improvement of N metabolism and photosynthesis, the accumulation of proline and arginine, and delayed degradation of storage protein in senescing leaves are the result of sufficient N supply and low N remobilization. Proteome further showed that energy generation proteins and glutamate synthase were hub proteins affecting N remobilization. In addition, N requirement of mature leaves is likely met by soil supply at high N nutrition, thereby resulting in low N remobilization. These results provide insight into N remobilization mechanisms of citrus that are of significance for N fertilizer management in orchards.

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.

The Dynamics of NO3- and NH4+ Uptake in Duckweed Are Coordinated with the Expression of Major Nitrogen Assimilation Genes

Duckweed plants play important roles in aquatic ecosystems worldwide. They rapidly accumulate biomass and have potential uses in bioremediation of water polluted by fertilizer runoff or other chemicals. Here we studied the assimilation of two major sources of inorganic nitrogen, nitrate (NO3- ) and ammonium (NH4+), in six duckweed species: Spirodela polyrhiza, Landoltia punctata, Lemna aequinoctialis, Lemna turionifera, Lemna minor, and Wolffia globosa. All six duckweed species preferred NH4+ over NO3- and started using NO3- only when NH4+ was depleted. Using the available genome sequence, we analyzed the molecular structure and expression of eight key nitrogen assimilation genes in S. polyrhiza. The expression of genes encoding nitrate reductase and nitrite reductase increased about 10-fold when NO3- was supplied and decreased when NH4+ was supplied. NO3- and NH4+ induced the glutamine synthetase (GS) genes GS1;2 and the GS2 by 2- to 5-fold, respectively, but repressed GS1;1 and GS1;3. NH4+ and NO3- upregulated the genes encoding ferredoxin- and NADH-dependent glutamate synthases (Fd-GOGAT and NADH-GOGAT). A survey of nitrogen assimilation gene promoters suggested complex regulation, with major roles for NRE-like and GAATC/GATTC cis-elements, TATA-based enhancers, GA/CTn repeats, and G-quadruplex structures. These results will inform efforts to improve bioremediation and nitrogen use efficiency.

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.

RNA-Seq-Based Profiling of pl Mutant Reveals Transcriptional Regulation of Anthocyanin Biosynthesis in Rice (Oryza sativa L.)

Purple-colored leaves in plants attain much interest for their important biological functions and could be a potential source of phenotypic marker in selecting individuals in breeding. The transcriptional profiling helps to precisely identify mechanisms of leaf pigmentation in crop plants. In this study, two genetically unlike rice genotypes, the mutant purple leaf (pl) and wild (WT) were selected for RNA-sequencing and identifying the differentially expressed genes (DEGs) that are regulating purple leaf color. In total, 609 DEGs were identified, of which 513 and 96 genes were up- and down-regulated, respectively. The identified DEGs are categorized into metabolic process, carboxylic acid biosynthesis, phenylpropanoids, and phenylpropanoid biosynthesis process enrichment by GO analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) confirmed their association with phenylpropanoid synthesis, flavonoid synthesis, and phenylalanine metabolism. To explore molecular mechanism of purple leaf color, a set of anthocyanin biosynthetic and regulatory gene expression patterns were checked by qPCR. We found that OsPAL (Os02g0626100, Os02g0626400, Os04g0518400, Os05g0427400 and Os02g0627100), OsF3H (Os03g0122300), OsC4HL (Os05g0320700), and Os4CL5 (Os08g0448000) are associated with anthocyanin biosynthesis, and they were up-regulated in pl leaves. Two members of regulatory MYB genes (OsMYB55; Os05g0553400 and Os08g0428200), two bHLH genes (Os01g0196300 and Os04g0300600), and two WD40 genes (Os11g0132700 and Os11g0610700) also showed up-regulation in pl mutant. These genes might have significant and vital roles in pl leaf coloration and could provide reference materials for further experimentation to confirm the molecular mechanisms of anthocyanin biosynthesis in rice.

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.

Biochemical and Genetic Approaches Improving Nitrogen Use Efficiency in Cereal Crops: A Review

Nitrogen is an essential nutrient required in large quantities for the proper growth and development of plants. Nitrogen is the most limiting macronutrient for crop production in most of the world's agricultural areas. The dynamic nature of nitrogen and its tendency to lose soil and environment systems create a unique and challenging environment for its proper management. Exploiting genetic diversity, developing nutrient efficient novel varieties with better agronomy and crop management practices combined with improved crop genetics have been significant factors behind increased crop production. In this review, we highlight the various biochemical, genetic factors and the regulatory mechanisms controlling the plant nitrogen economy necessary for reducing fertilizer cost and improving nitrogen use efficiency while maintaining an acceptable grain yield.

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.

Hydrogen sulfide and rhizobia synergistically regulate nitrogen (N) assimilation and remobilization during N deficiency-induced senescence in soybean

Hydrogen sulfide (H2 S) is emerging as an important signalling molecule that regulates plant growth and abiotic stress responses. However, the roles of H2 S in symbiotic nitrogen (N) assimilation and remobilization have not been characterized. Therefore, we examined how H2 S influences the soybean (Glycine max)/rhizobia interaction in terms of symbiotic N fixation and mobilization during N deficiency-induced senescence. H2 S enhanced biomass accumulation and delayed leaf senescence through effects on nodule numbers, leaf chlorophyll contents, leaf N resorption efficiency, and the N contents in different tissues. Moreover, grain numbers and yield were regulated by H2 S and rhizobia, together with N accumulation in the organs, and N use efficiency. The synergistic effects of H2 S and rhizobia were also demonstrated by effects on the enzyme activities, protein abundances, and gene expressions associated with N metabolism, and senescence-associated genes (SAGs) expression in soybeans grown under conditions of N deficiency. Taken together, these results show that H2 S and rhizobia accelerate N assimilation and remobilization by regulation of the expression of SAGs during N deficiency-induced senescence. Thus, H2 S enhances the vegetative and reproductive growth of soybean, presumably through interactions with rhizobia under conditions of N deficiency.

ES5 is involved in the regulation of phosphatidylserine synthesis and impacts on early senescence in rice (Oryza sativa L.)

Leaf senescence, which affects plant growth and yield in rice, is an ideal target for crop improvement and remarkable advances have been made to identify the mechanism underlying this process. We have characterized an early senile mutant es5 (early leaf senescence 5) in rice exhibiting leaf yellowing phenotype after the 4-leaf stage. This phenotype was confirmed by the higher accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA), the disintegration of chloroplasts, reduction in chlorophyll content and photosynthetic rate and up-regulation of senescence-associated genes (SAGs) like Osh36, OsI57, and OsI85. Positional cloning revealed that the es5 phenotype is the result of one base substitution in ES5, encoding phosphatidylserine synthase (PSS) family protein, which is involved in the base-exchange type reaction to synthesize the minor membrane phospholipid phosphatidylserine. Functional complementation of ES5 in the es5 plants completely restored the wild-type phenotype. Ultra-high-performance liquid chromatography (UHPLC) analysis showed that es5 plants had increased levels of phosphatidylserine (PS) and decreased level of phosphatidylcholine (PC). These results provide evidence about the role of PS in rice leaf senescence.

ES5 is involved in the regulation of phosphatidylserine synthesis and impacts on early senescence in rice (Oryza sativa L.)

Leaf senescence, which affects plant growth and yield in rice, is an ideal target for crop improvement and remarkable advances have been made to identify the mechanism underlying this process. We have characterized an early senile mutant es5 (early leaf senescence 5) in rice exhibiting leaf yellowing phenotype after the 4-leaf stage. This phenotype was confirmed by the higher accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA), the disintegration of chloroplasts, reduction in chlorophyll content and photosynthetic rate and up-regulation of senescence-associated genes (SAGs) like Osh36, OsI57, and OsI85. Positional cloning revealed that the es5 phenotype is the result of one base substitution in ES5, encoding phosphatidylserine synthase (PSS) family protein, which is involved in the base-exchange type reaction to synthesize the minor membrane phospholipid phosphatidylserine. Functional complementation of ES5 in the es5 plants completely restored the wild-type phenotype. Ultra-high-performance liquid chromatography (UHPLC) analysis showed that es5 plants had increased levels of phosphatidylserine (PS) and decreased level of phosphatidylcholine (PC). These results provide evidence about the role of PS in rice leaf senescence.

A Novel Stay-Green Mutant of Rice with Delayed Leaf Senescence and Better Harvest Index Confers Drought Tolerance

Three Ethyl methansulphonate (EMS)-induced stay-green mutants (SGM-1, SGM-2 and SGM-3) and their wild-type (WT), were tested for their Stay-Green (SG) and drought tolerance nature as the relation between these two attributes is not yet established in rice. In the dark induced senescence assay, SGM-3 showed delayed senescence while SGM-1 and SGM-2 showed complete lack of senescence. Mutants showed stable transcript abundance over time, for 15 candidate genes (CGs) associated with senescence, compared to the WT. SGM-3 however showed moderately increasing transcript abundance over time for ATG6a, ATG4a, NYC1, NOL and NYC3. Only SGM-3 performed better than the WT for yield and harvest index under well irrigated as well as drought conditions, though all the mutants showed better performance for other agronomic traits under both the conditions and ascorbate peroxidase activity under drought. Thus, SG trait showed positive correlation with drought tolerance though only SGM-3 could convert this into higher harvest index. Sequence analysis of 80 senescence-associated genes including the 15 CGs showed non-synonymous mutations in four and six genes in SGM-1 and SGM-2 respectively, while no SNPs were found in SGM-3. Analysis of the earlier reported Quantitative Trait Loci (QTL) regions in SGM-3 revealed negligible variations from WT, suggesting it to be a novel SG mutant.

Transcriptional Profile Corroborates that bml Mutant Plays likely Role in Premature Leaf Senescence of Rice (Oryza sativa L.)

Leaf senescence is the last period of leaf growth and a dynamic procedure associated with its death. The adaptability of the plants to changing environments occurs thanks to leaf senescence. Hence, transcriptional profiling is important to figure out the exact mechanisms of inducing leaf senescence in a particular crop, such as rice. From this perspective, leaf samples of two different rice genotypes, the brown midrib leaf (bml) mutant and its wild type (WT) were sampled for transcriptional profiling to identify differentially-expressed genes (DEGs). We identified 2670 DEGs, among which 1657 genes were up- and 1013 genes were down-regulated. These DEGs were enriched in binding and catalytic activity, followed by the single organism process and metabolic process through gene ontology (GO), while the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the DEGs were related to the plant hormone signal transduction and photosynthetic pathway enrichment. The expression pattern and the clustering of DEGs revealed that the WRKY and NAC family, as well as zinc finger transcription factors, had greater effects on early-senescence of leaf compared to other transcription factors. These findings will help to elucidate the precise functional role of bml rice mutant in the early-leaf senescence.

Candidate genes and genome-wide association study of grain protein content and protein deviation in durum wheat

Stable QTL for grain protein content co-migrating with nitrogen-related genes have been identified by the candidate genes and genome-wide association mapping approaches useful for marker-assisted selection. Grain protein content (GPC) is one of the most important quality traits in wheat, defining the nutritional and end-use properties and rheological characteristics. Over the years, a number of breeding programs have been developed aimed to improving GPC, most of them having been prevented by the negative correlation with grain yield. To overcome this issue, a collection of durum wheat germplasm was evaluated for both GPC and grain protein deviation (GPD) in seven field trials. Fourteen candidate genes involved in several processes related to nitrogen metabolism were precisely located on two high-density consensus maps of common and durum wheat, and six of them were found to be highly associated with both traits. The wheat collection was genotyped using the 90 K iSelect array, and 11 stable quantitative trait loci (QTL) for GPC were detected in at least three environments and the mean across environments by the genome-wide association mapping. Interestingly, seven QTL were co-migrating with N-related candidate genes. Four QTL were found to be significantly associated to increases of GPD, indicating that selecting for GPC could not affect final grain yield per spike. The combined approaches of candidate genes and genome-wide association mapping led to a better understanding of the genetic relationships between grain storage proteins and grain yield per spike, and provided useful information for marker-assisted selection programs.

A guanine insert in OsBBS1 leads to early leaf senescence and salt stress sensitivity in rice (Oryza sativa L.)

A rice receptor-like kinase gene OSBBS1/OsRLCK109 was identified; this gene played vital roles in leaf senescence and the salt stress response. Early leaf senescence can cause negative effects on rice yield, but the underlying molecular regulation is not fully understood. bilateral blade senescence 1 (bbs1), an early leaf senescence mutant with a premature senescence phenotype that occurs mainly performing at the leaf margins, was isolated from a rice mutant population generated by ethylmethane sulfonate (EMS) treatment. The mutant showed premature leaf senescence beginning at the tillering stage and exhibited severe symptoms at the late grain-filling stage. bbs1 showed accelerated dark-induced leaf senescence. The OsBBS1 gene was cloned by a map-based cloning strategy, and a guanine (G) insertion was found in the first exon of LOC_Os03g24930. This gene encodes a receptor-like cytoplasmic kinase and was named OsRLCK109 in a previous study. Transgenic LOC_Os03g24930 knockout plants generated by a CRISPR/Cas9 strategy exhibited similar early leaf senescence phenotypes as did the bbs1 mutant, which confirmed that LOC_Os03g24930 was the OsBBS1 gene. OsBBS1/OsRLCK109 was expressed in all detected tissues and was predominantly expressed in the main vein region of mature leaves. The expression of OsBBS1 could be greatly induced by salt stress, and the bbs1 mutant exhibited hypersensitivity to salt stress. In conclusion, this is the first identification of OsRLCKs participating in leaf senescence and playing critical roles in the salt stress response in rice (Oryza sativa L.).

The Brown Midrib Leaf (bml) Mutation in Rice (Oryza sativa L.) Causes Premature Leaf Senescence and the Induction of Defense Responses

Isolating and characterizing mutants with altered senescence phenotypes is one of the ways to understand the molecular basis of leaf aging. Using ethyl methane sulfonate mutagenesis, a new rice (Oryza sativa) mutant, brown midrib leaf (bml), was isolated from the indica cultivar ‘Zhenong34’. The bml mutants had brown midribs in their leaves and initiated senescence prematurely, at the onset of heading. The mutants had abnormal cells with degraded chloroplasts and contained less chlorophyll compared to the wild type (WT). The bml mutant showed excessive accumulation of reactive oxygen species (ROS), increased activities of superoxide dismutase, catalase, and malondialdehyde, upregulation of senescence-induced STAY-GREEN genes and senescence-related transcription factors, and down regulation of photosynthesis-related genes. The levels of abscisic acid (ABA) and jasmonic acid (JA) were increased in bml with the upregulation of some ABA and JA biosynthetic genes. In pathogen response, bml demonstrated higher resistance against Xanthomonas oryzae pv. oryzae and upregulation of four pathogenesis-related genes compared to the WT. A genetic study confirmed that the bml trait was caused by a single recessive nuclear gene (BML). A map-based cloning using insertion/deletion markers confirmed that BML was located in the 57.32kb interval between the L5IS7 and L5IS11 markers on the short arm of chromosome 5. A sequence analysis of the candidate region identified a 1 bp substitution (G to A) in the 5′-UTR (+98) of bml. BML is a candidate gene associated with leaf senescence, ROS regulation, and disease response, also involved in hormone signaling in rice. Therefore, this gene might be useful in marker-assisted backcrossing/gene editing to improve rice cultivars.

Genetic variations in ARE1 mediate grain yield by modulating nitrogen utilization in rice

In crops, nitrogen directly determines productivity and biomass. However, the improvement of nitrogen utilization efficiency (NUE) is still a major challenge in modern agriculture. Here, we report the characterization of are1, a genetic suppressor of a rice fd-gogat mutant defective in nitrogen assimilation. ARE1 is a highly conserved gene, encoding a chloroplast-localized protein. Loss-of-function mutations in ARE1 cause delayed senescence and result in 10-20% grain yield increases, hence enhance NUE under nitrogen-limiting conditions. Analysis of a panel of 2155 rice varieties reveals that 18% indica and 48% aus accessions carry small insertions in the ARE1 promoter, which result in a reduction in ARE1 expression and an increase in grain yield under nitrogen-limiting conditions. We propose that ARE1 is a key mediator of NUE and represents a promising target for breeding high-yield cultivars under nitrogen-limiting condition.

Genetic Dissection of Leaf Senescence in Rice

Leaf senescence, the final stage of leaf development, is a complex and highly regulated process that involves a series of coordinated actions at the cellular, tissue, organ, and organism levels under the control of a highly regulated genetic program. In the last decade, the use of mutants with different levels of leaf senescence phenotypes has led to the cloning and functional characterizations of a few genes, which has greatly improved the understanding of genetic mechanisms underlying leaf senescence. In this review, we summarize the recent achievements in the genetic mechanisms in rice leaf senescence.