Emerging role of jasmonic acid in woody plant development

Jasmonic acid is a crucial phytohormone that plays a pivotal role,serving as a regulator to balancing plant development and resistance.However,there are analogous and distinctive characteristics exhibited in JA biosynthesis,perception,and signal transduction pathways in both herbaceous and woody plants.Moreover,the majority of research subjects have predominantly focused on the function of JA in model or herbaceous plants.Consequently,there is a significant paucity of studies investigating JA regulation networks in woody plants,particularly concerning post-transcriptional regulatory events such as alternative splicing(AS).This review article aims to conduct a comprehensive summary of advancements that JA signals regulate plant development across various woody species,comparing the analogous features and regulatory differences to herbaceous counterparts.In addition,we summarized the involvement of AS events including splicing factor(SF)and transcripts in the JA regulatory network,highlighting the effectiveness of high-throughput proteogenomic methods.A better understanding of the JA signaling pathway in woody plants has pivotal implications for forestry production,including optimizing plant management and enhancing secondary metabolite production.

CsbZIP1-CsMYB12 mediates the production of bitter-tasting flavonols in tea plants (Camellia sinensis) through a coordinated activator–repressor network

Under high light conditions or UV radiation,tea plant leaves produce more flavonols,which contribute to the bitter taste of tea;however,neither the flavonol biosynthesis pathways nor the regulation of their production are well understood.Intriguingly,tea leaf flavonols are enhanced by UV-B but reduced by shading treatment.CsFLS,CsUGT78A14,CsMYB12,and CsbZIP1 were upregulated by UV-B radiation and downregulated by shading.CsMYB12 and CsbZIP1 bound to the promoters of CsFLS and CsUGT78A14,respectively,and activated their expression individually.CsbZIP1 positively regulated CsMYB12 and interacted with CsMYB12,which specifically activated flavonol biosynthesis.Meanwhile,CsPIF3 and two MYB repressor genes,CsMYB4 and CsMYB7,displayed expression patterns opposite to that of CsMYB12.CsMYB4 and CsMYB7 bound to CsFLS and CsUGT78A14 and repressed their CsMYB12-activated expression.While CsbZIP1 and CsMYB12 regulated neither CsMYB4 nor CsMYB7,CsMYB12 interacted with CsbZIP1,CsMYB4,and CsMYB7,but CsbZIP1 did not physically interact with CsMYB4 or CsMYB7.Finally,CsPIF3 bound to and activated CsMYB7 under shading to repress flavonol biosynthesis.These combined results suggest that UV activation and shading repression of flavonol biosynthesis in tea leaves are coordinated through a complex network involving CsbZIP1 and CsPIF3 as positive MYB activators and negative MYB repressors,respectively.The study thus provides insight into the regulatory mechanism underlying the production of bitter-tasting flavonols in tea plants.

MORN motifs in plant PIPKs are involved in the regulation of subcellular localization and phospholipid binding

Multiple repeats of membrane occupation and recognition nexus (MORN) motifs were detected in plant phosphatidylinositl monophosphate kinase (PIPK), a key enzyme in PI-signaling pathway. Structural analysis indicates that all the MORN motifs (with varied numbers at ranges of 7-9), which shared high homologies to those of animal ones, were located at N-terminus and sequentially arranged, except those of OsPIPK1 and AtPIPK7, in which the last MORN motif was separated others by an -100 amino-acid "island" region, revealing the presence of two kinds of MORN arrangements in plant PIPKs. Through employing a yeast-based SMET (sequence of membrane-targeting) system, the MORN motifs were shown being able to target the fusion proteins to cell plasma membrane, which were further confirmed by expression of fused MORN-GFP proteins. Further detailed analysis via deletion studies indicated the MORN motifs in OsPIPK 1, together with the 104 amino-acid "island" region are involved in the regulation of differential subcellular localization, i.e. plasma membrane or nucleus, of the fused proteins. Fat Western blot analysis of the recombinant MORN polypeptide, expressed in Escherichia coli, showed that MORN motifs could strongly bind to PA and relatively slightly to PI4P and PI(4,5)P2. These results provide informative hints on mechanisms of subcellular localization, as well as regulation of substrate binding, of plant PIPKs.

Multiomics-based dissection of citrus flavonoid metabolism using a Citrus reticulata × Poncirus trifoliata population

Deciphering the genetic basis of plant secondary metabolism will provide useful insights for genetic improvement and enhance our fundamental understanding of plant biological processes.Although citrus plants are among the most important fruit crops worldwide,the genetic basis of secondary metabolism in these plants is largely unknown.Here,we use a high-density linkage map to dissect large-scale flavonoid metabolic traits measured in different tissues(young leaf,old leaf,mature pericarp,and mature pulp)of an F_(1) pseudo-testcross citrus population.We detected 80 flavonoids in this population and identified 138 quantitative trait loci(QTLs)for 57 flavonoids in these four tissues.Based on transcriptional profiling and functional annotation,twenty-one candidate genes were identified,and one gene encoding flavanone 3-hydroxylase(F3H)was functionally verified to result in naturally occurring variation in dihydrokaempferol content through genetic variations in its promoter and coding regions.The abundant data resources collected for diverse citrus germplasms here lay the foundation for complete characterization of the citrus flavonoid biosynthetic pathway and will thereby promote efficient utilization of metabolites in citrus quality improvement.

Decoding altitude-activated regulatory mechanisms occurring during apple peel ripening

Apple(Malus domestica Borkh)is an important fruit crop cultivated in a broad range of environmental conditions.Apple fruit ripening is a physiological process,whose molecular regulatory network response to different environments is still not sufficiently investigated and this is particularly true of the peel tissue.In this study,the influence of environmental conditions associated with low(20 m)and high(750 m)altitude on peel tissue ripening was assessed by physiological measurements combined with metabolomic and proteomic analyses during apple fruit development and ripening.Although apple fruit ripening was itself not affected by the different environmental conditions,several key color parameters,such as redness and color index,were notably induced by high altitude.Consistent with this observation,increased levels of anthocyanin and other phenolic compounds,including cyanidin-3-O-galactoside,quercetin-3-O-rhamnoside,quercetin-3-O-rutinoside,and chlorogenic acid were identified in the peel of apple grown at high altitude.Moreover,the high-altitude environment was characterized by elevated abundance of various carbohydrates(e.g.,arabinose,xylose,and sucrose)but decreased levels of glutamic acid and several related proteins,such as glycine hydroxymethyltransferase and glutamate–glyoxylate aminotransferase.Other processes affected by high altitude were the TCA cycle,the synthesis of oxidative/defense enzymes,and the accumulation of photosynthetic proteins.From the obtained data we were able to construct a metabolite-protein network depicting the impact of altitude on peel ripening.The combined analyses presented here provide new insights into physiological processes linking apple peel ripening with the prevailing environmental conditions.

A Pin gene families encoding components of auxin efflux carriers in Brassica juncea

Based on the sequence information of Arabidopsis PIN1, two cDNAs encoding PIN homologues fromBrassica juncea, Bjpin2 and Bjpin3, were isolated through cDNA library screening. Bjpin2 and Bjpin3encoded proteins containing 640 and 635 amino acid residues, respectively, which shared 97.5% identities witheach other and were highly homologous to Arabidopsis PIN1, PIN2 and other putative PIN proteins. BjPIN2and BjPIN3 had similar structures as AtPIN proteins. Northern blot analysis indicated that Bjpin2 wasexpressed in stem, leaf and floral tissues, while Bjpin3 was expressed predominantly in stem and hypocotyls.Two promoter fragments of pin genes, Bjpin-X and Bjpin-Z, were isolated by 'genome walking' techniqueusing primers at 5'-end of pin cDNA. Promoter-gus fusion studies revealed the GUS activities driven byBjpin-X were at internal side of xylem and petal; while those driven by Bjpin-Z were detected at leaf vein,epidermal cell and cortex of stem, vascular tissues and anther. Results of the pin genes with differentexpression patterns in B. juncea suggested the presence of a gene family.

WTV2.0:A high-coverage plant volatilomics method with a comprehensive selective ion monitoring acquisition mode

Volatilomics is essential for understanding the biological functions and fragrance contributions of plant volatiles.However,the annotation coverage achieved using current untargeted and widely targeted volatomics(WTV)methods has been limited by low sensitivity and/or low acquisition coverage.Here,we introduce WTV 2.0,which enabled the construction of a high-coverage library containing 2111 plant volatiles,and report the development of a comprehensive selective ion monitoring(cSIM)acquisition method,including the selection of characteristic qualitative ions with the minimal ion number for each compound and an optimized segmentation method,that can acquire the smallest but sufficient number of ions for most plant volatiles,as well as the automatic qualitative and semi-quantitative analysis of cSIM data.Importantly,the library and acquisition method we developed can be self-expanded by incorporating compounds not present in the library,utilizing the obtained cSIM data.We showed that WTV 2.0 increases the median signal-to-noise ratio by 7.6-fold compared with the untargeted method,doubled the annotation coverage compared with the untargeted and WTV 1.0 methods in tomato fruit,and led to the discovery of menthofuran as a novel flavor compound in passion fruit.WTV 2.0 is a Python library with a user-friendly interface and is applicable to profiling of volatiles and primary metabolites in any species.

Characterization of PetM cytochrome b6f subunit 7 domain-containing protein in tomato

In recent years,multiple advances have been made in understanding the photosynthetic machinery in model organisms.Knowledge transfer to horticultural important fruit crops is challenging and time-consuming due to restrictions in gene editing tools and prolonged life cycles.Here,we characterize a gene encoding a PetM domain-containing protein in tomato.The CRISPR/Cas9 knockout lines of the PetM showed impairment in the chloroplastic electron transport rate(ETR),reduced CO_(2) assimilation,and reduction of carotenoids and chlorophylls(Chl)under several light conditions.Further,growth-condition-dependent elevation or repression of Chl a/b ratios and de-epoxidation states were identified,underlining possible impairment compensation mechanisms.However,under low light and glasshouse conditions,there were basal levels in CO_(2) assimilation and ETR,indicating a potential role of the PetM domain in stabilizing the cytochrome b6f complex(Cb6f)under higher light irradiance and increasing its quantum efficiency.This suggests a potential evolutionary role in which this domain might stabilize the site of the Cb6f regulating ratios of cyclic and linear electron transport and its potential importance during the conquest of terrestrial ecosystems during which plants were exposed to higher irradiance.Finally,the results are discussed with regard to metabolism and their implication to photosynthesis from an agronomic perspective.

Nitric oxide regulation of plant metabolism

Nitric oxide(NO)has emerged as an important signal molecule in plants,having myriad roles in plant devel-opment.In addition,NO also orchestrates both biotic and abiotic stress responses,during which intensive cellular metabolic reprogramming occurs.Integral to these responses is the location of NO biosynthetic and scavenging pathways in diverse cellular compartments,enabling plants to effectively organize signal transduction pathways.NO regulates plant metabolism and,in turn,metabolic pathways reciprocally regu-late NO accumulation and function.Thus,these diverse cellular processes are inextricably linked.This re-view addresses the numerous redox pathways,located in the various subcellular compartments that pro-duce NO,in addition to the mechanisms underpinning NO scavenging.We focus on how this molecular dance is integrated into the metabolic state of the cell.Within this context,a reciprocal relationship be-tween NO accumulation and metabolite production is often apparent.We also showcase cellular pathways,including those associated with nitrate reduction,that provide evidence for this integration of NO function and metabolism.Finally,we discuss the potential importance of the biochemical reactions governing NO levels in determining plant responses to a changing environment.

Understanding source-sink interactions: Progress in model plants and translational research to crops

Agriculture is facing a massive increase in demand per hectare as a result of an ever-expanding population and environmental deterioration.While we have learned much about how environmental conditions and diseases impact crop yield,until recently considerably less was known concerning endogenous factors,including within-plant nutrient allocation.In this review,we discuss studies of source-sink interactions covering both fundamental research in model systems under controlled growth conditions and how the findings are being translated to crop plants in the field.In this respect we detail efforts aimed at improving and/or combining C3,C4,and CAM modes of photosynthesis,altering the chloroplastic electron transport chain,modulating photorespiration,adopting bacterial/algal carbon-concentrating mechanisms,and enhancing nitrogen-and water-use efficiencies.Moreover,we discuss how modulating TCA cycle activities and primary metabolism can result in increased rates of photosynthesis and outline the opportunities that evaluating natural variation in photosynthesis may afford.Although source,transport,and sink functions are all covered in this review,we focus on discussing source functions because the majority of research has been conducted in this field.Nevertheless,considerable recent evidence,alongside the evidence from classical studies,demonstrates that both transport and sink functions are also incredibly important determinants of yield.We thus describe recent evidence supporting this notion and suggest that future strategies for yield improvement should focus on combining improvements in each of these steps to approach yield optimization.

At Long Last： Evidence for Pexophagy in Plants

Peroxisomes are highly dynamic single-membrane-bound eukaryotic organelles displaying great variability in enzymatic content （Platta and Erdmann, 2007）. Plant peroxisomes function in a plethora of crucial development and stress ameliorating processes. Among the functions of plant peroxisomes are 13-oxidation of fatty acids, phytohormone production, participation in photorespiration, the glyoxyalte cycle, detoxification processes, and signal molecule generation （Hu et al., 2012）.

Doubled haploid technology and synthetic apomixis:Recent advances and applications in future crop breeding

Doubled haploid(DH)technology and synthetic apomixis approaches can considerably shorten breeding cycles and enhance breeding efficiency.Compared with traditional breeding methods,DH technology offers the advantage of rapidly generating inbred lines,while synthetic apomixis can effectively fix hybrid vigor.In this review,we focus on(i)recent advances in identifying and characterizing genes responsible for haploid induction(Hl),(ii)the molecular mechanisms of Hl,(ili)spontaneous haploid genome doubling,and(iv)crop synthetic apomixis.We also discuss the challenges and potential solutions for future crop breeding programs utilizing DH technology and synthetic apomixis.Finally,we provide our perspectives about how to integrate DH and synthetic apomixis for precision breeding and de novo domestication.

A metabolic roadmap of waxy corn flavor

As well as being a popular vegetable crop worldwide,waxy corn represents an important amylopectin source,but little is known about its breeding history and flavor characteristics.In this study,through comparative-omic analyses between 318 diverse waxy corn and 507 representative field corn inbred lines we revealed that many metabolic pathways and genes exhibited selection characteristics during the breeding history of waxy corn,contributing to the divergence between waxy and field corn.We showed that waxy corn is not only altered in its glutinous property but also its sweetness,aroma,and palatability are all significantly affected.A substantial proportion(43%)of flavor-related metabolites have pleiotropic effects,affecting both flavor and yield characteristics,and 27%of these metabolites are related to antagonistic outcomes on yield and flavor.Furthermore,through multiple concrete examples,we demonstrated how yield and quality are coordinately or antagonistically regulated at the genetic level.In particular,some sweet molecules,such as DIMBOA and raffinose,which do not participate in the starch biosynthesis pathway,were identified as potential targets for breeding a new type of“sweet-waxy”corn.Taken together,our findings shed light on the historical selection of waxy corn and demonstrate the genetic and metabolic basis of waxy corn flavor,collectively providing valuable resources and knowledge for future crop breeding for improved nutritional quality.

Transition of primary to secondary cell wall synthesis

The construction of a secondary cell wall is an important and necessary developmental decision that sup- ports cell function and plant stature. Unlike the primary cell walls, which are initiated during cell division and develop along with the expansion of the cells, secondary cell walls are constructed after the cells have stopped growing. Hence, the transition from primary to secondary wall synthesis marks an important and distinct metabolic investment by the plant. This transition requires a coordi- nated change of a plethora of cellular processes, including hormonal, transcriptional and post-transcriptional activi- ties, metabolic flux re-distributions and enzymatic activities. In this review, we briefly summarize the hormonal and transcriptional control of the primary to secondary wall transition, and highlight important gaps in our under- standing of the metabolic framework that support the transition. Several tools that may aid in future research efforts to better understand the changes in cell wall synthesis during the trans-differentiation are also discussed.

The Past, Present, and Future of Maize Improvement: Domestication, Genomics, and Functional Genomic Routes toward Crop Enhancement

After being domesticated from teosinte,cultivated maize(Zea mays ssp.mays)spread worldwide and now is one of the most important staple crops.Due to its tremendous phenotypic and genotypic diversity,maize also becomes to be one of the most widely used model plant species for fundamental research,with many important discoveries reported by maize researchers.Here,we provide an overview of the history of maize domestication and key genes controlling major domestication-related traits,review the currently available resources for functional genomics studies in maize,and discuss the functions of most of the maize genes that have been positionally cloned and can be used for crop improvement.Finally,we provide some perspectives on future directions regarding functional genomics research and the breeding of maize and other crops.

Passing the Baton: Substrate Channelling in Respiratory Metabolism

Despite species-specifc diferences in the pathways of respiratory metabolism are remarkably conserved across the kingdoms of life with glycolysis,the tricarboxylic acid cycle,and mitochondrial electron transport chain representing the major components of the process in the vast majority of organisms.In addition to being of critical importance in fueling life itself these pathways serve as interesting case studies for substrate channelling with research on this theme having been carried out for over 40 years.Here we provide a cross-kingdom review of the ample evidence for protein-protein interaction and enzyme assemblies within the three component pathways as well as describing the scarcer available evidence for substrate channelling itself.

A heavy metal transporter gene ZmHMA3a promises safe agricultural production on cadmium-polluted arable land

In China,19%of agricultural soils contain harmful heavy metal pollutants at levels exceeding environmentally recommended standards,whilst around 3 million hectares of arable land are too polluted to grow crops on(Zhao et al.,2015;Hu et al.,2016).Among the deleterious heavy metals,cadmium(Cd)is the most bioavailable toxic metallic pollutant and is rapidly transferable through the food chain(Wang et al.,2019).Concerning the current dilemma of the enhanced food demands of a rising population and decreasing availability of arable land,it is promising to cultivate field crops that produce enough safe foods for human consumption and simultaneously remove the pollutants from contaminated arable lands.

Exploring the genic resources underlying metabolites throughmGWASandmQTL inwheat: From large-scale gene identification and pathway elucidation to crop improvement

Common wheat(Triticum aestivum L.)is a leading cereal crop,but has lagged behind with respect to the interpretation of the molecular mechanisms of phenotypes compared with other major cereal crops such as rice and maize.The recently available genome sequence of wheat affords the pre-requisite information for efficiently exploiting the potential molecular resources for decoding the genetic architecture of complex traits and identifying valuable breeding targets.Meanwhile,the successful application of metabolomics as an emergent large-scale profiling methodology in several species has demonstrated this approach to be accessible for reaching the above goals.One such productive avenue is combining metabolomics approaches with genetic designs.However,this trial is not as widespread as that for sequencing technologies,especially when the acquisition,understanding,and application of metabolic approaches in wheat populations remain more difficult and even arguably underutilized.In this review,we briefly introduce the techniques used in the acquisition of metabolomics data and their utility in large-scale identification of functional candidate genes.Considerable progress has been made in delivering improved varieties,suggesting that the inclusion of information concerning these metabolites and genes and metabolic pathways enables a more explicit understanding of phenotypic traits and,as such,this procedure could serve as an-omics-informed roadmap for executing similar improvement strategies in wheat and other species.

Watermelon domestication was shaped by stepwise selection and regulation of the metabolome

Although crop domestication has greatly aided human civilization,the sequential domestication and regulation of most quality traits remain poorly understood.Here,we report the stepwise selection and regulation of major fruit quality traits that occurred during watermelon evolution.The levels of fruit cucurbitacins and flavonoids were negatively selected during speciation,whereas sugar and carotenoid contents were positively selected during domestication.Interestingly,fruit malic acid and citric acid showed the opposite selection trends during the improvement.We identified a novel gene cluster(CGC1,cucurbitacin gene cluster on chromosome 1)containing both regulatory and structural genes involved in cucurbitacin biosynthesis,which revealed a cascade of transcriptional regulation operating mechanisms.In the CGC1,an allele caused a single nucleotide change in Cl ERF1 binding sites(GCC-box)in the promoter of Cl Bh1,which resulted in reduced expression of Cl Bh1 and inhibition of cucurbitacin synthesis in cultivated watermelon.Functional analysis revealed that a rare insertion of 244 amino acids,which arose in C.amarus and became fixed in sweet watermelon,in Cl OSC(oxidosqualene cyclase)was critical for the negative selection of cucurbitacins during watermelon evolution.This research provides an important resource for metabolomics-assisted breeding in watermelon and for exploring metabolic pathway regulation mechanisms.

Population analysis reveals the roles of DNA methylation in tomato domestication and metabolic diversity

DNA methylation is an important epigenetic marker,yet its diversity and consequences in tomato breeding at the population level are largely unknown.We performed whole-genome bisulfite sequencing(WGBS),RNA sequencing,and metabolic profiling on a population comprising wild tomatoes,landraces,and cultivars.A total of 8,375 differentially methylated regions(DMRs)were identified,with methylation levels progressively decreasing from domestication to improvement.We found that over 20%of DMRs overlapped with selective sweeps.Moreover,more than 80%of DMRs in tomato were not significantly associated with single-nucleotide polymorphisms(SNPs),and DMRs had strong linkages with adjacent SNPs.We additionally profiled 339 metabolites from 364 diverse accessions and further performed a metabolic association study based on SNPs and DMRs.We detected 971 and 711 large-effect loci via SNP and DMR markers,respectively.Combined with multi-omics,we identified 13 candidate genes and updated the polyphenol biosynthetic pathway.Our results showed that DNA methylation variants could complement SNP profiling of metabolite diversity.Our study thus provides a DNA methylome map across diverse accessions and suggests that DNA methylation variation can be the genetic basis of metabolic diversity in plants.