Arabidopsis R2R3-MYB transcription factor AtMYB60 functions as a transcriptional repressor of anthocyanin biosynthesis in lettuce (Lactuca sativa)

Reactive oxygen species act as the key signaling molecules mediating light-induced anthocyanin biosynthesis in Eucalyptus

Light plays a pivotal role in regulating anthocyanin biosynthesis in plants, and the early light-responsive signals that initiate anthocyanin biosynthesis remain to be elucidated. In this study, we showed that the anthocyanin biosynthesis in Eucalyptus is hypersensitive to increased light intensity. The combined transcriptomic and metabolomic analyses were conducted on Eucalyptus leaves after moderate (ML; 100 μmol m-2 s-1) and high (HL; 300 μmol m-2 s-1) light intensity treatments. The results identified 1940, 1096, 1173, and 2756 differentially expressed genes at 6, 12, 24, and 36 h after HL treatment, respectively. The metabolomic results revealed the primary anthocyanin types, and other differentially accumulated flavonoids and phenylpropane intermediates that were produced in response to HL, which well aligned with the transcriptome results. Moreover, biochemical analysis showed that HL inhibited peroxidase activity and increased the ROS level in Eucalyptus leaves. ROS depletion through co-application of the antioxidants rutin, uric acid, and melatonin significantly reduced, and even abolished, anthocyanin biosynthesis induced by HL treatment. Additionally, exogenous application of hydrogen peroxide efficiently induced anthocyanin biosynthesis within 24 h, even under ML conditions, suggesting that ROS played a major role in activating anthocyanin biosynthesis. A HL-responsive MYB transcription factor EgrMYB113 was identified to play an important role in regulating anthocyanin biosynthesis by targeting multiple anthocyanin biosynthesis genes. Additionally, the results demonstrated that gibberellic acid and sugar signaling contributed to HL-induced anthocyanin biosynthesis. Conclusively, these results suggested that HL triggers multiple signaling pathways to induce anthocyanin biosynthesis, with ROS acting as indispensable mediators in Eucalyptus.

Genome-Wide Identification and Characterization of the GRAS Gene Family in Lettuce Revealed That Silencing LsGRAS13 Delayed Bolting

Lettuce is susceptible to high-temperature stress during cultivation, leading to bolting and affecting yield. Plant-specific transcription factors, known as GRAS proteins, play a crucial role in regulating plant growth, development, and abiotic stress responses. In this study, the entire lettuce LsGRAS gene family was identified. The results show that 59 LsGRAS genes are unevenly distributed across the nine chromosomes. Additionally, all LsGRAS proteins showed 100% nuclear localization based on the predicted subcellular localization and were phylogenetically classified into nine conserved subfamilies. To investigate the expression profiles of these genes in lettuce, we analyzed the transcription levels of all 59 LsGRAS genes in the publicly available RNA-seq data under the high-temperature treatment conducted in the presence of exogenous melatonin. The findings indicate that the transcript levels of the LsGRAS13 gene were higher on days 6, 9, 15, 18, and 27 under the high-temperature (35/30 °C) treatment with melatonin than on the same treatment days without melatonin. The functional studies demonstrate that silencing LsGRAS13 accelerated bolting in lettuce. Furthermore, the paraffin sectioning results showed that flower bud differentiation in LsGRAS13-silenced plants occurred significantly faster than in control plants. In this study, the LsGRAS genes were annotated and analyzed, and the expression pattern of the LsGRAS gene following melatonin treatment under high-temperature conditions was explored. This exploration provides valuable information and identifies candidate genes associated with the response mechanism of lettuce plants high-temperature stress.

De novo domestication: what about the weeds?

Most high-yielding crops are susceptible to abiotic and biotic stresses, making them particularly vulnerable to the potential effects of climate change. A possible alternative is to accelerate the domestication of wild plants that are already tolerant to harsh conditions and to increase their yields by methods such as gene editing. We foresee that crops' wild progenitors could potentially compete with the resulting de novo domesticated plants, reducing yields. To improve the recognition of weeds, we propose using gene editing techniques to introduce traits into de novo domesticated crops that will allow for visual recognition of the crops by weeding robots that have been trained by machine learning.

Mechanistic and structural insight into R2R3-MYB transcription factor in plants: molecular dynamics based binding free energy analysis

The MYB transcription factor (TF) family is essential for various plant growth and development processes, including responses to biotic and abiotic stresses. This study investigated the R2R3-MYB protein structure from five plants, including cereal crops. The R2R3-MYB protein structure was docked with the DNA structure, and the best complexes were selected for two runs of molecular dynamics (MD) simulations to investigate the key interacting residues and conformational changes in the R2R3-MYB proteins caused by DNA binding. The MM/PBSA method calculated the binding free energy for each R2R3-MYB protein-DNA complex, showing strong interaction. Hydrophobic and hydrogen bonds significantly stabilized the R2R3-MYB protein-DNA complexes. The principal component analysis showed high restrictions on the movement of protein atoms in the phase space. A similar MD simulation analysis was performed using the crystal structure of the R2R3-MYB protein-DNA complex from Arabidopsis thaliana, and the generated complexes resembled the X-ray crystal structure. This is the first detailed study on the R2R3-MYB protein-DNA complex in cereal crops, providing a cost-effective solution to identify the key interacting residues and analyze the conformational changes in the MYB domain before and after DNA binding.Communicated by Ramaswamy H. Sarma.

The long noncoding RNAs lnc10 and lnc11 regulating flavonoid biosynthesis in Ginkgo biloba

Although long non-coding RNAs have been recognized to play important roles in plant, their possible functions and potential mechanism in Ginkgo biloba flavonoid biosynthesis are poorly understood. Flavonoids are important secondary metabolites and healthy components of Ginkgo biloba. They have been widely used in food, medicine, and natural health products. Most previous studies have focused on the molecular mechanisms of structural genes and transcription factors that regulate flavonoid biosynthesis. Few reports have examined the biological functions of flavonoid biosynthesis by long non-coding RNAs in G. biloba. Long noncoding RNAs associated with flavonoid biosynthesis in G. biloba have been identified through RNA sequencing, but the function of lncRNAs has not been reported. In this study, the expression levels of lnc10 and lnc11 were identified. Quantitative real-time polymerase chain reaction analysis revealed that lnc10 and lnc11 were expressed in all detected organs, and they showed significantly higher levels in immature and mature leaves than in other organs. In addition, to fully identify the function of lnc10 and lnc11 in flavonoid biosynthesis in G. biloba, lnc10 and lnc11 were cloned from G. biloba, and were transformed into Arabidopsis and overexpressed. Compared with the wild type, the flavonoid content was increased in transgenic plants. Moreover, the RNA-sequencing analysis of wild-type, lnc10-overexpression, and lnc11-overexpression plants screened out 2019 and 2552 differentially expressed genes, and the transcript levels of structural genes and transcription factors associated with flavonoid biosynthesis were higher in transgenic Arabidopsis than in the wild type, indicating that lnc10 and lnc11 activated flavonoid biosynthesis in the transgenic lines. Overall, these results suggest that lnc10 and lnc11 positively regulate flavonoid biosynthesis in G. biloba.

Epicuticular wax accumulation and regulation of wax pathway gene expression during bioenergy Sorghum stem development

Bioenergy sorghum is a drought-tolerant high-biomass C4 grass targeted for production on annual cropland marginal for food crops due primarily to abiotic constraints. To better understand the overall contribution of stem wax to bioenergy sorghum's resilience, the current study characterized sorghum stem cuticular wax loads, composition, morphometrics, wax pathway gene expression and regulation using vegetative phase Wray, R07020, and TX08001 genotypes. Wax loads on sorghum stems (~103-215 µg/cm2) were much higher than Arabidopsis stem and leaf wax loads. Wax on developing sorghum stem internodes was enriched in C28/30 primary alcohols (~65%) while stem wax on fully developed stems was enriched in C28/30 aldehydes (~80%). Scanning Electron Microscopy showed minimal wax on internodes prior to the onset of elongation and that wax tubules first appear associated with cork-silica cell complexes when internode cell elongation is complete. Sorghum homologs of genes involved in wax biosynthesis/transport were differentially expressed in the stem epidermis. Expression of many wax pathway genes (i.e., SbKCS6, SbCER3-1, SbWSD1, SbABCG12, SbABCG11) is low in immature apical internodes then increases at the onset of stem wax accumulation. SbCER4 is expressed relatively early in stem development consistent with accumulation of C28/30 primary alcohols on developing apical internodes. High expression of two SbCER3 homologs in fully elongated internodes is consistent with a role in production of C28/30 aldehydes. Gene regulatory network analysis aided the identification of sorghum homologs of transcription factors that regulate wax biosynthesis (i.e., SbSHN1, SbWRI1/3, SbMYB94/96/30/60, MYS1) and other transcription factors that could regulate and specify expression of the wax pathway in epidermal cells during cuticle development.

Development and Application of CRISPR/Cas9 to Improve Anthocyanin Pigmentation in Plants: Opportunities and Perspectives

Since its discovery in 2012, the novel technology of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) has greatly contributed to revolutionizing molecular biology. It has been demonstrated to be an effective approach for identifying gene function and improving some important traits. Anthocyanins are secondary metabolites responsible for a wide spectrum of aesthetic coloration in various plant organs and are beneficial for health. As such, increasing anthocyanin content in plants, especially the edible tissue and organs, is always a main goal for plant breeding. Recently, CRISPR/Cas9 technology has been highly desired to enhance the amount of anthocyanin in vegetables, fruits, cereals, and other attractive plants with more precision. Here we reviewed the recent knowledge concerning CRISPR/Cas9-mediated anthocyanin enhancement in plants. In addition, we addressed the future avenues of promising potential target genes that could be helpful for achieving the same goal using CRISPR/Cas9 in several plants. Thus, molecular biologists, genetic engineers, agricultural scientists, plant geneticists, and physiologists may benefit from CRISPR technology to boost the biosynthesis and accumulation of anthocyanins in fresh fruits, vegetables, grains, roots, and ornamental plants.

Overexpression of CaMYB78 transcription factor enhances resistance response in chickpea against Fusarium oxysporum and negatively regulates anthocyanin biosynthetic pathway

Chickpea, an important grain legume, suffers from considerable loss of yield due to Fusarium wilt disease. Inaccessibility of resistant gene pool among cultivars and lack of report of resistance, genes from alien sources have been the major constraints for resistance development in this valuable crop. However, along with some other transcription factors, MYB78 was significantly upregulated during chickpea-Fusarium interplay in resistant chickpea genotype. Being a highly recalcitrant species, the transformation of this important crop remained non-reproducible until recently. Following a tissue culture independent plumular meristem transformation protocol, introgression of CaMYB78 TF finally became feasible in chickpea. The overexpressed plants developed resistance against the pathogen but the anthocyanin production in transformed flowers was perturbed. In silico analyses of the anthocyanin biosynthetic key gene promoters reported the occurrence of multiple MYB-binding cis elements. Detailed molecular analyses establish the differential regulatory roles of CaMYB78, resistance response against Foc1 on one hand and suppression of pigmentation during flower development on the other, which is an innovative finding of its kind.

LettuceGDB: The community database for lettuce genetics and omics

As a globally popular leafy vegetable and a representative plant of the Asteraceae family, lettuce has great economic and academic significance. In the last decade, high-throughput sequencing, phenotyping, and other multi-omics data in lettuce have accumulated on a large scale, thus increasing the demand for an integrative lettuce database. Here, we report the establishment of a comprehensive lettuce database, LettuceGDB (https://www.lettucegdb.com/). As an omics data hub, the current LettuceGDB includes two reference genomes with detailed annotations; re-sequencing data from over 1000 lettuce varieties; a collection of more than 1300 worldwide germplasms and millions of accompanying phenotypic records obtained with manual and cutting-edge phenomics technologies; re-analyses of 256 RNA sequencing datasets; a complete miRNAome; extensive metabolite information for representative varieties and wild relatives; epigenetic data on the genome-wide chromatin accessibility landscape; and various lettuce research papers published in the last decade. Five hierarchically accessible functions (Genome, Genotype, Germplasm, Phenotype, and O-Omics) have been developed with a user-friendly interface to enable convenient data access. Eight built-in tools (Assembly Converter, Search Gene, BLAST, JBrowse, Primer Design, Gene Annotation, Tissue Expression, Literature, and Data) are available for data downloading and browsing, functional gene exploration, and experimental practice. A community forum is also available for information sharing, and a summary of current research progress on different aspects of lettuce is included. We believe that LettuceGDB can be a comprehensive functional database amenable to data mining and database-driven exploration, useful for both scientific research and lettuce breeding.

Cloning and Functional Analysis of NoMYB60 Gene Involved in Flavonoid Biosynthesis in Watercress (Nasturtium officinale R. Br.)

The MYB60 gene belongs to the R2R3-MYB subfamily, which includes the MYB31/30/96/94 genes. Although these genes have been shown to respond to heat and drought stresses, their role in flavonoid synthesis remains unclear. In this study, NoMYB60 was cloned from watercress and its structure and function were analyzed. Sequence structure analysis showed that NoMYB60 had a highly conserved R2R3 DNA-binding region at the N-terminus. Under the treatment of ABA, SA or MeJA, the expression level of NoMYB60 first significantly increased and then decreased, indicating that ABA, SA and MeJA positively regulated NoMYB60. The subcellular localization of NoMYB60-GFP indicated that NoMYB60 was localized in the nuclear region, which is consistent with the molecular characterization of the transcription factor. Gene silencing experiments were also performed to further test the function of NoMYB60. The result showed that virus-induced silencing of NoMYB60 affected the expression of enzyme genes in flavonoid synthesis pathways and promoted the synthesis of flavonoids. Moreover, we discovered that NoMYB60 interacts with NoBEH1/2. In this study, provides a reference for research on the regulation mechanism of flavonoid synthesis in Cruciferae and other crops.

Mining of the CULLIN E3 ubiquitin ligase genes in the whole genome of Salvia miltiorrhiza

CULLIN (CUL) proteins are E3 ubiquitin ligases that are involved in a wide variety of biological processes as well as in response to stress in plants. In Salvia miltiorrhiza, CUL genes have not been characterized and its role in plant development, stress response and secondary metabolite synthesis have not been studied. In this study, genome-wide analyses were performed to identify and to predict the structure and function of CUL of S. miltiorrhiza. Eight CUL genes were identified from the genome of S. miltiorrhiza. The CUL genes were clustered into four subgroups according to phylogenetic relationships. The CUL domain was highly conserved across the family of CUL genes. Analysis of cis-acting elements suggested that CUL genes might play important roles in a variety of biological processes, including abscission reaction acid (ABA) processing. To investigate this hypothesis, we treated hairy roots of S. miltiorrhiza with ABA. The expression of CUL genes varied obviously after ABA treatment. Co-expression network results indicated that three CUL genes might be involved in the biosynthesis of phenolic acid or tanshinone. In summary, the mining of the CUL genes in the whole genome of S. miltiorrhiza contribute novel information to the understanding of the CUL genes and its functional roles in plant secondary metabolites, growth and development.

Anthocyanin Biosynthesis Induced by MYB Transcription Factors in Plants

Anthocyanins act as polyphenolic pigment that is ubiquitously found in plants. Anthocyanins play a role not only in health-promoting as an antioxidant, but also in protection against all kinds of abiotic and biotic stresses. Most recent studies have found that MYB transcription factors (MYB TFs) could positively or negatively regulate anthocyanin biosynthesis. Understanding the roles of MYB TFs is essential in elucidating how MYB TFs regulate the accumulation of anthocyanin. In the review, we summarized the signaling pathways medicated by MYB TFs during anthocyanin biosynthesis including jasmonic acid (JA) signaling pathway, cytokinins (CKs) signaling pathway, temperature-induced, light signal, 26S proteasome pathway, NAC TFs, and bHLH TFs. Moreover, structural and regulator genes induced by MYB TFs, target genes bound and activated or suppressed by MYB TFs, and crosstalk between MYB TFs and other proteins, were found to be vitally important in the regulation of anthocyanin biosynthesis. In this study, we focus on the recent knowledge concerning the regulator signaling and mechanism of MYB TFs on anthocyanin biosynthesis, covering the signaling pathway, genes expression, and target genes and protein expression.

Integrated Metabolomic and Transcriptomic Analysis Reveals Differential Flavonoid Accumulation and Its Underlying Mechanism in Fruits of Distinct Canarium album Cultivars

Canarium album fruit has great potential to be consumed as a raw material not only for food but also medicine. The diverse active metabolites composition and content of C. album fruits greatly affect their pharmacological effects. However, up to now, there has been no report on the global metabolome differences among fruits from distinct C. album cultivars. In our present study, by using non-targeted metabolomics techniques, we identified 87 DAMs (differentially accumulated metabolites) including 17 types of flavonoids from fruits of four different C. album cultivars. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis revealed that the flavone and flavonol biosynthesis- and flavonoid biosynthesis-related DAMs were major factors determining their metabolome differences. Comparative transcriptomic analysis revealed that 15 KEGG pathways were significantly enriched by genes of the identified 3655 DEGs (differentially expressed genes) among different C. album cultivars. Consistent with the metabolome data, flavonoid biosynthesis-related DEGs, including eight key structural genes (such as FLS, CCoAOMT, CHI, C4H, DFR, LAR, and C3′H, etc.) and several regulatory transcription factor (TF) genes (including 32 MYBs and 34 bHLHs, etc.), were found to be significantly enriched (p < 0.01). Our study indicated that the differential expression of flavonoid biosynthesis-related genes and accumulation of flavonoids played dominant roles in the various metabolome compositions of fruits from different C. album cultivars.

Influence of cultivar and season on carotenoids and phenolic compounds from red lettuce influence of cultivar and season on lettuce

This paper presents complete HPLC profiles and MS spectrometric data of bioactive compounds from four cultivars of red lettuce produced in winter and summer and their antioxidant capacity. The experiment was carried out in a greenhouse, where red curly lettuce was cultivated: Mila, Maira, Carmin and Scarlet. The cultivar and season have not influenced the qualitative profile of carotenoids (CAR) and phenolic compounds (PC) of red lettuce. Instead, the season influenced the concentration of these components in all cultivars. The levels of phenolic compounds were significantly higher in winter, while the levels of carotenoids were higher in summer. Ten anthocyanins were identified (cyanidins and delphinidins). The main carotenoid found was the all-trans-β-carotene (45-48%), followed by lutein (13-20%) and zeaxanthin (11-15%). Major phenolic compounds include 5-caffeoylquinic acid, rutin and amentoflavone. Red lettuce cultivars have their main bioactive compounds described and compared within the variety and within the growing season. Different season and different lettuce cultivars may differ in the content of their bioactive compounds and in their antioxidant capacity.

Metabolomic and Transcriptomic Analyses of the Flavonoid Biosynthetic Pathway for the Accumulation of Anthocyanins and Other Flavonoids in Sweetpotato Root Skin and Leaf Vein Base

Sweetpotato [Ipomoea batatas (L.) Lam.] is a major tuberous root crop that is rich in flavonoids. Here, we discovered a spontaneous mutation in the color of the leaf vein base (LVB) and root skin (RS) in the Zheshu 81 cultivar. The flavonoid and anthocyanin metabolites and molecular mechanism were analyzed using metabolome and transcriptome data. Compared to the wild type, 13 differentially accumulated metabolites (DAMs) in the LVB and 59 DAMs in the RS were all significantly downregulated. Moreover, all the anthocyanin metabolites decreased significantly. The differentially expressed genes (DEGs) encoding the key enzymes in the later enzymatic reaction of anthocyanin and flavonoid were significantly downregulated in the mutant. The expression trends of the transcription factor MYB were evidently related to the anthocyanin content. These results offer insights into the coloration in the LVB and RS and a theoretical basis for determining the regulation of flavonoid and anthocyanin synthesis in sweetpotato.

Environmental and Genetic Factors Involved in Plant Protection-Associated Secondary Metabolite Biosynthesis Pathways

Plant specialized metabolites (PSMs) play essential roles in the adaptation to harsh environments and function in plant defense responses. PSMs act as key components of defense-related signaling pathways and trigger the extensive expression of defense-related genes. In addition, PSMs serve as antioxidants, participating in the scavenging of rapidly rising reactive oxygen species, and as chelators, participating in the chelation of toxins under stress conditions. PSMs include nitrogen-containing chemical compounds, terpenoids/isoprenoids, and phenolics. Each category of secondary metabolites has a specific biosynthetic pathway, including precursors, intermediates, and end products. The basic biosynthetic pathways of representative PSMs are summarized, providing potential target enzymes of stress-mediated regulation and responses. Multiple metabolic pathways share the same origin, and the common enzymes are frequently to be the targets of metabolic regulation. Most biosynthetic pathways are controlled by different environmental and genetic factors. Here, we summarized the effects of environmental factors, including abiotic and biotic stresses, on PSM biosynthesis in various plants. We also discuss the positive and negative transcription factors involved in various PSM biosynthetic pathways. The potential target genes of the stress-related transcription factors were also summarized. We further found that the downstream targets of these Transcription factors (TFs) are frequently enriched in the synthesis pathway of precursors, suggesting an effective role of precursors in enhancing of terminal products. The present review provides valuable insights regarding screening targets and regulators involved in PSM-mediated plant protection in non-model plants.

Characterization of the MYB Genes Reveals Insights Into Their Evolutionary Conservation, Structural Diversity, and Functional Roles in Magnaporthe oryzae

The myeloblastosis (MYB) transcription factor family is evolutionarily conserved among plants, animals, and fungi, and contributes to their growth and development. We identified and analyzed 10 putative MYB genes in Magnaporthe oryzae (MoMYB) and determined their phylogenetic relationships, revealing high divergence and variability. Although MYB domains are generally defined by three tandem repeats, MoMYBs contain one or two weakly conserved repeats embedded in extensive disordered regions. We characterized the secondary domain organization, disordered segments, and functional contributions of each MoMYB. During infection, MoMYBs are distinctively expressed and can be subdivided into two clades of being either up- or down-regulated. Among these, MoMYB1 and MoMYB8 are up-regulated during infection and vegetative growth, respectively. We found MoMYB1 localized predominantly to the cytosol during the formation of infection structures. ΔMomyb1 exhibited reduced virulence on intact rice leaves corresponding to the diminished ability to form hypha-driven appressorium (HDA). We discovered that MoMYB1 regulates HDA formation on hard, hydrophobic surfaces, whereas host surfaces partially restored HDA formation in ΔMomyb1. Lipid droplet accumulation in hyphal tips and expression of HDA-associated genes were strongly perturbed in ΔMomyb1 indicating genetic interaction of MoMYB1 with downstream components critical to HDA formation. We also found that MoMYB8 is necessary for fungal growth, dark-induced melanization of hyphae, and involved in higher abiotic stress tolerance. Taken together, we revealed a multifaceted picture of the MoMYB family, wherein a low degree of conservation has led to the development of distinct structures and functions, ranging from fungal growth to virulence.

Recent Advanced Metabolic and Genetic Engineering of Phenylpropanoid Biosynthetic Pathways

The MYB transcription factors (TFs) are evolving as critical role in the regulation of the phenylpropanoid and tanshinones biosynthetic pathway. MYB TFs relate to a very important gene family, which are involved in the regulation of primary and secondary metabolisms, terpenoids, bioactive compounds, plant defense against various stresses and cell morphology. R2R3 MYB TFs contained a conserved N-terminal domain, but the domain at C-terminal sorts them different regarding their structures and functions. MYB TFs suppressors generally possess particular repressive motifs, such as pdLNLD/ELxiG/S and TLLLFR, which contribute to their suppression role through a diversity of complex regulatory mechanisms. A novel flower specific "NF/YWSV/MEDF/LW" conserved motif has a great potential to understand the mechanisms of flower development. In the current review, we summarize recent advanced progress of MYB TFs on transcription regulation, posttranscriptional, microRNA, conserved motif and propose directions to future prospective research. We further suggest there should be more focus on the investigation for the role of MYB TFs in microalgae, which has great potential for heterologous protein expression system for future perspectives.

Integrated Metabolomic and Transcriptomic Analysis Reveals the Flavonoid Regulatory Network by Eutrema EsMYB90

Flavonoids are representative secondary metabolites with different metabolic functions in plants. Previous study found that ectopic expression of EsMYB90 from Eutremasalsugineum could strongly increase anthocyanin content in transgenic tobacco via regulating the expression of anthocyanin biosynthesis genes. In the present research, metabolome analysis showed that there existed 130 significantly differential metabolites, of which 23 metabolites enhanced more than 1000 times in EsMYB90 transgenic tobacco leaves relative to the control, and the top 10 of the increased metabolites included caffeic acid, cyanidin O-syringic acid, myricetin and naringin. A total of 50 markedly differential flavonoids including flavones (14), flavonols (13), flavone C-glycosides (9), flavanones (7), catechin derivatives (5), anthocyanins (1) and isoflavone (1) were identified, of which 46 metabolites were at a significantly enhanced level. Integrated analysis of metabolome and transcriptome revealed that ectopic expression of EsMYB90 in transgenic tobacco leaves is highly associated with the prominent up-regulation of 16 flavonoid metabolites and the corresponding 42 flavonoid biosynthesis structure genes in phenylpropanoid/flavonoid pathways. Dual luciferase assay documented that EsMYB90 strongly activated the transcription of NtANS and NtDFR genes via improving their promoter activity in transiently expressed tobacco leaves, suggesting that EsMYB90 functions as a key regulator on anthocyanin and flavonoid biosynthesis. Taken together, the crucial regulatory role of EsMYB90 on enhancing many flavonoid metabolite levels is clearly demonstrated via modulating flavonoid biosynthesis gene expression in the leaves of transgenic tobacco, which extends our understanding of the regulating mechanism of MYB transcription factor in the phenylpropanoid/flavonoid pathways and provides a new clue and tool for further investigation and genetic engineering of flavonoid metabolism in plants.

Evolution of the Subgroup 6 R2R3-MYB Genes and Their Contribution to Floral Color in the Perianth-Bearing Piperales

Flavonoids, carotenoids, betalains, and chlorophylls are the plant pigments responsible for floral color. Anthocyanins, a class of flavonoids, are largely responsible for the red, purple, pink, and blue colors. R2R3-MYB genes belonging to subgroup 6 (SG6) are the upstream regulatory factors of the anthocyanin biosynthetic pathway. The canonical members of these genes in Arabidopsis include AtMYB75, AtMYB90, AtMYB113, and AtMYB114. The Aristolochiaceae is an angiosperm lineage with diverse floral groundplans and perianth colors. Saruma henryi exhibits a biseriate perianth with green sepals and yellow petals. All other genera have sepals only, with colors ranging from green (in Lactoris) to a plethora of yellow to red and purple mixtures. Here, we isolated and reconstructed the SG6 R2R3-MYB gene lineage evolution in angiosperms with sampling emphasis in Aristolochiaceae. We found numerous species-specific duplications of this gene lineage in core eudicots and local duplications in Aristolochiaceae for Saruma and Asarum. Expression of SG6 R2R3-MYB genes examined in different developmental stages and plant organs of four Aristolochiaceae species, largely overlaps with red and purple pigments, suggesting a role in anthocyanin and flavonoid synthesis and accumulation. A directed RNA-seq analysis corroborated our RT-PCR analyses, by showing that these structural enzymes activate during perianth development in Aristolochia fimbriata and that the regulatory genes are expressed in correlation with color phenotype. Finally, the reconstruction of the flavonoid and anthocyanin metabolic pathways using predicted peptides from transcriptomic data show that all pivotal enzymes are present in the analyzed species. We conclude that the regulatory genes as well as the biosynthetic pathway are largely conserved across angiosperms. In addition, the Aristolochiaceae emerges as a remarkable group to study the genetic regulatory network for floral color, as their members exhibit an outstanding floral diversity with elaborate color patterns and the genetic complement for SG6 R2R3-MYB genes is simpler than in core eudicot model species.

Exploring genetic architecture for pod-related traits in soybean using image-based phenotyping

Mature pod color (PC) and pod size (PS) served as important characteristics are used in the soybean breeding programs. However, manual phenotyping of such complex traits is time-consuming, laborious, and expensive for breeders. Here, we collected pod images from two different populations, namely, a soybean association panel (SAP) consisting of 187 accessions and an inter-specific recombinant inbred line (RIL) population containing 284 RILs. An image-based phenotyping method was developed and used to extract the pod color- and size-related parameters from images. Genome-wide association study (GWAS) and linkage mapping were performed to decipher the genetic control of pod color- and size-related traits across 2 successive years. Both populations exhibited wide phenotypic variations and continuous distribution in pod color- and size-related traits, indicating quantitative polygenic inheritance of these traits. GWAS and linkage mapping approaches identified the two major quantitative trait loci (QTL) underlying the pod color parameters, i.e., qPC3 and qPC19, located to chromosomes 3 and 19, respectively, and 12 stable QTLs for pod size-related traits across nine chromosomes. Several genes residing within the genomic region of stable QTL were identified as potential candidates underlying these pod-related traits based on the gene annotation and expression profiling data. Our results provide the useful information for fine-mapping/map-based cloning of QTL and marker-assisted selection of elite varieties with desirable pod traits.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01223-2.

A Roadmap to Modulated Anthocyanin Compositions in Carrots

Anthocyanins extracted from black carrots have received increased interest as natural colorants in recent years. The reason is mainly their high content of acylated anthocyanins that stabilizes the color and thereby increases the shelf-life of products colored with black carrot anthocyanins. Still, the main type of anthocyanins synthesized in all black carrot cultivars is cyanidin limiting their use as colorants due to the narrow color variation. Additionally, in order to be competitive against synthetic colors, a higher percentage of acylated anthocyanins and an increased anthocyanin content in black carrots are needed. However, along with the increased interest in black carrots there has also been an interest in identifying the structural and regulatory genes associated with anthocyanin biosynthesis in black carrots. Thus, huge progress in the identification of genes involved in anthocyanin biosynthesis has recently been achieved. Given this information it is now possible to attempt to modulate anthocyanin compositions in black carrots through genetic modifications. In this review we look into genetic modification opportunities for generating taproots of black carrots with extended color palettes, with a higher percentage of acylated anthocyanins or a higher total content of anthocyanins.

Enhanced Biosynthesis of Chlorogenic Acid and Its Derivatives in Methyl-Jasmonate-Treated Gardenia jasminoides Cells: A Study on Metabolic and Transcriptional Responses of Cells

Chlorogenic acid and its derivatives (CQAs) are considered as important bioactive secondary metabolites in Gardenia jasminoides Ellis (G. jasminoides). However, few studies have investigated the biosynthesis and regulation of CQAs in G. jasminoides. In this study, methyl jasmonate (MeJA) was used to enhance CQAs accumulation in cultured G. jasminoides cells. Moreover, the possible molecular mechanism of MeJA-mediated accumulation of CQAs is also explored. To this end, time-course transcriptional profiles of G. jasminoides cells responding to MeJA were used to investigate the mechanism from different aspects, including jasmonate (JAs) biosynthesis, signal transduction, biosynthesis of precursor, CQAs biosynthesis, transporters, and transcription factors (TFs). A total of 57,069 unigenes were assembled from the clean reads, in which 80.7% unigenes were successfully annotated. Furthermore, comparative transcriptomic results indicated that differentially expressed genes (DEGs) were mainly involved in JAs biosynthesis and signal transduction (25 DEGs), biosynthesis of precursor for CQAs (18 DEGs), CQAs biosynthesis (19 DEGs), and transporters (29 DEGs). Most of these DEGs showed continuously upregulated expressions over time, which might activate the jasmonic acid (JA) signal transduction network, boost precursor supply, and ultimately stimulate CQAs biosynthesis. Additionally, various TFs from different TF families also responded to MeJA elicitation. Interestingly, 38 DEGs from different subgroups of the MYB family might display positive or negative regulations on phenylpropanoids, especially on CQAs biosynthesis. Conclusively, our results provide insight into the possible molecular mechanism of regulation on CQAs biosynthesis, which led to a high CQAs yield in the G. jasminoides cells under MeJA treatment.

Transcriptomic and Metabolomic Analyses Reveals That Exogenous Methyl Jasmonate Regulates Galanthamine Biosynthesis in Lycoris longituba Seedlings

The Amaryllidaceae alkaloid galanthamine (Gal) in Lycoris longituba is a secondary metabolite that has been used to treat Alzheimer's disease. Plant secondary metabolism is affected by methyl jasmonate (MeJA) exposure, although the regulatory mechanisms of MeJA on L. longituba seedlings remains largely unknown. In the present study, 75, 150, and 300 μM MeJA were used as treatments on L. longituba seedlings for 7, 14, 21, and 28 days, while 0 μM MeJA was used as the control (MJ-0). The effect of exogenous MeJA on Gal synthesis in L. longituba was then investigated using transcriptomic sequencing and metabolite profiling via GC-MS and LC-MS analysis. Galanthamine (Gal), lycorine (Lyc), and lycoramine (Lycm) abundances were 2. 71-, 2. 01-, and 2.85-fold higher in 75 μM MeJA (MJ-75) treatment plants compared to MJ-0 treatment plants after 7 days of cultivation. Transcriptomic analysis further showed that MJ-75 treatment significantly induced the expression of norbelladine synthase (NBS) and norbelladine 4'-O-methyltransferase (OMT), which are involved in the Gal biosynthesis pathway. In addition, increased expression was observed in MJ-75 treatment plants for genes in the JA synthesis and JA signaling pathways including those of allene oxide cyclase (AOC), 12-oxo-phytodienoic acid reductase (OPR), jasmonic acid amino acid synthase (JAR), and transcription factor MYC. The L. longituba tyrosine decarboxylase (LlTYDC) enzyme was identified and proposed to be involved in the Gal biosynthetic pathway. Metabolomics results demonstrated that the accumulation of Amaryllidaceae alkaloids, and especially alkaloids in the Gal biosynthesis pathway, could be induced by MJ-75 treatment. Interestingly, metabolites in the JA synthesis pathway were also affected by MeJA treatment. Overall, this multi-omics study suggests that both the JA synthesis/JA signaling and Gal biosynthesis pathways were affected by exogenous MeJA treatment. This comprehensive study of gene expression and metabolite contents can help us better understand the molecular mechanisms underlying MeJA-mediated Gal biosynthesis in L. longituba.

Genetic and Physical Localization of the Gene Controlling Leaf Pigmentation Pattern in Medicago truncatula

In Medicago truncatula, some ecotypes form a black or purple stain in the middle of adaxial leaf surface due to accumulation of anthocyanins. However, this morphological marker is missing in some other ecotypes, although anthocyanin biosynthesis pathway is not disrupted. Genetic analysis indicated that the lack of the leaf spot of anthocyanins accumulation is a dominant trait, which is controlled by a single gene, LPP1. Genetic mapping indicated that the LPP1 gene was delimited to a 280 kb-region on Chromosome 7. A total of 8 protein-coding genes were identified in the LPP1 locus through gene annotation and sequence analysis. Of those, two genes, putatively encoding MYB-transcriptional suppressors, were selected as candidates for functional validation.

Parallel Transcriptional Regulation of Artemisinin and Flavonoid Biosynthesis

Plants regulate the synthesis of specialized compounds through the actions of individual transcription factors (TFs) or sets of TFs. One such compound, artemisinin from Artemisia annua, is widely used as a pharmacological product in the first-line treatment of malaria. However, the emergence of resistance to artemisinin in Plasmodium species, as well as its low production rates, have required innovative treatments such as exploiting the synergistic effects of flavonoids with artemisinin. We overview current knowledge about flavonoid and artemisinin transcriptional regulation in A. annua, and review the dual action of TFs and structural genes that can regulate both pathways simultaneously. Understanding the concerted action of these TFs and their associated structural genes can guide the development of strategies to further improve flavonoid and artemisinin production.

Genome and Transcriptome Analyses Provide Insight Into the Omega-3 Long-Chain Polyunsaturated Fatty Acids Biosynthesis of Schizochytrium limacinum SR21

Schizochytrium sp. is the best natural resource for omega-3 long-chain polyunsaturated fatty acids. We report a high-quality genome sequence of Schizochytrium limacinum SR21, which has a 63 Mb genome size, with a contig N50 of 2.67 Mb and 6,838 protein-coding genes. Phylogenomic and comparative genomic analyses revealed that DHA-producing Schizochytrium and Aurantiochytrium strains were highly similar and possessed similar genes. Analysis of the fatty acid synthase (FAS) for LC-PUFAs production results in the annotation of all genes in map00062 and map01212. A gene cluster and 10 ORFs related to PKS pathway were found in the genome. 1,402 differentially expressed genes (DEGs) of the treated groups (0.5 g/L yeast extract) were identified by comparing with the control groups (1.0 g/L yeast extract) at 36 h. A weighted gene coexpression network analysis revealed that 2 of 7 modules correlated highly with the fatty acid and DHA contents. The DEGs and transcription factors were significantly correlated with fatty acid biosynthesis, including MYB, Zinc Finger and ACOX. The results showed that these hub genes are regulated by genes involved in fatty acid biosynthesis pathways. The results providing an important reference for further research on promoting fatty acid and DHA accumulation in S. limacinum SR21.

Transcriptome Analysis of Different Tissues Reveals Key Genes Associated With Galanthamine Biosynthesis in Lycoris longituba

L ycoris longituba is a traditional medicinal plant containing the bioactive compound galanthamine (Gal), a type of Amaryllidaceae alkaloid and can be used to treat Alzheimer's disease. However, research on its genome or transcriptome and associated genes in the biosynthetic pathway is incomplete. In this study, we estimated the nuclear genome size of this species to be 29.33 Gb by flow cytometry. Then, RNA sequencing of the leaves, roots, and bulbs of L. longituba was carried out. After de novo assembly, 474,589 all-transcripts and 333,440 all-unigenes were finally generated. In addition, the differentially expressed genes (DEGs) were identified, and genes involved in the galanthamine metabolic pathway encoding tyrosine decarboxylase (TYDC), phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), p-coumarate 3-hydroxylase (C3H), norbelladine synthase (NBS), norbelladine 4'-O-methyltransferase (OMT), and noroxomaritidine synthase (CYP96T1) were detected and validated by real-time quantitative PCR analysis. One candidate gene, Lycoris longituba O-Methyltransferase (LlOMT), was identified in the proposed galanthamine biosynthetic pathway. Sequence analysis showed that LlOMT is a class I OMT. LlOMT is localized in the cytoplasm, and biochemical analysis indicated that the recombinant LlOMT catalyzes norbelladine to generate 4'-O-methylnorbelladine. The protoplast transformation result showed that the overexpression of LlOMT could increase the Gal content. Our results indicate that LlOMT may play a role in galanthamine biosynthesis in L. longituba. This work provides a useful resource for the metabolic engineering of Amaryllidaceae alkaloids.

Identification of novel MYB transcription factors involved in the isoflavone biosynthetic pathway by using the combination screening system with agroinfiltration and hairy root transformation

Soybean isoflavones are functionally important secondary metabolites that are mainly accumulated in seeds. Their biosynthetic processes are regulated coordinately at the transcriptional level; however, screening systems for key transcription factors (TFs) are limited. Here we developed a combination screening system comprising a simple agroinfiltration assay and a robust hairy root transformation assay. First, we screened for candidate MYB TFs that could activate the promoters of the chalcone synthase (CHS) gene GmCHS8 and the isoflavone synthase (IFS) genes GmIFS1 and GmIFS2 in the isoflavone biosynthetic pathway. In the agroinfiltration assay, we co-transformed a LjUbi (Lotus japonicus polyubiquitin gene) promoter-fused MYB gene with target promoter-fused GUS (β-glucuronidase) gene constructs, and identified three genes (GmMYB102, GmMYB280, and GmMYB502) as candidate regulators of isoflavone biosynthesis. We then evaluated the functional regulatory role of identified three MYB genes in isoflavone biosynthesis using hairy roots transformation assay in soybean for the accumulation of isoflavones. Three candidate MYB genes showed an increased accumulation of total isoflavones in hairy root transgenic lines. Accumulation of total isoflavones in the three MYB-overexpressing lines was approximately 2-to 4-folds more than that in the vector control, confirming their possible role to regulate isoflavone biosynthesis. However, the significant accumulation of authentic GmCHS8, GmIFS1, and GmIFS2 transcripts could not be observed except for the GmMYB502-overexpressing line. Therefore, the analysis of isoflavone accumulation in transgenic hairy root was effective for evaluation of transactivation activity of MYB TFs for isoflavone biosynthetic genes. Our results demonstrate a simple and robust system that can potentially identify the function of orphan TFs in diverse plant metabolic pathways.

Prospects for economical natural colorants: insights from maize

Anthocyanin pigments from maize offer a natural yet economical alternative to artificial dyes. Breeding for optimal colorant production requires understanding and integrating all facets of anthocyanin chemistry and genetics research. Replacing artificial dyes with natural colorants is becoming increasingly popular in foods and beverages. However, natural colorants are often expensive, have lower stability, and reduced variability in hue. Purple corn is rich in anthocyanins and offers a scalable and affordable alternative to synthetic dyes ranging in color from orange to reddish-purple. This diversity is attributable to differences in anthocyanin composition and concentration. Here we review the chemistry, biosynthesis, and genetics of purple corn and outline key factors associated with the feasibility of producing an economical source of natural colorants. Anthocyanin compositional modifications including acylation, methylation, and polymerization with flavan-3-ols can influence color stability and hue, yet there is more to learn regarding the genetic factors responsible for these modifications. Activators and repressors of anthocyanin biosynthesis structural genes as well as factors controlling trafficking and storage largely control anthocyanin yield. Further knowledge of these mechanisms will allow breeders to apply molecular strategies that accelerate the production of purple corn hybrids to meet growing demands for natural colorants.

Anthocyanin Accumulation in the Leaves of the Purple Sweet Potato (Ipomoea batatas L.) Cultivars

Sweet potato anthocyanins are water-soluble pigments with many physiological functions. Previous research on anthocyanin accumulation in sweet potato has focused on the roots, but the accumulation progress in the leaves is still unclear. Two purple sweet potato cultivars (Fushu No. 23 and Fushu No. 317) with large quantities of anthocyanin in the leaves were investigated. Anthocyanin composition and content were assessed with ultra-performance liquid chromatography diode-array detection (UPLC-DAD) and ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS), and the expressions of genes were detected by qRT-PCR. The two cultivars contained nine cyanidin anthocyanins and nine peonidin anthocyanins with an acylation modification. The acylation modification of anthocyanins in sweet potato leaves primarily included caffeoyl, p-coumaryl, feruloyl, and p-hydroxy benzoyl. We identified three anthocyanin compounds in sweet potato leaves for the first time: cyanidin 3-p-coumarylsophoroside-5-glucoside, peonidin 3-p-coumarylsophoroside-5-glucoside, and cyanidin 3-caffeoyl-p-coumarylsophoroside-5-glucoside. The anthocyanidin biosynthesis downstream structural genes DFR4, F3H1, anthocyanin synthase (ANS), and UDP-glucose flavonoid 3-O-glucosyltransferase (UFGT3), as well as the transcription factor MYB1, were found to be vital regulatory genes during the accumulation of anthocyanins in sweet potato leaves. The composition of anthocyanins (nine cyanidin-based anthocyanins and nine peonidin-based anthocyanins) in all sweet potato leaves were the same, but the quantity of anthocyanins in leaves of sweet potato varied by cultivar and differed from anthocyanin levels in the roots of sweet potatoes. The anthocyanidin biosynthesis structural genes and transcription factor together regulated and controlled the anthocyandin biosynthesis in sweet potato leaves.

Reduced nitrogen supply enhances the cellular antioxidant potential of phenolic extracts through alteration of the phenolic composition in lettuce (Lactuca sativa L.)

BACKGROUND

Nitrogen availability is an important environmental factor that determines the production of phenolic compounds in vegetables, but the relationship between low nitrogen-induced alterations of phenolic compounds in vegetable crops and the cellular antioxidant activities of these compounds remains unclear. This study investigated the effect of reduced nitrogen supply (0.05 mmol L-1 nitrate) on phenolic metabolism in lettuce and the protective role of phenolic extracts against H2 O2 -induced oxidative stress in Caco-2 cells by determining cell damage, reactive oxygen species (ROS) content and antioxidant enzyme activities.

RESULTS

Reduced nitrogen supply significantly improved the accumulation of phenolic compounds in lettuce, which was partially correlated with the upregulation of genes related to the phenolic synthesis pathway. Phenolic extracts from lettuce cultivated in low-nitrogen medium exhibited a better protective effect against H2 O2 -induced oxidative damage in Caco-2 cells than those from lettuce cultivated with adequate nitrogen. These extracts act by increasing the activities of antioxidant enzymes and, subsequently, by inhibiting ROS overproduction, which leads to a decrease in mitochondrial membrane and DNA damage. The results of HPLC and correlation analyses implied that the improvement in the protective capacity of lettuce extracts after low-nitrogen treatment may be related, not only to the increased content of phenolic compounds, but also to the increased percentage contribution of chlorogenic acid and quercetin derivatives to the total phenolic content.

CONCLUSION

Reduction in nitrogen supply can be a powerful strategy to modify phenolic metabolism and composition in lettuce and, consequently, to improve their antioxidant capacity. © 2019 Society of Chemical Industry.

Transcriptome landscape of the early Brassica napus seed

Brassica napus L. (canola) is one of the world's most economically important oilseeds. Despite our growing knowledge of Brassica genetics, we still know little about the genes and gene regulatory networks underlying early seed development. In this work, we use laser microdissection coupled with RNA sequencing to profile gene activity of both the maternal and filial subregions of the globular seed. We find subregions of the chalazal end including the chalazal endosperm, chalazal proliferating tissue, and chalazal seed coat, have unique transcriptome profiles associated with hormone biosynthesis and polysaccharide metabolism. We confirm that the chalazal seed coat is uniquely enriched for sucrose biosynthesis and transport, and that the chalazal endosperm may function as an important regulator of the maternal region through brassinosteroid synthesis. The chalazal proliferating tissue, a poorly understood subregion, was specifically enriched in transcripts associated with megasporogenesis and trehalose biosynthesis, suggesting this ephemeral structure plays an important role in both sporophytic development and carbon nutrient balance, respectively. Finally, compartmentalization of transcription factors and their regulatory circuits has uncovered previously unknown roles for the chalazal pole in early seed development.

Advance of the negative regulation of anthocyanin biosynthesis by MYB transcription factors

Anthocyanins are secondary metabolites derived from the specific branch of the flavonoid pathway, responsible for red, purple and blue coloration display in the flowers and fruits. The functions of anthocyanins are diverse, including acting as visual signals to pollinators, defense against biotic and abiotic stresses. Thus, anthocyanins have been the most intensely studied secondary metabolite pathway. From model plants to horticultural crops, numerous studies have resulted in the discovery of highly conserved MYB-bHLH-WDR (MBW) transcriptional complex for the regulation of anthocyanin biosynthesis in plants. Recent discoveries have revealed that the anthocyanin biosynthesis pathway is also controlled by MYB repressors. Here we focus on the research progress into the role of MYB repressors in anthocyanin biosynthesis. In particular, we will discuss their functions and relationship to the MBW complex in the control of anthocyanin accumulation. In addition, an integrated regulatory network of anthocyanin biosynthesis controlled by MYB repressors and MBW activation complex is built based on the significant progress.

A R2R3-MYB Transcription Factor, VvMYBC2L2, Functions as a Transcriptional Repressor of Anthocyanin Biosynthesis in Grapevine (Vitis vinifera L.)

In grapevine, the MYB transcription factors play an important role in the flavonoid pathway. Here, a R2R3-MYB transcription factor, VvMYBC2L2, isolated from Vitis vinifera cultivar Yatomi Rose, may be involved in anthocyanin biosynthesis as a transcriptional repressor. VvMYBC2L2 was shown to be a nuclear protein. The gene was shown to be strongly expressed in root, flower and seed tissue, but weakly expressed during the fruit development in grapevine. Overexpressing the VvMYBC2L2 gene in tobacco resulted in a very marked decrease in petal anthocyanin concentration. Expression analysis of flavonoid biosynthesis structural genes revealed that chalcone synthase (CHS), dihydroflavonol 4-reductase (DFR), leucoanthocyanidin reductase (LAR) and UDP glucose flavonoid 3-O-glucosyl transferase (UFGT) were strongly down-regulated in the VvMYBC2L2-overexpressed tobacco. In addition, transcription of the regulatory genes AN1a and AN1b was completely suppressed in transgenic plants. These results suggested that VvMYBC2L2 plays a role as a negative regulator of anthocyanin biosynthesis.

Short-Term Nitrate Limitation Prior to Harvest Improves Phenolic Compound Accumulation in Hydroponic-Cultivated Lettuce ( Lactuca sativa L.) without Reducing Shoot Fresh Weight

Long-term exposure to a low nitrogen supply could effectively improve phenolic content in vegetables, but it also greatly decreases the yield. Therefore, it is necessary to develop cost-effective strategies of nitrogen management to overcome these obstacles. Here, we find that decreasing the nitrogen (NO3-) supply from 8.0 to below 2.0 mM during the last 7 days before harvest significantly increases phenolic levels and antioxidant capacity of the soluble fraction in two hydroponic-cultivated lettuces, which is demonstrated by the up-regulation of related genes ( PAL1, CHS, F3H, DFR, F35H, and UFGT) involved in the phenolic synthesis pathway. Importantly, short-term nitrate limitation before harvest does not affect yield production unless nitrogen supply is reduced below 1.0 and 0.5 mM for Ziluoma and Lvluo, respectively. These findings suggest that appropriate short-term nitrate limitation before harvest, considering genotype variation, is feasible for improving the phenolic content and antioxidant capacity of vegetables without reducing their yield.

Anthocyanins accumulation and molecular analysis of correlated genes by metabolome and transcriptome in green and purple asparaguses (Asparagus officinalis, L.)

Asparagus (A. officinalis L.) is a highly nutrition vegetable crop. Here, three purple asparagus cultivars, namely, Jing Zi-2, Purple Passion and Pacific Purple, and one green cultivar, namely, Jing Lv-1 were studied. At least 16 kinds of anthocyanins were identified in purple and green cultivars, and peonidin, cyanidin and their glycoside derivatives were found to be the major anthocyanins. Transcriptome data showed that most anthocyanin biosynthetic genes and at least 5 kinds of transcription factors were significantly differentially expressed significantly between the green and purple cultivars. Dark-treated experiments revealed that anthocyanins are not produced in the absence of light, and both the anthocyanin biosynthetic and regulatory genes were down-regulated greatly in the dark, implying that anthocyanins accumulation in asparagus is light-dependent. Overall, the results of this study provide useful information for understanding anthocyanin accumulation and the molecular mechanism of anthocyanin biosynthesis in asparagus.

Transcriptome Analysis Reveals Molecular Signatures of Luteoloside Accumulation in Senescing Leaves of Lonicera macranthoides

Lonicera macranthoides is an important medicinal plant widely used in traditional Chinese medicine. Luteoloside is a critical bioactive compound in L. macranthoides. To date, the molecular mechanisms underlying luteoloside biosynthesis are still largely unknown. In this work, high performance liquid chromatography (HPLC) was employed to determine the luteoloside contents in leaves, stems, and flowers at different developmental stages. Results showed that senescing leaves can accumulate large amounts of luteoloside, extremely higher than that in young and semi-lignified leaves and other tissues. RNA-Seq analysis identified that twenty-four differentially expressed unigenes (DEGs) associated with luteoloside biosynthesis were significantly up-regulated in senescing leaves, which are positively correlated with luteoloside accumulation. These DEGs include phenylalanine ammonia lyase 2, cinnamate 4-hydroxylase 2, thirteen 4-coumarate-CoA ligases, chalcone synthase 2, six flavonoid 3'-monooxygenase (F3'H) and two flavone 7-O-β-glucosyltransferase (UFGT) genes. Further analysis demonstrated that two F3'Hs (CL11828.Contig1 and CL11828.Contig2) and two UFGTs (Unigene2918 and Unigene97915) might play vital roles in luteoloside generation. Furthermore, several transcription factors (TFs) related to flavonoid biosynthesis including MYB, bHLH and WD40, were differentially expressed during leaf senescence. Among these TFs, MYB12, MYB75, bHLH113 and TTG1 were considered to be key factors involved in the regulation of luteoloside biosynthesis. These findings provide insights for elucidating the molecular signatures of luteoloside accumulation in L. macranthoides.

Ectopic Overexpression of a Novel R2R3-MYB, NtMYB2 from Chinese Narcissus Represses Anthocyanin Biosynthesis in Tobacco

R2R3 MYB transcription factors play key functions in the regulation of secondary metabolites. In the present study, a R2R3 MYB transcriptional factor NtMYB2 was identified from Chinese narcissus (Narcissus tazetta L. var. Chinensis Roem) and functionally characterized. NtMYB2 belongs to subgroup 4 of the R2R3 MYB transcription factor family that are related to repressor MYBs involved in the regulation of anthocyanin and flavonoids. Transient expression confirmed that NtMYB2 strongly reduced the red pigmentation induced by MYB- anthocyanin activators in agro-infiltrated tobacco leaves. Ectopic expression of NtMYB2 in tobacco significantly reduced the pigmentation and altered the floral phenotypes in transgenic tobacco flowers. Gene expression analysis suggested that NtMYB2 repressed the transcript levels of structural genes involved in anthocyanin biosynthesis pathway, especially the UFGT gene. NtMYB2 gene is expressed in all examined narcissus tissues; the levels of transcription in petals and corona is higher than other tissues and the transcription level at the bud stage was highest. These results show that NtMYB2 is involved in the regulation of anthocyanin biosynthesis pathway and may act as a repressor by down regulating the transcripts of key enzyme genes in Chinese narcissus.

A wheat MYB transcriptional repressor TaMyb1D regulates phenylpropanoid metabolism and enhances tolerance to drought and oxidative stresses in transgenic tobacco plants

MYB transcription factors are involved in the regulation of plant development and response to biotic and abiotic stress. In this study, TaMyb1D, a novel subgroup 4 gene of the R2R3-MYB subfamily, was cloned from wheat (Triticum aestivum L.). TaMyb1D was localized in the nucleus and functioned as a transcriptional repressor. The overexpression of TaMyb1D in tobacco (Nicotiana tabacum) plants repressed the expression of genes related to phenylpropanoid metabolism and down-regulated the accumulation of lignin in stems and flavonoids in leaves. These changes affected plant development under normal conditions. The expression of TaMyb1D was ubiquitous and up-regulated by PEG6000 and H2O2 treatments in wheat. TaMyb1D-overexpressing transgenic tobacco plants exhibited higher relative water content and lower water loss rate during drought stress, as well as higher chlorophyll content in leaves during oxidative stress. The transgenic plants showed a lower leakage of ions as well as reduced malondialdehyde and H2O2 levels during conditions of drought and oxidative stresses. In addition, TaMyb1D up-regulated the expression levels of ROS- and stress-related genes in response to drought stress. Therefore, the overexpression of TaMyb1D enhanced tolerance to drought and oxidative stresses in tobacco plants. Our study demonstrates that TaMyb1D functions as a negative regulator of phenylpropanoid metabolism and a positive regulator of plant tolerance to drought and oxidative stresses.

Characterization and functional analysis of a MYB gene (GbMYBFL) related to flavonoid accumulation in Ginkgo biloba

Flavonoids are a group of metabolites in Ginkgo biloba thought to provide health benefits. R2R3-MYB transcription factors (TFs) play key roles in the transcriptional regulation of the flavonoid biosynthesis in plants. In this study, an R2R3-MYB transcription factor gene, GbMYBFL, was isolated from G. biloba and characterized. Results of bioinformatic analysis indicated that GbMYBFL is more closely related to the R2R3-MYB involved in flavonoid biosynthesis and displayed high similarity to MYB from other plants. The genmomic sequence of GbMYBFL had three exons and two introns, with its upstream sequence containing cis-acting regulatory elements Myb binding site, Myc recognition sites, and light, SA, MeJA responsive elements. Subcellular localization analysis indicates that GbMYBFL was located in the nucleus. Quantitative real-time PCR revealed that GbMYBFL was expressed in leaves, stems, roots, young fruits, male flower and female flower, and the level of transcription in male flower and leaves were higher than that in female flower, stems, roots, and young fruits. During G. biloba leaf growth, the transcription of GbMYBFL is positively correlated with the flavonoid content, suggesting that the GbMYBFL is involved in the flavonoid biosynthesis. Overexpression of GbMYBFL under the control of the CaMV35S promoter in Ginkgo callus notably enhanced the accumulation of flavonoids and anthocyanin compared with non-transformed callus. This finding suggested that GbMYBFL positively related to flavonoid biosynthesis, and the overexpression of GbMYBFL was sufficient to induce flavonoids and anthocyanin accumulation.

PbrMYB21, a novel MYB protein of Pyrus betulaefolia, functions in drought tolerance and modulates polyamine levels by regulating arginine decarboxylase gene

MYB comprises a large family of transcription factors that play significant roles in plant development and stress response in plants. However, knowledge concerning the functions of MYBs and the target genes remains poorly understood. Here, we report the identification and functional characterization of a novel stress-responsive MYB gene from Pyrus betulaefolia. The MYB gene, designated as PbrMYB21, belongs to the R2R3-type and shares high degree of sequence similarity to MdMYB21. The transcript levels of PbrMYB21 were up-regulated under various abiotic stresses, particularly dehydration. PbrMYB21 was localized in the nucleus with transactivation activity. Overexpression of PbrMYB21 in tobacco conferred enhanced tolerance to dehydration and drought stresses, whereas down-regulation of PbrMYB21 in Pyrus betulaefolia by virus-induced gene silencing (VIGS) resulted in elevated drought sensitivity. Transgenic tobacco exhibited higher expression levels of ADC (arginine decarboxylase) and accumulated larger amount of polyamine in comparison with wild type (WT). VIGS of PbrMYB21 in Pyrus betulaefolia down-regulated ADC abundance and decreased polyamine level, accompanied by compromised drought tolerance. The promoter region of PbrADC contains one MYB-recognizing cis-element, which was shown to be interacted with PbrMYB21, indicating the ADC may be a target gene of PbrMYB21. Take together, these results demonstrated that PbrMYB21 plays a positive role in drought tolerance, which may be, at least in part, due to the modulation of polyamine synthesis by regulating the ADC expression.

Isolation and characterization of GmMYBJ3, an R2R3-MYB transcription factor that affects isoflavonoids biosynthesis in soybean

Isoflavonoids are secondary metabolites that play a variety of roles in plant-microbe interactions and plant defenses against abiotic stresses. Here we report a new MYB transcription factor (TF) gene, GmMYBJ3, that is involved in the isoflavonoids biosynthesis. The GmMYBJ3 gene is 1,002 bp long and encodes a protein of 333 amino acids. Amino acid sequence analysis showed that GmMYBJ3 is a typical R2R3 MYB TF. Yeast expression experiment demonstrated that GmMYBJ3 has its transcription activity in the nucleus and is transiently expressed in onion epidermal cells. The GmMYBJ3 gene was transformed into soybean and the expression activity of the GmMYBJ3 gene was significantly positively correlated with total isoflavonoid accumulation in soybean. Transient expression assays indicated that GmMYBJ3 can activate CHS8 expression. Furthermore, we analyzed the expressions of several genes known involved in the isoflavonoid biosynthesis, including CHS8, CHI1A, PAL1, IFS2 and F3H, in the GmMYBJ3 transgenic plants. The results showed that the expression levels of CHS8 and CHI1A were significantly increased in the transgenic plants compared to wild-type plants, but those of PAL1, IFS2 and F3H remained similar between the transgenic and wild-type plants. These results suggest that GmMYBJ3 participates in the isoflavonoid biosynthesis through regulation of CHS8 and CHI1A in soybean.

Establishment of the model system between phytochemicals and gene expression profiles in Macrosclereid cells of Medicago truncatula

Macrosclereid cells, which are a layer in the seed coat of Medicago truncatula, accumulate large amounts of phytochemicals during their development. But little is known about the complex and dynamic changes during macrosclereid cell development. To characterize the phytochemicals and the related gene expression during the development of M. truncatula macrosclereid cells, a high performance liquid chromatography-mass spectrometry (HPLC-MS) assay and microarray study were conducted on transcriptome changes from macrosclereid cell during seed development. A total of 16 flavonoids by HPLC-MS and 4861 genes exhibited significant differences at transcript levels by microarray analysis were identified for macrosclerid cells at six different time points during seed development. 815 abiotic and biotic stress genes, 223 transcriptional factors (TFs), and 155 annotated transporter proteins exhibited differential expression during the development of macrosclereid cells. A total of 102 genes were identified as involved in flavonoid biosynthesis, phenypropanoid biosynthesis, and flavone and flavonol biosynthesis. We performed a weighted gene co-regulatory network (WGCNA) to analyze the gene-flavonoid association and rebuilt the gene regulatory network during macrosclereid cell development. Our studies revealed that macrosclereid cells are, beside as the first barrier of defense against diseases, an excellent model system to investigate the regulatory network that governs flavonoid biosynthesis.

Overexpression of AmRosea1 Gene Confers Drought and Salt Tolerance in Rice

Ectopic expression of the MYB transcription factor of AmROSEA1 from Antirrhinum majus has been reported to change anthocyanin and other metabolites in several species. In this study, we found that overexpression of AmRosea1 significantly improved the tolerance of transgenic rice to drought and salinity stresses. Transcriptome analysis revealed that a considerable number of stress-related genes were affected by exogenous AmRosea1 during both drought and salinity stress treatments. These affected genes are involved in stress signal transduction, the hormone signal pathway, ion homeostasis and the enzymes that remove peroxides. This work suggests that the AmRosea1 gene is a potential candidate for genetic engineering of crops.

Molecular candidates for early-stage flower-to-fruit transition in stenospermocarpic table grape (Vitis vinifera L.) inflorescences ascribed by differential transcriptome and metabolome profiles

Flower-to-fruit transition depends of nutrient availability and regulation at the molecular level by sugar and hormone signalling crosstalk. However, in most species, the identities of fruit initiation regulators and their targets are largely unknown. To ascertain the main pathways involved in stenospermocarpic table grape fruit set, comprehensive transcriptional and metabolomic analyses were conducted specifically targeting the early phase of this developmental stage in 'Thompson Seedless'. The high-throughput analyses performed disclosed the involvement of 496 differentially expressed genes and 28 differently accumulated metabolites in the sampled inflorescences. Our data show broad transcriptome reprogramming of molecule transporters, globally down-regulating gene expression, and suggest that regulation of sugar- and hormone-mediated pathways determines the downstream activation of berry development. The most affected gene was the SWEET14 sugar transporter. Hormone-related transcription changes were observed associated with increased indole-3-acetic acid, stimulation of ethylene and gibberellin metabolisms and cytokinin degradation, and regulation of MADS-box and AP2-like ethylene-responsive transcription factor expression. Secondary metabolism, the most representative biological process at transcriptome level, was predominantly repressed. The results add to the knowledge of molecular events occurring in grapevine inflorescence fruit set and provide a list of candidates, paving the way for genetic manipulation aimed at model research and plant breeding.

New member of the R2R3-MYB transcription factors family in grapevine suppresses the anthocyanin accumulation in the flowers of transgenic tobacco

In grapevine, anthocyanins and proanthocyanidins are the main flavonoids in berries, which are associated to organoleptic properties in red wine such as color and astringency. Flavonoid pathway is specifically regulated at transcriptional level and several R2R3-MYB proteins have shown to act as positive regulators. However, some members of this family have shown to repress the flavonoid biosynthesis. In this work, we present the characterization of VvMYB4-like gene, which encodes a putative transcriptional factor highly expressed in the skin of berries at the pre veraison stage in grapevine. Its over-expression in tobacco resulted in the loss of pigmentation in flowers due a decrease in anthocyanin accumulation. Severity in anthocyanin suppression observed in petals could be associated with the expression level of the VvMYB4-like transgene. Expression analysis of flavonoid structural genes revealed the strong down-regulation of the flavonoid-related genes anthocyanidin synthase (ANS) and dihydroflavonol reductase (DFR) genes and also the reduction of the anthocyanin-related gene UDP glucose:flavonoid 3-O-glucosyl transferase (UFGT), which was dependent of the transgene expression. In addition, expression of VvMYB4-like in the model plant Arabidopsis showed similar results, with the higher down-regulation observed in the AtDFR and AtLDOX genes. These results suggest that VvMYB4-like may play an important role in regulation of anthocyanin biosynthesis in grapevine acting as a transcriptional repressor of flavonoid structural genes.

The soybean R2R3 MYB transcription factor GmMYB100 negatively regulates plant flavonoid biosynthesis

Soybean flavonoids, a group of important signaling molecules in plant-environment interaction, ubiquitously exist in soybean and are tightly regulated by many genes. Here we reported that GmMYB100, a gene encoding a R2R3 MYB transcription factor, is involved in soybean flavonoid biosynthesis. GmMYB100 is mainly expressed in flowers, leaves and immature embryo, and its level is decreased after pod ripening. Subcellular localization assay indicates that GmMYB100 is a nuclear protein. GmMYB100 has transactivation ability revealed by a yeast functional assay; whereas bioinformatic analysis suggests that GmMYB100 has a negative function in flavonoid biosynthesis. GmMYB100-overexpression represses the transcript levels of flavonoid-related genes in transgenic soybean hairy roots and Arabidopsis, and inhibits isoflavonoid (soybean) and flavonol (Arabidopsis) production in transgenic plants. Furthermore, the transcript levels of six flavonoid-related genes and flavonoid (isoflavonoid and flavone aglycones) accumulation are elevated in the GmMYB100-RNAi transgenic hairy roots. We also demonstrate that GmMYB100 protein depresses the promoter activities of soybean chalcone synthase and chalcone isomerase. These findings indicate that GmMYB100 is a negative regulator in soybean flavonoid biosynthesis pathway.