Search Results (1,562)

Salvia miltiorrhiza Bunge is a traditional Chinese medicinal plant whose roots are rich in water-soluble phenolic acids. Rosmarinic acid and salvianolic acid B are representative components that confer antibacterial, antioxidant, and cardio-cerebrovascular protective activities. However, these metabolites often accumulate at low and unstable levels in planta, which limits their efficient development and use. This review summarises recent advances in understanding salvianolic acid biosynthesis and its transcriptional regulation in S. miltiorrhiza. Current evidence supports a coordinated pathway composed of the phenylpropanoid route and a tyrosine-derived branch, which converge to generate rosmarinic acid and subsequently more complex derivatives through oxidative coupling reactions. Key findings on transcription factor families that fine-tune pathway flux by regulating core structural genes are synthesised. Representative positive regulators such as SmMYB111, SmMYC2, and SmTGA2 activate key nodes (e.g., PAL, TAT/HPPR, RAS, and CYP98A14) to promote phenolic acid accumulation. Conversely, negative regulators such as SmMYB4 and SmMYB39 repress pathway genes and/or interfere with activator complexes. Major regulatory features include hormone-inducible signalling, cooperative regulation through transcription factor complexes, and emerging post-transcriptional and post-translational controls. Future directions and challenges are discussed, including overcoming regulatory redundancy and strong spatiotemporal specificity of transcriptional control. Integrating spatial and single-cell omics with functional genomics (e.g., genome editing and rational TF stacking) is highlighted as a promising strategy to enable predictive metabolic engineering for the stable, high-yield production of salvianolic acid-type compounds. Full article

As cold-sensitive fruits, loquats easily develop chilling injury (CI) during cold storage, which leads to quality deterioration and economic losses. Our prior research indicated that exogenous melatonin (MT) treatment can mitigate CI in postharvest loquats by regulating reactive oxygen species (ROS) metabolism, but the underlying molecular mechanism remains unclear. The primary objective of this study is to decipher the molecular regulatory pathway by which MT alleviates CI in postharvest loquats, focusing on the role of MYB transcription factors (TFs) in modulating antioxidant enzyme genes. Here, MT treatment remarkably reduced CI severity in loquat fruits, as reflected by lower CI index, reduced cell membrane permeability, decreased firmness, lower a* and b* values, and higher L* value, compared with the control group. Moreover, a cold-induced MYB TF, designated EjMYB15, was identified. Compared to non-treated fruits, the expression level of EjMYB15 was maintained at higher levels in MT-treated loquats. Subcellular localization and transactivation assays demonstrated that EjMYB15 is a nuclear-localized transcriptional activator. Electrophoretic mobility shift assay (EMSA) and dual-luciferase reporter (DLR) assays showed that EjMYB15 binds the MYB-binding sites (MBS) in the promoters of four antioxidant enzyme genes (EjCAT1, EjCAT2, EjGST1, and EjGST2), thereby activating their transcription. Taken together, these findings indicate that EjMYB15 positively regulates cold tolerance of loquat fruits by improving ROS scavenging capacity. These results elucidate the regulatory pathway by which MYB TFs mitigate CI and provide new theoretical support for the application of MT in alleviating CI in postharvest fruits. Full article

Fragaria vesca L., a widely distributed model species, serves as a key resource for studying the evolution and genetics of the Fragaria genus. Research has shown that R2R3-MYB transcription factors are crucial for plant growth and development. However, their specific role in cold resistance in F. vesca is not well understood. In this study, we used the latest genome data for the strawberry (F. vesca v6.0). We performed a genome-wide identification of the R2R3-MYB gene family in F. vesca. We identified a total of 106 R2R3-FvMYBs. Based on their predicted functions in plants, we classified these genes into 25 distinct subfamilies. We then conducted a comprehensive bioinformatics analysis of this family. We performed a detailed examination of the R2R3-FvMYBs structures and physicochemical properties. This analysis provided five key parameters for each protein: molecular weight, the number of amino acids, theoretical isoelectric point, grand average of hydropathicity (GRAVY), and instability index. Gene duplication analysis suggested that segmental duplications were a primary driver of the proliferation of this gene family. Promoter cis-acting element prediction revealed that a large proportion of R2R3-FvMYBs possess elements predominantly associated with phytohormone responsiveness and biotic/abiotic stress responses. Quantitative real-time reverse transcription PCR (qRT-PCR) results confirmed that the expression levels of several R2R3-FvMYBs were upregulated under cold stress. Furthermore, compared to wild-type controls, the overexpression of FvMYB103 in Arabidopsis thaliana enhanced cold tolerance, accompanied by increases in the relevant physiological indices. Collectively, these findings support further investigation into R2R3-MYB gene family to directly assess their contribution to cold resistance. Full article

Gloriosa superba ‘Passion Flame’ (flame lily) is a distinctive ornamental plant characterized by its striking floral structure and vivid coloration. During flower development, flame lily tepals undergo a pronounced color transition from green at the bud stage to bright red with a yellow base at maturity, providing an excellent system for studying flower pigmentation in monocots. Here, we applied a multi-omics approach to examine metabolite accumulation and gene expression dynamics across four stages of flower development. Metabolomic profiling identified 240 flavonoids and four anthocyanins, among which pelargonidin-3-O-glucoside showed the highest relative abundance among red pigmentation. Transcriptome analysis revealed that seven key anthocyanin structural genes showed strong correlations with anthocyanin accumulation. In parallel, several chlorophyll degradation genes, including GsSGR and GsPPH, were upregulated during tepal maturation, suggesting transcriptional activation of chlorophyll degradation pathways concurrent with pigment accumulation. Co-expression network analysis further identified GsMYB75 and GsMYB114 as temporally distinct regulators associated with anthocyanin biosynthesis, acting together with bHLH, NAC, and AP2/ERF transcription factors. This study provides new insights into the pigment regulation in G. superba ‘Passion Flame’ and offers candidate regulatory components for future functional studies and the improvement of ornamental traits in monocotyledonous plants. Full article

The pigmentation patterns of potato tubers are complex and diverse, often exhibiting significant tissue specificity. This study was conducted to elucidate the molecular mechanisms underlying the differential pigmentation in different parts of potato tubers using two cultivars, ‘Huashu 12’ and 15EM36-26, which exhibit opposite pigmentation patterns between the bud eyes and the tuber periderm. Metabolomic analysis revealed that cyanidin, pelargonidin, and malvidin are the key anthocyanin components responsible for the observed pigmentation differences. A total of 118 common differentially expressed genes in the differentially pigmented tissues of both cultivars were identified in transcriptomic analysis, including key structural genes of the anthocyanin biosynthesis pathway (such as StPAL, StCHS, and StDFR). Weighted gene co-expression network analysis was further employed to screen modules significantly correlated with pigmentation phenotypes, and 28 candidate genes associated with anthocyanin biosynthesis were identified. Expression validation demonstrated that the expression of StbHLH14 was significantly higher in non-pigmented tissues compared to pigmented tissues. Functional analysis revealed that StbHLH14 can inhibit the activation of structural gene promoters (such as StCHS and StDFR) via the MYB transcription factor StAN2, thereby negatively regulating anthocyanin biosynthesis. This study unveils the metabolic and transcriptional basis of tissue-specific pigmentation in potato tubers and clarifies the negative regulatory role of StbHLH14. Full article

Lateral Organ Boundaries Domain (LBD) proteins are plant-specific transcription factors characterized by a typical N-terminal LOB domain and are critical for plant growth, development, and stress response. Currently, LBD genes have been investigated in various plant species, but they have yet to be identified in Neolamarckia cadamba, known as a ‘miracle tree’ for its fast growth and acknowledged for its potential medicinal value in tropical and subtropical areas of Asia. In this study, a total of 65 NcLBD members were identified in N. cadamba by whole-genome bioinformatics analysis. Phylogenetic analysis revealed their classification into two clades with seven distinct groups, and their uneven distribution across 18 chromosomes, along with 6 tandem repeats and 58 segmental duplications. Furthermore, enrichment analysis of transcription factor binding motifs within NcLBD promoters identified the MYB-related and WRKY families exhibited the most significant enrichment in the NcLBD promoter. Protein interaction network analysis revealed potential interactions among NcLBD proteins, as well as their interactions with various transcription factors. RNA-seq and qRT-PCR analyses of NcLBDs transcript levels showed distinct expression patterns both across various tissues and under different hormone and abiotic stress conditions. Specifically, NcLBD3, NcLBD37, and NcLBD47 were highly expressed in vascular cells and induced by abiotic stress, including cold, drought, and salt, suggesting their significant role in the processes. In summary, our genome-wide analysis comprehensively identified and characterized LBD gene family in N. cadamba, laying a solid foundation for further elucidating the biological functions of NcLBD genes. Full article

Schima superba, belonging to the genus Schima of Theaceae, is a common large tree in evergreen broad-leaved forests in subtropical regions of China. As one of the largest transcription factor families in plants, MYB transcription factors play an important role in plant stress response by specifically binding to cis-acting elements in different gene promoter regions to accurately regulate gene expression. However, there are few studies on MYB transcription factors in S. superba. The MYB transcription factor family of S. superba was found and examined in this study using the genomic and transcriptome data of the S. superba. A set of 220 MYB transcription factors was identified from S. superba and classified into four subfamilies. These transcription factors were unevenly distributed on 18 chromosomes of S. superba. The conserved domains of the same subfamily members are highly similar to the conserved motifs. The collinearity analysis between species showed that there were few orthologous genes located on chromosome 18 of S. superba. Numerous elements linked to phytohormone response, stress adaptation, and growth control can be found in the promoter regions of the S. superba MYB transcription factor family, according to an analysis of the promoter cis-acting elements. Verification via qRT-PCR showed that among 15 SsMYBs genes tested, SsMYB24 expression peaked at 96 h of drought stress, followed by a rapid downregulation upon rewatering to initial levels. This expression pattern aligned with the transcriptome data. This study is helpful to further identify the function of SsMYB transcription factors and provide a new molecular mechanism for improving drought tolerance of S. superba. Full article

The corolla of Rehmannia glutinosa typically exhibits a stable reddish-purple color, but a naturally occurring yellow-flowered variant has recently been identified. To clarify the molecular basis of flower color variant, metabolomics, transcriptomics, and variant analyses were integrated. Metabolomic profiling revealed that the yellow phenotype was associated with lower anthocyanin levels and higher carotenoid levels. Specifically, the decreased cyanidin-3-O-glucoside led to a loss of red, while increased lutein provided the basis for the yellow color. Transcriptomic analysis revealed a downregulation of anthocyanin biosynthetic genes, including CHS, CHI, F3H, DFR, and ANS, in the yellow-flowered variant, and three S6-subgroup R2R3-MYB genes, including the known anthocyanin activator RgMYB41 (gene-DH2020_015992), were downregulated. Variant analysis showed that A12S and G255E in the gene-DH2020_015992 transcription factor were predicted to markedly alter protein conformation and potentially impair regulatory function. Subcellular localization and transcriptional activation assays further supported the functional characterization of gene-DH2020_015992 as a transcription factor. Collectively, these findings suggest that flower color variation in R. glutinosa is driven by MYB-mediated repression of anthocyanin biosynthesis and by carotenoid accumulation. This study provides a comprehensive genetic explanation for flower color variation in R. glutinosa and offers a theoretical foundation for floral pigmentation in plants. Full article

Soil salinity is a major constraint on global crop production, disrupting photosynthesis, ion homeostasis, and growth. Beyond the roles of classic osmoprotectants and antioxidant enzymes, flavonoids have emerged as versatile mediators of salt stress tolerance at the interface of redox control, hormone signaling, and developmental plasticity. This review summarizes current evidence on how salinity remodels flavonoid biosynthesis, regulation, and function from cellular to whole-plant scales. We first outline the phenylpropanoid–flavonoid pathway, with emphasis on transcriptional control by MYB, bHLH, and NAC factors and their integration with ABA, JA, and auxin signaling. We then discussed how post-synthetic modifications such as glycosylation and methylation adjust flavonoid stability, compartmentation, and activity under salt stress. Functional sections highlight roles of flavonoids in ROS scavenging, Na⁺/K⁺ homeostasis, membrane integrity, and the modulation of ABA/MAPK/Ca²⁺ cascades and noncoding RNA networks. Spatial aspects, including root–shoot communication and rhizosphere microbiota recruitment, are also considered. Based on this synthesis, we propose a flavonoid-centered stress network (FCSN), in which specific flavonoids function as key nodes that connect metabolic flux with hormonal crosstalk and stress signaling pathways. We argue that reconceptualizing flavonoids as central stress network regulators, rather than generic antioxidants, provides a basis for metabolic engineering, bio-stimulant design, and breeding strategies aimed at improving crop performance on saline soils. Full article

The color and scent of flowers are vital ornamental attributes influenced by a complex interaction of metabolic and transcriptional mechanisms. Comparative analyses were performed to determine the molecular rationale for these features in Hydrangea arborescens, between the white-flowered variety ‘Annabelle’ (An) and its pink-flowered variant ‘Pink Annabelle’ (PA). Gas chromatography–mass spectrometry (GC–MS) detected 25 volatile organic compounds (VOCs) in ‘An’ and 21 in ‘PA’, with 18 chemicals common to both types. ‘An’ exhibited somewhat higher VOC diversity, whereas ‘PA’ emitted much bigger quantities of benzenoid and phenylpropanoid volatiles, including benzaldehyde, benzyl alcohol, and phenylethyl alcohol, resulting in a more pronounced floral scent. UPLC–MS/MS metabolomic analysis demonstrated obvious clustering of the two varieties and underscored the enrichment of phenylpropanoid biosynthesis pathways in ‘PA’. Transcriptomic analysis revealed 11,653 differentially expressed genes (DEGs), of which 7633 were elevated and linked to secondary metabolism. Key biosynthetic genes, including PAL, 4CL, CHS, DFR, and ANS, alongside transcription factors such as MYB—specifically TRINITY_DN5277_c0_g1, which is downregulated in ‘PA’ (homologous to AtMYB4, a negative regulator of flavonoid biosynthesis)—and TRINITY_DN23167_c0_g1, which is significantly upregulated in ‘PA’ (homologous to AtMYB90, a positive regulator of anthocyanin synthesis), as well as bHLH, ERF, and WRKY (notably TRINITY_DN25903_c0_g1, highly upregulated in ‘PA’ and homologous to AtWRKY75, associated with jasmonate pathway), demonstrating a coordinated activation of color and fragrance pathways. The integration of metabolomic and transcriptome data indicates that the pink-flowered ‘PA’ variety attains its superior coloring and aroma via the synchronized transcriptional regulation of the phenylpropanoid and flavonoid pathways. These findings offer novel molecular insights into the genetic and metabolic interplay of floral characteristics in Hydrangea. Full article

Drought severely limits plant growth, threatening global food security and biodiversity. This review provides a comprehensive overview of the recent advances in plant responses to drought, ranging from initial sensing to physiological adaptation, as well as guidelines for experimental design. We focus on key regulatory components, specifically the ABA signaling core (PYR/PYL/RCARs, PP2C phosphatases, and SnRK2 kinases) and ROS signaling. We provide a detailed description of transcriptional networks, highlighting the pivotal roles of DREB, NAC, and MYB transcription factors in coordinating gene expression. Furthermore, we explore downstream tolerance strategies, including osmoprotectant (e.g., proline) accumulation, cell wall remodeling involving expansins and pectin methylesterases, as well as stomatal regulation. We also discuss how combining genetics with multi-omics and high-throughput phenotyping bridges the gap between molecular mechanisms and whole-plant physiological performance. Ultimately, these insights provide a foundation for refining research approaches and accelerating the development of drought-resilient crops to sustain agricultural productivity and ecosystem stability in increasingly arid environments. Full article

Soluble sugars are key determinants of fruit quality, directly influencing sensory attributes such as sweetness and flavor, as well as nutritional value and texture. Their content and composition are precisely regulated by sugar-metabolizing enzymes. Key enzymes, including invertase (INV), sucrose phosphate synthase (SPS), sucrose synthase (SUS), fructokinase (FRK), and hexokinase (HXK), play pivotal roles in these processes. However, a systematic and in-depth analysis of their regulatory mechanisms is currently lacking, which hinders a comprehensive understanding of the regulatory network governing fruit sugar metabolism. This review employs bibliometric analysis to systematically examine research trends in fruit sugar metabolism. Furthermore, it synthesizes recent advances in the coordinated regulatory mechanisms from the perspectives of transcriptional regulation, epigenetic modifications, and signal transduction, aiming to provide a clearer framework for future research. At the transcriptional level, transcription factor families such as MYB, WRKY, NAC, and MADS-box achieve precise regulation of sugar metabolism-related genes by specifically binding to the promoters of their target genes. Regarding epigenetic regulation, mechanisms including histone modifications, non-coding RNAs, and DNA methylation influence the expression of sugar-metabolizing enzymes at the post-transcriptional level by modulating chromatin accessibility or mRNA stability. Signaling pathways integrate hormonal signals (e.g., ABA, ethylene), environmental signals (e.g., temperature, light), and sugar-derived signals into the regulatory network, forming complex feedback mechanisms. These regulatory mechanisms not only directly affect sugar accumulation in fruits but also participate in fruit quality formation by modulating processes such as cell turgor pressure and carbon allocation. By integrating recent findings on transcriptional regulation, epigenetics, and signaling pathways, this review provides a theoretical foundation for fruit quality improvement and targeted breeding. Full article

To elucidate the physiological and molecular mechanisms underlying cold tolerance in the mangrove species Kandelia obovata Sheue & al, this study measured the antioxidant enzyme activities and photosynthetic pigment contents of two populations—cold-tolerant and -sensitive—under natural overwintering conditions. In addition, transcriptome sequencing was performed to analyze differentially expressed genes (DEGs), transcription factor families, single nucleotide polymorphisms (SNPs), and alternative splicing events. The results showed that catalase activity was significantly elevated in the cold-tolerant population, which enhanced the efficiency of hydrogen peroxide scavenging. In contrast, although the superoxide dismutase activity was relatively high in the cold-sensitive population, its downstream scavenging capacity was insufficient, resulting in an overall lower antioxidant efficiency. The KEGG enrichment analysis indicated that pathways such as phenylpropanoid biosynthesis, amino sugar metabolism, and plant hormone signal transduction might be involved in the response to low-temperature stress. Further analysis revealed that transcription factors such as WRKY, NAC, MYB, and ERF were differentially expressed at significant levels in the cold-tolerant population, suggesting that they may play important roles in low-temperature adaptation. In addition, the diversity of SNPs and alternative splicing events may enhance protein function and contribute to improved cold tolerance. In summary, the cold-tolerant K. obovata population achieves low-temperature tolerance through multiple mechanisms, including antioxidant defense, metabolic regulation, and transcriptional as well as post-transcriptional regulation. This study provides a theoretical basis for elucidating the molecular foundations of cold tolerance in K. obovata. Full article

As a coastal brush, Atalantia buxifolia is a good rootstock of citrus plants around sea shores, but its salt tolerance has not been studied. In order to explore the salt tolerance of A. buxifolia, its seeds and seedlings were subjected to NaCl stress treatment, followed by phenotypic observation and biochemical and transcriptome analysis. Results showed that the increase in NaCl concentrations resulted in the decrease in germination rates, germination potential, germination index, and vigor index of A. buxifolia seeds, as well as growth of epicotyl and radicle, and biomass of A. buxifolia seedlings. However, the seeds of A. buxifolia could adapt to the growth of 100 mM NaCl concentration to a certain extent. The levels of malondialdehyde (MDA) and relative electrolyte leakage increased with the increase in NaCl concentrations. However, under treatment of 100 mM NaCl, the biomass, POD, CAT, APX, GSH, AsA, H₂O₂, MDA, and relative electrolyte leakage of A. buxifolia seedlings did not show significant changes compared with the control treatment. Transcriptome analysis showed that expression of differential genes increased with the increase in NaCl concentrations. GO enrichment showed that the most annotated genes were metabolic process, cell and cell composition, and binding. The KEGG pathway annotation shows that differential genes were mainly enriched in some pathways, such as photosynthesis antenna proteins, plant hormone signal transduction, glutathione metabolism, and starch and sucrose metabolism. In addition, differentially expressed genes had been annotated into 45 transcription factor families, including the largest number of bHLH, NAC, WRKY, MYB, and bZIP families. The results provide a basis for further understanding the salt tolerance mechanism and exploring related salt tolerance genes of A. buxifolia. Full article

The genus Pinus (~115 species) represents a cornerstone of boreal and temperate forests and plays a central role in global forestry, industrial applications, and carbon sequestration. Their distinctive biology—including exceptionally large genomes, guaiacyl-rich lignin, tracheid-based xylem, and pronounced seasonal growth regulation—makes pines both scientifically compelling and technically challenging to study. Recent advances in genomics and transcriptomics, supported by emerging multi-omics and computational frameworks, have significantly advanced our understanding of the molecular architecture of wood formation, including key processes such as NAC–MYB regulatory cascades, lignin biosynthesis pathways, and adaptive processes such as compression wood development. Yet functional studies remain limited by low transformation efficiency, regeneration difficulties, and a scarcity of conifer-optimized genetic tools. This review highlights recent breakthroughs in single-cell and spatial transcriptomics, CRISPR-based genome editing, synthetic promoter design, and machine learning-driven regulatory network prediction and comprehensively examines translational applications in biomass improvement, lignin engineering, stress resilience, and industrial biotechnology. By expanding the research frontiers of Pinus, we aim to connect molecular discovery with applied forestry and climate mitigation strategies. Full article