Search Results (1,906)

Phenolic acids and flavonoids are major bioactive constituents of Sparganium stoloniferum tubers (SL), yet their spatial organization within this medicinal organ remains insufficiently characterized, limiting understanding of how anatomical structure relates to metabolite distribution. To address this, we integrated mass spectrometry imaging (MSI), non-targeted LC–MS and targeted LC–MS/MS metabolomics, and reverse transcription quantitative polymerase chain reaction (RT–qPCR) analysis to characterize the spatial patterns of phenylpropanoid- and auxin-related metabolites and selected transcripts in SL. MSI and non-targeted LC–MS profiling showed that phenylpropanoid- and flavonoid-related metabolites were preferentially accumulated in the peripheral cortex rather than in the stele, although the stele constitutes the dominant internal tissue of the tuber. Targeted LC–MS/MS further confirmed that representative hydroxycinnamic acids and caffeoylquinic acid derivatives were enriched in the cortex and, for most validated metabolites, in the cell wall-enriched fraction. Notably, spatial metabolomic profiling also revealed a contrasting stele-biased distribution of indole-related metabolites, including indole-3-acetamide-related features detected by MSI and non-targeted LC–MS and indole-3-acetic acid (IAA) enrichment validated by targeted LC–MS/MS. RT–qPCR analysis showed that phenylpropanoid biosynthetic genes were generally more highly expressed in the cortex and cell wall-enriched fraction, whereas auxin-related genes showed higher expression in the stele. Together, these results show cortex-biased phenylpropanoid accumulation, preferential association of most validated phenylpropanoid-related metabolites with the cell wall-enriched fraction, and stele-associated IAA accumulation and auxin-related transcript expression. This study provides a spatial framework for understanding metabolite partitioning in medicinal aquatic storage organs and highlights the importance of integrating anatomical, metabolomic, and gene expression information in medicinal plant research. Full article

Plant specialized metabolites connect genetic programs and environmental responses with ecologically and economically valuable natural products. Their accumulation is rarely constitutive, varying instead with tissue identity, developmental stage, stress exposure, hormone signaling, and cellular storage capacity. This review examines basic helix-loop-helix (bHLH) transcription factors as regulatory switch points in plant specialized metabolism, with emphasis on the jasmonate-JAZ-MYC module. In resting tissues, JAZ repressors constrain MYC/bHLH activity; after wounding, herbivory, pathogen challenge, or elicitation, jasmonoyl-isoleucine triggers COI1-dependent JAZ turnover, releasing MYC factors to bind E-box/G-box motifs, recruit coregulators such as MED25, and activate biosynthetic genes or downstream transcription-factor cascades. Plant lineages have repeatedly adapted this regulatory logic to control terpenoids, alkaloids, phenylpropanoids, flavonoids, glucosinolates, phytoalexins, and related metabolites. Comparative examples include Arabidopsis sesquiterpenes and glucosinolates, Taxus taxanes, Artemisia artemisinin, Catharanthus terpenoid indole alkaloids, Salvia phenolic acids and tanshinones, Ginkgo terpene trilactones, rice diterpenoid phytoalexins, and cotton gossypol. Across these systems, bHLH output depends on dimer choice, promoter grammar, chromatin accessibility, hormone crosstalk, partner transcription factors, and cell-type competence. Six shared principles emerge: signal gating, topology matched to pathway architecture, partner-dependent promoter decoding, spatial competence, feedback rheostats, and evidence-dependent transferability. We further discuss evidence standards, multi-omics-guided factor discovery, miRNA-mediated post-transcriptional control, and engineering strategies for crop defense, food quality, medicinal-metabolite production, and synthetic biology. Unlike pathway- or MYC2-centered surveys, this review organizes the literature within a direct–cascade–hybrid framework that integrates promoter grammar, spatial competence, storage anatomy, and an explicit evidence hierarchy. Full article

Petal blight caused by Neopestalotiopsis clavispora infection in Rhododendron delavayi petals severely reduces their ornamental value; however, the metabolic and transcriptional responses of petals to this pathogen remain unclear. In this study, we integrated widely targeted metabolomic and transcriptomic analyses to systematically characterize the response mechanisms of R. delavayi petals at early (1 day post-infection), middle (2 days post-infection), and late (4 days post-infection) stages of N. clavispora infection. A total of 1251 metabolites were identified, and K-means clustering analysis revealed that the differentially accumulated metabolites (DAMs) in Subclass 1 were significantly enriched in flavonoid, phenylpropanoid, and glutathione metabolic pathways. Transcriptomic analysis identified 3744, 6986, and 5407 differentially expressed genes (DEGs) at early, middle and late stages, respectively. Weighted gene co-expression network analysis (WGCNA) indicated that the key hub genes at early, middle, and late stages were mainly involved in maintaining reactive oxygen species (ROS) homeostasis, plant–pathogen interaction signal transduction, and cell wall remodeling, respectively. Joint metabolomic and transcriptomic analysis showed that phenylpropanoid, flavonoid, and glutathione pathways were commonly and significantly enriched. In vitro antifungal assays demonstrated that 2000 mg/L phloretin significantly inhibited mycelial growth of N. clavispora and effectively alleviated petal infection. Collectively, R. delavayi petals exhibit stage-specific defense strategies against N. clavispora: in the early stage, by inducing H₂O₂ accumulation and ROS homeostasis; in the middle stage, by activating immune signaling pathways; and in the late stage, by enhancing cell wall remodeling and antioxidant capacity. This study provides a theoretical basis and a candidate compound for green control of petal blight. Full article

Waterlogging is a major abiotic stress that restricts maize growth and yield. WRKY transcription factors play important roles in plant stress responses; however, the functions of many maize WRKY members in waterlogging tolerance remain poorly understood. In this study, we investigated the role of ZmWRKY83 in maize responses to waterlogging. ZmWRKY83 expression was significantly downregulated in maize roots under waterlogging stress. Functional analysis showed that ZmWRKY83-overexpressing lines exhibited growth comparable to that of wild-type plants under normal conditions but more severe growth inhibition and lower shoot and root fresh weights after waterlogging treatment. Physiological analyses further revealed that ZmWRKY83 overexpression impaired adventitious root formation, increased membrane damage, and reduced antioxidant capacity under waterlogging conditions. Transcriptome analysis revealed that the differentially expressed genes were primarily enriched in plant hormone signal transduction, secondary metabolism, and phenylpropanoid biosynthesis. Further investigation identified the auxin-responsive gene ZmIAA7 as a potential downstream target of ZmWRKY83. qRT-PCR, DLR, and Y1H assays indicated that ZmWRKY83 directly binds to the ZmIAA7 promoter and represses its transcriptional activity. Collectively, these findings suggest that ZmWRKY83 negatively regulates maize waterlogging tolerance by suppressing auxin-related responses through ZmIAA7, expanding the regulatory network underlying WRKY-mediated responses to waterlogging in maize. Full article

For the evaluation of the chemical composition of Inula hookeri f. major Ling, ultra-high-performance liquid chromatography quadrupole-Exactive Orbitrap mass spectrometry (UHPLC-Q-Exactive-Orbitrap MS) was integrated with feature-based molecular networking (FBMN) and SIRIUS. The chromatographic separation of the chemical components from Inula hookeri f. major Ling was conducted on a Hypersil GOLD™ aQ C₁₈ (100 mm × 2.1 mm, 1.9 μm) using gradient elution, with a 0.1% formic acid aqueous solution and acetonitrile as the mobile phase. Mass spectrometric analysis was performed in both positive and negative ion modes using an electrospray ionization (ESI) source. Based on the obtained high-resolution fragment ions, FBMN was conducted to enable the clustering and visualization of structurally similar compounds. Molecular formulas were predicted and MS/MS fragment ions were interpreted with the assistance of SIRIUS. A total of 162 compounds were tentatively annotated from Inula hookeri f. major Ling, including terpenoids, phenylpropanoids, fatty acids, organic acids, and other types of compounds. The application of the strategy incorporating UHPLC-Q-Exactive-Orbitrap MS, FBMN, and SIRIUS enables the systematic characterization of the chemical composition of Inula hookeri f. major Ling. Full article

Understanding whether long-term vascular cambium vitality in ancient trees reflects progressive decline or adaptive reprogramming is central to grasping woody plant longevity. We performed an integrative analysis of functional traits, transcriptome profiles, and metabolomic landscapes of cambial zone enriched from 80-, 500-, and 1000-year-old Styphnolobium japonicum trees. With increasing tree age, the vascular cambium showed fewer cell layers, reduced thickness, and lower auxin, gibberellin, and IAA/ABA ratios, whereas bark thickness, malondialdehyde, abscisic acid, jasmonic acid, and salicylic acid contents increased. Transcriptomic and metabolomic analyses revealed that differentially expressed genes and metabolites were primarily enriched in the cell cycle, phytohormone signaling, and phenylpropanoid biosynthesis pathways. Specifically, genes associated with cell division were down-regulated in millennial trees, whereas phenolic acids, flavonoids, and lignin-related metabolites significantly accumulated. Piecewise structural equation modeling suggested associations among tree age, transcription factors, structural genes, metabolites, and cambial functional traits. These results indicate that cambial senescence is not a simple linear decay but a highly coordinated remodeling process, providing crucial evidence for delayed senescence in long-lived woody species. Full article

Background: Imidacloprid, a widely used neonicotinoid insecticide, is routinely applied to control pests in Astragalus membranaceus var. mongholicus, a crucial medicinal herb producing Astragali Radix. However, the early short-term transcriptional and metabolic responses of its seedlings under imidacloprid gradient stress remain poorly characterized. Methods: In this study, 80-day seedlings were subjected to three foliar spray treatments: blank control (CK), the recommended imidacloprid concentration (2000-fold dilution, 475 mg·L⁻¹), and an excessively high concentration (500-fold dilution, 1900 mg·L⁻¹). Leaf samples were harvested 24 h post-treatment for untargeted ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC–MS/MS) metabolomics (6 biological replicates) and RNA-seq transcriptome sequencing (3 biological replicates). Results: The low- and high-dose treatments induced 1076 and 860 differential metabolites and 6818 and 7283 differentially expressed genes, respectively. Flavonoids, saponins, terpenoids, amino acid metabolites, and energy-related pathways were prominently affected. KEGG enrichment indicated activation of flavone/flavonol biosynthesis, phenylpropanoid metabolism, amino acid metabolism, MAPK signaling, cutin/suberin/wax biosynthesis, and ABC transporter pathways, whereas high-dose exposure was associated with stronger changes in genes related to DNA replication and cell wall remodeling. Integrated network analysis highlighted CHS, PAL, MYC2, KCS, and ABCG40 as candidate regulators linking stress signaling, secondary metabolism, and metabolite transport. Conclusions: Seedlings of A. membranaceus var. mongholicus exhibit dose-dependent acute responses to imidacloprid. Moderate pesticide exposure primarily activates defensive secondary metabolism, whereas excessive dosage triggers genome-wide transcriptional reprogramming. This work identifies key metabolic pathways and hub genes, offering candidate molecular markers for investigating pesticide stress adaptation in medicinal Astragalus and guiding standardized pesticide application in cultivation. Full article

Gardenia fruit, a medicinal and edible resource rich in bioactive compounds, faces several limitations, including low extraction efficiency, poor stability, and intense bitterness. In this study, gardenia fruit powder at varying concentrations (2.5%, 5.0%, 7.5%, 10.0%, and 12.5%) was mixed with a kombucha inoculum and fermented for 8 days to develop functional beverages. The results demonstrated that fermentation with gardenia fruit powder effectively supported SCOBY growth. The 5.0% addition of gardenia fruit (G5Fer) produced thicker bacterial cellulose, higher total titratable acidity (10.43 g/L), and increased total polyphenols (37.12 mg GAE/100 mL) after 8 days of fermentation. G5Fer also achieved the highest sensory scores, especially in aroma, flavor, and overall acceptance. Higher doses of gardenia fruit (≥7.5%) caused turbidity, dark color, and strong sourness, leading to lower sensory scores. Non-targeted metabolomics revealed that kombucha fermentation reshaped the metabolic profile, enriching phenolic acids (e.g., gallic acid and caffeic acid) and flavonol glycosides (e.g., kaempferol-3-O-rutinoside) via the biosynthesis of phenylpropanoid pathways while antioxidant activity (DPPH and ABTS⁺ scavenging rate) was well maintained. Overall, G5Fer achieved the best balance among acidity, bioactive compounds, and consumer preference. In conclusion, gardenia fruit represents a promising substrate for developing a functional, palatable kombucha-like beverage, aligning with the growing demand for value-added fermented products. Full article

Qamgur is a widely consumed vegetable and is also used in traditional medicine because of its extensive health benefits. White and yellow are the two main varieties. However, the mechanisms underlying quality development in these varieties, particularly in yellow Qamgur, remain unclear. This study compared nutritional and functional components throughout development. Total phenols and total isothiocyanates showed similar trends and levels in both varieties, whereas total free amino acids showed related but distinct patterns. Yellow Qamgur accumulated significantly higher levels of carotenoids. The integrated use of widely targeted and targeted metabolomics revealed stage-specific metabolites. White Qamgur showed stronger enrichment in secondary metabolite pathways, such as anthocyanin, flavonoid, steroid, terpenoid, and phenylpropanoid biosynthesis. In contrast, yellow Qamgur showed stronger enrichment in primary metabolic pathways, including amino acid biosynthesis. In addition, carotenoid biosynthesis may be the primary pathway responsible for the yellow coloration. Carotenoid profiling revealed that lycopene (28.94 mg/kg) was the predominant carotenoid in yellow Qamgur, followed by violaxanthin, γ-carotene, phytoene, β-cryptoxanthin laurate, and β-carotene. Full article

Cotton damping-off caused by Rhizoctonia solani restricts seedling establishment, and locally adapted biocontrol isolates are potential components of sustainable disease management. This study evaluated Pseudomonas chlororaphis-like isolate M6 and tested whether molecular profiles in M6-protected plants differed from those in Pathogen-infected plants in directions that moved toward Healthy Control levels. Culturable bacteria from root-associated soils were screened against R. solani by dual-culture assays, and M6 was evaluated in a greenhouse cotton damping-off assay. RNA sequencing (RNA-seq) and untargeted liquid chromatography–mass spectrometry (LC–MS) data from Healthy Control, Pathogen-infected, and M6-protected plants at 0 and 7 d were analyzed using the Pathogen-infected versus Healthy Control and M6-protected versus Pathogen-infected contrasts. M6 produced the highest inhibition among the candidate isolates (81.9%). Under greenhouse conditions, the M6-protected treatment had lower disease incidence (22.2% versus 88.9%) and disease index (16.4 versus 76.8) than the Pathogen-infected treatment. At 7 d, the primary false-discovery-rate-controlled analysis identified 4457 transcripts and 1620 LC–MS features for which the change between M6-protected and Pathogen-infected plants was opposite to the pathogen-associated change and the M6-protected group mean was closer to the Healthy Control mean. Additional nominal-p-value-only results were retained as exploratory. The two contrasts involved redox regulation, phenylpropanoid/benzenoid-related metabolism, hormone/defense signaling, protein synthesis and central metabolism. Antioxidant enzyme and quantitative reverse transcription PCR (qRT-PCR) data provided independent support for selected redox- and defense-associated differences. Because pathogen biomass, bacterial colonization and antagonism-deficient mutants were not assessed, the molecular profiles are interpreted as association-based features of the protected state rather than evidence that host recovery caused disease reduction. Most LC–MS annotations are putative and were not confirmed with authentic standards. Full article

Bamboo shoots, as the most nutritionally valuable food source for giant pandas during key reproductive seasons, are critical for conservation because their availability and timing directly influence panda foraging and habitat use. However, the molecular mechanisms through which altitudinal temperature variation governs rhizome shooting in staple food bamboos remain largely unknown. Here, we performed integrated metabolomic and transcriptomic analyses of Fargesia rufa rhizomes collected along an elevational gradient (1000 m, 1500 m, and 2000 m), with a critical paired comparison at 2000 m between a non-shooting cold gully-edge site (16.4 °C) and a shooting warm gully-center site (21.1 °C), where soil temperature is elevated by approximately 4 °C due to prolonged solar exposure. Our results demonstrate that soil temperature, rather than elevation per se, acts as the primary driver of rhizome shooting, with an apparent threshold near 20 °C. A core shooting metabolome (CSM) comprising 843 metabolites was consistently accumulated across all shooting conditions, which featured gibberellin/auxin precursors, TCA cycle intermediates, and phenylpropanoid compounds. Correspondingly, a core shooting transcriptome (Rh_shooting) of 10,970 genes was identified, which resolved into three functionally distinct temporal clusters: “shooting-on” (activated upon threshold crossing, enriched in hormone signaling and cell wall metabolism), “temperature-dose” (progressively upregulated with rising temperature, enriched in energy metabolism and defense), and “microenvironment-enhanced” (specifically upregulated in the high-elevation warm gully, enriched in photosynthesis and antioxidant pathways). Integrative network analysis further revealed zeatin riboside and multiple hub genes as central coordinators linking hormone signaling, energy metabolism, and cell wall remodeling. Collectively, these findings establish a molecular framework linking altitudinal temperature variation to bamboo rhizome regeneration—a process that directly determines the spatiotemporal availability of bamboo shoots for giant pandas. This work provides mechanistic insights into giant panda foraging ecology and has direct implications for predicting habitat quality under climate change and informing evidence-based conservation strategies for this flagship species and its critical food resource. Full article

Tephritid flies, highlighting Anastrepha fraterculus and Ceratitis capitata, cause substantial economic losses and trigger strict quarantine measures worldwide. In response, research is looking for eco-friendly alternatives and, in this study, we evaluated 7 terpenes/terpenoids (α-pinene, β-pinene, β-caryophyllene, γ-terpinene, ρ-cymene, citronellal and geropine) and 3 phenylpropanoids (isoeugenol, methyl cinnamate and coumarin) commonly found in a diverse group of aromatic plants tested against A. fraterculus and C. capitata adults. Subsequently, their selectivity for the egg–larvae endoparasitoid Doryctobracon areolatus was also assessed. Ingestion and topical application bioassays (range = 100–6000 mg L⁻¹) revealed that isoeugenol caused the highest mortality (≥75%) in both fruit fly species. Concentration–response indicated a similar toxicity of this compound to A. fraterculus (ingestion: LC₅₀ ≅ 34.2 mg L⁻¹, LC₉₀ ≅ 105.7 mg L⁻¹; topical: LC₅₀ ≅ 33.7 mg L⁻¹, LC₉₀ ≅ 121.3 mg L⁻¹) and C. capitata (ingestion: LC₅₀ ≅ 33.2 mg L⁻¹, LC₉₀ ≅ 125.5 mg L⁻¹; topical: LC₅₀ ≅ 31.4 mg L⁻¹, LC₉₀ ≅ 129.2 mg L⁻¹). None of the tested compounds (α-pinene, β-pinene, ρ-cymene, β-caryophyllene, isoeugenol, γ-terpinene, coumarin, citronellal, geropine and methyl cinnamate) reduced the number of oviposition punctures on grape berries by either fruit fly species. In contrast, all compounds caused lower mortality in D. aerolatus (≤17%) and did not impair parasitism, with a range of 43.21–62.13% among the tested compounds. Overall, our findings indicate that selected phytocompounds, particularly isoeugenol and citronellal, show strong insecticidal activity against A. fraterculus and C. capitata while having low toxicity to D. areolatus, supporting their use into sustainable pest management programs. Full article

Verticillium dahliae is a devastating soil-borne fungal pathogen that causes severe yield losses in melon (Cucumis melo L.) and other crops. Identifying novel resistance genes is crucial for sustainable disease management. In this study, we characterized the function of CmVQ23, a candidate gene previously identified through QTL mapping, in mediating defense against V. dahliae using heterologous expression in Arabidopsis thaliana. Subcellular localization assays revealed that the CmVQ23-eGFP fusion protein predominantly localized to the nucleus, consistent with its predicted role as a co-factor of transcription factor. Upon V. dahliae inoculation, CmVQ23-overexpressing Arabidopsis lines exhibited significantly reduced disease indices and restricted fungal proliferation compared with wild-type and mutant plants, although these lines displayed altered vegetative growth, including delayed bolting and reduced plant height. Mechanistically, CmVQ23 overexpression promoted reactive oxygen species (ROS) accumulation and hypersensitive response (HR)-mediated cell death at infection sites, as evidenced by intensified DAB and trypan blue staining. Furthermore, transgenic lines maintained higher photosynthetic efficiency, enhanced antioxidant enzyme activities, and increased lignin deposition via upregulation of phenylalanine ammonia-lyase (PAL) and polyphenol oxidase (PPO). Notably, CmVQ23 overexpression markedly upregulated both salicylic acid (SA)- and jasmonic acid/ethylene (JA/ET)-responsive marker genes, including AtPR1, AtPR2, AtPR5, AtPAD4, AtPDF1.2, and AtVSP2 upon infection. Collectively, these findings demonstrate that CmVQ23 functions as a positive regulator of resistance to Verticillium dahliae by orchestrating ROS/HR-mediated cell death, antioxidant defense, phenylpropanoid pathway activation, and phytohormone signaling crosstalk, offering a promising genetic resource for improving Verticillium wilt resistance in crops. Full article

Background and Objectives: Baccharis dracunculifolia DC. (Asteraceae), the main botanical source of Brazilian green propolis, is recognized for its high content of bioactive secondary metabolites. Given this potential, this study aimed to characterize the chemical profile of the crude extract (CE) from the aerial parts of B. dracunculifolia and to investigate its anti-inflammatory, antiproliferative, antioxidant, and photoprotective properties. Predictive computational analyses were used to assist the interpretation of the experimental findings. Methods: The CE was obtained by dynamic maceration with ethanol and chemically characterized by UHPLC-MS/MS using external calibration curves. Anti-inflammatory activity was evaluated by inhibiting nitric oxide (NO) in RAW 264.7 macrophages, while cellular antioxidant activity (CAA) was determined in the same model. Antiproliferative activity was evaluated against the human tumor cell lines AGS, Caco-2, MCF-7, and NCI-H460, as well as non-tumor VERO cells. Additionally, antioxidant potential was investigated using classical colorimetric methods (DPPH, FRAP, and ABTS). The extract was also quantified for total phenolic and flavonoid content, as well as sun protection factor (SPF). Furthermore, complementary computational analyses included PASS prediction, SwissTargetPrediction, Gene Ontology enrichment using PANTHER, SwissADME profiling, and toxicity prediction with ProTox-III. Results: UHPLC-MS/MS analysis revealed a profile rich in flavonoids and phenolic acids and led to the identification of 14 compounds not previously reported in B. dracunculifolia according to the literature examined, notably the flavonoid morin and the phenylpropanoid coniferaldehyde detected at comparatively high concentrations (>600 µg/g). CE inhibited NO production (IC₅₀ = 62.00 µg/mL) suggesting anti-inflammatory activity, and reduced intracellular oxidation by 81% (at 2000 µg/mL) in RAW 264.7 macrophages. The extract showed total phenolic content (83.62 to 540.40 µg gallic acid equivalents/mg of CE) and high levels of flavonoids (472.00–515.00 µg quercetin equivalents/mg of CE), antioxidant activity in the DPPH assay (IC₅₀ = 0.86 mg/mL), and relevant photoprotective potential (SPF = 7.79–19.30). Antiproliferative activity was moderate to weak (GI₅₀ = 165.00–257.00 µg/mL). In silico analyses identified predicted activities, molecular targets, and enriched biological processes related to redox homeostasis, inflammation, apoptosis, and cellular responses to UV radiation, suggesting biological functions potentially associated with the identified metabolites. Conclusions: The crude extract of B. dracunculifolia demonstrated significant cellular anti-inflammatory and antioxidant activities, likely associated with its phenolic composition and the presence of metabolites reported in this study for the first time in this species, particularly morin and coniferaldehyde. These findings expand the phytochemical knowledge of B. dracunculifolia and reinforce its potential as a source of bioactive compounds for pharmaceutical, nutraceutical, and photoprotective applications. Full article

Background: Anthocyanin accumulation is a developmentally regulated trait shaped by complex interactions between metabolic and transcriptional networks. However, dissecting the regulatory mechanisms underlying anthocyanin biosynthesis is often complicated by confounding variation in plant growth and environmental conditions. Methods: Here, we used a time-resolved multi-omics approach to investigate anthocyanin accumulation in maize seedlings by comparing an anthocyanin-rich inbred line PH19401 with an anthocyanin-deficient line YPX across five developmental stages. Results: Untargeted metabolomic and transcriptomic profiling revealed progressive divergence between the two lines beginning at early development stages. Using a dual-line, intersection-based filtering strategy, we identified a refined set of metabolites and genes closely associated with anthocyanin accumulation. These candidates were enriched in pathways related to phenylpropanoid metabolism, energy metabolism, and redox regulation. Weighted gene co-expression network analysis (WGCNA) identified two transcriptional modules that showed opposing associations with anthocyanin content. The positively associated module was centered on MYB transcription factors, consistent with canonical regulation of flavonoid biosynthesis, whereas the negatively associated module was enriched in genes involved in primary metabolism and signaling. Integration of transcriptomic and metabolomic datasets further revealed coordinated relationships between MYB hub genes and flavonoid intermediates, linking transcriptional regulation with metabolic output. Together, these results support a model in which anthocyanin accumulation is associated with activation of MYB-centered transcriptional programs and broader metabolic reprogramming that enhances precursor supply and redox balance, while competing transcriptional programs favor primary metabolism. Conclusions: This study provides a systems-level perspective on anthocyanin biosynthesis in maize seedlings and establishes an analytical framework for dissecting developmentally regulated metabolic traits. Full article