Search Results (295)

A major Chinese woody oil plant with unsaturated-fatty-acid-rich seeds for biodiesel and edible oil, Xanthoceras sorbifolium tolerates drought but not waterlogging; salicylic acid (SA), a key stress response signal, is inexpensive, safe, and effective for enhancing stress tolerance. Two-year-old saplings of Xanthoceras sorbifolium were used as materials. They were sprayed with 0.5 mmol·L⁻¹ SA for 3 days (based on prior studies), and then waterlogged for 10 days; physiological and transcriptomic data were collected. SA significantly increased height, diameter, and root dry weight by 392.6%, 450.0%, and 242.4% compared to water control; enhanced osmotic regulatory substances, antioxidant enzyme activities, secondary metabolites, and root activity; and reduced malondialdehyde content and relative electrical conductivity by 23.40% and 148.7%. SA-enhanced antioxidant defense correlated with synergistic transcriptional regulation. Transcriptome analysis showed that SA up-regulated key enzyme genes involved in flavonoid synthesis, such as PAL and 4CL, and regulated hormone signal transduction-related genes such as SAUR and DELLA. Key transcription factor genes were also screened, mainly including members of the MYB, bHLH, and ERF families. SA alleviated waterlogging damage. Meanwhile, this study provides valuable insights into the molecular basis of the response to waterlogging stress regulated by salicylic acid, and offers important theoretical and practical significance for the promotion and cultivation of Xanthoceras sorbifolium in rainy southern regions of China. Full article

Plants must continuously balance the trade-offs between growth and defense, a constraint that is exacerbated by biotic and abiotic stresses, particularly when they occur together. Ethylene (ET) serves as a central, integrative regulatory node controlling this by linking developmental programs to stress-responsive signaling networks. Advances at the molecular and systems levels have revealed that ET mediates the redistribution of metabolic resources via coordinated regulation of its synthesis, perception, and downstream signaling. The ETR (Ethylene Receptor)-CTR1 (Constitutive Triple Response 1)-EIN2 (Ethylene Insensitive 2)-EIN3(Ethylene Insensitive 3) signaling module lies at the core of this network, integrating multiple hormonal pathways. Through dynamic crosstalk with jasmonic acid (JA), salicylic acid (SA), abscisic acid (ABA), auxin (AUX), and gibberellins (GA), ET enables the fine-tuned coordination of growth inhibition, immune activation, and stress acclimation in response to environmental fluctuations. Processes such as induced systemic resistance, programmed cell death, and architectural plasticity further reinforce this regulatory framework, with ethylene-responsive transcription factors, including ERFs (ethylene responsive factor gene family) and WRKYs, acting as critical convergence points. Emerging insights into ACC (1-aminocyclopropane-1-carboxylic acid)-dependent signaling, chromatin remodeling, and tissue-specific regulation expand the functional scope of ET beyond traditional hormone paradigms. At the same time, the ability of pathogens to manipulate ET signaling underscores its dual role in both promoting immunity and facilitating susceptibility. By integrating molecular, physiological, and ecological perspectives, this review highlights ET as a central coordinator of plant stress resilience and growth optimization, providing a unifying framework for understanding how plants adapt to complex and dynamic environments. Full article

Tree peony (Paeonia suffruticosa Andr.) is a traditional ornamental plant of high economic and cultural value, but its flower longevity is often limited by petal water loss. Cuticular wax serves as an essential barrier against non-stomatal water loss, and the AP2/EREBP (APETALA2/Ethylene-Responsive Element Binding Protein) transcription factor family is known to regulate wax biosynthesis. However, little information is available on the roles of AP2/EREBP genes in petal cuticle formation in tree peony. In this study, we performed transcriptome sequencing on petals of the tree peony cultivar ‘Bai Wang Shi Zi’ at three developmental stages (early, middle, and late). Using the assembled transcriptomic data, we identified 29 high-confidence AP2/EREBP family members, which were phylogenetically classified into AP2, ERF, and DREB subfamilies. Expression profiling revealed that 18 of these genes exhibited stage-specific expression patterns during petal development. Among them, two homologs of Arabidopsis SHN1 (SHINE 1) and WRI3 (WRINKLED 3), designated PsSHN1 and PsWRI3, showed peak expression at the middle stage. By co-expression analysis and phylogenetic comparison, three downstream candidate genes were identified and named PsCER2, PsKAS1, and PsLTPG1, based on their homology with known wax-related genes. Dual-luciferase reporter assays indicated that PsSHN1 and PsWRI3 can activate the promoters of PsCER2, PsKAS1, and PsLTPG1, suggesting a possible cooperative regulation of cuticle formation. Collectively, our findings provide promising candidate genes for prolonging floral lifespan by improving petal cuticular wax accumulation, and lay a preliminary foundation for molecular breeding and quality improvement of tree peony and other ornamental flowers. Full article

Salt stress is a major abiotic stress that threatens citrus yield and quality. To elucidate the molecular mechanisms underlying differential salt tolerance in citrus rootstocks, we performed an integrative transcriptomic and metabolomic analysis of salt-sensitive trifoliate orange (Poncirus trifoliata) and salt-tolerant Goutoucheng (Citrus aurantium) under 60 mM NaCl treatment for 12 h and 24 h. Physiological observations confirmed that Goutoucheng exhibited less growth inhibition and leaf damage than trifoliate orange. Transcriptome sequencing identified 2081 and 1588 differentially expressed genes (DEGs) in trifoliate orange at 12 h and 24 h, respectively, compared with 1166 and 997 DEGs in Goutoucheng. Metabolome profiling revealed 217 and 173 differentially accumulated metabolites (DAMs) in trifoliate orange versus 162 and 239 DAMs in Goutoucheng at the two time points. KEGG pathway analysis showed that DEGs were mainly enriched in the Mitogen-activated protein kinase (MAPK) signaling pathway—plant, plant hormone signal transduction, and flavonoid biosynthesis—and DAMs were mainly enriched in flavonoid biosynthesis, starch and sucrose metabolism, and glutathione metabolism. Integrative nine-quadrant and two-way orthogonal partial least squares analyses further pinpointed flavonoid biosynthesis as a central hub in salt response. Notably, quercetin derivatives accumulated preferentially in the salt-tolerant rootstock Goutoucheng. Several transcription factor families—including HSF, MYB, NAC, HB-HD-ZIP, C2H2, bHLH, AP2/ERF, and Trihelix—may enhance antioxidant capacity under salt stress by regulating flavonoid accumulation. Collectively, these results indicated that coordinated regulation of flavonoids contributed critically to salt stress adaptation in citrus rootstocks. The identified DEGs, DAMs, and transcription factors provide candidate targets for genetic improvement of salt tolerance in citrus. Full article

Gerbera hybrida, a model plant for studying the development and evolution of complex inflorescences, has been recognized as a valuable source of colorants and natural coatings. Previously, we demonstrated that inoculation with Piriformospora indica, an endophytic fungus, could enhance the resistance of gerbera to Phytophthora cryptogea, which causes root rot disease. Here, to dissect the underlying molecular mechanism, comparative transcriptomic analyses of gerbera roots from P. indica-colonized (PI), P. cryptogea-inoculated (PC), and P. cryptogea-inoculated P. indica-colonized (PP), along with the non-inoculated control (CK) groups were conducted. In total, we identified 15,763 differentially expressed genes (DEGs) among CK vs. PI, CK vs. PC, and PI vs. PP comparisons, together with PC vs. PP comparisons. Of them, 743 DEGs encode transcription factor (TF) proteins, with the AP2/ERF family members occupying the majority. An ERF gene (GhERF) was identified as one of the 30 common DEGs among the four comparisons. Notably, its transient overexpression in tobacco leaves reduced the lesion area caused by P. cryptogea inoculation to 65.36% of the empty vector control. Many defense response- and secondary metabolism-related DEGs were expressed higher in the PP group than in the PC group. Moreover, P. indica-colonization up-regulated the expression of hormone signaling- and MAPK signaling-related genes, thereby activating the defense responses against the pathogen infection. Our study is helpful for understanding the molecular mechanism underlying P. indica-enhanced root rot resistance in gerbera. Full article

Background/Objectives: Sunflower (Helianthus annuus L.) is one of the four major oil crops worldwide and possesses strong stress tolerance. However, salt stress remains limiting in the improvement of sunflower yield and quality. Methods: In this study, the salt-tolerant cultivar P50 and salt-sensitive cultivar P29 were used as experimental materials to conduct transcriptome sequencing on root and leaf samples treated with NaCl. Subsequently, the molecular mechanisms underlying salt tolerance in sunflower were revealed through assembly and splicing, functional annotation, differential expression analysis, enrichment analysis, and transcription factors (TFs) prediction. Results: Results showed that 54,860,184 and 60,601,572 high-quality clean reads were obtained from the two cultivars, respectively. A total of 110,751 all-unigenes were generated after assembly and clustering, of which 77,536 were functionally annotated. A total of 21,332 differentially expressed genes (DEGs) were identified, including 10,306 upregulated and 11,026 downregulated genes. Quantitative real-time PCR validation of 15 DEGs showed a 93.33% consistency rate with the sequencing data. GO enrichment analysis indicated that DEGs were significantly enriched in pathways related to antioxidant enzyme activities. KEGG enrichment analysis demonstrated that DEGs were primarily involved in 15 carbohydrate metabolism pathways, especially starch and sucrose metabolism. In addition, 67 differentially expressed TF families containing 528 DEGs were identified, including bHLH, AP2/ERF-ERF, MYB, C3H, WRKY, EREBP, B3-ARF, and NAC. Conclusions: Our study constructed a comprehensive transcription map of the sunflower response to salt stress and systematically elucidated the molecular mechanisms underlying salt tolerance. The salt-tolerant sunflower cultivar P50 exhibits an efficient salt stress defense system via three core strategies: (i) activating the antioxidant system to rapidly scavenge excess reactive oxygen species and mitigate oxidative damage; (ii) regulating carbohydrate metabolism through starch and sucrose redistribution to provide energy and osmotic protection against physiological drought; and (iii) mobilizing multiple TF families to establish a complex regulatory network for the precise control of downstream functional genes. Full article

Intensifying drought stress under global climate change poses a significant threat to woody plants, highlighting the critical need to identify key genes conferring drought tolerance. Here, we characterized PsnSAUR6, a Small Auxin Upregulated RNA (SAUR) family gene from poplar (Populus simonii × P. nigra) that is responsive to drought and abscisic acid (ABA). Overexpression of PsnSAUR6 in transgenic tobacco conferred superior drought tolerance, evidenced by increased biomass, enhanced root elongation, improved stomatal regulation, and favorable physiological responses, including higher proline content and peroxidase (POD) activity but lower malondialdehyde (MDA). Transcriptome analysis revealed that under water deficit, PsnSAUR6 suppressed the ABA negative regulator PP2C37 while upregulating key antioxidant defense-related transcription factors (ERF020, NAC83, MYB2) and the potassium transporter HAK5. Collectively, these findings establish PsnSAUR6 as a positive regulator in ABA-mediated drought adaptation, presenting it as a promising genetic target for enhancing the climate resilience of woody plants. Full article

Dihydroflavonol 4-reductase (DFR) plays a pivotal role in regulating flavonoid and anthocyanin biosynthesis, governing the accumulation of plant secondary metabolites. This study aimed to characterize the DFR gene family in Ginkgo biloba and elucidate the function of the predominant gene GbDFR2 in the flavonoid metabolic network. Through transcriptome analysis, three differentially expressed GbDFR genes were identified. Bioinformatic analysis revealed that all three GbDFR proteins are hydrophilic and acidic and belong to the NADB_Rossmann superfamily. RT-qPCR analysis of different tissues of ginkgo revealed that all three GbDFR genes exhibited the highest expression levels in the leaves. An overexpression vector of GbDFR2 was constructed and stably transformed into Nicotiana benthamiana. Metabolomic and qPCR analyses showed that heterologous GbDFR2 expression significantly remodeled the flavonoid profile, upregulating sakuranetin and 3,7-Di-O-methylquercetin while downregulating narcissin and naringenin chalcone. Additionally, it upregulated endogenous NbCHI and NbDFR, and suppressed the transcription factors NbMYL2b and NbERF4a. These findings suggest that GbDFR2 can act as a regulator of flavonol biosynthesis and provide a candidate gene for the metabolic engineering of flavonoids in woody plants. Full article

Background/Objectives: Environmental conditions in natural and cultivation-managed habitats strongly influence plant physiology and medicinal quality. However, the molecular mechanisms underlying metabolic differentiation in Anoectochilus roxburghii remain poorly understood. This study aimed to elucidate the metabolic and transcriptional differences between wild and cultivated A. roxburghii and to identify the regulatory mechanisms driving habitat-associated variation in metabolite profiles. Methods: We applied integrated non-targeted metabolomics and transcriptomics to compare metabolic profiles and gene expression in the leaves and stems of 15-month-old wild and cultivated A. roxburghii plants. Gene–metabolite correlation analysis was performed to identify coordinated correlation networks associated with key biosynthetic pathways. Results: Our analyses revealed clear differences in metabolite composition and transcriptional patterns between habitat types, suggesting distinct strategies of metabolic resource allocation. Wild plants showed significant enrichment of amino acids and other primary metabolites, whereas cultivated plants accumulated higher levels of flavonoids. Gene–metabolite correlation analysis indicated that multiple flavonoid metabolites were closely associated with key structural genes, including F3H, C12RT1, and HHT1, forming a tightly connected correlation network. In addition, several transcription factor families, including MYB, bHLH, WRKY, and AP2/ERF, showed strong correlations with genes involved in the flavonoid pathway, suggesting that flavonoid accumulation in cultivated plants may be associated with coordinated transcriptional control. Conclusions: Taken together, these findings suggest that habitat conditions are associated with differences in metabolic networks and resource allocation in A. roxburghii. This work provides new insight into the metabolic plasticity of this medicinal plant and highlights potential factors associated with molecular mechanisms that may contribute to variation in medicinal quality. Full article

ERF/AP2 is a family of transcription factors that plays a broad role in plant growth and development and in responses to various environmental stresses. In our previous studies, we found that the transcription factor LoERF4 indirectly induces the breaking of dormancy in lily bulbs by regulating its downstream gene, LoXTH23. To further investigate the function of LoERF4, we overexpressed it in Arabidopsis thaliana. Paraffin section analysis revealed that root cells in OE-LoERF4 transgenic Arabidopsis thaliana lines exhibited significantly longer average cell lengths compared to the wild type. In the overexpression lines, the expression of multiple modified genes, including AtXTHs and AtEXPAs was significantly upregulated, and these lines exhibited earlier lateral root emergence and a significant increase in primary root length. Under 100 mM sodium chloride treatment, the overexpression lines exhibited significantly higher numbers of lateral roots, true leaves, and primary root length compared with the wild type (WT). In the OE-LoERF4 line, antioxidant enzyme (SOD, POD, CAT) activity was enhanced, oxidative damage was reduced (decreased MDA content), and root survival rate was improved (as reflected by TTC reduction). This confirms that LoERF4 may promote root development in the overexpression line by positively regulating downstream AtXTHs and AtEXPAs, while simultaneously enhancing the salt tolerance of the overexpression line. Full article

Cotton Verticillium wilt seriously threatens global cotton production, necessitating the development of resistant cultivars through molecular breeding. Members of the ethylene response factor (ERF) family function as pivotal transcriptional regulators of the ethylene signaling pathway, orchestrating plant defensive responses against pathogen invasion. Here, through comprehensive phenotypic and transcriptional analyses of lignin biosynthesis genes in AtERF49-overexpressing lines, loss-of-function mutants, dominant repressor plants, and GhERF49-silenced cotton plants (TRV-VIGS), we demonstrate that AtERF49 functions as a negative regulator of Verticillium wilt resistance. Overexpression of AtERF49 significantly compromised defense responses in Arabidopsis thaliana, whereas GhERF49 silencing enhanced cotton resistance to Verticillium wilt. Transcription analysis showed that ERF49-mediated susceptibility correlates with suppression of lignin biosynthesis-related genes following pathogen challenge, suggesting that ERF49 interferes with inducible cell wall fortification. These findings elucidate a previously unrecognized negative regulatory node linking ethylene signaling to lignin-mediated disease resistance, providing promising biotechnological targets for engineering durable Verticillium wilt resistance in cotton and related crops. Full article

Epimedium brevicornu is an important medicinal plant in China, whose main bioactive components are flavonoid glycosides. UDP-glycosyltransferases (UGTs) play key roles in flavonoid glycosylation and metabolic diversification. In this study, transcriptome data from four representative production regions in Gansu Province were used to systematically identify and analyze the UGT gene family in E. brevicornu. A total of 359 UGT members were identified, and 168 homologous genes with clear expression evidence were obtained from four geographical populations. Molecular evolutionary analysis showed that most UGT genes were under purifying selection, whereas UGT2, UGT52, UGT57, UGT241, UGT269, and UGT271 exhibited significant signals of positive selection in specific lineages (p < 0.05). Protein interaction analysis indicated that many UGT proteins were closely associated with key enzymes involved in flavonoid biosynthesis, including CHS (TT4), CHI (TT5), F3H, FLS, and DFR, suggesting their potential involvement in flavonoid metabolism. Promoter analysis further revealed a high enrichment of ERF (11,169 occurrences) and MYB (7673 occurrences) transcription factor binding sites in the upstream regions of UGT genes. In addition, UGT57 and UGT241 showed significantly higher expression levels in the QLH population. Molecular docking analysis indicated relatively strong binding affinities with quercetin, with binding energies of −7.23 kcal/mol and −4.62 kcal/mol, respectively. These results suggest that the sequence variation and differential expression of UGT genes may be associated with flavonoid glycosylation and ecological adaptation in Epimedium. This study provides a basis for understanding the evolutionary characteristics and expression patterns of the UGT gene family and offers candidate genes for future studies on flavonoid metabolism. Full article

DREB (Dehydration-Responsive Element-Binding Protein) transcription factors are a subfamily of the AP2/ERF transcription factor family and play a crucial role in the regulation of plant responses to abiotic stress. In this study, we successfully cloned the IbDREB1d gene from the leafy sweet potato cultivar Fucaishu18. The open reading frame (ORF) of the IbDREB1d gene comprises 792 base pairs and encodes a protein consisting of 263 amino acids. Protein sequence analysis indicates that IbDREB1d is characterized by acidic, hydrophilic, and unstable properties, with its closest phylogenetic relationships to Ipomoea trifida and Ipomoea triloba. Quantitative real-time PCR (RT-qPCR) analysis revealed that IbDREB1d is expressed in the roots, stems, and leaves of sweet potato, with increased expression under low temperature, hydrogen peroxide (H₂O₂), and drought conditions. Overexpression of IbDREB1d in sweet potato resulted in transgenic plants exhibiting dwarfism, shortened internode lengths, smaller leaf size, and microscopic evidence of impaired vascular tissue development. Hormonal analysis indicated significant reductions in the levels of indole-3-acetic acid, indole-3-butyric acid, salicylic acid, and zeatin in these transgenic plants. These decreases may explain the observed phenotypic changes, such as inhibited growth and reduced leaf size. This study provides novel theoretical insights into the role of IbDREB1d in stress-responsive expression and modulating plant growth in sweet potato. Full article

Salt, drought and freezing stress were major abiotic factors limiting plant growth, development and yield. Halostachys caspica (Amaranthaceae), a halophyte native to saline-arid desert regions, tolerated multiple abiotic stresses, but its molecular mechanisms of stress tolerance remain unclear. By integrating the small RNA library and transcriptome data of H. caspica under high salinity, HcmiR172e was identified as a differentially expressed miRNA and selected for the study of multiple abiotic stress responses. Using its mature sequence (20 nt) to align with upregulated genes from the transcriptome, HcTOE3 (AP2 subfamily transcription factor belonging to the AP2/ERF family) was preliminarily predicted as its target gene through bioinformatic analysis. Our previous work demonstrated that HcTOE3 was strongly upregulated by multiple abiotic stresses, including salinity, drought, heat and low temperature. Furthermore, overexpression of HcTOE3 conferred freezing tolerance to Arabidopsis throughout the entire growth period. In this study, miRNA expression analyses showed that HcmiR172e was significantly downregulated in the assimilating branches of H. caspica under low temperature, heat, salt, drought, oxidative stress and abscisic acid (ABA) application. Tobacco transient expression assays and 5′RLM-RACE confirmed that HcmiR172e directly cleaved HcTOE3 transcripts in the region close to the 5′end of the ORF. HcmiR172e-overexpressing Arabidopsis displayed increased sensitivity to salt, drought, freezing stresses and ABA treatment, along with enhanced growth inhibition, elevated reactive oxygen species (ROS) accumulation, decreased osmolyte content and downregulation of stress-responsive genes. In contrast, HcTOE3-overexpressing Arabidopsis exhibited the opposite phenotypes, physiological responses and corresponding gene expression patterns under multiple stress treatments. These findings collectively elucidated the antagonistic regulatory roles of HcmiR172e and HcTOE3 in plant abiotic stress responses, providing novel molecular targets for engineering stress-tolerant crops for saline, arid, freezing environments. Full article

Cold stress limits sorghum productivity, yet the temporal organization of its molecular response remains incompletely understood. In this study, a multi-layered transcriptomic approach was employed to analyze the cold response of sorghum across 6 h, 12 h, and 24 h. By integrating differential expression, weighted gene co-expression network analysis (WGCNA), and alternative splicing (AS) profiling, a phase-dependent regulatory model was proposed. Quantitatively, the network was initially resolved into 17 co-expression modules, which were subsequently consolidated into 10 final modules. A core set of 147 transcription factors (predominantly AP2/ERF and NAC families) was consistently associated with the response across time points. During the early shock phase (6 h), the broad repression of energy-associated transcripts suggests rapid intracellular stabilization. The transition phase (12 h) was characterized by transcriptomic shifts suggestive of chromatin-level regulation and post-transcriptional adjustments. By late acclimation (24 h), the reorganization of stress-associated modules indicates a progression toward a stabilized regulatory state. Furthermore, the identification of dynamic AS events across multiple regulatory families suggests that isoform diversification is a crucial parallel regulatory layer. Moving beyond static expression profiling, this study provides a comprehensive temporal framework of sorghum cold acclimation and identifies phase-specific candidate genes for future experimental validation in C4 crops. Full article