Search Results (821)

Biological invasions threaten tropical biodiversity, yet the molecular mechanisms underlying successful invaders remain poorly understood. Thunbergia alata (Black-eyed Susan) is an aggressive “genomic orphan” invader in Andean forests, causing significant ecological disruption. This study contributes as one of the few transcriptomic profiles of light vs. shade responses in T. alata, providing a foundational molecular resource for this species. We performed differential expression analysis under varying light conditions, revealing a massive transcriptomic shift involving over 4000 differentially expressed genes. Our findings suggest a robust and stable homeostatic adaptation mechanism, characterized by the up-regulation of SnRK1 subunits for energy sensing and strategic management of Reactive Oxygen Species (ROS) within the thylakoid membrane. Furthermore, the fine-tuning of PIF/Auxin modules and the condition-specific induction of NAC and WRKY transcription factors facilitate shade avoidance and rapid vertical growth. The identification of a substantial reservoir of species-specific “not classified” genes suggests that novel genetic elements contribute to T. alata’s adaptive success. By elucidating these key regulatory networks, this research provides an important genomic baseline for future studies on adaptive evolution and the development of molecularly informed strategies for managing and controlling this invasive species in new environments. Full article

Perilla (Perilla frutescens) is an important oil-bearing crop rich in α-linolenic acid (ALA), and seed oil quality varies greatly among different germplasms. However, the molecular and metabolic mechanisms underlying genotypic differences in ALA accumulation remain unclear. In this study, four Perilla varieties with distinct seed phenotypic traits were used to investigate the variations in seed quality, metabolome, and transcriptome. Significant genotypic differences were observed in seed color, thousand-grain weight, and oil content. QO8 showed the highest seed oil content, while QS5 and QO10 exhibited relatively lower oil accumulation levels. Metabolome analysis revealed that lipid metabolism was the dominant metabolic category in Perilla seeds. Multiple differentially accumulated metabolites (DAMs), including ALA, stearic acid, traumatic acid, and 10-OPDA, displayed genotype-specific accumulation patterns. KEGG enrichment demonstrated that α-linolenic acid metabolism and unsaturated fatty acid biosynthesis were the most significantly divergent pathways among different Perilla germplasms. Transcriptome analysis identified numerous differentially expressed genes (DEGs) involved in fatty acid and ALA biosynthesis, such as FAD2, LOX, AOS, AOC, OPR, KAT, ECH, and ACOX. Integrated transcriptome and metabolome analysis further confirmed that the differential expression of structural genes altered the metabolic flux of the ALA and downstream jasmonic acid pathway, resulting in varied accumulation of core lipid intermediates. In addition, WRKY and MYB transcription factors were identified as key upstream regulators that positively or negatively modulated ALA metabolic homeostasis. This study systematically clarified the phenotypic, metabolic, and transcriptional differences in seeds of different Perilla varieties and revealed the core regulatory network of ALA biosynthesis. These findings provide valuable candidate genes and a theoretical foundation for elucidating the molecular mechanism of high ALA accumulation and quality improvement in Perilla seeds. Full article

Green tea quality is largely determined by the metabolite profile of fresh leaves. However, the time-of-day-dependent dynamics of these metabolites remain largely unknown in Xinyang Maojian (XYMJ), a premium Chinese green tea. In this study, we performed the first integrative transcriptomic and metabolomic analysis of Camellia sinensis cv. Xinyang 10 shoots (one bud and one leaf) sampled at 7:00, 13:00, and 18:00 under field conditions with light intensities of 19.2, 113, and 5.4 klx, respectively. We identified 525 differentially accumulated metabolites and 19,767 differentially expressed genes exhibiting distinct time-of-day-dependent patterns. Physiological measurements confirmed significant fluctuations in starch, soluble sugars, chlorophyll, relative water content, and polyphenols throughout the daytime. A key finding was a daytime carbon allocation trade-off: primary metabolism (starch biosynthesis, glycolysis, TCA cycle) peaked at 13:00, whereas secondary metabolism (flavonoids, theaflavins, phenolic acids, anthocyanins) dominated at 18:00, supported by strong negative correlations between primary and secondary metabolic modules. Chlorophyll and oligomeric catechins peaked at 7:00; theaflavins at 13:00; and starch, soluble sugars, theanine, and organic acids at 18:00. Light-responsive transcription factors (bZIP, NF-Y, HD-Zip, SPL, ARF, MADS) and other regulators (MYB, AP2/ERF, WRKY, NAC, GRAS, bHLH) exhibited time-specific expression, sequentially modulating flavonoid, caffeine, and theanine biosynthesis, along with specific gene modules including SS3/SS4 (starch synthesis), BAM3 (starch degradation), FBA1 (carbon fixation), CYP72A219 (terpenoid metabolism), and L7A (theaflavin biosynthesis). Evening-harvested leaves accumulated higher levels of theanine (umami) and soluble sugars (sweetness), whereas morning leaves were enriched in astringent catechins and flavonols. This multi-omics dissection of time-of-day-dependent metabolism in XYMJ tea provides a scientific basis for time-of-day harvesting strategies and graded processing of tea products. Full article

Annamocarya sinensis is a Plant Species with Extremely Small Populations (PSESP) of great ecological and research value. Water conditions serve as a key environmental factor that profoundly shapes its growth, physiological homeostasis and stress adaptation. WRKY transcription factor families constitute the core molecular regulatory modules orchestrating plant responses to water-related stresses and environmental fluctuations. This study performs a systematic identification and bioinformatics analysis of the WRKY gene family in A. sinensis, combined with RT-qPCR to verify and analyze its expression patterns under water stress. The results identified a total of 92 WRKY genes unevenly distributed across 16 chromosomes, classified into three distinct subfamilies with obvious conservation of conserved motifs; the gene promoters were enriched with drought cis-elements, and fragment duplication drove the expansion of the family; this family had a high collinearity with the homologous genes of Arabidopsis thaliana, and its evolutionary function was conserved. RT-qPCR confirmed that AsWRKY3, AsWRKY11, AsWRKY17, AsWRKY53 and AsWRKY72 showed differential expression under water stress and were involved in regulating the processes of drought and waterlogging tolerance. Under drought stress, all five genes exhibited an upregulation trend, albeit with slightly varying response intensities; under waterlogging stress, AsWRKY3 and AsWRKY17 demonstrated strong enhanced responses, AsWRKY11 and AsWRKY53 showed early-response patterns, whereas AsWRKY72 exhibited a downregulation trend. In summary, fragment duplication and family differentiation enhanced the functional diversity of the WRKY family, providing a genetic basis for the adaptation of A. sinensis to changes in water availability. The research findings not only provide crucial theoretical clues for exploring the potential environmental adaptation and molecular evolution mechanisms of extremely small population plants, but also offer essential genetic resources and scientific foundations for species conservation, restoring wild populations, and conducting stress-resistant molecular breeding. Full article

Populus hopeiensis is an important native poplar species in northern China, but herbivorous insect damage seriously affects its growth and ecological function. WRKY transcription factors play important roles in plant stress responses; however, the function of WRKY23 homologs in woody plant resistance to chewing herbivores remains unclear. In this study, a herbivore-responsive WRKY transcription factor gene, PhWRKY23, was identified from P. hopeiensis. PhWRKY23 expression was significantly induced by Spodoptera litura feeding, with a maximum increase of approximately 69.71-fold the control level at the highest damage level, and the encoded protein was predominantly localized in the nucleus. To investigate its function, PhWRKY23-overexpressing and RNA interference transgenic lines were generated. In the choice feeding assay, the consumed leaf area of PhWRKY23-overexpressing plants was approximately 85.5% lower than that of WT plants after 8 h. In the no-choice feeding assay, the total larval mass after 6 d was approximately 38.8% lower in larvae fed on overexpression plants and 51.0% higher in larvae fed on RNAi plants than in those fed on WT plants. Physiological analysis showed that RNAi plants accumulated significantly more MDA than WT and overexpression plants, whereas overexpression plants had higher chlorophyll a, chlorophyll b, and carotenoid contents than the other genotypes. Phytohormone analysis further showed that PhWRKY23-overexpressing plants accumulated higher levels of jasmonic acid, jasmonoyl-L-isoleucine, and salicylic acid, whereas abscisic acid showed no significant difference among genotypes. Yeast two-hybrid screening identified several candidate PhWRKY23-interacting proteins, and pairwise validation confirmed that PhWRKY23 interacted with PhDOX1 in yeast. These results indicate that PhWRKY23 positively contributes to herbivore resistance in P. hopeiensis and that this resistance phenotype is associated with changes in JA, JA-Ile, and SA accumulation and defense-related physiological traits. Full article

Plant diseases impose major constraints on global crop productivity and pose a major threat to food security. Here, we review transcription factors (TFs) as central orchestrators of plant defense, consolidating recent advances in how these regulators connect pathogen perception to immune signaling, transcriptional reprogramming, and durable defense responses. Initially, we combined a literature-based synthesis with a natural language processing (NLP) analysis of 1647 PubMed abstracts published between 2021 and 2026 to map dominant and underexplored TF families associated with plant immunity. WRKY, MYB, AP2/ERF, bHLH/MYC, and NAC dominated the recent literature, whereas families such as NF-Y, Trihelix, PLATZ, TCP, and GRAS represent emerging regulatory actors. Across these and other families, TFs integrate pattern- and effector-triggered immunity, hormone crosstalk, chromatin dynamics, non-coding RNA regulation, post-translational modifications, and metabolic remodeling, in addition to cell-type-specific expression. Further evidence indicates that pathogens frequently manipulate TFs to weaken host defense, underscoring their central position in plant molecular physiology and plant-pathogen coevolution. The data emphasize that TF function is context-dependent and influenced by multilayered regulation, cell type, pathogen lifestyle, and host genetic background. This review provides a framework for understanding TFs in plant immune control and highlights TF-centered strategies for engineering durable crop resistance, along with future challenges. Full article

Vegetative propagation of recalcitrant woody species is a challenging task that limits biotechnological exploitation of economically relevant trees. In the case of chestnut, a severe decline in its ability to form adventitious roots is imposed during maturation. In previous reports, both juvenile-like and mature microshoots were subject to different hormonal treatments to gain deeper insights into the molecular processes driving the formation of adventitious roots while allowing us to increase our understanding of failed treatments. In the present work, RNAseq libraries from those treatments were used to develop a Weighted Gene Co-expression Network Analysis in order to identify gene modules correlated with the formation of adventitious roots. Hub genes within relevant modules were then used for promoter region analysis to identify transcription factor families that may play a role in the process by controlling the expression of the genes within those modules. bZIP and bHLH families in juvenile-like microshoots and WRKY and SBP families in mature microshoots were found to be particularly relevant for this developmental process. Specific transcription factors, like CsbHLH30 and CsbZIP44, seem to play key roles in the rooting process, while the activity of CsWRKY75 is putatively related to recalcitrant responses in mature shoots. Full article

Background: Nitrogen (N) availability is an important factor affecting soybean growth, photosynthetic capacity, and seed development. Identification of genomic regions associated with N-responsive traits may enable the development of cultivars with enhanced performance under reduced fertilizer inputs. Methods: A soybean diversity panel consisting of 193 accessions was evaluated under N-deficient (N−) and N-sufficient (N+) conditions during the 2024 and 2025 growing seasons. Best linear unbiased predictors were estimated for SPAD area under the curve (SPAD AUC) and 1000-seed weight (SW) under N− and N+ conditions and used for genome-wide association analysis with 37,429 single-nucleotide polymorphism (SNP) markers. Results: Six loci associated with SPAD AUC under N−, four with SW under N−, and 10 with SW under N+ exceeded the Bonferroni-corrected significance threshold, whereas no significant loci were detected for SPAD AUC under N+. Candidate genes near significant loci encoded proteins including receptor-like kinases, WRKY transcription factors, peroxidases, and protein kinases, which are involved in signal transduction, transcriptional regulation, oxidative stress responses, carbohydrate metabolism, and developmental processes. Allelic effect analyses revealed significant phenotypic differences between favorable and unfavorable alleles at representative loci, supporting the biological relevance of the identified associations. Conclusions: These findings provide insight into the genetic architecture of chlorophyll accumulation and seed weight under contrasting N environments and identify candidate loci that may facilitate the improvement of nitrogen-use efficiency and agronomic performance in soybean. Full article

Strawberry is a globally important yet stress-sensitive crop, increasingly threatened by combined abiotic and biotic stresses. Unlike single stresses, combined stresses elicit unique, non-additive responses through complex signaling and gene regulatory networks. This review synthesizes current knowledge on the molecular mechanisms underlying strawberry responses to combined stresses, focusing on signal perception and transduction as well as gene regulation. We examine how combined stresses are perceived by membrane-localized sensors and calcium channels, and how these signals are transduced through MAPK (mitogen-activated protein kinase) cascades, CDPKs (calcium-dependent protein kinases), and hormonal crosstalk involving ABA (abscisic acid), JA (jasmonic acid), and ethylene. At the gene regulation level, we discuss the roles of key transcription factors (WRKY, NAC (NAM, ATAF1, ATAF2 and CUC2), GRAS (GAI-RGA-and-SCR), DREB (Dehydration-Responsive Element-Binding protein), bZIP (basic leucine zipper transcription factor), CAMTA (calmodulin-binding transcription activator), ARF (auxin response factor), and LAV (Leafy Cotyledon2–Abscisic Acid Insensitive3–Val)), transcriptional cascades, epigenetic regulation via DNA methylation, and post-transcriptional (miRNAs such as Fan-miR73) and post-translational (ubiquitination and phosphorylation) control mechanisms. The review also evaluates emerging mitigation strategies informed by these molecular insights, including genomic selection, and explores future directions such as CRISPR (clustered regularly interspaced short palindromic repeats)-based genome editing and multi-omics integration. We conclude that understanding the integrated signaling and gene regulatory networks is essential for developing climate-resilient strawberry cultivars capable of withstanding increasingly complex stress combinations. 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

Exserohilum spike blight, caused by Exserohilum rostratum, is an emerging constraint in wheat production, and improving host resistance is a sustainable strategy because the disease is governed largely by quantitative, environment-responsive loci rather than single major genes. Identifying genomic regions and biological pathways underlying quantitative resistance is therefore essential for developing durable resistant varieties. In this study, the Wheat Association Mapping Initiative spring wheat panel (n = 289) was evaluated across two contrasting Indian agroclimatic zones over two seasons. Resistance was quantified using two traits: incubation period (IP) and area under the disease progress curve (AUDPC). Significant genotype, environment, and genotype × environment interaction effects were observed for both traits (p < 0.001). IP and AUDPC were weakly correlated (r = −0.18 to 0.16), indicating that these traits represent partially distinct resistance components. Genome-wide association mapping identified 25 marker–trait associations, 13 for AUDPC and 12 for IP, with most associations showing environment dependence. Putative candidate genes highlighted defense-relevant loci, including an LRR receptor-like kinase and a WRKY transcription factor for IP, and an RGA2-like resistance gene and PHLOEM UNLOADING MODULATOR-like gene for AUDPC. These findings provide the first GWAS-based framework for E. rostratum resistance in wheat, prioritizing loci for validation and marker deployment. Full article

Background/Objectives: Whole-genome duplication (WGD) and transposed duplication (TRD) are two principal evolutionary drivers of plant genome expansion, yet the molecular mechanisms underlying their divergent co-expression patterns remain poorly characterized. Methods: In this study, based on the reference genome of tea plant (Camellia sinensis ‘Yunkang 10’, YK10), we integrated publicly available transcriptomic, ATAC-seq, H3K27ac ChIP-seq, whole-genome bisulfite sequencing (WGBS), and SNP data from eight tissues and performed a multi-layered analysis of co-expression divergence across 4071 WGD and 10,174 TRD gene pairs. Results: WGD gene pairs exhibited significantly higher co-expression rates (44.3%) than TRD pairs (33.0%), with gene length and sequence similarity jointly promoting co-expression. Chromatin accessibility and H3K27ac modification were each positively correlated with expression and co-expression; however, under equivalent chromatin accessibility conditions, TRD gene expression remained systematically attenuated, and this reduced expression state was significantly associated with elevated levels of CG, CHG, and CHH methylation, suggesting that these epigenetic marks may collectively participate in the transcriptional repression of TRD genes. Promoter-proximal SNPs exerted disproportionately deleterious effects on TRD co-expression, demonstrating that the combined effects of genetic variation and epigenetic modifications are associated with enhanced transcriptional divergence. Weighted gene co-expression network analysis (WGCNA) revealed that WGD modules showed significant associations with EC, GC, and EGC accumulation, whereas WRKY and bHLH transcription factors in the TRD MEblue module exhibited strong associations with EGCG and ECG. Conclusions: This study systematically characterizes multi-omics association patterns related to duplicate gene co-expression divergence, providing insights into potential hierarchical regulation. It offers mechanistic clues for catechin metabolic regulation and provides candidate targets for metabolite-directed breeding. Full article

Cereal crops including wheat, rice, maize, barley, and sorghum collectively supply most global caloric and protein requirements, yet their productivity is increasingly constrained by combined abiotic stresses that co-occur under field conditions. Simultaneous drought, heat, salinity, and cold impose yield losses that consistently exceed those caused by individual stresses and elicit molecular responses that are qualitatively distinct from single-stress reactions and cannot be inferred from them. Despite this agronomic reality, the molecular mechanisms governing combined stress responses in cereals remain poorly resolved, and no integrated framework connecting the transcriptional, epigenetic, and genome-editing dimensions of combined stress tolerance has previously been articulated for this crop group. This review proposes a three-tier integrated framework for understanding and engineering combined abiotic stress tolerance in major cereals. The first tier encompasses transcription factor networks, including bZIP, WRKY, NAC, AP2/ERF, DREB, MYB, and HSF families, that translate combined stress signals into transcriptional reprogramming through ABA-dependent and ABA-independent pathways, hormonal crosstalk, and osmoprotectant and antioxidant defence systems. The second tier addresses the epigenetic regulatory layer, encompassing DNA methylation, histone modifications, and non-coding RNA pathways that gate TF binding site accessibility and encode stress memory in cereals. The third tier examines CRISPR-based tools, including multiplexed Cas9 editing and dCas9-based epigenome editing, that engineer validated targets from both tiers, while confronting polyploid off-target effects, growth penalties, and a laboratory-to-field validation gap. The three tiers are mechanistically coupled, with TF activity shaping epigenetic landscapes, epigenetic states gating TF access, and both providing precision engineering targets. Critical gaps include the absence of combined-stress epigenomic datasets, limited characterisation in barley and sorghum, and early-stage combined-stress-specific strategies. Full article

Soil salinization has become a major global abiotic threat restricting sustainable viticulture, especially in coastal and inland saline–alkali zones. Unlike cereal crops mainly suffering from sodium toxicity, grapevine (Vitis vinifera L.) is a typical chloride-sensitive woody perennial, subjected to superimposed damages of osmotic stress, ionic imbalance and secondary oxidative injury under saline conditions which severely suppress vegetative growth and degrade berry quality. This review systematically summarizes the multi-layered physiological adaptive mechanisms of grapevine against salt stress, including ion homeostasis maintained by salt overly sensitive (SOS), Na⁺/H⁺ exchanger (NHX) and chloride channel (CLC) transporter families, active accumulation of osmoprotectants, synergistic enzymatic and non-enzymatic antioxidant systems, and phytohormone crosstalk networks formed by endogenous phytohormones (abscisic acid, ABA; jasmonic acid, JA; salicylic acid, SA; brassinosteroid, BR) and small signaling molecules. We further elaborate comprehensive molecular regulatory cascades governing salt tolerance, covering core functional genes for ion transport, master transcription factor families WRKY, MYB, APETALA2/Ethylene Response Factor (AP2/ERF), NAC, basic helix–loop–helix (bHLH) and emerging epigenetic regulatory layers mediated by deoxyribonucleic acid (DNA) methylation, microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). In addition, we integrate four categories of field mitigation strategies for saline vineyards: germplasm improvement via salt-tolerant rootstock grafting, rhizosphere soil basal amendment, exogenous biostimulant regulation, and precision agronomic optimization. Current experimental systems do not fully recapitulate complex field combined-stress conditions, as most studies rely on laboratory single-salt stress simulation. Meanwhile, multi-omics, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) gene editing and high-throughput phenotyping tools provide promising approaches to deepen our understanding of grape salt tolerance. This review constructs a comprehensive theoretical framework linking physiological responses, molecular regulatory networks and practical field technologies, offering systematic theoretical references and technical guidance for salt-tolerant germplasm innovation and environmentally sustainable viticulture on saline soils. Full article

Lignin deposition in fruit trees represents a fundamental physiological trade-off: essential for structural integrity and stress adaptation, yet excessive or mistimed activation compromises fruit texture, palatability, and market value. This review synthesizes advances in lignin biosynthesis and its multilayered regulation in commercial fruit species. We describe how abiotic (drought, salinity, temperature extremes) and biotic (pathogens, pests) stresses trigger lignification through transcriptional, post-transcriptional, hormonal, and epigenetic mechanisms, centered on the conserved NAC-MYB cascade. This core module integrates WRKY/ERF transcription factors (TFs), microRNA networks, and hormone signaling. Transcriptional programs are further refined by microRNAs, alternative splicing, DNA methylation, histone acetylation, and phytohormone crosstalk (abscisic acid, ABA; jasmonic acid, JA; salicylic acid, SA; and brassinosteroids, BRs). We emphasize molecular crosstalk integrating abiotic and biotic stress signaling via shared TFs, reactive oxygen species (ROS), and epigenetic memory. We critically examine lignification’s dual nature during development and postharvest storage, contributing to desirable traits (stone formation and skin toughness) but also driving defects (stone cell gritty texture and chilling-induced wooliness). Finally, we propose a strategic framework leveraging molecular breeding, targeted gene editing, and precision horticulture to fine-tune lignification, enabling climate-resilient cultivars without compromising fruit quality. Full article