Search Results (328)

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

MYB transcription factors (TFs) serve pivotal regulatory functions in plant pigmentation; however, the composition of the MYB family in Bougainvillea spp. and the regulatory mechanisms underlying bract coloration have not yet been systematically examined. Here, 163 BbMYB TFs were detected from the Bougainvillea genome through bioinformatic methods and categorized into three subfamilies: 1R-MYB (13 members), R2R3-MYB (144 members), and 3R-MYB (six members). Phylogenetic analysis further assigned the BbMYB proteins to 15 subgroups. Conserved motif analysis showed that most BbMYB proteins contained conserved motifs at the N-termini and that the R2 and R3 repeat regions of R2R3-MYB proteins collectively possessed five highly conserved tryptophan residues. Gene structure analysis demonstrated that BbMYB genes contained 0 to 12 introns and exhibited conserved intron distribution patterns within the same subgroups. Promoter cis-acting element analysis revealed 54 total elements, classified into four categories: hormone-responsive, stress-responsive, development-related, and light-responsive elements. According to transcriptomic data and reverse transcription quantitative polymerase chain reaction validation, BbMYB6, BbMYB8, and BbMYB10 were significantly upregulated in yellow bracts, whereas BbMYB69, BbMYB89, and BbMYB148 were significantly upregulated in red bracts. Virus-induced gene silencing experiments further demonstrated that silencing BbMYB6 caused fading in yellow bracts and a significant reduction in flavonoid content, whereas silencing BbMYB69 caused fading in red bracts and a significant decrease in betacyanin content, suggesting that these two genes are involved in positively regulating the coloration of yellow and red bracts, respectively. This work comprehensively analyzed the MYB gene family in Bougainvillea, pinpointed essential candidate genes linked to bract coloration, and established a theoretical basis, along with genetic resources, for molecular breeding of bract color in Bougainvillea. Full article

Phellodendron amurense Rupr. is a native tree species in China, well known for its significant medicinal value. Its pharmacological activity mainly derives from the abundant isoquinoline alkaloids in its bark. Berberine serves as the key compound underlying the multiple pharmacological effects of P. amurense and exhibits organ-specific accumulation. However, the genetic mechanisms governing this organ-specific accumulation remain unclear. Genes encoding O-methyltransferase (OMT) and cytochrome P450 (CYP) may play an important role in this regulatory process. In this study, by integrating transcriptomic and metabolomic data from the leaves and stems of P. amurense plantlets, we identified core candidate genes and transcription factors (TFs) that regulate the differential biosynthesis of berberine between these two organs. The results showed that 37 metabolites were significantly upregulated in stems, including main medicinal components such as berberine and jatrorrhizine, while 8497 genes were differentially expressed between leaves and stems. Among these, downstream genes in the berberine biosynthesis pathway, including OMTs and CYPs, were predominantly highly expressed in stems. A co-expression regulatory network identified some TFs such as PaBES1, PaWRKY12/13, PaNAC5, and PaMYB12 as the key nodes regulating the differential biosynthesis of berberine. Phylogenetic analysis classified the 97 PaOMTs into four subgroups. Core candidate genes such as PaOMT7 and PaOMT9 were contained in subgroup IV, potentially contributing to the specific modification of characteristic alkaloids in P. amurense. This study reveals the transcriptional regulatory networks underlying the organ-specific accumulation of berberine in P. amurense plantlets, providing key targets and theoretical support for the targeted improvement and development of elite medicinal varieties. Full article

Leaf senescence, the final developmental stage of a leaf, is a highly regulated process that is vital for the recycling of nutrients and the maintenance of plant fitness. Its control operates at multiple levels, including chromatin remodeling, transcription, post-transcriptional regulation, translation, and post-translational modifications. This review summarizes recent advances in understanding the roles of key transcription factor (TF) families—WRKY, NAC, and MYB—in modulating leaf senescence in Arabidopsis thaliana. We detail how these TFs integrate internal and external signals to regulate senescence-associated genes (SAGs). In addition, we explore the pivotal role of microRNAs (miRNAs) in post-transcriptional control of senescence, focusing on their regulation of these TF families. In conjunction with the transcriptome data of Arabidopsis miRNAs under conditions of dark-induced senescence, we also highlight several novel senescence-associated miRNAs. Integrating transcriptional and post-transcriptional perspectives, this review presents an updated regulatory network for leaf senescence and discusses potential applications for manipulating senescence in crops to improve yield and quality. Full article

Leaf senescence is a critically regulated developmental process that determines crop yield and quality. MYB and NAC transcription factors (TFs) are central regulators within this network, yet the crosstalk between these TF families and their connection to the gibberellin (GA) pathway remain poorly understood. This study revealed that overexpression of DIV1, a MYB-like TF, leads to significantly reduced chlorophyll content and precocious leaf senescence. Based on the public transcriptome profiling of DIV1-overexpression leaves, 37 senescence-associated differentially expressed genes (DEGs), including the highly upregulated NAC59 and NAC92, were identified. Molecular assays confirmed that DIV1 directly binds to the promoters of NAC59 and NAC92 and activates their transcription. Meanwhile, yeast two-hybrid and split-luciferase assays demonstrated that DIV1 physically interacts with the GA biosynthetic enzyme ent-kaurene oxidase (KO1) both in vitro and in vivo. The promoted senescence phenotype in DIV1-overexpression lines was rescued by treatment with paclobutrazol (PAC), a GA biosynthesis inhibitor. In summary, our findings reveal a dual mechanism whereby DIV1 integrates the GA pathway and NAC-mediated transcription to regulate leaf senescence. This work provides new insights into the coordination between MYB and NAC TFs during hormone-mediated senescence. Full article

Nitrogen (N) availability is a critical determinant of grain yield and protein quality in wheat (Triticum aestivum L.). To elucidate the molecular mechanisms underlying nitrogen response associated with nitrogen use efficiency (NUE), a comparative transcriptomic analysis of high grain protein content (HP) and low grain protein content (LP) wheat lines during N resupply at the seedling stage is conducted in this study, with sampling conducted at T1 (one day after treatment) and T3 (three days after treatment). Our results reveal that the HP line exhibits an early-responsive and well-coordinated metabolic pattern, whereas the LP line shows a distinct temporal response characterized by delayed adjustments. Integrated GSEA and KEGG analyses demonstrated that the HP line prioritized protein processing in the endoplasmic reticulum and diterpenoid biosynthesis, potentially associated with enhanced protein quality control and early signaling efficacy. This allows the HP line to synchronize its N assimilation machinery with the transient peak of N availability at T1 and establishes a robust foundation for protein accumulation. Conversely, the LP line redirected its metabolic resources toward glutathione metabolism and flavonoid biosynthesis to mitigate N-induced oxidative instability. This metabolic shift increases the energetic usage required for antioxidant defense and subsequently deviates resources away from productive N assimilation. These divergent metabolic landscapes were orchestrated by a hierarchical network of transcription factors (TFs). In leaves, the MYB and NAC families showed a more disciplined and immediate increase in the HP line, whereas the LP line demonstrated a delayed peak at T3. In root tissues, while Dof and NAC families were rapidly induced and concluded in the HP line, the LP line exhibited a sluggish sensing-to-response mechanism with prolonged or specific late-stage activation at T3. These results indicate that the capacity for rapid metabolic synchronization and disciplined transcriptomic mobilization is a key physiological indicator of high-protein potential in wheat. This insight provides essential molecular targets for breeding programs aimed at improving NUE and grain quality. Full article

The discovery of bidirectional microRNA transfer between two organisms during plant–microbe interactions and the ability of some fungal pathogens to absorb double-stranded RNA (dsRNA) or short interfering RNA (siRNA) from the environment provided an impetus for exploiting this mechanism in plant defense against pathogens. In this study, we investigated the role of conserved wheat microRNAs (miRNAs), miRNA408 and miRNA159, in inducing plant defense responses and suppressing the virulence of the phytopathogenic ascomycete fungus Parastagonospora nodorum, mediated by necrotrophic effectors (NEs) encoded by SnTox genes regulated by fungal transcription factors (TFs). The foliar spraying with in vitro synthesized siRNA408 and siRNA159 duplexes before inoculation with SnTox3-producing P. nodorum isolate increased wheat plant resistance to the SnB isolate and suppressed the pathogen growth and development. Most likely, silencing of the miRNA408 target genes TaCAT-2A, TaCAT-2B, and TaCLP1, and the miRNA159 target gene TaMYB65, led to the induction of a defense response of wheat plants against P. nodorum. This defense response was characterized by a decrease in the catalase activity, accumulation of hydrogen peroxide, activation of the expression of salicylic acid signaling pathway genes (TaWRKY13, TaPR1), and suppression of the expression of ethylene signaling pathway genes (TaEIN3, TaPR3). We demonstrated for the first time the ability of siRNA159 and siRNA408 to penetrate the mycelium of the pathogen P. nodorum and be involved in the cross-kingdom regulation of fungal genes to suppress the expression of some genes of NE (SnToxA, SnTox3) and fungal TFs (SnStuA). We predicted potential targets for wheat miRNA408 and miRNA159 in the P. nodorum transcriptome, making spray-induced gene silencing (SIGS) promising for use against this pathogen. These results provide valuable insights for studying the cross-kingdom transfer of plant miRNAs. Full article

R2R3-MYB and bHLH transcription factors (TFs) are key regulators of floral secondary metabolism and epidermal development in flowering plants. Orchids exhibit remarkable floral diversity, which is critical for pollination success and ornamental value, yet the evolutionary and functional diversification of these TF families within the genus remains largely unexplored. Here, we conducted a comprehensive pan-genome dissection of R2R3-MYB and bHLH TF families across 18 Dendrobium species, integrating orthologs assignment, phylogenetics, duplication profiling, cis-regulatory annotation, and tissue-specific expression analysis. We identified 3074 R2R3-MYB and 2282 bHLH genes, classified into 69 and 61 orthologous gene groups (OGGs), respectively. Core OGGs accounted for two-thirds of both families, indicating strong evolutionary conservation, whereas variable OGGs reflected lineage-specific diversification. Phylogenetic analyses resolved R2R3-MYBs into 24 canonical subfamilies and revealed conserved heterogeneous expansion patterns in bHLH subfamilies. Promoter architectures of R2R3-MYB genes were enriched in hormone-, stress-, and light-responsive elements, whereas bHLH promoters were dominated by development-related motifs. Tissue-specific expression profiling in Dendrobium ‘Chao Praya Smile’ showed that floral bud-enriched genes were associated with flavonoid/anthocyanin biosynthesis, whereas root-enriched genes were linked to stress and hormone responses. Integration of pan-genomics and transcriptomics highlighted evolutionary trajectory and functional divergence between core and variable gene sets within Dendrobium. Our study establishes a comprehensive, genus-wide framework for understanding the evolutionary and functional characteristics of MYB–bHLH regulatory networks in Dendrobium. These findings provide valuable genetic resources and key candidate targets for functional characterization and molecular breeding, with important implications for genetic improvement of reproductive traits, floral quality, stress resistance, and ornamental and agronomic value in orchids. Full article

MYB transcription factors (TFs) are crucial for plant growth, development, and response to abiotic stress. However, their exact functions in abiotic stress responses in rapeseed remain largely unexplored. In this study, we identified and characterized BnaMYB73, a member of the R2R3-MYB subfamily, and investigated its role in abiotic stress tolerance. The transcription level of BnaMYB73 was significantly upregulated in response to salt and osmotic stress. Transgenic Arabidopsis thaliana lines expressing BnaMYB73 displayed significantly enhanced tolerance to salt and osmotic stress, while showing no phenotypic differences in growth compared with wild-type (WT) plants under normal conditions. Physiological analyses revealed that the BnaMYB73-expressing plants accumulated higher proline levels, exhibited elevated superoxide dismutase (SOD) and peroxidase (POD) activities, and reduced malondialdehyde (MDA) content under stress conditions. Moreover, the BnaMYB73-expressing plants significantly upregulated key stress-responsive genes, including AtRD29B, AtDREB2A, AtRAB18, AtP5CS1, AtSOS1 and AtCAT1. Collectively, these findings establish BnaMYB73 functions as a stress-responsive transcription factor that enhances abiotic stress tolerance and provide a promising target for breeding stress-resilient rapeseed cultivars. Full article

Cibotium barometz (L.) J. Sm., a medicinally significant fern in traditional Chinese medicine, is little explored at the genomic level regarding its bioactive compounds. Using an integrated approach combining Illumina and PacBio sequencing technologies, we profiled its root, rachis, and pinna transcriptomes, identifying 12,718, 21,341, and 11,441 unigenes, respectively. Our analysis systematically characterized the transcriptional features of transcription factors (TFs), simple sequence repeats (SSRs), long non-coding RNAs (lncRNAs), and differentially expressed genes (DEGs). Enrichment analyses highlighted the roles of highly expressed unigenes in secondary metabolism. Seventeen key enzymes involved in polysaccharide biosynthesis showed tissue-specific expression patterns. Notably, total polysaccharide content correlated positively with UDP-arabinose 4-epimerase (UXE) expression but negatively with phosphoglucomutase (PGM) and 3,5-epimerase/4-reductase (UER1). Flavonoid accumulation inversely correlated with chalcone synthase (CHS) expression. Two lignin pathways (H-lignin and G-lignin) were characterized, with phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H), and cinnamyl alcohol dehydrogenase (CAD) as key genes. The absence of ferulate-5-hydroxylase (F5H) explains the undetected S-lignin pathway. Regulatory network analysis revealed positive correlations between PAL expression and NAC72/NAC78/WRKY35 and C4H expression and WRKY65/WRKY69/WRKY71, while a negative correlation was revealed between flavonoid 3′,5′-hydroxylase (F3′5′H) and MYB3R4. This study provides comprehensive transcriptomic insights into C. barometz bioactive compound biosynthesis, serving as a foundation for mechanistic research. Full article

Cadmium (Cd) toxicity threatens global food security and agricultural sustainability. Transcription factors (TFs) act as master regulators of the complex molecular networks involved in Cd detoxification. This review provides a focused synthesis of the molecular mechanisms governing Cd tolerance in plants, encompassing antioxidant defense, Cd chelation and sequestration, Cd uptake and transport, signal transduction, and damage repair pathways. We highlight the pivotal roles of key TFs in these specific processes, such as OsMYB45 in antioxidant defense, OsIRO2 in regulating chelation and storage, OsNAC5 in modulating Cd transport, and OsE2F in facilitating the repair of DNA and protein damage. Furthermore, we evaluate the potential of harnessing these TF-mediated regulatory mechanisms for developing low-Cd rice varieties. By delineating precise correlations between specific TFs and detoxification pathways, this review proposes actionable molecular strategies to mitigate Cd contamination, thereby contributing to ecological and food safety. Full article

Transcription factors (TFs) are ubiquitously distributed in plants and play pivotal roles in regulating plant growth and development. The present study aims to elucidate the function of transcription factors (TFs) in highland barley’s response to selenium stress. The results show that 89, 218, 141, 92, 23, and 34 genes were identified from the bHLH, MYB, NAC, WRKY, GATA, and HSF families, respectively. We analyzed the physicochemical properties of the transcription factor family, including amino acid number and molecular weight, theoretical PI, instability index, hydrophilicity index, and subcellular location. The majority of proteins encoded by these gene families are hydrophilic and predominantly localized in the nucleus. Structural analysis demonstrates that each family contains conserved motifs and domains. Most bHLH genes, such as KAE8811666.1 and KAE8789390.1, contain bHLH_SF superfamily domains. 45 MYB genes possess the myb_SHAQKYF domain. Most NAC genes possess typical NAM domains. Most WRKY proteins showed the WRKY superfamily domain. The 22 members of GATA possess the ZnF_GATA domain. HSF gene family showed that 24 gene family members contained HSF domains. Systematic evolutionary analysis indicates that the bHLH and NAC families can each be divided into nine subfamilies, while the remaining four families are categorized into five to eight subfamilies, respectively. Based on transcriptome data, under low selenium treatment, 56.25%, 76%, 67.39%, 47.37%, 50%, and 56.25% of the genes belonging to the bHLH, MYB, NAC, WRKY, GATA, and HSF transcription factor families were significantly upregulated, respectively. In contrast, under high selenium treatment, the proportions of upregulated genes in these families were 81.25%, 80%, 65.22%, 63.16%, 75%, and 75%, respectively. Additionally, qRT-PCR results were consistent with the trends of the transcriptome expression data, corroborating the reliability and accuracy of the transcriptomic findings. These results elucidate the molecular characteristics and response patterns of six transcription factor families to selenium stress in highland barley, laying a foundation for further in-depth research on the functions of transcription factors in highland barley plants. Full article

Powdery mildew (PM) is a major disease affecting bitter gourd cultivation, and resolving the molecular regulatory mechanisms underlying PM resistance is important for bitter gourd molecular breeding for resistance. In this study, morphological and molecular methods were used to identify the PM pathogen in bitter gourd, and comparative transcriptome analysis was performed on leaves of the resistant cultivar R and the susceptible cultivar S after PM infection. The morphological and molecular identification results showed that the PM pathogen in bitter gourd was Podosphaera xanthii. Scanning electron microscopy results revealed that the P. xanthii exhibited distinct growth patterns in the R and S after P. xanthii infection. Compared to the S, the R exhibited 3966, 2729, 5891, and 3878 differentially expressed genes (DEGs) at 0, 2, 3, and 4 days after P. xanthii infection, respectively. KEGG enrichment analysis showed that DEGs were primarily enriched in plant–pathogen interactions, MAPK signaling pathway plants, and plant hormone signal transduction pathways. Transcription factor (TF) analysis of differentially expressed genes revealed that MYB, bHLH, and ERF family members could be involved in the defense process against the P. xanthii infection. Moreover, the analysis of the MLO genes revealed that Moc10g30350.1 could be involved in regulating PM resistance. These findings could enrich the molecular theoretical basis for resistance to PM, and provide new insights for the molecular breeding process of bitter gourd resistance to PM. Full article

Seed germination is a critical developmental stage exhibiting high vulnerability to salt stress. The role of MYB transcription factors (TFs) in mediating this process in Cannabis sativa L. remains largely unexplored. In this study, we performed a genome-wide analysis and identified 115 CsMYB genes, which were phylogenetically classified into 12 distinct subgroups. In silico promoter analysis revealed a significant enrichment of abscisic acid (ABA)- and methyl jasmonate (MeJA)-responsive cis-elements, suggesting their potential linkage to phytohormone signaling pathways under stress conditions. To investigate their expression during salt stress, we profiled a subset of candidate CsMYB genes during seed germination under 150 mM NaCl treatment based on RNA-seq screening at 24 h post-imbibition (hpi) under salt stress. These candidates exhibited distinct temporal expression profiles: CsMYB33 and CsMYB44 were transiently induced at the early stage (12 h post-imbibition), while CsMYB14, CsMYB78, and CsMYB79 showed sustained upregulation from 24 h to 5 days. In contrast, CsMYB58 and CsMYB110 were downregulated. Synteny analysis indicated a closer evolutionary relationship between CsMYBs and their Arabidopsis thaliana orthologs compared to those in monocots. Protein–protein interaction predictions, based on orthology, further implicated these CsMYBs within putative ABA signaling and reactive oxygen species (ROS) homeostasis networks. Collectively, our findings provide a systematic genomic identification and genomic characterization of the CsMYB family and propose a model for the potential multi-phase involvement of selected CsMYBs in the salt stress response during seed germination. This work establishes a foundational resource and identifies key candidate genes for future functional validation aimed at enhancing salt tolerance in C. sativa. Full article

Plant roots form highly specialized apoplastic barriers that regulate the exchange of water, ions, and solutes between the soil and vascular tissues, thereby protecting plant survival under environmental stress. Among these barriers, the endodermis and exodermis play essential roles, enhanced by suberin lamellae and lignin-rich Casparian strips (CS). Recent advances have shown that these barriers are not static structures but are dynamic systems, rapidly adapting in response to drought, salinity and nutrient limitation. The R2R3-MYB transcription factor (TF) family is essential to this adaptive plasticity. These TFs serve as key regulators of hormonal and developmental signals to regulate suberin and lignin biosynthesis. Studies across different species demonstrate both conserved regulatory structure and species-specific adaptations in barrier formation. Suberization provides a hydrophobic structure that limits water loss and ion toxicity, while lignification supports structural resilience and pathogen defense, with the two pathways exhibiting adaptive and interactive regulation. However, significant knowledge gaps remain regarding MYB regulation under combined abiotic stresses, its precise cell-type-specific activity, and the associated ecological and physiological trade-offs. This review summarizes the central role of root barrier dynamics in plant adaptation, demonstrating how MYB TFs regulate suberin and lignin deposition to enhance crop resilience to environmental stresses. Full article