Search Results (357)

Akebia trifoliata is an important Chinese traditional medicinal plant, and its abundant triterpenoids are the primary active medicinal components. However, the oxidosqualene cyclase (OSC) gene family responsible for constructing their triterpenoid skeletons has not yet been systematically characterized. In this study, nine AktOSC genes were identified genome-wide in A. trifoliata. Phylogenetic analysis revealed that most AktOSC members formed independent evolutionary subclades. Synteny and selective pressure analyses indicated that multiple duplication modes collectively contributed to the expansion of the AktOSC family, and all members were subjected to strong purifying selection. Sequence alignment showed that all members possess the characteristic motifs of the OSC family, whereas amino acid substitutions at critical active-site residues hinted at potential catalytic product diversity. Cis-acting element prediction revealed an abundance of environmental and phytohormone responsiveness elements within the AktOSC promoter regions. Expression profiling revealed that AktOSC genes exhibited distinct expression patterns across tissues, developmental stages, and disease-susceptibility groups. Finally, AktOSC8, which was specifically and highly expressed in the pericarp, was identified as a highest-priority candidate gene. Collectively, these findings provide essential foundational insights for further elucidating the mechanisms underlying triterpenoid biosynthesis and accumulation in A. trifoliata. Full article

The RING-type E3 ubiquitin ligase plays a significant role in plant responses and adaptations to abiotic stresses such as drought. However, few studies have explored the role of E3 ubiquitin ligases in potato drought stress, especially DRIP1. In this study, 172 StHCa genes were identified across the potato genome. These genes were unevenly distributed on twelve chromosomes and divided into six subclades (group I–VI). The molecular weight of potato HCa proteins ranges from 5445.38 to 143,293.69 Da. More than half of them are acidic proteins and most are unstable. There are 161 hydrophilic proteins, and the subcellular localization analysis indicated that they were mainly located in the nucleus. The co-linearity analysis of StHCa genes showed that 172 genes underwent 40 tandem duplications and 28 segmental duplication events. Potato and tomato share a recent common ancestor and exhibit highly similar evolutionary trajectories. Promoter sequence analysis of the StHCa family identified abundant cis-acting elements associated with light signal transduction, hormone responses, plant growth and development, and abiotic stress responses. These results suggest that the StHCa genes may play important regulatory roles in different environmental signals and developmental stages. Expression profiling revealed that StDRIP1 exhibited higher transcript levels in potato roots than in stems and leaves, and its expression was significantly induced by drought stress. Physiological phenotyping demonstrated that StDRIP1-overexpressing (OE) plants displayed reduced root growth compared with wild-type (WT) plants, with decreases in root length, total root area, total root volume, and root vitality. Under 20% PEG-6000-simulated drought stress, the root expression level of StDRIP1 was higher in OE lines than in WT plants. Furthermore, StDRIP1 overexpression suppressed the activities of antioxidant enzymes (POD, CAT, and SOD) and weakened their osmotic adjustment ability by reducing proline (Pro) accumulation. At the late stage of stress treatment (9 h), the SOD, POD, and CAT activities of OE plants were 5.0%, 19.9%, and 25.1% lower than those of WT plants, respectively. These physiological alterations exacerbated oxidative damage, as evidenced by increased malondialdehyde (MDA) content and elevated electrolyte leakage in OE plants. In summary, this study comprehensively characterized the StHCa gene family in potato, providing a valuable theoretical basis for elucidating the functional mechanism of StDRIP1 in modulating drought stress responses. Collectively, StDRIP1 acts as a negative regulator of potato drought tolerance through two primary mechanisms: (1) repressing root growth and weakening root vitality, thereby reducing the water absorption capacity of roots; and (2) diminishing antioxidant enzyme activities and impairing osmotic homeostasis, which further exacerbates oxidative damage under drought stress. Full article

WOX transcription factors play conserved roles in plant adventitious root development, but the WOX family in pepino (Solanum muricatum) has not been systematically characterized. To investigate this family, genome-wide identification and expression analysis were performed. A total of 15 SmWOX genes were identified, unevenly distributed across 12 chromosomes and phylogenetically divided into three clades: WUS (11), Intermediate (3), and Ancient (1). RT-qPCR revealed that most SmWOX genes showed the highest expression in apical buds and the lowest in leaves; among them, SmWOX5 and SmWOX15 exhibited significantly higher expression in roots. These two genes were subsequently cloned and subjected to subcellular localization analysis. SmWOX5 (492 bp, 163 amino acids) and SmWOX15 (2514 bp, 837 amino acids) were both predicted as non-transmembrane, non-secretory proteins, with differences in phosphorylation site distribution and structural conformations. Subcellular localization showed that SmWOX5 is exclusively nuclear, whereas SmWOX15 is predominantly nuclear with partial plasma membrane distribution. The WOX family in pepino exhibits evolutionary conservation with signs of functional divergence. The high root expression and differential localization of SmWOX5 and SmWOX15 suggest their distinct regulatory roles in root development and adventitious root formation, providing candidate genes for improving cutting propagation efficiency in pepino (Solanum muricatum). Full article

Reverse transcription quantitative PCR (RT-qPCR) is one of the most widely used techniques for gene expression analysis in molecular biology. However, the accuracy of relative gene expression quantification largely depends on the stability of the reference genes used for normalization. Sambucus nigra L. (elderberry) is a valuable medicinal and edible plant rich in anthocyanins and other bioactive compounds. Despite its increasing research and application value, no reference genes have been validated for this species. In this study, we applied RT-qPCR alongside four algorithms (GeNorm, NormFinder, BestKeeper, and RefFinder) to assess the expression stability of nine candidate reference genes across ten samples representing five tissue types (including stems, flowers, leaves, roots, fruits) at different developmental stages. The results showed that VAMP and Pol were the most suitable reference gene combination for normalization across different tissues of S. nigra. For studies involving only vegetative tissues (leaves and stems), our results recommend that RPB2 and RPB5 are the most stable and suitable reference genes. This study provides reliable reference genes for accurate RT-qPCR-based gene expression analysis in S. nigra and establishes a useful methodological basis for future functional genomics and molecular breeding studies in this species. Full article

Flavonoids, prominent bioactive compounds in citrus fruits, exhibit diverse health-promoting properties. However, the dynamic compositional changes in flavonoids during fruit development remain insufficiently characterized in Citrus reticulata ‘Shiyue Ju’ (STJ) and C. reticulata ‘Denglong Ju’ (DLJ). In this study, a comprehensive untargeted metabolomics approach was employed to systematically analyze the flavonoid profiles in both peel and flesh tissues across six key developmental stages, leading to the putative annotation of 205 flavonoids. Heatmap analysis revealed higher flavonoid levels in SP-4 (STJ peel in stage 4) compared to DP-4 (DLJ peel in stage 4), potentially resulting from the substantial upregulation of genes involved in flavonoid biosynthesis during this period. Furthermore, S-plot analysis identified salvigenin, demethylnobiletin, and nobiletin as key discriminators in the peel of STJ (SP), whereas sinensetin, tangeretin, and 3′,4′,5,7-tetramethoxyflavone were predominant in the peel of DLJ (DP). These compounds could represent potential biochemical markers for varietal differentiation. Notably, SP exhibited higher levels of neohesperidin, hesperidin, naringin, and naringenin, suggesting enhanced health-promoting properties. The results enhance our understanding of flavonoid dynamics during citrus development and provide valuable implications for quality-oriented cultivation and genetic improvement. Full article

Vitamin D comprises a group of fat-soluble secosteroids traditionally associated with animal physiology, calcium-phosphate homeostasis, and skeletal metabolism. However, vitamin D and related compounds have also been reported in taxonomically distinct non-animal systems, including fungi, microalgae, other algae, phytoplankton, and higher plants, although the strength of evidence differs substantially among these groups. This review synthesizes current knowledge on the occurrence, structural chemistry, UV-B-driven photochemical mechanisms, environmental determinants, analytical challenges, and biofortification potential of vitamin D formation in photosynthetic organisms and fungi. Vitamin D synthesis is initiated by UV-B radiation, primarily within the 290–315 nm range, which converts sterol precursors such as 7-dehydrocholesterol and ergosterol into previtamin D intermediates and is followed by thermal isomerization to the corresponding vitamin D forms. Continued irradiation may additionally generate lumisterol, tachysterol, and other photoproducts, thereby limiting net vitamin D accumulation. This non-enzymatic mechanism supports the interpretation that vitamin D formation can occur outside vertebrates when an appropriate 5,7-diene sterol precursor is accessible to a sufficient UV-B dose. In photosynthetic organisms and fungal matrices, net vitamin D accumulation is constrained by the spectral dose of UV-B, environmental exposure, tissue architecture, sterol localization, oxygen availability, antioxidant capacity, and ROS-mediated degradation. Studies of microalgae and phytoplankton, including reports concerning Emiliania huxleyi, suggest the occurrence or UV-B-dependent formation of both vitamin D₂ and vitamin D₃. However, these findings require evaluation according to the analytical method, use of authentic standards, experimental conditions, and confidence of compound identification. In fungi, the UV-B-induced conversion of abundant ergosterol to vitamin D₂ is well established. Microalgae represent a developing source of vitamin D₂ and vitamin D₃, whereas evidence for nutritionally relevant vitamin D accumulation in higher plants remains limited and heterogeneous. Although higher plants contain diverse phytosterols, the formation of vitamin D₄, vitamin D₅, or related analogues requires appropriate photoreactive 5,7-diene precursors and should not be inferred directly from the presence of common phytosterols such as β-sitosterol. Analytical detection remains challenging because of low concentrations, complex lipophilic matrices, and structural similarity among secosteroids and photoproducts; therefore, reliable identification requires validated analytical procedures. LC-MS/MS provides high sensitivity and selectivity but should be supported by authentic standards, preferably isotope-labelled internal standards, retention-time agreement, quantitative and qualifying ions, matrix-recovery assessment, limits of detection and quantification, and evaluation of ion suppression. Structurally similar analogues and photoproducts may additionally require orthogonal confirmation. Nutritionally, post-harvest UV-B enrichment of edible mushrooms is currently the best-validated strategy for increasing non-animal vitamin D₂ content. Microalgae constitute a developing platform for vitamin D₂ and vitamin D₃ production, whereas biofortification of higher plants remains experimental. Full article

Japonica soft rice varieties possess excellent eating quality, and their cultivation area has been steadily expanding in recent years. This study aimed to analyze japonica soft rice varieties cultivated in the Yangtze River Delta region of China at the genome level and to provide a theoretical basis for optimizing disease resistance and other important traits. Genotypic characterization and evaluation of ten major japonica soft rice varieties from the Yangtze River Delta region were conducted using a genome-wide single nucleotide polymorphism (SNP) chip. The experimental results indicated that the soft rice varieties in the Yangtze River Delta region had a relatively high japonica component and were all classified as typical japonica rice varieties. Specifically, the highest (95.6%) and lowest (91.5%) proportions of japonica genomic segments were detected in Tai’an 1 and Zhehexiang 2, respectively. Japonica soft rice varieties from Shanghai exhibited a closer genetic distance to those from Jiangsu Province than to those from Zhejiang Province. Genomic identity was highest between Tai’an 1 and Nanjing 46 (87.9%) and lowest between Tai’an 1 and Jia 67 (74.4%). Based on the results of the chip assay, a total of twenty-six functional genes controlling key traits, such as yield, quality, and resistance to biotic and abiotic stresses, were identified in the ten analyzed varieties. Among them, Zhehexiang 2 carried the broad-spectrum blast resistance genes Pi2 and Pita, which is useful for improving the blast resistance of japonica soft rice varieties. The findings of this study provide genetic resources and carrier materials for the efficient molecular improvement of japonica soft rice varieties. Full article

N6-methyladenosine (m6A) is the most prevalent internal modification of eukaryotic mRNA and a central regulator of plant development and stress adaptation. The plant m6A writer complex requires two MT-A70 family proteins, the catalytic subunit MTA70 and its non-catalytic partner MTB, yet the evolutionary basis and structural logic underlying this functional division remain unresolved across land plant lineages. Here, we present an integrative computational analysis of MTA70 and MTB across 15 phylogenetically representative species spanning bryophytes, lycophytes, charophyte algae, monocots, and dicots. Phylogenomic reconstruction resolved three strongly supported clades, namely MTA70, MTB, and an intermediate MTA70-like group, demonstrating that catalytic-to-regulatory divergence predates the separation of major land plant lineages. MTA70 proteins exhibited strict conservation of gene structure, catalytic motifs, and domain architecture, reflecting selective constraint at functionally critical residues, whereas MTB showed extensive divergence in exon–intron organization and surface-exposed residues, consistent with relaxed structural constraints. AlphaFold2-based structural modeling and data-driven protein–protein docking predicted a stable MTA70–MTB heterodimer with a buried surface area of 1435 Ų and a binding free energy of −8.1 kcal/mol, with Lys746 and Lys637 of MTB identified as primary interface hotspots by computational alanine scanning. Expression profiling across six species revealed preferential MTB accumulation in reproductive tissues, while promoter analysis identified statistically significant enrichment of jasmonate-responsive elements (TGACG-motif) in MTB promoters (Mann–Whitney U, p = 0.025) and a 3.4-fold higher abundance of ABA-responsive elements (ABRE) in MTB relative to MTA70, suggesting potential responsiveness to multiple phytohormone signals. Together, these findings establish an evolutionary and regulatory framework for MTB as a conserved scaffold coupling m6A deposition to developmental and environmental signaling in land plants. Full article

Salinity stress affects not only the survival and productivity of halophytic plants, but also the composition, structure and processability of their biomass. In Salicornia spp., salt-induced regulation of ion transport, osmotic adjustment, reactive oxygen species signaling, antioxidant defense, and cell wall remodeling can directly influence residual salinity, water retention, texture, extractability, drying behavior, and oxidative stability of plant biomass. However, most existing transcriptomic studies of Salicornia and related halophytes have focused mainly on salt tolerance mechanisms, whereas the connection between stress-regulated molecular networks and processing-related biomass traits remains insufficiently systematized. This review addresses this gap by proposing a mechanistic framework that links salinity perception, ROS-mediated signaling, ABA and MAPK pathways, antioxidant gene families, transcription factor networks and processing-oriented quality traits. Special attention is given to enzymatic antioxidant systems, including SOD, CAT, APX, POD and components of the ascorbate-glutathione cycle, as well as to non-enzymatic defense mechanisms involving ascorbate, glutathione, phenolic compounds, carotenoids, proline and glycine betaine. The review also discusses the regulatory roles of WRKY, DREB/CBF, NAC, bZIP and MYB transcription factor families as molecular control points connecting salinity stress responses with downstream metabolic and structural traits. Network-based approaches, including WGCNA, pathway signatures and transcript panels, are considered more informative than single-gene markers for predicting complex quality traits in Salicornia biomass. In addition, recent genomic and computational strategies, including CRISPR/Cas-mediated functional validation, GWAS, genomic selection, multi-omics integration and AI-assisted modeling, are discussed as emerging tools for candidate-gene prioritization and predictive assessment of stress-dependent biomass quality. Overall, this review shifts the interpretation of Salicornia transcriptomics from a descriptive salt-tolerance model toward a mechanistic and application-oriented framework for improving halophytic raw materials for food, feed and bioprocessing applications. Full article

Salinity stress has a debilitating effect on crop productivity and triggers complex molecular changes in plants, and understanding these responses is important for improving stress tolerance. This study investigated transcriptomic changes in the salt-tolerant barley line CC89/Giza123 by analyzing gene expression in roots and leaves following exposure to 200 mM NaCl for 12 and 24 h. The number of differentially expressed genes (DEGs) showed a much stronger response in roots than in leaves. At 12 h, roots showed 1836 DEGs, and this number increased to 2696 at 24 h, whereas leaves showed 256 DEGS at 12 h, and 787 at 24 h. The presence of strong and early activation in roots appears to indicate that roots play a key role in the adaptive response to salinity stress initiation. GO and KEGG analyses of differentially expressed genes revealed tissue- and time-specific responses. Roots showed rapid activation of ribosome and secondary-metabolite pathways at 12 h, followed by shifts toward carbon fixation and energy-related pathways at 24 h. Leaves responded early by adjusting photosynthesis-antenna proteins and later expanded their response to defense-related and amino-acid biosynthesis pathways. Important salt-responsive genes were identified in both tissues, including protein kinases, protein phosphatases 2C (PP2Cs), phospholipases, aquaporins, detoxification enzymes, molecular chaperones, and Late Embryogenesis Abundant (LEA) proteins. These results highlight clear tissue-specific and time-dependent differences in how plants respond to salt stress, providing insights into the metabolic and regulatory mechanisms involved in salt tolerance. Overall, these results provide evidence that the response of barley to salinity is achieved by using coordinated and dynamic molecular changes in different tissues. The transcriptomic dataset is a useful source of candidate genes for further functional studies and is a significant resource for breeding and biotechnological approaches to the production of salt-tolerant cereal crops. Full article

Soil salinization represents one of the most severe abiotic constraints on global forest productivity. Populus, the most widely cultivated fast-growing timber tree and a premier model woody plant, exhibits striking intrageneric variation in salt tolerance—from the extremely halophytic Populus euphratica to highly salt-sensitive cultivated clones. Understanding the molecular basis of this variation has profound implications for saline–alkali land reclamation and salt-tolerant variety breeding. This review systematically synthesizes current knowledge on Populus salt-stress responses, covering three primary injury mechanisms (osmotic stress, ionic toxicity, and oxidative damage) and the corresponding physiological countermeasures. We further survey functional genes across four major categories: ion transporters, osmotic-adjustment enzymes, antioxidant-defense components, and transcription factors. Crucially, we extend beyond the herbaceous-plant paradigm by examining salt-tolerance strategies that are specific to the woody architecture of Populus: long-distance radial and axial Na⁺ transport through tall stems, salt sequestration in senescent bark and wood parenchyma, and deep-root ion exclusion strategies. Comparative insights from other woody genera are incorporated to highlight convergent and divergent mechanisms. On this basis, we propose an integrated multi-level regulatory model in which Na⁺ compartmentalization/efflux serves as the core, ROS homeostasis as the key regulatory axis, and osmotic adjustment as the auxiliary strategy. Outstanding challenges—including unresolved primary salt-signal perception, insufficient pathway integration, and limited in planta gene-function verification—are critically assessed, and future research priorities encompassing multi-omics integration, CRISPR-based gene editing, and natural-population genomics are outlined. Full article

The rapid proliferation of genetically modified (GM) crops and the uncontrolled distribution of GM-based food and feed have become a growing global concern, posing new challenges for regulatory oversight and traceability. The traditional PCR detection method cannot simultaneously meet the needs of high-throughput, high-specificity and high-sensitivity detection of transgenic organisms. In this study, a multiplex fluorescence PCR-capillary electrophoresis platform was developed by labeling primers of endogenous and exogenous genes with different fluorescent groups. The system enabled the simultaneous detection of 27 GM-related genes and events in a single analytical workflow. The results demonstrated accurate identification of all seven GM maize events, with correct detection achieved for each individual strain. In addition, the method enabled precise discrimination of a mixed sample containing five GM maize varieties. The assay also achieved a detection sensitivity of 0.1% in gradient mixtures with different GM contents. Our platform integrates a larger number of targets into a single PCR reaction, thereby simplifying the detection workflow while maintaining high analytical performance. Furthermore, the combination of multicolor fluorescence labeling and capillary electrophoresis provides high-resolution fragment discrimination and robust multiplex detection capability. This platform provides a novel and effective tool for rapid detection in food safety of transgenic crops and related areas, and can be applied in import/export inspection, quarantine, and biosafety surveillance. Full article

The continued rise in atmospheric carbon dioxide (CO₂) concentrations presents a strategic opportunity to harness climate change variables within the framework of precision agriculture. Despite the well-established role of elevated CO₂ (eCO₂) in enhancing biomass accumulation, its largely underexplored potential to drive the biosynthesis of secondary metabolites represents a more significant and promising avenue of investigation. This review appraises the physiological and molecular mechanisms through which eCO₂ enrichment redirects metabolic flux toward secondary metabolite biosynthesis, with far-reaching implications for plant productivity and resilience. Special emphasis is placed on critically evaluating the scientific literature to explore how CO₂-mediated modulation of the carbon–nutrient balance (CNB) can be strategically leveraged to enhance secondary metabolite yields. Moving from observation to application, integrated strategies are proposed to exploit CO₂ enrichment in advanced bioreactor systems and controlled-environment greenhouses as a means of maximizing bioactive compound production in ginseng. Pinpointing the regulatory sweet spots at which carbon saturation elicits maximum ginsenoside expression opens a promising avenue for engineering ginseng cultivation systems with sustainable potency and superior bioactivity. Though the full molecular architecture of these pathways in Panax awaits elucidation, converging evidence from related plant systems furnishes a credible mechanistic scaffold for future research. Full article

Pathogenesis-related (PR) proteins are crucial for plant defense against pathogen infection. However, the specific role of thaumatin-like proteins (TLPs), which comprise the PR-5 family, in plant immune responses has not been thoroughly investigated. Filipendula ulmaria is a medicinal plant with valuable pharmacological properties, including antimicrobial, anti-inflammatory, gastroprotective, immunomodulatory, and anticancer activities. The structure of the TLP family and its role in the immune system of meadowsweet have not been studied so far. The goal of this study was to analyze in detail the TLP gene family in meadowsweet and explore its response to fungal infection. In the meadowsweet genome, we identified 27 putative TLP genes, examined their structure and location on chromosomes, analyzed cis-regulatory elements in the promoter regions, predicted the structure and physicochemical characteristics of the encoded proteins, and performed a phylogenetic analysis. We also studied the differential expression of TLP genes under Bipolaris sorokiniana infection. Of six differentially expressed genes, three genes were up-regulated 48 h post-infection, suggesting their involvement in defense response to the fungus. The results obtained shed light on the role of the TLP gene family in the immune system of F. ulmaria and form the foundation for the creation of disease-resistant crops in agriculture and the development of bio-based antimicrobials in medicine. Full article