Search Results (423)

The three-amino-acid-loop-extension (TALE) gene family encodes a group of plant-specific homeodomain transcription factors that play indispensable roles in plant growth, development, and adaptation to environmental stresses. Although TALE genes have been extensively investigated in several plant species, their genome-wide characteristics and potential functions in maize, particularly in response to phosphorus deficiency, remain poorly understood. In the present study, a comprehensive genome-wide identification and characterization of the maize TALE gene family were conducted using bioinformatics approaches, followed by an investigation of their transcriptional responses to low-phosphorus (LP) stress. A total of 40 ZmTALE genes (ZmTALE1–ZmTALE40) were identified and phylogenetically classified into four subfamilies: BEL1-like, KNOX I, KNOX II, and KNOX III. Members within the same subfamily exhibited highly conserved gene structures and motif compositions, reflecting their evolutionary conservation. Chromosomal localization and synteny analyses demonstrated that segmental duplication has been the predominant force driving the expansion of the ZmTALE gene family during maize evolution. Promoter analysis revealed that the upstream regulatory regions of ZmTALE genes were enriched in light-responsive, phytohormone-responsive, and abiotic stress-related cis-acting regulatory elements, implying their potential involvement in multiple developmental and stress-responsive pathways. Expression profiling under LP conditions revealed pronounced genotype-dependent transcriptional responses among different maize inbred lines. Notably, ZmTALE1/5/12/14/18/30/31/33/36 were significantly induced by LP stress, whereas ZmTALE10 and ZmTALE37 were markedly repressed. These differentially expressed genes represent promising candidates for further functional investigation of phosphorus-deficiency tolerance in maize. Furthermore, ZmTALE10, ZmTALE14, and ZmTALE31 are nuclear-localized transcriptional activators. Taken together, these findings provide valuable insights into the evolutionary characteristics and potential biological functions of the maize TALE gene family and offer candidate genes for developing phosphorus-efficient maize cultivars through molecular breeding. Full article

Fruit firmness is a pivotal agronomic and commercial trait that determines the storability, transport tolerance and edible quality of tomato (Solanum lycopersicum L.). Fruit softening severely restricts postharvest performance and economic benefits of tomato products worldwide. This review summarizes the latest research progress on factors and regulatory mechanisms governing tomato fruit firmness. Multiple environmental factors including temperature, light, moisture and atmospheric composition jointly affect cell wall structure and metabolism, thereby altering fruit firmness. Mineral nutrition, postharvest handling and pathogen infection also exert profound impacts on texture characteristics by modulating physiological activities and cell wall integrity. Phytohormones such as gibberellin, ethylene, abscisic acid, jasmonic acid and salicylic acid form complex signaling crosstalk to mediate fruit softening processes. Furthermore, we elaborate on the functions of transcription factors, quantitative trait loci, and key functional genes, as well as research advances in transcriptomics and metabolomics, including transcriptome analyses identifying differentially expressed genes related to cell wall remodeling, and metabolomic profiling revealing hydroxyproline and galacturonic acid as firmness-associated markers. Cell wall metabolism is confirmed as the core pathway controlling fruit softening. Finally, future research directions are proposed, focusing on single-cell and spatial transcriptomics to map softening regulatory networks, AI-driven predictive modeling for softening kinetics and shelf-life optimization, and CRISPR/Cas9-based gene editing for precise trait improvement. Full article

Wheat is a globally important staple crop, whose growth and yield formation rely on the precise regulation of phytohormone signaling. The PR10/Bet v 1 (Pathogenesis-related protein 10/Betula verrucosa 1) family consists of conserved small-molecule ligand-binding proteins that participate in phytohormone signaling and plant development; however, systematic investigations of this family in wheat remain limited. Here, we performed a genome-wide identification of 75 PR10/Bet v 1 members in wheat, which were phylogenetically classified into three subfamilies: 21 known members belonging to the PYL (Pyrabactin resistance 1-like) subfamily, and 54 members assigned to two previously uncharacterized subfamilies. Bioinformatic analyses revealed that whole-genome/segmental duplication has driven the expansion of this gene family, which has evolved under strong purifying selection. Expression profiling and promoter analysis revealed differential expression patterns, along with abundant cis-acting elements responsive to multiple hormones. Quantitative RT-PCR (qRT-PCR) of 12 representative genes revealed marked transcriptional changes in several members within 1 h of treatment with BR (Brassinosteroid), ABA (Abscisic acid), CK (Cytokinin), or SA (Salicylic acid) suggesting that these genes may be directly involved in hormone-regulated processes. This study provides a fundamental framework for exploring the regulatory functions of the wheat PR10/Bet v 1 family, and valuable hormone-responsive candidate genes for the genetic improvement of wheat agronomic traits. Full article

Somatic embryogenesis (SE) is an indispensable biotechnological platform for plant regeneration, micropropagation and genetic modification. Members of WUSCHEL-related homeobox (WOX) transcription factor family are key regulators in SE, yet their roles in Catalpa bungei remain largely unexplored. C. bungei is a high-quality ornamental tree species endemic to China with prominent horticultural ornamental value. Here, we present the first genome-wide identification and expression profiling of the CbWOX gene family during SE in C. bungei. Fourteen CbWOX genes were identified and phylogenetically classified into three major clades. These genes are distributed across the 11 chromosomes of C. bungei, and their promoter regions are enriched with cis-regulatory elements associated with phytohormone response, stress adaptation, and growth/development. Integrated transcriptome and quantitative real-time PCR (qPCR) data indicated that CbWOX2, CbWOX5, CbWOX8, and CbWOX9 were highly expressed in embryogenic callus (EC), while CbWOX1.1 and CbWOX13 were predominantly expressed in non-embryogenic callus (NEC). Notably, only eight of the fourteen CbWOX genes were significantly expressed during SE, with distinct expression profiles across developmental stages. CbWOX4.1 and CbWOX4.2 were specifically associated with yellow-green hypocotyl callus development, while CbWOX2 and CbWOX8 were highly expressed at the EC stage. During later SE stages, CbWOX1.2, CbWUS, CbWOX5, and CbWOX13 showed significant expression at the globular embryo (GE) stage, while CbWOX1.3 was specifically upregulated at the cotyledon embryo (CE) stage. Our study provides a comprehensive genomic and transcriptomic foundation for the CbWOX family in C. bungei and reveals candidate genes with stage-specific expression during SE. These findings lay a solid basis for subsequent functional research to boost SE efficiency and advance the large-scale propagation of this precious ornamental tree. Full article

The calcium ion-transporting ATPase (Ca²⁺-ATPase) gene family maintains plant intracellular Ca²⁺ homeostasis and regulates growth, development and stress immunity; however, its functions remain poorly characterized in Malus domestica. Here, we performed a genome-wide identification of apple Ca²⁺-ATPase genes and obtained 45 members, which were classified into MdACA (39) and MdECA (6) subfamilies and unevenly distributed on 14 chromosomes. Phylogenetic analysis of Ca²⁺-ATPase genes from Malus domestica, Arabidopsis thaliana, and Oryza sativa classified these proteins into five subgroups. The ACA and ECA subfamilies were highly conserved across species, whereas Group D was apple-specific. Collinearity and Ka/Ks analyses indicated that segmental duplication and purifying selection dominated the evolution of apple Ca²⁺-ATPase genes. Promoter cis-element prediction uncovered numerous regulatory elements related to phytohormone signaling, growth, development and stress defense. Codon usage bias analysis indicated that AUG (methionine) was the dominant codon. Tissue expression profiles showed differential expression of apple Ca²⁺-ATPase genes in various organs. Quantitative real-time PCR (qRT-PCR) assays demonstrated widespread responses of Ca²⁺-ATPase genes to Alternaria alternata infection, exogenous CaCl₂, salicylic acid (SA) and methyl jasmonate (MeJA), among which MdACA39 was strongly induced under all treatments. Subcellular localization verified that MdACA39 resides on the plasma membrane. Moreover, transient overexpression of MdACA39 significantly enhanced apple resistance to A. alternata, likely due to the activation of SA, MeJA and Ca²⁺ signaling-mediated immune pathways, the induction of disease resistance-related genes, and elevated antioxidant enzyme activity. Collectively, this study systematically characterizes the apple Ca²⁺-ATPase family and identifies MdACA39 as a key regulator of fungal resistance, providing valuable gene resources for dissecting Ca²⁺ signaling-mediated disease resistance in apple. Full article

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 ubiquitous use of the plant hormone indole-3-acetic acid (IAA) or auxin in modern agriculture has led to its emergence as a water contaminant, necessitating efficient removal technologies. Addressing the need for high-performance sorbent materials, this study reports the synthesis and characterization of four novel nanocomposites based on halloysite (Hal), bentonite (Ben), sepiolite (Sep), and diatomaceous earth (DE) functionalized with silver nanoparticles (AgNPs). Successful immobilization and morphological features were confirmed via XRD and SEM-EDS. Crucially, post-adsorption EDS analysis provided direct solid-state evidence of pollutant capture through the distinct quantification of organic carbon. High-Performance Liquid Chromatography (HPLC) tests demonstrated that all functionalized materials exhibited a drastically enhanced IAA adsorption capacity over their pristine counterparts during a 96-h kinetic monitoring window. Kinetic profiling revealed a biphasic adsorption pathway characterized by a rapid initial sequestration within the first 10 h followed by a diffusion-limited equilibration, while thermodynamic modeling converged excellently with Langmuir and Sips equations, confirming a surface-confined chemisorption mechanism governed by uniform monolayer deposition. Notably, the performance ranking was found to be primarily governed by the architectural accessibility of the silicate frameworks rather than the absolute magnitude of their specific surface area. Furthermore, solution-phase spectroscopic studies coupled with Dynamic Light Scattering (DLS) and Zeta Potential measurements unraveled a robust, surface-confined ligand exchange mechanism. Rather than triggering colloidal aggregation, IAA coordination induced a controlled, systematic development of an organic molecular shell around the individual silver cores. This work underscores the potential of these engineered AgNPs@silicate platforms as sustainable, high-efficiency materials for the environmental remediation of emerging phytohormone contaminants. Full article

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

Camellia oleifera is a significant woody oil tree species native solely to China. The bud–seedling grafting technique has been widely applied to this tree due to its significant advantages in improving propagation efficiency and shortening the growth cycle. However, the healing process and its underlying molecular regulatory mechanisms during interspecific heterografting in Camellia remain poorly understood. In this study, we established both homografting and heterografting systems using C. oleifera bud seedlings as rootstocks, grafted with scions from C. oleifera, C. meiocarpa, and C. weiningensis. We systematically investigated the response patterns and differences in metabolites and gene expression before and after grafting healing through endogenous hormone detection, LC-MS untargeted metabolomics, and transcriptomic sequencing. The results showed that the grafting survival rates between C. oleifera and the other species were high (>88%), indicating strong compatibility. Metabolomic analysis revealed that differential metabolites, such as Gibberellin A53, Sophoramine, and Morellin, accumulated significantly with prolonged grafting time, and interspecific grafting combinations exhibited specific highly expressed metabolite profiles. We integrated multi-dimensional data comprising hormone levels, differential metabolites, and DEGs. A “hormone-gene” interaction network was constructed using WGCNA. The analysis revealed that key hub genes, including CYP73A, F3H, CHS, LHCA1, and LHCB5, were significantly correlated with flavonoid biosynthesis and elevated iPR content. We hypothesize that these genes enhance graft healing capacity by regulating secondary metabolism and hormone signaling pathways. The identified candidate genes, phytohormones, and metabolites provide potential molecular markers and regulatory targets for evaluating graft compatibility, selecting suitable rootstock–scion combinations, and optimizing grafting and propagation practices in C. oleifera, providing a crucial theoretical basis for superior cultivar breeding and the investigation of graft compatibility mechanisms. Full article

Seed germination of Paris polyphylla var. yunnanensis is intrinsically low, severely restricting its artificial propagation. Despite the known roles of ABA and GAs, the regulatory functions of other phytohormones in this process remain largely unexplored. In this study, we integrated transcriptomic and targeted metabolomic profiling to systematically investigate the dynamics of 34 phytohormones and global gene expression patterns across five germination stages of P. polyphylla seeds. Seven hormones showed significant changes during germination, including auxins, melatonin, cytokinins, and jasmonate, which exhibited distinct accumulation patterns. Integrative correlation analysis further uncovered candidate genes potentially involved in hormone biosynthesis and signaling. Collectively, our findings provide new insights into the hormonal regulation of seed germination in P. polyphylla, establish a foundational framework for understanding its germination mechanisms, and offer candidate molecular targets for improving seed propagation efficiency. Full article

Background: The urgent need for sustainable agricultural drives the search for effective microbial biostimulants. Cyanobacteria of the order Nostocales are promising candidates due to their nitrogen-fixing capabilities and bioactive secondary metabolites. However, the genomic potential of many soil strains from microorganism collection remains largely unexplored. Methods: We performed a targeted genomic screening of five cyanobacterial strains from the All-Russian Collection of Microorganisms (VKM): Nostoc commune VKM Al-35, Nostoc punctiforme VKM Al-37, Nostoc minutum VKM Al-168, Anabaena pirinica VKM Al-153, and Hassallia pseudoramosissima VKM Al-158. The workflow involved WGS, de novo assembly, and comparative metabolic profiling using KEGG, SEED, PLaBAse, antiSMASH, and RhizoSMASH to identify predicted plant growth-promoting (PGP) traits, biosynthetic gene clusters (BGCs), and rhizosphere competence mechanisms. Biosafety was evaluated via Comprehensive Antibiotic Resistance Database (CARD) and in silico toxomics screening. Results: High-quality genome assemblies were obtained for all strains (completeness > 99%). Functional annotation uncovered complete genetic machinery for nitrogen fixation, predicted phosphate mobilization, and phytohormone biosynthesis pathways. Comparative analysis revealed two distinct genomic strategies: a versatile support profile in Nostoc strains (expanded genomes and diverse accessory pathways) and a specialized stimulation profile in Anabaena and Hassallia strains (focused phytohormone pathways). Comprehensive CARD and antiSMASH screenings demonstrated an excellent biosafety profile, confirming the complete absence of regulated cyanotoxin clusters or acquired antibiotic resistance genes of clinical concern. Conclusions: This genome-based bioprospecting serves as a cost-effective pre-selection filter, providing a strong scientific rationale for downstream experimental validation of these strains. The presence of predicted gibberellin biosynthesis pathways and T6SS/T4SS secretion systems in H. pseudoramosissima VKM Al-158 represents a notable genomic feature among soil cyanobacteria. The identified genomic prerequisites suggest that these strains possess strong predictive potential for future development as safe biological resources for sustainable agriculture. Full article

Fusarium fujikuroi is an industrial producer of gibberellic acid (GA₃), a phytohormone of agricultural interest. Despite the high concentration of nutrients used for its production, GA₃ yields remain low, highlighting the importance of identifying the major metabolites synthesized during GA₃ synthesis. Therefore, the principal aim of this work was to evaluate organic acid production during F. fujikuroi batch cultures by determining GA₃ production and organic acid profiles using Fourier transform infrared spectroscopy (FTIR) and liquid chromatography (HPLC) analysis. Significant differences in compound quantification were found; five organic acids, namely lactic, malic, citric, succinic and maleic, were detected by HPLC (in g/L: 101.09, 10.66, 2.80, 6.94 and 1.07, respectively). In addition, eight organic acids were determined by FTIR, namely lactic, butyric, pyruvic, fumaric, malic, succinic, maleic and oxalic (in g/L: 62.97, 19.19, 11.92, 7.54, 2.30, 4.36, 1.25 and 1.06 g/L, respectively). GA₃ production was also quantified, reaching nearly 5.0 g/L as determined by HPLC and UV-Vis, and FTIR yielded 2.20 g/L. This report found that the low yields obtained in GA₃ production are related to the side conversion of raw materials into organic acids as byproducts. In addition, the FTIR technique can be employed as an innovative strategy for the quantification of metabolites to provide relevant information on F. fujikuroi metabolic regulation. This enables the spread of its application as a biotechnological tool in high-value-added processes with potential for industrial-scale GA₃ production. 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

Aerobic composting of food waste (FW) is constrained by delayed temperature increase initially. This study evaluated the use of high-solid anaerobic digestion (HSAD) biogas residue as a composting initiator. In the co-composting treatment containing biogas residue and FW (C3), the temperature peaked at 69.8 °C on day 5. In comparison, the FW composting alone (C1) reached a lower peak temperature of 67.1 °C on day 8. Similarly, C3 sustained the thermophilic phase (>55 °C) for 10 days, comparable to the 11 days observed in C1. The incorporation of biogas residue adjusted the pH of FW toward neutrality, helping to reduce nitrogen loss. C3 also demonstrated a distinctive phytohormone profile, with salicylic acid (SA) content reaching 42.62 ng g⁻¹, significantly exceeding that of C1 (31.54 ng g⁻¹), suggesting enhanced bio-stimulatory potential. Compared with C1, N₂O emissions in C3 were both reduced and delayed, while cumulative CH₄ emissions were lower than those in the biogas-residue-alone composting (C2). Biogas residue addition introduced thermotolerant microbes, reduced acidification by suppressing acidophiles, and enhanced humification via cooperative networks. Metagenomics revealed that C3 developed a denitrification gene profile favoring net N₂O consumption under high pH. These results demonstrate that HSAD biogas residue can serve as an effective initiator for FW composting. Full article

Rho GTPase-activating proteins (RhoGAPs) are characterized by a conserved RhoGAP domain and function as negative regulators of Rho GTPases, playing important roles in plant growth, development, and responses to environmental stimuli. In this study, 19 GmRhoGAP genes were identified in the soybean genome and found to be unevenly distributed across 11 chromosomes. Comprehensive analyses were performed, including gene structure, conserved motifs, protein domains, gene duplication, synteny, cis-acting elements, tissue-specific expression, and quantitative real-time PCR under rhizobial infection. Structural analysis revealed substantial diversity in intron-exon organization but high conservation of motif composition, with all members containing the conserved RhoGAP domain. A total of 20 segmentally duplicated gene pairs were identified, indicating expansion of the GmRhoGAP family in soybean. Inter-species synteny analysis showed closer evolutionary relationships with Arabidopsis than with rice, and Ka/Ks analysis suggested strong purifying selection during evolution. Promoter analysis indicated potential involvement in development, phytohormone signaling, stress responses, and light responsiveness. Expression profiling demonstrated distinct tissue-specific patterns. qRT-PCR further showed that GmRhoGAP genes respond differentially to rhizobial infection, with 10 generally upregulated genes and 4 downregulated genes. These analyses provide a framework for understanding this gene family and identify candidate genes for future research. Full article