Search Results (1,771)

Trihelix is a class of transcription factors unique to plants that play a major role in abiotic and biotic stress responses, seed isolate development, floral organ morphogenesis, and plant photomorphogenesis. Nevertheless, the Trihelix transcription factor family in Gardenia jasminoides (G. jasminoides) has not been systematically characterized. In this study, 11 GjTrihelix genes were identified from the G. jasminoides genome, unevenly distributed across five chromosomes, and can be classified into four subfamilies: GT-1, GT-2, SIP and SH4. Gene structure and functional motif analyses revealed high conservation within the same subfamily. Cis-acting element analysis showed that these genes are closely related to hormone responses, stress responses, and growth and development processes. Intraspecific synteny analysis showed a segmental duplication between GjTrihelix-3 and GjTrihelix-10. Interspecific collinearity analysis revealed that G. jasminoides shared 21 collinear gene pairs with soybean, compared with five pairs with Arabidopsis and 13 with Populus, indicating greater syntenic block conservation between G. jasminoides and soybean. Transcriptome data analysis demonstrated distinct spatiotemporal expression specificity of this gene family. Several genes were constitutively expressed in fruits; GjTrihelix-1 and GjTrihelix-3 were predominantly expressed in green fruits, while GjTrihelix-11 was highly expressed in red fruits. Under melatonin treatment, five GjTrihelix genes showed significant up-regulation and obvious transcriptional suppression of another five genes. Following infection by Botryosphaeria dothidea, GjTrihelix-5 and GjTrihelix-7 were progressively induced and peaked at 72 h. qRT-PCR results indicated that most GjTrihelix genes were highly expressed in leaves, while GjTrihelix-11 was highly expressed in flowers. Most GjTrihelix genes were significantly down-regulated under NaCl, ABA, GA₃ and IAA stresses. This study provides new insights into the potential association of the Trihelix transcription factor family in G. jasminoides growth, development, and stress adaptation, offering theoretical references for stress-resistant G. jasminoides breeding. Full article

Sucrose non-fermenting protein 7 (SNF7) is a core operator of the endosomal sorting complex required for transport III (ESCRT-III) component mediating protein sorting and degradation. To date, the SNF7 gene family remains poorly characterized in plants, particularly in maize (Zea mays L.). Here, we integrated bioinformatic and transcriptomic analyses to systematically characterize the ZmSNF7 gene family and its regulatory potential in stress responses. In total, 20 ZmSNF7 genes were identified genome-wide and classified into three phylogenetic clades, with conserved motifs and similar tertiary structures within the same clade. Abundant hormone- and stress-responsive cis-elements were detected in their promoters. Protein interaction prediction indicated ZmSNF7 proteins interact with intra-family members and other ESCRT components. Gene Ontology (GO) enrichment analysis suggested ZmSNF7s are primarily involved in endomembrane system organization and vesicular trafficking. Transcriptomic data revealed divergent ZmSNF7 expression patterns under drought, Rice black-streaked dwarf virus (RBSDV) infection, Colletotrichum graminicola (C. graminicola) inoculation and Asian corn borer (ACB) infestation. Collectively, this study comprehensively characterized the ZmSNF7 gene family and broadened our functional understanding of ZmSNF7 in mediating plant responses to biotic and abiotic stresses. Full article

Endo-β-1,4-mannanases (MANs) are glycoside hydrolase family 5 (GH5) enzymes that degrade cell wall mannan polysaccharides and participate in plant growth and stress adaptation. This gene family has not been systematically characterized in common wheat (Triticum aestivum L.). Here, we identified 24 TaMAN genes (TaMAN1–TaMAN24) genome-wide and analyzed their phylogeny, gene structures, chromosomal distribution, synteny, and promoter cis-acting elements. Expression profiles under biotic and abiotic stresses were investigated using public databases, salt-stress RNA-seq, and RT-qPCR. TaMAN proteins (386–475 aa) were mainly predicted to localize in the extracellular space. Phylogenetic analysis divided them into three groups, with Groups II and III representing monocot-specific expansions. Family expansion was driven primarily by whole-genome duplication, supplemented by tandem duplication on homoeologous group 6. Promoters were enriched in hormone- and stress-responsive cis-acting elements (ABRE, as-1/CGTCA-motif, W box). TaMAN1, TaMAN5, TaMAN8, TaMAN9, TaMAN16 and TaMAN19 were significantly induced by powdery mildew, while TaMAN3, TaMAN4 and TaMAN19–TaMAN22 rapidly responded to salt stress. This study provides candidate genes for disease-resistant and salt-tolerant wheat breeding. Full article

Background: Glutathione S-transferases (GSTs) play pivotal roles in plant growth, abiotic stress responses, detoxification of xenobiotics, and maintenance of redox homeostasis. Methods: In this study, transcriptomic analysis was employed to identify differentially expressed genes (DEGs) in the pea cultivar DX27 under freezing stress (−4 °C) at 3, 6, and 12 h. Results:GO and KEGG enrichment analyses of global transcriptomic data further reveal that DEGs are significantly enriched in the following functional categories: oxidation–reduction processes, stress responses, glutathione metabolism, and secondary metabolite biosynthesis. A total of 52 PsatGST genes were identified and classified into nine subfamilies based on phylogenetic relationships. Chromosomal localization revealed a non-random distribution across seven chromosomes. Promoter cis-element analysis indicated that PsatGST genes harbor diverse regulatory elements associated with light responsiveness, hormone signaling (auxin, abscisic acid, gibberellin, salicylic acid, and MeJA), and abiotic/biotic stress responses. PsatGSTF2 expression analysis showed pronounced up-regulation under freezing stress (−4 °C) at 3, 6, and 12 h. Conclusions: These findings provide a foundational framework for understanding the evolutionary history and functional diversification of the PsatGST gene family and offer valuable candidate genes for the breeding of stress-tolerant pea varieties. Full article

Members of the EPIDERMAL PATTERNING FACTOR (EPF) and EPF-Like (EPFL) families perform diverse regulatory functions in plant tissue morphogenesis, controlling the development of stomata, awns, shoot apical meristems (SAMs), and inflorescences. Nevertheless, the biological functions of OsEPF/EPFL family members in mediating responses to biotic/abiotic stresses are not yet widely characterized. Here, we demonstrated abundant cis-acting elements in the putative promoters of OsEPF/EPFL genes, including those associated with dehydration-, MeJA-, MYB binding site for drought, stress-, and ABA-responsive element. We performed a systematic analysis of the expression patterns of all OsEPF/EPFL family members under heat, cold, drought, and salt stress treatments. Among these genes, OsEPFL9 and OsEPFL10 exhibited rapid and sustained up-regulation across all four stress conditions. Furthermore, the majority of OsEPF/EPFL members were up-regulated specifically in response to salt stress. In terms of biotic stress responses, OsEPF2/5/7/10 were rapidly induced as early as 12 h post-infection (hpi) with the rice blast pathogen (Magnaporthe oryzae). Functional validation further revealed that its deficiency causes increased sensitivity to both M. oryzae and Xanthomonas oryzae pv. oryzae (Xoo). Collectively, our research will provide significant insights into the multifunctional roles of the OsEPF/EPFL gene family, particularly in stress responses. This work also establishes a theoretical basis and scientific reference for the application of plant small secreted peptides (SSPs) in crop disease resistance breeding and stress tolerance improvement. Full article

Background/Objectives: Phytocystatins are plant-specific inhibitors of papain-like cysteine proteinases that participate in plant development and responses to biotic and abiotic stresses. The roles of rice (Oryza sativa L.) phytocystatins under cold stress remain poorly understood. Xiaomagu (XMG), a cold-tolerant japonica rice landrace, provides valuable material for exploring phytocystatin transcript responses to low-temperature stress. This study characterizes 12 rice phytocystatin genes isolated from XMG and investigates their transcript profiles under cold and abscisic acid (ABA) treatments. Methods: Twelve phytocystatin genes were isolated from the cold-tolerant japonica rice landrace Xiaomagu. Sequence characterization and conserved domain analysis were performed for these phytocystatin family members. Real-time quantitative PCR was performed to examine transcript abundance of phytocystatin genes: low-temperature stress was applied to leaf and root tissues, while ABA treatment was carried out for leaf tissues only. Results: Conserved domain analysis revealed structural differences among the identified phytocystatin members. Real-time quantitative PCR detected distinct transcriptional responses to cold stress among these phytocystatin genes. In leaves, OsCST1, OsCST8, and OsCST12 were up-regulated, whereas OsCST11 was down-regulated. In roots, OsCST2, OsCST3, OsCST6, and OsCST12 showed increased transcript levels, while OsCST1 and OsCST11 were down-regulated. OsCST2, OsCST6, and OsCST11 exhibited significantly altered transcript abundance under ABA treatment. Conclusions: This study characterizes transcript-level responses of 12 phytocystatin genes from the cold-tolerant rice landrace Xiaomagu (XMG) under cold and ABA treatments. The detected expression changes reflect stress-responsive transcriptional regulation of rice phytocystatin family genes. Further in planta functional assays and comparisons with cold-sensitive genotypes are needed to elucidate their precise roles in rice cold adaptation. Full article

Grafting profoundly influences fruit tree performance, yet the molecular mechanisms underlying rootstock–scion interactions in mulberry (Morus multicaulis) remain poorly understood. To investigate the regulatory networks linking grafting to scion physiology, we performed an integrated analysis combining small RNA sequencing, transcriptome-based KEGG pathway assessment, and qRT-PCR validation of key target genes across five rootstock–scion combinations. High-throughput miRNA profiling of phloem tissues identified 71 conserved and 156 novel miRNAs, which exhibited distinct, genotype-dependent expression patterns. Recurrent activation of nutrient- and stress-responsive families (e.g., miR399, miR397, and miR395) was observed. Target prediction and functional enrichment analyses revealed that these miRNAs likely regulate pathways related to metabolic processes, hormone signaling, cell wall modification, and stress responses. The expression trends of their predicted target genes—including TCP4, Laccase-3, and ATP sulfurylase 1—were subsequently confirmed by qRT-PCR, revealing significant rootstock-specific regulation. Collectively, this study establishes a reference framework for elucidating the molecular mechanisms underlying scion biological processes in Morus species, which is of great significance for improving fruit quality, enhancing abiotic and biotic stress resistance, and boosting long-term planting productivity. Full article

The Andes serve as natural laboratories where biomes shape faunal communities into mosaics of habitats prone to fragmentation, making protected areas such as the Chimborazo Reserve (RC) critical refuges in the face of climate change. Based on this premise, patterns of biotic specialization and inter-biome faunal connectivity were evaluated through the ordering and co-scaling of family-level taxa in factorial space. A geospatial design was employed, stratifying the area into 400 ha cells, which were distributed across the high-Andean tundra (T), paramo grassland (G), and Andean forest (F) biomes and selected via simple proportional random sampling. A validated database of 2511 occurrences was compiled for the classes reptilia, aves, mammalia, amphibia, and insecta, comprising a total of 48 families, integrating records from global platforms and field surveys. The resulting matrix of 102 sampling cells (across three biomes) with 48 taxonomic families was analyzed using principal component analysis (HJ-biplot), k-means clustering, and bidirectional biclustering. It was found that Cluster 3 reflected a marked ecotone effect and faunal connectivity between F and G, dominated by generalist families with high evolutionary success such as Thraupidae, Tyrannidae, and waterbirds. In contrast, Clusters 1 and 2 revealed structural discontinuities and high biogeographic specialization in response to abiotic stress in the tundra, isolating taxa adapted to extreme conditions (Tropiduridae, Cricetidae, and Thinocoridae). Biclustering confirmed that the heterogeneity of the terrain mitigates climatic severity at the forest edge, acting as a microclimatic refuge for specialized nectar-eaters (Trochilidae) associated with Chuquiraga jussieui. The zoological structure of the RC reflects a distinct and predictable faunal partition that is strongly influenced by the interaction between the altitudinal gradient and microtopography. The coexistence of zones of diffuse transitions that promote biotic connectivity alongside nuclei of maximum specialization and ecological isolation was confirmed, which is essential for planning conservation measures. Full article

Moruga Hill Rice (MHR) is an African rice (Oryza glaberrima Steud.) brought to Trinidad by formerly enslaved African Americans and has been grown for many generations in Trinidad at subsistence and commercial scale. Despite its historical and agricultural significance, genomic resources specific to MHR remain unexplored, and its genetic composition, evolutionary history, and potential agronomic traits have not been characterized. This current study presents the first draft genome assembly of the MHR genome using a hybrid sequencing approach. The MHR genome size was found to be ~372.9 Mb with 56,073 predicted genes. Variant analysis revealed a total of 3,318,242 variants, of which 2,440,476 were SNPs, and 877,766 were InDels. Several candidate genes encoding proteins with orthology to previously characterized biotic resistance and abiotic stress-responsive genes in rice were identified. Potential gene families identified prompt further investigation of their roles in MHR drought and salt stress responses. Phylogenomic analysis of O. glaberrima landraces suggests that MHR shares close genetic affinity with the IRGC−104595 Malian landrace, consistent with historical records. This assembly thus expands the African rice genomic repository, providing a foundation to understand the genetic architecture underlying key phenotypic traits and identifying potential novel gene sources in MHR for rice improvement in the Caribbean region. Full article

Brassinosteroids (BRs) are essential steroidal phytohormones that regulate plant growth, development, and responses to environmental stresses. Recent studies have demonstrated the important roles of BRs in enhancing plant tolerance to abiotic stresses, including drought, salinity, temperature extremes, heavy metal toxicity, and oxidative stress, as well as biotic stresses caused by pathogens and herbivores. This review summarizes current advances in BR biosynthesis, metabolism, transport, and signaling pathways, focusing on key components that mediate stress adaptation. We discuss the physiological and molecular mechanisms through which BRs improve stress tolerance, including regulation of antioxidant defense, ion homeostasis, osmotic adjustment, and stress-responsive gene expression. Particular attention is given to the extensive cross talk between BRs and other phytohormones, such as abscisic acid, jasmonic acid, salicylic acid, ethylene, auxin, and gibberellins, which enables plants to balance growth and defense under adverse conditions. Furthermore, we highlighted the potential applications of BRs in crop improvement through exogenous treatments, genetic engineering, and genome-editing approaches. However, the effectiveness of BR-based strategies is highly dependent on crop species, developmental stage, stress type, BR concentration, application method, and environmental conditions. In addition, excessive BR accumulation or application may result in undesirable growth responses, and further multi-location field validation is required before widespread agricultural implementation. Finally, we discuss emerging research trends, current knowledge gaps, and future perspectives for exploring BR signaling to develop climate-resilient crops. Overall, BRs represent promising targets for improving crop stress resilience; however, optimizing BR-mediated strategies and validating their long-term performance under diverse field conditions will be essential for their successful application in sustainable agriculture. Full article

Background: Autophagy plays a central role in maintaining cellular homeostasis, regulating growth and development, and responding to multiple stresses. Autophagy-related genes (ATGs) play critical roles in autophagy, yet their functional diversity in soybean (Glycine max) remains underexplored. Methods: Genome-wide identification of GmATG genes was performed using sequence similarity and domain-based searches against the Wm82.gnm4 reference genome, followed by characterization of physicochemical properties, chromosomal distribution, phylogenetic relationships, gene duplication, conserved motifs, gene structure, three-dimensional structural, and promoter cis-acting elements. Tissue-specific expression and multiple stresses response were examined using transcriptome data and profiled by RT-qPCR. Results: A total of 60 GmATG genes belonging to 20 subfamilies were identified in soybean. Gene family expansion was predominantly driven by fragment duplication (33 gene pairs), with the ATG8 family expanding to 12 members, and pan-genomic analysis uncovered prominent copy number variation (6–9 copies) in the ATG18 family. GmATG genes showed distinct expression patterns in response to multiple abiotic and biotic stresses. Specifically, GmATG18f was significantly induced by phosphorus deficiency in the low-phosphorus-tolerant soybean variety Nannong 94-156. GmATG8g, GmATG9d and GmATG13d showed a typical expression trend of initial increase followed by decrease, with expression levels peaking at 6–12 h after salt stress treatment. GmATG8g and GmATG9d were rapidly upregulated at the early drought stress stage, while GmATG13a maintained sustained upregulation. In response to Phomopsis stem rot, GmATG7a/8h/8i/11/13d/18e/18f displayed differential expression in resistant and susceptible soybean materials. Conclusions: This study systematically characterizes the composition, expansion and stress response patterns of the GmATG gene family, revealing functional differentiation among family members. The identified key candidate genes, including abiotic-stress-regulated GmATG8g/9d/13d/18f and biotic-stress-regulated GmATG7a/8h/8i/11/13d/18e/18f, provide valuable genetic resources for the molecular breeding of stress-tolerant soybean. Full article

The Bcl-2-associated athanogene (BAG) gene family plays vital roles in plant growth, development, and biotic and abiotic stress responses. Previous work has demonstrated that tomato SlBAG9, a group II BAG member, negatively regulates plant thermotolerance. However, the regulatory mechanisms governing SlBAG9 expression remain poorly understood. In this study, we isolated and characterized the authentic 1486 bp full-length promoter (P1) of SlBAG9 from the tomato genome. Building upon our previous transcript-level observations, we provide here a detailed functional characterization of this promoter at the cellular and tissue level. In silico analysis identified several key cis-acting regulatory elements, including abscisic acid-responsive elements (ABRE), anaerobic response elements (ARE), and a heat shock element (HSE1). We used stable transgenic tomato plants carrying SlBAG9pro::GUS to verify that the full-length promoter was capable of driving the expression of β-glucuronidase reporter gene (GUS) in transgenic tomato plants, showing GUS staining was detectable in the roots, stems, leaves, flowers, fruits, and seeds, with the highest activity in red-ripe fruits. Notably, GUS activity was significantly upregulated by high temperature (HT) but not by PEG, NaCl, ABA, or cold treatments. To further dissect the HT-responsive regulatory module, we generated three 5′-terminal deletion fragments (−386 bp, P2; −239 bp, P3; and −113 bp, P4) and fused them to GUS. Under HT stress, the smallest deletion P4 showed negligible GUS activity, whereas P1, P2, and P3 retained significant activity. Furthermore, site-directed deletion of the HSE1 element in the full-length context (MU-P1) abolished HT inducibility, confirming that HSE1 serves as a critical positive HT-responsive element. Collectively, these findings confirm and extend our observations that SlBAG9 is a stress-responsive gene, and the characterized HSE1-dependent promoter module represents a promising candidate for genetic engineering aimed at enhancing thermotolerance in crops. Full article

Olive leaves represent a metabolically active tissue that plays an important role in plant responses to biotic stress. The present study comprised two independent experiments investigating biochemical responses of olive leaves to bacterial and fungal challenge under controlled conditions. Changes in primary metabolites (sugars, organic acids and free amino acids), phenolic compounds and lipid peroxidation were analyzed using chromatographic and spectrophotometric methods. In the bacterial experiment, pronounced differences were observed in primary metabolism. Tryptophan concentrations ranged from approximately 50 mg kg⁻¹ DW to more than 360 mg kg⁻¹ DW in ‘Istarska bjelica’, while sucrose concentrations reached up to 87 g kg⁻¹ DW, demonstrating cultivar-dependent differences in carbohydrate metabolism. Phenolic profiling showed that secoiridoids were the dominant phenolic class, with oleuropein concentrations exceeding 27 g kg⁻¹ DW across bacterial treatments. In the fungal experiment, amino acids showed greater variability than sugars and phenolic compounds, whereas MDA concentrations ranged from approximately 190 to 300 nmol g⁻¹ DW but did not differ significantly among pathogen treatments. Overall, the two experiments showed distinct patterns of metabolite variation associated with bacterial and fungal challenge. These findings contribute to a better understanding of cultivar-dependent metabolic responses and provide a basis for future studies of olive–microbe interactions. Full article

Background: Histone 3 lysine 27 tri-methylation (H3K27me3) is a chromatin mark typically associated with transcriptional repression. Histone demethylation, and particularly the removal of H3K27me3, has been linked to abiotic stress tolerance in plants. However, less is known about its role in biotic stress responses. Methods: We exploited immunity-related transcriptomics data combined with chromatin-state data to identify an association between chromatin modifications and plant immunity in Arabidopsis thaliana. We also measured the expression and H3K27me3 levels at immune-responsive loci, at Col-0 and at histone deacetylase mutants. Results: We identified H3K27me3 as a mark correlated with the silencing of defence gene loci. Moreover, we showed that the expression of a subset of flg22-induced genes is repressed by H3K27me3 prior to elicitation, and that expression negatively correlates with the mark upon activation of immunity. Notably, our studies also revealed a role for the H3K27 demethylase REF6 in plant defence. Loss of REF6 allows ectopic H3K27me3 deposition at target genes, revealing that these loci are actively regulated by the demethylase. Conclusions: Our data provide insight into the regulation of plant immune responses through chromatin dynamics. Full article

Trifoliate orange (Poncirus trifoliata L.), a citrus rootstock valued for its cold hardiness and resistance to broad biotic stress, produces desiccation-sensitive seeds whose successful germination requires optimized pre-sowing treatments for reliable sexual propagation. This study investigated whether chitosan-based coating systems, incorporating glycerol as a plasticizer combined with either an amino acid biostimulant (betaine-proline) or gibberellic acid (GA₃), could improve germination kinetics and seedling establishment. Seeds from mature fruits were subjected to 18 treatments across Petri dish and soil bioassays. In Petri dishes, the germination percentage remained uniformly high (86.67–100%), with GA₃-containing formulations promoting shoot elongation and proline-betaine combinations favoring root development. In soil, treatments primarily modulated germination kinetics: GA₃ combined with chitosan (1.5–2%) increased the germination speed by approximately 3.0–3.4 times relative to the control, while 1.5% chitosan with proline-betaine and glycerol yielded the fastest germination overall. Biomass responses were strongly formulation-dependent: 2% chitosan with GA₃ maximized shoot and total dry weight, whereas 2% chitosan with proline-betaine and glycerol substantially improved root dry biomass and overall seedling quality. Glycerol exerted context-dependent effects, enhancing amino acid formulations while reducing performance in GA₃ mixtures. These findings support the use of optimized chitosan-based treatments as effective tools for accelerating emergence and improving seedling robustness in rootstock production. Full article