Search Results (813)

Salt stress is a major form of abiotic stress that disrupts soybean germination and early seedling establishment. In this study, physiological, biochemical, and transcriptomic analyses—including germination index, antioxidant enzyme activity, and RNA-seq profiling—were conducted during soybean germination to elucidate early responses to salt stress and biostimulant treatment. A preliminary screening of six biostimulants (nanoparticle zinc oxide (NP-ZnO), nanoparticle silicon dioxide (NP-SiO₂), silicon dioxide (SiO₂), glucose, humic acid, and fulvic acid) revealed NP-SiO₂ as the most effective in promoting germination under salt stress. Under 150 mM NaCl, NP-SiO₂ increased the germination rate and length of the radicle compared with the control, also enhancing peroxidase and ascorbate peroxidase activities while reducing malondialdehyde accumulation, suggesting alleviation of oxidative stress. RNA sequencing revealed extensive transcriptional reprogramming under salt stress, identifying 4579 differentially expressed genes (DEGs) compared with non-stress conditions, while NP-SiO₂ treatment reduced this number to 2734, indicating that NP-SiO₂ mitigated the transcriptional disturbance caused by salt stress and stabilized gene expression networks. Cluster analysis showed that growth- and hormone-related genes suppressed by salt stress were restored under NP-SiO₂ treatment, whereas stress-responsive genes that were induced by salt were attenuated. Hormone-related DEG analysis revealed that NP-SiO₂ down-regulated the overactivation in the abscisic acid, jasmonic acid, and salicylic acid pathways while partially restoring gibberellin, auxin, cytokinin, and brassinosteroid signaling. Overall, NP-SiO₂ at 100 mg/L mitigated salt-induced oxidative stress and promoted early soybean growth by fine-tuning physiological and transcriptional responses, representing a promising nano-based biostimulant for enhancing salt tolerance in plants. Full article

MicroRNAs (miRNAs) are key post-transcriptional regulators of plant development and stress responses, with many being conserved across diverse plant lineages. In this study, we investigated the expression profiles of miRNAs and their corresponding target genes in Arachis stenosperma, a wild peanut relative that exhibits robust resistance to root-knot nematodes (RKN). Small RNA sequencing of nematode-infected roots identified 107 miRNA loci, of which 93 corresponded to conserved miRNA families and 14 represented novel candidates, designated as miRNOVO. Among these, 18 miRNAs belonging to 11 conserved families were identified as differentially expressed (DEMs). Notably, miR399 and miR319 showed the highest upregulation (logFC = 4.25 and 4.20), while miR393 and miR477 were the most downregulated (logFC = −0.83 and −0.79). Integrated analysis of miRNA and transcriptome data revealed several regulatory interactions involving key defense-related genes. These included NLR genes targeted by miR393 and miR477, hormone signaling components such as the auxin response factor ARF8 targeted by miR167, and the growth regulator GRF2 targeted by miR396. Additionally, miR408 was predicted to target laccase3, a gene involved in the oxidation of phenolic compounds, lignin biosynthesis, copper homeostasis and defense responses. Remarkably, four immune receptor genes belonging to the nucleotide-binding site leucine-rich repeat (NLR) family displayed inverse expression patterns relative to their regulatory miRNAs, suggesting miRNA-mediated post-transcriptional control during the early stages of nematode infection. These findings reveal both conserved and species-specific miRNA–mRNA modules associated with nematode resistance in A. stenosperma, highlighting promising targets for developing RKN-tolerant peanut cultivars through miRNA-based strategies. Full article

Antimony (Sb), a toxic metalloid, inhibits plant growth and threatens human health. Yellow Stripe-Like (YSL) proteins play crucial roles in metal ion transport and cellular homeostasis. While the OPT gene family has been characterized in some species, its genome-wide organization and functional involvement in Sb stress response remain unexplored in Brassica juncea. Here, we identified 47 high-confidence BjOPT genes and combined transcriptomic approaches to elucidate their regulatory roles under Sb stress. Phylogenetic tree, conserved motifs, and gene structure analyses consistently distinguished the BjOPT and BjYSL subfamilies. Comparative and collinearity analyses indicated that OPT genes in Brassica species (including B. rapa, B. nigra, and B. juncea) expanded independently of whole-genome triplication events. Transcriptomic profiling revealed significant enrichment of differentially expressed genes (DEGs) related to key biological processes (oxidative and toxic stress response, metal ion transport, and auxin efflux) and pathways (glutathione metabolism, MAPK signaling, and phytohormone transduction), highlighting their roles in Sb detoxification and tolerance. Notably, three BjYSL3 (BjA10.YSL3, BjB02.YSL3, and BjB05.YSL3) genes exhibited strong up-regulation under Sb stress. Heterologous expression in yeast demonstrated that both BjA10.YSL3 and BjB02.YSL3 enhance Sb tolerance, suggesting their potential role in transporting Sb–nicotianamine (NA) or phytosiderophore (PS) complexes. These findings advance our understanding of Sb tolerance mechanisms and provide a basis for developing metal-resistant crops and phytoremediation strategies. Full article

Melatonin (MT), an antioxidant and growth regulator, interacts with almost all phytohormones, but the molecular mechanisms of these interactions are poorly understood. Using mRNA sequencing (mRNA-seq) technology, we analysed the global regulation of MT-induced expression of genes involved in metabolism, signalling and responses to major phytohormones under prolonged high-intensity light (HL) stress. Plants respond to MT through the activation of auxin and brassinosteroid (BS) response genes, which were identified among the enriched categories of differentially expressed genes (DEGs) with increased expression, and the suppression of abscisic acid and ethylene signalling and response genes, which were among the enriched downregulated categories. MT also suppressed growth-inhibiting genes involved in jasmonic acid (JA) and salicylic acid (SA) signalling and response and activated genes encoding the growth-promoting hormones gibberellins and cytokinins (CKs), which is consistent with the role of MT in stress alleviation. However, the expression of some unique genes, which are positively or negatively modulated by stress, was reinforced by MT treatment, illustrating the extraordinary type of regulation that enhances the action of specific hormone-mediated mechanisms. The study of signal integration between MT and hormones with the involvement of signalling mutants revealed that some interactions are regulated at the transcriptional level and require the activity of relevant signalling pathways. Disruption of CAND2 completely abolished melatonin-dependent activation of the mitogen-activated protein kinases MAP3K17 and MKK7, suggesting that the MAP3K17-MKK7 module is an important player in the MT-triggered MAPK pathway, acting downstream of CAND2. Full article

Zygotic embryogenesis is a key process in the development and propagation of avocado (Persea americana). Plant growth regulators, particularly auxins and cytokinins, play a crucial role in regulating this process. In this study, a transcriptomic analysis was performed to identify and characterize the expression of genes related to biosynthesis, transport, signaling, or response to auxins and cytokinins during different stages of embryonic development, as defined by the varying sizes of collected fruits. Additionally, several transcription factors and genes related to embryogenesis were analyzed. The results reveal dynamic patterns of gene expression that suggest a coordinated interaction between these PGRs in embryo formation and differentiation. This study provides key insights into the molecular mechanisms that regulate avocado zygotic embryogenesis, with potential applications in biotechnology and plant propagation. Full article

Global temperature rise has become a critical challenge to agricultural sustainability, severely affecting crop growth, productivity, and survival. Human-induced climate change and greenhouse gas emissions cause heat stress, disrupting plant metabolism and physiology at all developmental stages from germination to harvest. Elevated temperatures during germination impair water uptake, enzyme activity, and energy metabolism, leading to poor or uneven seedling emergence. At key phases such as flowering and grain filling, heat stress limits photosynthesis and transpiration by inducing stomatal closure, restricting carbon dioxide intake, and reducing photosynthetic efficiency. The reproductive stage is particularly vulnerable to high temperatures, impairing pollen viability, preventing anther dehiscence, and reducing fertilization success. Membrane instability further accelerates chlorophyll degradation and leaf senescence. Heat stress also alters biochemical and hormonal balances by disrupting the synthesis and signaling of auxins, gibberellins, and abscisic acid (ABA). Elevated ABA promotes stomatal closure to enhance stress tolerance, while increased ethylene levels trigger premature leaf senescence and abscission. These hormonal shifts and oxidative stress hinder plant growth and reproduction, threatening global food security. Although plants employ adaptive mechanisms such as heat shock protein expression and stress-responsive gene regulation, current strategies remain inadequate, highlighting the urgent need for innovative approaches to improve crop resilience under rising temperatures. Full article

Oat (Avena sativa L.) is a vital cereal and feed crop grown worldwide, but its production is increasingly threatened by barley yellow dwarf virus (BYDV) and aphid infestations in arid and semi-arid regions, particularly in northern China. This study explores the transcriptomic and physiological responses of two oat cultivars MN10253 (resistant) and Qingyin 1 (susceptible) to BYDV at 0, 2, 8, 24, and 48 h post-infection. A combination of phytohormone profiling, differential gene expression analysis, and pathway enrichment was employed to identify mechanisms underpinning disease resistance. Comparative time-course transcriptome analysis revealed 9285 and 8904 differentially expressed genes (DEGs) in MN10253 and Qingyin 1, respectively. Key pathways such as MAPK signaling, plant–pathogen interaction, and hormone signal transduction were significantly enriched. The resistant cultivar exhibited robust activation of pattern-triggered immunity and effector-triggered immunity pathways, marked by upregulation of genes like RPS2, HSP90, and WRKY33, alongside higher expression of salicylic acid (SA)-responsive genes, such as NPR1 and PAL. Conversely, the susceptible cultivar displayed weaker or delayed activation of these defense pathways. Hormonal analysis further demonstrated higher SA accumulation in MN10253 during early infection, correlating with enhanced defense responses. In contrast, Qingyin 1 showed elevated levels of auxin and abscisic acid, which are linked to suppressed immunity. This study underscores the central role of immunity responses and phytohormone pathways in mediating oat resistance to BYDV, highlighting the tradeoff between growth and defense modulated by hormonal crosstalk. These findings advance our understanding of host–pathogen dynamics in oats and provide valuable insights for breeding disease-resistant cultivars. Full article

The morphological traits of Vaccinium uliginosum L., including plant height, leaf area, and fruit weight, have changed significantly across an elevational gradient in the Changbai Mountains. To elucidate the molecular mechanisms underlying these morphological variations, RNA-Seq technology was employed to identify differentially expressed genes (DEGs), key metabolic pathways, and associated biological functions of V. uliginosum at seven elevations in the Changbai Mountains. A total of 1190 DEGs significantly associated with morphological variations were identified. These genes are mainly involved in lipid synthesis, carbohydrate metabolism, energy metabolism, and signal transduction. Redundancy analysis (RDA) revealed that fatty acyl-ACP thioesterase B (FATB) and ribulose-bisphosphate carboxylase small subunit (cbbS) exhibited a significant association with morphological variation. Integrated analysis indicated that high-altitude plants likely enhance lipid synthesis and cell wall stability while also inhibiting photosynthesis and carbohydrate metabolism. The regulatory mechanisms underlying hormone signal transduction may be relatively complex, as evidenced by the enhanced activity of gibberellin and reduced biological effects of auxin, abscisic acid, and ethylene. This study is the first to provide transcriptomic evidence elucidating the genetic basis of altitudinal morphological adaptation in V. uliginosum, integrating phenotypic traits with gene expression profiles across an elevational gradient. Full article

Drought is a leading constraint on plant productivity and will intensify with climate change. Plant acclimation emerges from a multilayered regulatory system that integrates signaling, transcriptional reprogramming, RNA-based control, and chromatin dynamics. Within this hierarchy, non-coding RNAs (ncRNAs) provide a unifying regulatory layer; microRNAs (miRNAs) modulate abscisic acid and auxin circuits, oxidative stress defenses, and root architecture. This balances growth with survival under water-deficient conditions. Small interfering RNAs (siRNAs) include 24-nucleotide heterochromatic populations that operate through RNA-directed DNA methylation, which positions ncRNA control at the transcription–chromatin interface. Long non-coding RNAs (lncRNAs) act in cis and trans, interact with small RNA pathways, and can serve as chromatin-associated scaffolds. Circular RNAs (circRNAs) are increasingly being detected as responsive to drought. Functional studies in Arabidopsis and maize (e.g., ath-circ032768 and circMED16) underscore their regulatory potential. This review consolidates ncRNA biogenesis and function, catalogs drought-responsive modules across model and crop species, especially cereals, and outlines methodological priorities, such as long-read support for isoforms and back-splice junctions, stringent validation, and integrative multiomics. The evidence suggests that ncRNAs are tractable entry points for enhancing drought resilience while managing growth–stress trade-offs. Full article

Dongxiang wild rice (DXWR, Oryza rufipogon Griff.), the northernmost known wild rice species, exhibits exceptional tolerance to combined low-temperature and anaerobic stress during seed germination, providing a unique model for understanding plant adaptation to complex environmental constraints. Here, we employed an integrated multi-omics approach combining genomic, transcriptomic, and metabolomic analyses to unravel the synergistic regulatory mechanisms underlying this tolerance. Genomic comparative analysis categorized DXWR genes into three evolutionary groups: 18,480 core genes, 15,880 accessory genes, and 6822 unique genes. Transcriptomic profiling identified 10,593 differentially expressed genes (DEGs) relative to the control, with combined stress triggering the most profound changes, specifically inducing the upregulation of 5573 genes and downregulation of 5809 genes. Functional characterization revealed that core genes, including DREB transcription factors, coordinate energy metabolism and antioxidant pathways; accessory genes, such as glycoside hydrolase GH18 family members, optimize energy supply via adaptive evolution; and unique genes, including specific UDP-glycosyltransferases (UDPGTs), confer specialized stress resilience. Widely targeted metabolomics identified 889 differentially accumulated metabolites (DAMs), highlighting significant accumulations of oligosaccharides (e.g., raffinose) to support glycolytic energy production and a marked increase in flavonoids (153 compounds identified, e.g., procyanidins) enhancing antioxidant defense. Hormonal signals, including jasmonic acid and auxin, were reconfigured to balance growth and defense responses. We propose a multi-level regulatory network based on a “core-unique-adaptive” genetic framework, centered on ERF family transcriptional hubs and coordinated through a metabolic adaptation strategy of “energy optimization, redox homeostasis, and growth inhibition relief”. These findings offer innovative strategies for improving rice stress tolerance, particularly for enhancing germination of direct-seeded rice under early spring low-temperature and anaerobic conditions, by utilizing key genes such as GH18s and UDPGTs, thereby providing crucial theoretical and technological support for addressing food security challenges under climate change. Full article

The Auxin-Regulated Gene Involved in Organ Size (ARGOS) proteins have crucial regulatory effects on organ size and responses to environmental stresses. Despite their importance, Brassica oleracea ARGOS gene members and their functions in response to abiotic stresses have not been thoroughly investigated. In this study, we identified 40 ARGOS genes via a genome wide analysis of cauliflower and two other B. oleracea morphotypes as well as Brassica rapa, Brassica nigra, and Raphanus sativus. Expression pattern analyses indicated that these genes are responsive to multiple abiotic stresses, including salinity, heat, cold, and diverse hormones. Notably, the expression of an ARGOS-like gene (BobARL2) was upregulated in cauliflower treated with 1-aminocyclopropane-1-carboxylic acid (ACC). Moreover, the overexpression of BobARL2 decreased ethylene sensitivity, resulting in less inhibition of root elongation compared to the wild-type. Additionally, the overexpression lines exhibited enhanced salt tolerance. A yeast two-hybrid assay and luciferase complementation imaging (LCI) assay confirmed that BobARL2 can interact with Reversion-to-ethylene sensitivity Like4 (BobRTL4), which negatively regulates ethylene signal transduction. These findings advance our understanding of the evolution and functional roles of ARGOS genes in cauliflower and other Brassicaceae species, particularly in relation to abiotic stress responses, while also offering valuable insights relevant to the genetic improvement and breeding of novel varieties. Full article

Calcium-dependent protein kinases (CDPKs) are key Ca²⁺ sensors in plants, mediating responses to abiotic stresses via phosphorylation signaling. In the halophyte Nitraria sibirica, which thrives in saline soils, we identified 19 CDPK genes (NsCDPKs) and classified them into four canonical angiosperm clades, highlighting conserved functional modules. Promoter analysis revealed diverse cis-acting elements responsive to light, hormones (ABA, MeJA, auxin, GA, SA), and abiotic stresses (drought, cold, wounding), along with numerous MYB binding sites, suggesting complex transcriptional regulation. Transcriptome profiling under salt stress (100 and 400 mM NaCl) showed induction of most NsCDPKs, with several genes significantly upregulated in roots and stems, indicating coordinated whole-plant activation. These salt-responsive NsCDPKs were also upregulated by cold but repressed under PEG-simulated drought, indicating stress-specific regulatory patterns. Fifteen MYB transcription factors, differentially expressed under salt stress, were predicted to interact with NsCDPK promoters, implicating them as upstream regulators. This study identified a potential salt- and cold-responsive CDPK regulatory module and a MYB-mediated transcriptional hierarchy in N. sibirica, providing insights into the molecular mechanisms of salinity adaptation and highlighting candidate genes that could be explored for improving salt tolerance in crop species. Full article

Brassinosteroids (BRs) are essential regulators of plant development and stress responses, but the distinct contributions of BR biosynthesis and signaling to hormonal crosstalk remain poorly defined. Here, we investigated the effects of the BR biosynthesis inhibitor brassinazole (BRZ) and the BR-insensitive mutant bri1-6 on endogenous phytohormone profiles in Arabidopsis thaliana. Using multivariate analysis and targeted hormone quantification, we show that BRZ treatment and BRI1 disruption alter hormone balance through partially overlapping but mechanistically distinct pathways. Principal component analysis (PCA) and hierarchical clustering revealed that BRZ and the bri1-6 mutation do not phenocopy each other and that BRZ still alters hormone profiles even in the bri1-6 mutant, suggesting potential BRI1-independent effects. Both BRZ treatment and the bri1-6 mutation tend to influence cytokinins and auxin conjugates divergently. On the contrary, their effects on stress-related hormones converge: BRZ decreases salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA) in the WT leaves; similarly, bri1-6 mutants show reduced SA, JA, and ABA. These results indicate that BR biosynthesis and BRI1-mediated perception may contribute independently to hormonal reprogramming, with BRZ eliciting additional effects, possibly via metabolic feedback, compensatory signaling, or off-target action. Hormone correlation analyses revealed conserved co-regulation clusters that reflect underlying regulatory modules. Altogether, our findings provide evidence for a partial uncoupling of BR levels and BR signaling and illustrate how BR pathways intersect with broader hormone networks to coordinate growth and stress responses. Full article

Irregular rooting in vitro is a major problem in the micropropagation of culinary rhubarb (Rheum rhaponticum), a vegetable crop rich in bioactive compounds. To date, little is known about the factors and mechanisms underlying adventitious root (AR) formation in rhubarb under in vitro conditions. Here, we studied the effects of indole-3-butyric acid (IBA) and its interaction with ethylene (ET) on AR development in rhubarb ‘Raspberry’ selection. To evaluate the ET-effect, we applied a precursor of ET biosynthesis—1 aminocyclopropane-1-carboxylic acid (ACC); an inhibitor of ET synthesis—aminoethoxyvinylglycine (AVG); and an inhibitor of ET action—silver nitrate (AgNO₃). The best results (96.9% rooting frequency, 12.7 roots/shoot) were obtained after adding ACC to the IBA-containing medium. The positive effect of ET was linked to decreased levels of cytokinin and auxins in the rhubarb shoot bases at the initiation and expression stages of rooting. Moreover, the enhanced expression levels of genes involved in auxin signalling and homeostasis (IAA17, GH3.1) and ABA catabolism (CYP707A1) were observed. The blocking of ethylene synthesis significantly increased JA production, and the rooting frequency decreased to 29.8%. The presence of AgNO₃ in the auxin medium resulted in a significant reduction in root number, which was consistent with the enhanced levels of ABA and the expression of genes related to ABA biosynthesis and signalling (PP2C49 and CBF4), as well as ET synthesis (ACO5). Full article

Lycoris longituba produces a single flower bearing six tepals. The double-petaled phenotype of L. longituba has gained significant interest in China due to its ornamental and commercial value in tourism industries. This double-petal phenotype, characterized by stamen petalization, shows improved esthetic characteristics compared with conventional single-petal form. However, the molecular mechanisms underlying this floral trait remain largely undefined. In this study, RNA-based comparative transcriptomic analysis was performed between single- and double-petaled flowers of L. longituba at the fully opened flower stage. Approximately 13,848 differentially expressed genes (DEGs) were identified (6528 upregulated and 7320 downregulated genes). Functional annotation through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed several DEGs potentially involved in double-petal development. Six candidate genes, including the hub genes LlbHLH49, LlNAC1, LlSEP, LlTIFY, and LlAGL11, were identified based on DEG functional annotation and weighted gene co-expression network analysis (WGCNA). Transcription factors responsive to phytohormonal signaling were found to play a pivotal role in modulating double-petal development. Specifically, 123 DEGs were involved in phytohormone biosynthesis and signal transduction pathways, including those associated with auxin, cytokinin, gibberellin, ethylene, brassinosteroid, and jasmonic acid. Moreover, 521 transcription factors (TFs) were identified, including members of the MYB, WRKY, AP2/ERF, and MADS-box families. These results improve the current understanding of the genetic regulation of the double tepal trait in L. longituba and offer a base for future molecular breeding strategies to enhance ornamental characteristics. Full article