The satellitome of Triticum aestivum cv. Chinese Spring consists of 36 satellite DNA (satDNA) families that were previously molecularly characterized and chromosomally mapped. The recent release of a complete gap-free telomere-to-telomere (T2T) assembly of the species offers a unique opportunity to refine the physical map and evolutionary interpretation of these sequences. Here, we re-evaluate the organization of the wheat satellitome by analyzing the T2T assembly with RepeatMasker and visualizing the results using the CHRISMAPP script. This research strengthens the notion that more than half of wheat satDNAs are connected to transposable elements (TEs) and enables us to propose a model of satDNA origin and evolution driven by TEs and other random genome sequences. By integrating T2T based physical mapping with previous FISH analyses, we refine the genomic distribution of tandem repeats, identify complex satellite organizations and length variants, and resolve several discrepancies between cytogenetic and genomic analyses. Finally, the detailed mapping of satDNA in centromeric and the subtelomeric regions highlight clear chromosome and subgenome specific patterns, suggesting potential roles of satellites in chromosome architecture. Together these findings provide the most complete and accurate satellitome map available for bread wheat, offering new insights into repeat evolution and genome organization in polyploid species. The organization of the different satellite DNA families that constitutes its satellitome is re-evaluated in light of the information provided by the new T2T assembly of the bread wheat genome, revealing relevant information about their origin and evolution, distribution, and role in centromeric and subtelomeric regions.
Disomic alien addition lines (DAALs, 2n = 42) were obtained from an intersubgeneric cross between Glycine max [L.] Merr. cv. Dwight (2n = 40, G1G1) and Glycine tomentella Hayata (PI 441001, 2n = 78, D3D3CC). These DAALs had two homologous G. tomentella chromosomes. In some progenies of the DAALs the extra G. tomentella chromosomes were eliminated. One objective of this research was to identify differences in gene expression between a DAAL (LG13-7552) and one of its 2n = 40 progenies (LG12-7063). RNA-sequencing documented that many genes critical to fundamental plant growth and related to stress and defense responses were differentially expressed. DNA and RNA-sequencing data showed that the gray pubescence of LG12-7063 was due to a novel adenine deletion in the T locus. When the DAALs were grown in the field, progeny were identified that possessed characteristics that were absent in both parents. Additional objectives of this research were to document this phenotypic variation and to determine the cause of these changes. All off-type progenies lost their G. tomentella chromosomes and reverted to the normal soybean chromosomal state (2n = 40). Significant variation was observed among the 2n = 40 progenies for the several qualitative and quantitative traits. Field research documented an average reversion frequency within the DAAL rows of 4
Blueberry (Vaccinium spp.) has gained worldwide popularity as a fruit crop of exceptional flavor and high nutritional value. Fruit acidity, a critical determinant of consumer preference in rabbiteye blueberry, is primarily governed by vacuolar malic acid accumulation; however, the underlying regulatory mechanism remains unclear. In the current study, VaALMT9, encoding an aluminum-activated malate transporter, was identified from rabbiteye blueberry transcriptome data. The full-length coding sequence encodes a 574 amino acid protein harboring the characteristic WEP fingerprint motif of the ALMT family. Subcellular localization analysis suggested that VaALMT9 localizes to the endomembrane system, most likely the tonoplast (vacuolar membrane). Expression analysis revealed that VaALMT9 transcript levels paralleled malate accumulation during fruit development, with both peaking at the purple stage and declining at the late ripening stage. Virus-induced gene silencing of VaALMT9 in blueberry fruits significantly reduced its transcript levels (by 96.74
Drought and salt stresses impose serious effects on plant proliferation and development, with multiple categories of transcription factors (TFs) playing important regulatory effects in modulation stress reaction. In this study, the apple R2R3 MYB TF, MdMYB73L, was cloned and characterized its role in conferring abiotic stress tolerance. Firstly, expression assays demonstrated that the transcript levels of MdMYB TFs changed substantially under salt and drought stresses. Subsequently, MdMYB73L-overexpressing transgenic Arabidopsis, apple calli and tomato plants all showed increased sensitivity to salt and drought treatments, manifesting as short roots and severe growth inhibition compared to controls. These results demonstrate that MdMYB73L functions as a key negative regulator in the response to drought and salt stresses. Overall, these research not only demonstrate the specific function of a MYB TF in stress responses but also provide a crucial framework for elucidating the broader effects of the apple MYB family in abiotic stress tolerance. MdMYB73L, an apple R2R3‑MYB transcription factor, negatively regulates drought and salt tolerance, as its overexpression consistently enhances stress sensitivity in Arabidopsis, apple calli, and tomato. This work provides novel insights into the regulatory roles of MYB proteins under abiotic stress.
Plants are continuously exposed to a wide range of abiotic stresses, including drought, salinity, temperature extremes, nutrient deficiency, and heavy metal toxicity, which severely constrain growth and productivity. To cope with these challenges, plants have evolved sophisticated regulatory networks involving phytohormones and non-coding RNAs (ncRNAs). This review provides a comprehensive overview of the biogenesis and functional roles of major ncRNA classes’ microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) and their dynamic interplay with phytohormonal signaling pathways under stress conditions. We highlight how ncRNAs modulate key hormonal pathways, including abscisic acid, auxin, jasmonic acid, ethylene, and gibberellins, to fine-tune stress-responsive gene expression and maintain cellular homeostasis. Special emphasis is placed on nutrient stress and heavy metal toxicity, where ncRNA-mediated regulation influences ion transport, autophagy, reactive oxygen species detoxification, and metabolic reprogramming. Emerging evidence on circRNAs as miRNA sponges further reveals an additional regulatory layer linking developmental processes with stress adaptation. The review also integrates recent advances in high-throughput sequencing, multi-omics approaches, and bioinformatics tools that have enabled large-scale identification and functional annotation of stress-responsive ncRNAs. Furthermore, the application of artificial intelligence and machine learning models in predicting ncRNA target interactions and regulatory networks is discussed as a transformative approach in plant stress biology. Collectively, this synthesis provides a systems-level understanding of ncRNA-phytohormone cross-talk and underscores its potential in developing climate-resilient crops through advanced molecular and computational strategies. ncRNA-mediated phytohormone signaling coordinates stress-responsive regulatory networks, providing a promising strategy to enhance plant resilience under abiotic stress.
Cucumber is an economically important vegetable crop cultivated worldwide, but its productivity is severely affected by destructive foliar diseases particularly powdery mildew and downy mildew. These pathogens cause significant yield and quality losses and the continuous emergence of new races makes disease management increasingly challenging. Conventional approaches including cultural, biological and chemical control often provide limited and short-term effectiveness. Therefore, the development of host plant resistance remains the most sustainable and environmentally sound strategy for long-term disease control. Recent advances in cucumber genomics and molecular breeding have enabled the identification of resistance-associated loci through SNP genotyping, QTL mapping, genome-wide association studies and marker-assisted selection. Furthermore, multi-omics approaches such as transcriptomics, proteomics and metabolomics combined with innovative technologies like CRISPR/Cas-mediated genome editing, genomic selection and speed breeding are transforming resistance breeding. Therefore, by integrating advanced molecular tools with omics-driven insights, this review aims to accelerate genetic gains and facilitate the development of durable, broad-spectrum mildew-resistant cucumber cultivars for sustainable and resilient production systems. Key Message Powdery mildew (PM) and downy mildew (DM) are major foliar diseases of cucumber that severely affect productivity and fruit quality worldwide. In this review, we highlighted the genetic resources, screening strategies, disease scoring systems, inheritance patterns, resistance-associated QTLs, molecular markers and candidate genes involved in cucumber mildew resistance. Furthermore, we discussed genome-assisted breeding approaches, including QTL mapping, genome-wide association studies, marker-assisted selection, CRISPR/Cas9-mediated genome editing, transgenic approaches and high-throughput phenotyping tools for improving resistance breeding efficiency. Therefore, this review focuses on integrating conventional breeding, molecular mapping, functional genomics and precise phenotyping approaches to understand PM and DM resistance mechanisms and accelerate the development of durable, broad-spectrum mildew-resistant cucumber cultivars.
Rice false smut (RFS) caused by Ustilaginoidea (U.) virens has become an emerging threat to global rice production, driven by complex host–pathogen interactions and stage-specific infection processes. We present a comprehensive review of the omics approach to delve into the interplay of genes and their functional validation in decoding the pathway of infection by U. virens and the resistance mechanism exhibited by rice. Firstly, the pathogenesis genes are discussed, which are triggered at spore germination, progressing to hyphal colonization of floral tissues and smut ball formation. Furthermore, these processes are a consequence of tightly regulated expression of genes of different pathways such as cAMP-MAPK signaling, transcriptional regulators, cell wall integrity factors, virulence determinants, secondary metabolites, and carbohydrate-active enzymes. The rice plants also respond by activating a plethora of defense genes such as phytoalexin biosynthesis, pathogenesis-related proteins, receptor-like kinases, transcription factors, anti-oxidation, etc. The mapping of these genes to related quantitative trait loci and short sequence repeat sequences may aid in gene pyramiding strategies for molecular-assisted breeding programs. The molecular manipulation of resistance genes using CRISPR-Cas9 may further facilitate targeted development of improved rice varieties. Overall, molecular insights of host–pathogen interactions offer decoding of sustainable strategies for developing resilient cultivars and effective management of false smut disease. This review synthesizes omics approaches to decipher the molecular interplay governing rice–Ustilaginoideavirens interactions, highlighting stage-specific pathogenicity genes and rice defense mechanisms that control false smut disease development.
Root traits during post-tillering stages in wheat are critical for adapting to moisture-deficit stress. This study mapped 24 traditional quantitative trait loci (QTLs) of root and yield traits in wheat across 14 chromosomes using 198 recombinant inbred lines (RILs), developed by crossing two contrasting parents, HD 3086 and HI 1500. Genotyping was done with the 35 K Axiom Wheat Breeder’s Array, followed by QTL mapping through Inclusive Composite Interval Mapping (ICIM) software. From the 5 conditional QTLs (Y75|Y45) mapped, QARFC.iari-2 A was mapped as the major stable QTL for root fresh weight, explaining 11.23
Engineering crop plants with the biological nitrogen fixation pathway is a longstanding goal of modern agriculture. Dinitrogenase reductase (NifH) is a critical component of the biological nitrogen fixation pathway, with multiple roles in metal cofactor assembly and catalysis. This enzyme must be folded correctly as a soluble homodimer and loaded with the [4Fe-4S] metallocluster for function. Previous studies have found that Klebsiella oxytoca (Ko) and Azotobacter vinelandii (Av) NifHs were mostly insoluble when targeted to plant mitochondria. Here we found that a translational fusion of two KoNifH or AvNifH monomers, forming KoNifHH or AvNifHH synthetic dimers, produced a soluble protein when targeted to plant mitochondria and co-expressed with the putative peptidyl-prolyl cis–trans isomerase NifM. KoNifHH isolated after expression in leaf mitochondria at ambient oxygen showed some acetylene reduction activity, which did not require co-expression of the nitrogenase-specific metallocluster machinery NifS and NifU. This activity increased after iron-sulfur cluster reconstitution in vitro with recombinant NifU. In a parallel study, we tested a translational fusion of a variant iron-only dinitrogenase reductase (AvAnfHv6) monomer that was soluble but not active as-isolated from plant mitochondria (AvAnfHHv6) (Gregg et al. 2025a). AvAnfHHv6 was abundant and fully soluble when isolated from plant mitochondria, like its monomer. AvAnfHHv6 was not active as-isolated but could be largely activated by iron-sulfur cluster reconstitution in vitro. This study demonstrates how translational fusions help improve solubility and have the potential to generate an active NifH enzyme within plant mitochondria. A translational fusion of two Klebsiella oxytoca dinitrogenase reductase monomers was soluble and functional when expressed in Nicotiana benthamiana mitochondria, demonstrating its applicability for nitrogen fixation in plants.
Sesame (Sesamum indicum L.), is one of the earliest domesticated oilseed crops. It is valued for its exceptional oil content, bioactive compounds, and adaptability to diverse agroclimatic conditions. However, its production remains highly susceptible to water scarcity particularly terminal drought and intermittent moisture deficits that in turn severely compromise the yield and oil quality. Recent advances in genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics have placed sesame as an emerging model for multi-omics-driven stress research. These approaches have uncovered key regulators of drought (NAC, MYB, WRKY), protective proteins (late embryogenesis abundant proteins, heat shock proteins, antioxidant enzymes), osmolyte- and redox-related metabolites, and hormonal signalling modules such as PYL-SnRK2-ABF (ABA), LOX/AOS/OPR (jasmonate), and EIN/ERF (ethylene). Addressing these gaps will require investments in precision phenotyping, robust pan-genomic databases, functional validation using CRISPR/Cas9 tools, and global data-sharing networks. This review highlights the current advances in sesame drought research across omics platforms, critically evaluates their relevance to breeding programs, and offers the first comprehensive multi-omics perspective on moisture-stress adaptation in sesame. Additionally, KEGG pathway-guided multi-omics integration connects ABA signaling, phenylpropanoid metabolism, and antioxidant pathways to drought adaptation in sesame. By bridging mechanistic insights with applied strategies, it highlights pathways to accelerate the development of climate-resilient sesame cultivars.
Understanding the biochemical basis of α-glucosidase inhibitory (AGI) activity in chili peppers (Capsicum annuum L.) is essential for their development as functional food ingredients. This study evaluated AGI activity and phytochemical profiles across four ripening stages in three C. annuum cultivars: Sumihyang (a cultivar derived from the Korean landrace Subicho), Dangjo (a functional antidiabetic cultivar), and Olbokhap (a disease-resistant commercial cultivar). Enzyme assays revealed that AGI activity peaked at the immature stage in all cultivars, with Sumihyang consistently exhibiting the highest activity across two harvest periods. Untargeted metabolomic profiling at the immature and turning stages identified two phenolamides, caffeoylputrescine and feruloylputrescine, that were selectively enriched in immature Sumihyang and strongly correlated with AGI activity (r > 0.92). While the AGI effect of caffeoylputrescine has been previously reported, feruloylputrescine was evaluated here for the first time under this assay system. In vitro validation confirmed their inhibitory activities, with half maximal inhibitory concentration (IC50) values of 193 µM for caffeoylputrescine and 291 µM for feruloylputrescine. These findings suggest that phenolamide composition, rather than total flavonoid content, is a key determinant of AGI activity in chili peppers. The selective accumulation of these phenolamides in immature Sumihyang highlights its potential as a genetic resource for developing antidiabetic functional foods. Immature fruits of Sumihyang uniquely accumulate phenolamides with α-glucosidase inhibitory activity, supporting its potential as a genetic source for developing antidiabetic functional peppers.
Pattern-recognition receptors (PRRs) initiate plant pattern-triggered immunity (PTI), encompassing receptor-like kinases (RLKs) and receptor-like proteins (RLPs). Eucalyptus grandis, an economically important species worldwide, is a long-lived organism that faces multiple disease pressures. The deployment of PRR-based breeding tools offers a route to broad, non-race-specific resistance that can remain effective across outbreaks. The objective of this work was to identify and characterise the PRR repertoire of E. grandis using public multi-omics data. Two state-of-the-art predictors were compared with a multi-species curation and a meta-analysis was conducted compiling transcriptomic data under biotic stress. A set of 730 RLKs/RLPs (PRR candidates) were consistently identified across three sources ( 1.6
Fruit growth is mediated by cell division and expansion. In tomato, the model for fleshy fruit development, both processes are tightly linked to changes in gene expression, including transcriptional regulation and RNA processing. While several transcription factors are implicated in fruit developmental programs, the role of splicing regulators remains largely unexplored. Expression profiling of splicing-related genes revealed expression patterns. The serine/arginine-rich splicing factor RS2Z36 is expressed in ovaries and during early fruit development. Loss-of-function mutations in RS2Z36 result in ovaries with altered patterning and in smaller, ellipsoid fruits. rs2z36 mutants display elongated pericarp cells along the longitudinal axis of pre-anthesis ovaries, indicating that RS2Z36-dependent expansion patterns are established before anthesis. Based on RNA-seq analysis we identified 230 genes with altered splicing profile in ovaries of rs2z36.1 compared to WT and 235 differentially expressed genes. Proteome analysis further revealed several differentially abundant isoforms, including several cell wall proteins and modifiers that might be involved in ovary patterning and fruit growth. In addition, rs2z36-1 pericarps show increased deposition of LM6-recognized arabinan and AGP epitopes. Together, these findings identify RS2Z36 as a regulator of ovary and fruit development and highlight a previously underappreciated role for splicing control in shaping early fruit morphology.
Ocimum, a widely used medicinal and culinary herb, is known for its health-promoting properties, yet most research has focused on its volatile oils, leaving the therapeutic potential and biosynthesis of its coumarins largely unexplored. Despite reports of coumarin bioactivity in other plants, a comprehensive understanding of coumarin diversity, pharmacology, and genetic regulation within Ocimum remains lacking—limiting both its breeding potential and pharmaceutical applications. Here, we applied an integrated multi-omics approach—including UPLC-MS/MS metabolomics, transcriptomics, network pharmacology, and molecular docking—to systematically profile coumarin metabolites, investigate their medicinal potential, and uncover their biosynthetic underpinnings across ten Ocimum accessions. A total of 59 coumarins were identified, 58 of which displayed significant variation among accessions, highlighting pronounced intra-genus metabolic diversity. Network pharmacology revealed that 35 bioactive coumarins potentially interact with 263 human targets, forming a rich metabolite–target–disease–pathway network. These coumarins were enriched in cancer- and inflammation-related KEGG pathways (e.g., PI3K-Akt, Ras/MAPK, endocrine resistance) and GO terms (e.g., tyrosine kinase activity), with hub compounds such as isodemethylwedelolactone, coumestrol, daphnetin, umbelliferone, and agrimonolide showing strong binding affinities to key proteins (e.g., EGFR, MAPK1, CCND1; docking scores ≤ − 6 kcal/mol). Coumarin biosynthetic pathways were reconstructed for several major compounds, revealing genotype-specific accumulation patterns and associated differentially expressed genes. These findings fill a critical knowledge gap regarding Ocimum coumarins by linking their metabolic diversity to pharmacological function and underlying gene expression. Our results lay the groundwork for breeding high-value Ocimum cultivars and developing coumarin-based functional foods or multi-target therapeutic agents, particularly for cancer and inflammatory diseases. Multi-omics profiling of Ocimum accessions bridges the gap between coumarin chemical diversity and genetic regulation, providing a foundation for breeding high-value cultivars and developing multi-target anticancer therapeutics.
Cold stress, especially freezing stress, is an important environmental factor that induces physiological damage in plants. In previous studies, we showed that ethanol application increases tolerance to high salinity, heat, high-intensity light, and drought, although the core mechanisms remain unclear. In this study, we investigated whether ethanol application could enhance freezing stress tolerance in Arabidopsis and sugar beet. Arabidopsis seedlings grown on agar plates were pretreated with 20 mM ethanol solution and then subjected to freezing. The survival ratio and growth indicators, including green leaf area, were higher in ethanol-pretreated seedlings than in water-pretreated seedlings. Similarly, in Arabidopsis seedlings grown in pots containing soil, 20 mM ethanol pretreatment increased the green leaf area after freezing treatment. Pretreatment with 80 mM ethanol solution of potted sugar beet seedlings grown in soil before exposure to freezing increased the survival ratio compared with that of water-pretreated seedlings. Transcriptome analysis using potted Arabidopsis plants grown in soil identified differentially expressed genes (DEGs), which included stress-related genes (LEA, DREB1A and ERF6) and anthocyanin biosynthesis-related genes (LDOX/ANS and DFR). Gene ontology analysis showed that DEGs associated with hypoxic response including oxidative stress response and anthocyanin-containing compound metabolic process were enriched in seedlings pretreated with 20 mM ethanol. Collectively, the results reveal that ethanol application effectively increases freezing stress tolerance and provide novel insights into the molecular mechanisms that underlie ethanol-mediated abiotic stress tolerance. Ethanol application enhances freezing stress tolerance through hypoxic response.
Climate change-induced abiotic stress, including heat, cold, salinity, and drought, increasingly threaten global crop productivity. These challenges highlight the need for complementary strategies alongside conventional genetic improvement. Reactive oxygen species (ROS) act both as cytotoxic molecules causing oxidative damage and as essential signaling regulators controlling redox homeostasis and stress adaptation. This review examines recent advances in engineering nanozymes (NZs) for targeted regulation of plant ROS networks. NZs exhibit dual functions as antioxidant ROS scavengers, and modulators of redox signaling, with nanoceria (CeO2), serving as key example due to its enzyme-mimetic antioxidant activity. Beyond ROS scavenging, emerging evidence suggests that nanoceria can modulate molecular stress signaling pathways, including Ca2⁺ fluxes and phytohormone interactions involving auxin (IAA), abscisic acid, and jasmonic acid. Such ROS reprogramming may trigger hormetic responses that enhance plant tolerance to environmental stress. We further discuss design of smart nanocarriers for targeted and stress-responsive modulation of plant defense pathways. Finally, we highlight future research directions, including experimental standardization and integration of artificial intelligence (AI) and machine learning (ML) to predict NZ–plant interactions based on physicochemical properties. Together, these advances position CeO2 NZs as a promising tool for molecular reprogramming of oxidative homeostasis toward improved climate resilience. CeO₂ nanozymes modulate ROS-mediated molecular signaling, including redox, Ca²⁺, and phytohormone networks, offering a promising strategy to enhance plant resilience under climate-induced abiotic stress.
Plants represent commercially relevant production systems for recombinant proteins and chemical compounds. Effective genetic engineering depends on precise control of heterologous gene expression, which remains challenging due to complex transcriptional and post-transcriptional regulation, endogenous gene silencing mechanisms, and notably because of limited number of tools for allowing robust, fine-tuned control of expression levels across different systems/organisms. Some of the most common issues associated with plant expression systems are addressed with our plant-optimized version of a previously developed fungal universal synthetic expression system (SES). Plant SES demonstrates several favorable characteristics for robust heterologous gene expression, including highly constitutive function with apparently reduced sensitivity to endogenous silencing in transient assays, without requiring p19 co‑expression under the tested conditions. These together provide simple, predictable tuning of gene expression levels, and the potential for very high expression levels of the target genes. In all these features, SES shows higher and more stable transcript levels than Cauliflower Mosaic Virus (CaMV) 35 S promoter-based constructs in our experimental setups. The functionality of plant SES was tested by expressing mCherry and three commercially relevant proteins: fungal glucose oxidase (GOX), protein A and human vascular endothelial growth factor 165 (VEGF16) from diverse organisms, supporting high-level accumulation of recombinant proteins. In addition, plant SES retains full functionality in both plant and fungal hosts, which makes this expression system a useful tool for a multitude of genetic engineering applications in other eukaryotic organisms. Plant synthetic expression system (SES) enables tunable transient expression of genes with high recombinant protein yields in Nicotiana benthamiana with the capability of inter-kingdom functionality.
Alfalfa (Medicago sativa L.), the world’s most widely cultivated perennial forage crop, is valued for its high-quality feed and broad environmental adaptability. However, soil alkalization poses a major constraint to its productivity in marginal lands, with the genetic basis of alkali tolerance remaining largely unexplored. This study identified a lead SNP (Chr7-16,804,032) via a genome-wide association study (GWAS), where the T/T genotype was strongly associated with enhanced alkali tolerance. Physiological analyses revealed that lines carrying the T/T genotype maintained higher chlorophyll and soluble protein content, lower malondialdehyde levels, elevated antioxidant enzyme activities, and better Na+/K+ homeostasis under alkali stress. Functional validation across five alfalfa cultivars, supported by field trials in natural saline-alkali soils, confirmed that the T/T genotype consistently promoted biomass accumulation. Within a 14.4 Kb region flanking Chr7-16,804,032, we identified MsFAI (F-box Associated Interaction domain), a gene specifically induced under alkali stress. Overexpression of MsFAI in Arabidopsis thaliana significantly improved alkali tolerance. Further transcriptomic profiling highlighted MsCDPK (Calcium-Dependent Protein Kinase) and MsPCO (Plant Cysteine Oxidase) as alkali-responsive genes, and their heterologous expression in A. thaliana likewise conferred alkali tolerance. Taken together, our work delineates a major genetic locus (Chr7-16,804,032) and key candidate genes (MsFAI, MsCDPK, and MsPCO) governing alkali tolerance in alfalfa. These findings provide important candidate loci and genes for future research on alkali tolerance mechanisms and may facilitate molecular breeding of alfalfa after further functional validation.
Bacterial expansins contribute to the virulence of diverse plant pathogens, yet their biological activity and molecular roles during host interactions remain to be elucidated. Expansin-like protein, Exl1, from phytopathogens from the genus Pectobacterium, activates defense responses in Arabidopsis thaliana involving production of reactive oxygen species (ROS), and the jasmonic acid (JA), ethylene (ET), and salicylic acid (SA) pathways, ultimately reducing disease symptoms upon subsequent infections with P. brasiliense and the fungus Botrytis cinerea. However, the target of Exl1 within the plant cell wall and the downstream pathways associated with these responses are yet to be identified. Here, we analyzed the transcriptomic profile of A. thaliana leaves treated with Exl1 protein to provide a genome-wide transcriptional framework associated with Exl1-triggered immunity. Comparative transcriptomic analysis of Arabidopsis thaliana Col-0 and JA-impaired mutant jar1-1 revealed distinct transcriptional patterns associated with JA-dependent responses at early time points. Abscisic acid (ABA)-related signaling was associated with later stages of the response, supported by the increased expression of the ABA-responsive gene CRK45 six hours after Exl1 treatment, and increased susceptibility of an ABA-impaired mutant. These findings suggest the involvement of multiple phytohormone-related pathways following Exl1 treatment. In parallel, extensive transcriptional reprogramming was observed, across diverse functional categories, reflecting a broad host response associated to the presence of Exl1. Together, these findings suggest that Exl1 induces an integrated signaling network that coordinates immune responses to strengthen plant defense, providing new insight for future functional studies on how bacterial expansins modulate plant-microbe interactions.
Plant viruses, which were previously considered only as agricultural threats, are becoming programmable vectors of transgene-free, tissue culture-independent genome editing. Engineered viral vectors can be used to precisely deliver genome-editing reagents far more expeditiously than classical techniques by harnessing their inherent ability to replicate and disseminate throughout the systemic space. These systems are 5–10 times faster to accomplish trait validation and overcome the tissue culture bottleneck, which continues to inhibit genome editing in more than 80 This review highlights how engineered plant viruses enable rapid, tissue culture-independent genome engineering and flowering regulation, offering practical tools for next-generation plant breeding.
