Search Results (2,832)

The SWEET (Sugars Will Eventually be Exported Transporter) family, a class of sugar transporters identified in recent years, plays important roles in plant growth and development. Increasing evidence suggests that SWEET genes are also involved in plant responses to abiotic stresses, including salt stress. However, the genome-wide composition and salt-responsive functions of SWEET genes in Elymus nutans Griseb. have not been systematically characterized to date. This study presents the first genome-wide identification of the SWEET gene family in E. nutans and functional characterization of EnSWEET15 in salt stress response, providing candidate genes and a theoretical basis for improving salt tolerance in this species. A total of 12 EnSWEET genes were identified from the E. nutans genome and were unevenly distributed across eight chromosomes. Phylogenetic analysis classified them into four subfamilies, and promoter analysis revealed abundant cis-elements related to hormone signaling and stress responses, suggesting roles in abiotic stress adaptation. Expression analysis showed that EnSWEET15 was significantly upregulated in both roots and leaves under salt stress. The full-length EnSWEET15 coding sequence (930 bp ORF) was cloned and functionally characterized. Heterologous overexpression in Arabidopsis thaliana indicated that EnSWEET15 enhances salt tolerance. Transgenic lines showed reduced reactive oxygen species (ROS) accumulation and increased activities of antioxidant enzymes, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), compared with wild-type plants under salt stress. Overall, this study identifies EnSWEET15 as a positive regulator of salt tolerance via modulating ROS homeostasis, providing novel insights into SWEET-mediated salt stress response in perennial forages and valuable genetic resources for salt-tolerant breeding of E. nutans. 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

Plant lipid transfer proteins (LTPs) are key components in defense against biotic and abiotic stresses, yet their functional diversity in Panax ginseng remains unclear. This study aimed to characterize LTP and evaluate its role in stress tolerance. The gene was identified from ginseng transcriptome data and analyzed using bioinformatics tools to determine its structural and physicochemical properties. Panax ginseng lipid transfer protein (PgLTP) was then heterologously expressed in Arabidopsis thaliana (A. thaliana). Transgenic lines were evaluated under fungal infection, drought, and salt stress conditions. Physiological and molecular responses, including reactive oxygen species(ROS) accumulation, malondialdehyde (MDA) content, proline levels, electrolyte leakage, and stomatal behavior under abscisic acid (ABA) treatment, were assessed. Bioinformatic analysis indicated that PgLTP encodes a small protein of approximately 12 kDa containing ten conserved cysteine residues, four α-helices, a signal peptide, and a transmembrane region, suggesting structural divergence from typical LTPs. Functional assays showed that transgenic plants exhibited significantly reduced disease indices under Fusarium oxysporum (F. oxysporum) and Cylindrocarpon destructans (C. destructans) infection. Under drought and salinity stress, transgenic lines demonstrated higher germination and survival rates, enhanced proline accumulation, reduced oxidative damage, and lower electrolyte leakage compared with the wild type. Additionally, PgLTP exhibited enhanced ABA-responsive stomatal closure, which was associated with reduced water loss. These findings indicate that PgLTP contributes to plant tolerance against both biotic and abiotic stresses, which is associated with changes in redox status, osmotic adjustment capacity, and stomatal responses. Full article

Seed protein content, oil content, and yield are key agronomic traits that determine the economic value of soybean. For decades, soybean has served as a leading source of plant protein for human and animal nutrition due to its high protein concentration. Manipulating amino acid transporters to regulate the direction of nitrogen allocation represents a promising strategy for improving seed protein content. Multiple studies have employed this strategy by targeting amino acid importers. Recently, the Usually Multiple Amino acids Move In and Out Transporter (UMAMIT) family has been characterized as amino acid exporters; nevertheless, their role in regulating the seed protein content of soybean has not yet been investigated. In this study, we identified 120 soybean UMAMIT genes via a genome-wide search and designated them according to chromosomal location. Phylogenetic analysis grouped these genes into 10 clades (A–J). Whole-genome duplication (WGD)/segmental duplication served as the main driver of the GmUMAMIT family expansion, followed by tandem duplication. By integrating transcriptome data with QTL/GWAS loci, we identified twelve candidate genes associated with seed protein content and verified their expression patterns during seed development via qPCR. One candidate gene, GmUMAMIT118, was selected and overexpressed in Arabidopsis thaliana, resulting in transgenic lines with significantly higher seed protein content and yield. Collectively, these results provided a comprehensive overview of the soybean UMAMIT family and offered a preliminary exploration of its role in improving seed protein content. Full article

Cutin matrices in the cuticle cover plant epidermis, facilitating plant adaptation to stressful environments. Although cutin biosynthesis is extensively explored in the model plant Arabidopsis thaliana, the molecular mechanism governing cutin biosynthesis in the agriculturally important crop bread wheat (Triticum aestivum L.) remains largely unknown. The aim of the study is the characterization of the function and transcriptional regulation of a wheat gene involved in cutin biosynthesis. Long-chain acyl-CoA synthetase TaLACS2 was identified as an essential component of the wheat cutin biosynthetic machinery. Silencing of the wheat TaLACS2 gene by barley stripe mosaic virus-induced gene silencing assay resulted in remarkably reduced cutin accumulation and increased cuticle permeability. Furthermore, wheat GT-1-like transcription factor TaGT-3b was identified as a positive regulator of cutin biosynthesis. Silencing of the wheat TaGT-3b gene led to significantly decreased cutin accumulation and enhanced cuticle permeability. Importantly, we found that TaGT-3b could occupy the promoter regions of the TaLACS2 gene and that it functions as a transcriptional activator to activate TaLACS2 gene transcription. Collectively, these results elucidated that wheat GT-1-like transcription factor TaGT-3b boosts cutin biosynthesis, probably by activating TaLACS2 gene transcription, contributing to genetically improving cutin-associated traits in bread wheat. Full article

Splicing factors, as core determinants of splice-site selection and dynamic spliceosome assembly, play pivotal roles in stress responses. This review systematically categorizes splicing factors involved in plant abiotic stress responses according to their functions as major spliceosomal components, dividing them into small nuclear ribonucleoproteins (snRNPs) and associated components, spliceosome assembly and disassembly factors, splicing regulatory factors, and proteins related to non-canonical RNA splicing. On this basis, we summarize their regulatory mechanisms of these factors under salt, drought, abscisic acid (ABA) signaling, temperature, and oxidative stresses. Through analyses across multiple species—including Arabidopsis thaliana, rice, maize, soybean, and wheat—we reveal both the evolutionary conservation and species-specific divergence of splicing-factor-mediated regulation. Currently, a large amount of research is still mainly at the transcriptome analysis or single phenotype validation stages, lacking in-depth analysis of direct targets, splicing isomer functions, and molecular mechanisms. Furthermore, current research is heavily concentrated on Arabidopsis, with relatively insufficient functional validation and breeding applications in crops such as maize and wheat. Despite substantial progress, several bottlenecks remain for translational applications in breeding, such as functional redundancy among splicing factor family members, growth penalties associated with overexpression, and tissue-specific and developmental-stage-dependent effects. To address these challenges, we discuss promising strategies, including CRISPR/Cas9-mediated splice-site editing, the use of inducible or tissue-specific promoters, and targeted modulation of upstream kinases, although extensive field trials and rigorous evaluations remain necessary. Collectively, this review provides a theoretical framework for understanding the roles of splicing factors in RNA-level regulation of plant stress adaptation and highlights their potential for breeding improvement. Full article

BRI1-EMS-SUPPRESSOR 1 (BES1)/BRASSINAZOLE-RESISTANT 1 (BZR1) transcription factors serve as core regulators of brassinosteroid (BR) signal in seed plants, where they control diverse developmental processes, including cell elongation, vascular development, and environmental responses; however, their evolutionary trajectory and functional diversification in early-diverging land plants remain poorly characterized. In this study, we systematically characterized the BES1/BZR1 gene family across 12 representative bryophyte species covering hornworts, liverworts and mosses, with Arabidopsis thaliana included as a vascular plant outgroup. In total, 19 non-redundant BES1/BZR1 homologs were identified within bryophyte genomes. Phylogenetic reconstruction, synteny analysis and Ka/Ks selection pressure analyses collectively revealed that this gene family is evolutionarily conserved throughout bryophytes, with moss-specific lineage expansion; most paralogous gene pairs have experienced strong purifying selection during evolution. Further analyses of gene structural organization, conserved protein motifs and cis-acting promoter elements uncovered universally conserved core domains alongside lineage-specific structural and regulatory variations. Subcellular localization assays demonstrated that the majority of tested bryophyte BES1/BZR1 proteins primarily accumulate in the nucleus, and autoluminescent reporter assays verified that multiple homologs modulate E-box-driven transcriptional activity. Transcriptional expression profiling indicated that BES1/BZR1 genes from Marchantia polymorpha and Sphagnum fallax are transcriptionally responsive to exogenous BR treatment, while several paralogs in S. fallax additionally exhibit altered expression under drought stress. Collectively, our results demonstrate that the BES1/BZR1 family originated at an early stage of land plant evolution, followed by lineage-specific gene expansion and divergent transcriptional regulation in bryophytes. This work advances our understanding of ancestral BR signaling and stress response modules in the early terrestrial plant lineages. Full article

Unlike conventional genetic polymorphisms, many induced epigenetic polymorphisms can be reset across generations, raising uncertainty about how consistently the same epigenetic loci and associated phenotypic effects can be recovered among independent studies. To address this problem, we designed our study specifically to maximize a lineage-matched, environmentally aligned cross-study comparability with the foundational work of Cortijo et al. by using seeds derived from the same epiRIL generation and grown under broadly similar environmental conditions. We mapped flowering time, as well as five non-flowering traits that had not previously been mapped in this epiRIL population: rosette diameter, basal branch number, lateral branch number, fruit number, and rosette leaf number. We detected significant epiQTLs for all traits except lateral branch number. We also reproduced a facsimile of the original computational pipeline. This design provides an approximate upper bound on expected reproducibility before additional generations of methylation resetting or divergence among seed stocks could substantially influence the results. We recovered two of Cortijo et al.’s previously reported epiQTLs, failed to recover another, and found a different one, with power analyses suggesting that the discrepancies may reflect statistical power. Within overlapping epiQTL intervals across the five traits that had significant intervals, we identified 69 candidate genes exhibiting gene body methylation. Overall, our results reproduced some but not all previous epiQTL signals when comparisons were made using closely matched source material under similar conditions. Full article

Caffeic acid O-methyltransferase (COMT) serves as a crucial rate-limiting enzyme within the melatonin biosynthesis pathway and is involved in various primary and secondary metabolic processes, significantly contributing to plant growth, development, and stress response. Nevertheless, a comprehensive characterization of the COMT gene family in citrus species, particularly with regard to its functional roles under salinity stress, remains unavailable. In the current study, we identified 47 COMT loci from the Poncirus trifoliata genome, and these genes were observed to be non-uniformly scattered across seven chromosomes. The majority of these genes are predicted to localize within the Golgi apparatus and nucleus. Each PtrCOMT gene contains between 2 and 19 exons and 1 and 18 introns, and they are categorized into four groups based on phylogenetic analysis. Collinearity analysis uncovered three intraspecific collinear gene pairs in Poncirus trifoliata. Three orthologous collinear pairs were detected between P. trifoliata and Arabidopsis thaliana, and one pair between P. trifoliata and Oryza sativa. Additionally, the promoter regions of PtrCOMT genes were found to contain 23 distinct cis-acting regulatory elements. Expression analysis indicated tissue-specific expression patterns, with higher expression levels observed in roots. Furthermore, qRT-PCR profiling detected increased expression of multiple candidate PtrCOMT genes upon high-salt treatment, hinting that members of this family may be implicated in plant salt stress regulatory processes. Overall, these findings provide a foundation for further investigation into the functional roles of PtrCOMT genes in response to salt stress. Full article

Background: Soybean is an important crop with multiple uses for oil, food, and feed, providing 50% of the vegetable protein and 20% of the edible oil in the world. The WD40 family genes play crucial regulatory roles in growth, development, secondary metabolism, and stress responses. However, the definition of WD40 family genes in soybean remained unclear, which limited their application potential in genetic improvement. Methods: To identify soybean WD40 family members and screen candidate genes for breeding improvement, this study performed genome-wide identification of the soybean WD40 gene family via bioinformatic approaches based on the latest Williams 82 reference genome (Wm82.a6.v1). Meanwhile, the function of the family gene GmWD40-257 regulating seed quality was analyzed. Results: The results showed that a total of 458 GmWD40 genes were identified, which were distributed on the 20 chromosomes. Subcellular localization showed that most members were mainly concentrated in the nucleus, chloroplast, and cytoplasm. Phylogenetic tree analysis divided the 458 GmWD40 genes into eight groups. Synteny analysis identified 160 syntenic genes between soybean and Arabidopsis thaliana. Conserved motif analysis identified ten core motifs. The promoter regions of GmWD40 contained 19 types of cis-acting elements. Functional analysis revealed that the nonsense mutation of GmWD40-257 significantly reduced the content of oil, palmitic acid, oleic acid, linoleic acid, α-linolenic acid and soluble sugar, while significantly increasing the contents of protein, γ-tocopherol and δ-tocopherol. Conclusions: A total of 458 members of the WD40 gene family were identified in soybean. Among these, GmWD40-257 was found to positively regulate the contents of soybean oil, palmitic acid, oleic acid, linoleic acid, α-linolenic acid and soluble sugar, while negatively regulating the contents of soybean protein, γ-tocopherol and δ-tocopherol. Full article

The UBP gene family plays a key role in various physiological processes, including cell cycle regulation, DNA repair, and stress responses. UBPs have been identified and analyzed in several species, including Moso Bamboo, Arabidopsis thaliana, Oryza sativa L., and Brachypodium distachyon. However, the UBP family within Prunus mume Siebold & Zucc. remains unexplored. In this study, 30 PmUBPs were identified and characterized, all of which contained the UCH conserved domain. They were grouped into 16 subfamilies via evolutionary analysis, revealing similarities in genome structure and motif distribution. PmUBPs were distributed on seven chromosomes and three scaffolds. Gene duplication events, including tandem duplication and segmental duplication, promoted the expansion of PmUBPs. Collinear analysis demonstrated the close relationship between P. armeniaca, P. persica, P. avium, and P. mume. Transcriptome data revealed distinct relative expression trends in PmUBP genes across different tissues. Promoter cis-acting element analysis revealed an abundance of hormone-, light-, and stress-responsive elements across all genes. Transcriptome and reverse transcription quantitative PCR (RT-qPCR) analysis showed that PmUBP2, PmUBP11, PmUBP13, PmUBP18, PmUBP22, and PmUBP26 exhibited relatively high expressions under low-temperature stress. This study provides a theoretical foundation for the role of PmUBP genes in response to low-temperature stress. Full article

The HAK/KUP/KT family represents a major group of plant potassium transporters involved in K⁺ uptake, ion homeostasis and stress responses. However, the accession-level diversity of HAK/KUP/KT genes in Brassica napus remains insufficiently characterized. In this study, we performed a pan-family analysis of HAK/KUP/KT genes across eight B. napus accessions. A total of 269 annotated HAK/KUP/KT family members were identified and classified into core, soft-core, dispensable and private orthogroups based on their representation across the analyzed genome annotations. Phylogenetic analysis grouped these proteins into four major clades together with reference HAK/KUP/KT members from Arabidopsis thaliana and rice. Ka/Ks analysis indicated that HAK/KUP/KT orthogroups were predominantly under purifying selection, while accession-variable orthogroups showed greater variation in sequence conservation. Gene structure, conserved domain, motif and predicted promoter cis-element analyses revealed conserved transporter-related protein features together with orthogroup-level structural and sequence variation. Expression profiling using the ZS11 BnIR dataset further revealed tissue-, hormone- and stress-responsive expression patterns among ZS11 HAK/KUP/KT genes. By integrating expression features, predicted promoter information, evolutionary characteristics, published salt GWAS context and BnVIR haplotype–phenotype information, BnaA08T0085800ZS was prioritized as a candidate locus located near salt-associated variation. This study provides a pan-genome perspective on HAK/KUP/KT family diversity in B. napus and establishes a framework for prioritizing candidate genes for future functional investigation. Full article

Drought stress severely restricts the growth and yield of woody nut crops. The xyloglucan endotransglucosylase/hydrolase (XTH) gene family participates in plant developmental and stress responses, yet its functions in pecan (Carya illinoinensis) under water limitation remain largely uncharacterized. Here, we performed a genome-wide identification of the XTH family in pecan, identifying 34 members distributed across four phylogenetic clades. Transcriptome-based expression analysis showed that several CiXTH genes responded to drought stress, among which CiXTH18 exhibited strong and sustained induction. To investigate its function, CiXTH18 was overexpressed in Arabidopsis thaliana. Under PEG-induced osmotic stress, CiXTH18-overexpressing lines exhibited significantly prolonged primary root lengths compared to wild-type plants. Furthermore, detached leaf assays revealed that transgenic plants had lower water loss rates under dehydration conditions. In addition, DAB staining indicated reduced H₂O₂ accumulation in CiXTH18-overexpressing plants under osmotic stress. Quantitative real-time PCR analysis revealed that the drought-responsive gene DREB2A and the ABA biosynthesis-related gene NCED3 were more strongly induced in transgenic lines than in wild-type plants after PEG treatment. Promoter activity assays confirmed that CiXTH18 was responsive to ABA treatment. Collectively, our findings indicate that heterologous expression of CiXTH18 is associated with improved performance of Arabidopsis under PEG-induced osmotic stress and support CiXTH18 as a promising candidate for further functional investigation. Full article

Sclareol, a natural diterpene, exhibits diverse physiological activities in plants, microorganisms, and animals. Exogenous application of sclareol to Arabidopsis thaliana leaves induces chlorosis-like symptoms accompanied by a reduction in chlorophyll content. In our previous study, a bioassay-guided fractionation approach was employed to isolate endogenous compounds responsible for this decrease, leading to the identification of campesterol and stigmasterol as active phytosterols. Notably, this approach also indicated the presence of additional active substances in fractions lacking these phytosterols. In the present study, we identified α-pinene, oleic acid, triolein, and pipecolic acid as additional compounds capable of reducing chlorophyll content. Exogenous application of each compound to Arabidopsis leaves resulted in a dose-dependent decline in chlorophyll levels. Furthermore, sclareol treatment increased the endogenous accumulation of these metabolites, along with the expression of genes involved in their biosynthesis. Because phytosterols, terpenoids, lipids, and pipecolic acid have been implicated in plant growth and development, stress responses, and disease resistance, the metabolites identified in this study are likely to contribute not only to sclareol-induced chlorophyll reduction but also to other physiological responses elicited by sclareol. Collectively, these findings suggest that sclareol triggers coordinated metabolic reprogramming in Arabidopsis, leading to the accumulation of multiple bioactive metabolites that mediate diverse physiological processes. Full article

Verticillium dahliae is a devastating soil-borne fungal pathogen that causes severe yield losses in melon (Cucumis melo L.) and other crops. Identifying novel resistance genes is crucial for sustainable disease management. In this study, we characterized the function of CmVQ23, a candidate gene previously identified through QTL mapping, in mediating defense against V. dahliae using heterologous expression in Arabidopsis thaliana. Subcellular localization assays revealed that the CmVQ23-eGFP fusion protein predominantly localized to the nucleus, consistent with its predicted role as a co-factor of transcription factor. Upon V. dahliae inoculation, CmVQ23-overexpressing Arabidopsis lines exhibited significantly reduced disease indices and restricted fungal proliferation compared with wild-type and mutant plants, although these lines displayed altered vegetative growth, including delayed bolting and reduced plant height. Mechanistically, CmVQ23 overexpression promoted reactive oxygen species (ROS) accumulation and hypersensitive response (HR)-mediated cell death at infection sites, as evidenced by intensified DAB and trypan blue staining. Furthermore, transgenic lines maintained higher photosynthetic efficiency, enhanced antioxidant enzyme activities, and increased lignin deposition via upregulation of phenylalanine ammonia-lyase (PAL) and polyphenol oxidase (PPO). Notably, CmVQ23 overexpression markedly upregulated both salicylic acid (SA)- and jasmonic acid/ethylene (JA/ET)-responsive marker genes, including AtPR1, AtPR2, AtPR5, AtPAD4, AtPDF1.2, and AtVSP2 upon infection. Collectively, these findings demonstrate that CmVQ23 functions as a positive regulator of resistance to Verticillium dahliae by orchestrating ROS/HR-mediated cell death, antioxidant defense, phenylpropanoid pathway activation, and phytohormone signaling crosstalk, offering a promising genetic resource for improving Verticillium wilt resistance in crops. Full article