Search Results (138)

The soil-borne fungal pathogen Verticillium dahliae causes devastating vascular wilt disease in numerous crops, including cotton. In this study, we reveal that VdSOX1, a highly conserved sarcosine oxidase gene, is significantly upregulated during host infection and plays a multifaceted role in fungal physiology and pathogenicity. Functional deletion of VdSOX1 leads to increased fungal virulence, accompanied by enhanced microsclerotia formation, elevated carbon source utilization, and pronounced upregulation of effector genes, including over 50 predicted secreted proteins genes. Moreover, the VdSOX1 knockout strains suppress the expression of key defense-related transcription factors in cotton, such as WRKY, MYB, AP2/ERF, and GRAS families, thereby impairing host immune responses. Transcriptomic analyses confirm that VdSOX1 orchestrates a broad metabolic reprogramming that links nutrient acquisition to immune evasion. Our findings identify VdSOX1 as a central regulator that promotes V. dahliae virulence by upregulating effector gene expression and suppressing host immune responses, offering novel insights into the molecular basis of host–pathogen interactions and highlighting potential targets for disease management. Full article

Apomixis-mediated fixation of heterosis could transform hybrid breeding in alfalfa (Medicago sativa), a globally important forage crop. The parthenogenesis-inducing morphogenetic regulator BABY BOOM (BBM) represents a promising candidate for enabling this advancement. Here, we identified BBM homologs from three alfalfa genomes, characterized their promoter regions, and cloned a 2082 bp MsBBM gene encoding a 694-amino acid nuclear-localized protein. Three alfalfa BBM gene promoters primarily contained light- and hormone-responsive elements. Phylogenetic and conserved domain analyses of the MsBBM protein revealed a high sequence similarity with M. truncatula BBM. Expression profiling demonstrated tissue-specific accumulation of MsBBM transcripts, with the highest expression in the roots and developing pods. Hormonal treatments differentially regulated MsBBM. Expression was upregulated by GA₃ (except at 4 h) and SA, downregulated by NAA, MeJA (both except at 8 h), and ABA (except at 4 h), while ETH treatment induced a transient expression peak at 2 h. As an AP2/ERF family transcription factor showing preferential expression in young embryos, MsBBM likely participates in reproductive development and may facilitate apomixis. These findings establish a molecular framework for exploiting MsBBM to enhance alfalfa breeding efficiency through heterosis fixation. Full article

Mung bean (Vigna radiata L.) is globally cultivated and has been widely used in the food industries. Other than nutrients, the composition of the volatile organic compounds (VOCs) often influences the quality of mung bean-based products. However, the dynamics of VOCs and the flavor changes during mung bean seed development remain unexplored. This study investigated the VOC and flavor composition in four mung bean varieties by integrating relative odor activity value (ROAV) evaluation and transcriptomic analysis. A total of 65 VOCs were identified, with eucalyptol serving as a key maturity indicator in LL655 and SH-1, while nonanal contributed significantly to the characteristic beany flavor across all varieties. Transcriptomic analysis revealed four downregulated geranylgeranyl diphosphate synthase genes during seed development, leading to terpenoid accumulation patterns. Terpenoids, including trans-beta ocimene and gamma-terpinene, appeared to be regulated by transcription factors (TFs) from the RLK-Pelle, WRKY, AP2/ERF, bHLH, and bZIP families. Additionally, two MYB TFs showed potential roles in modulating the accumulation of phenylpropanoid/benzenoid derivatives. This study provides a comprehensive understanding of the VOC accumulation and flavor variation during mung bean seed development, enriches the knowledge of flavor chemistry in mung bean varieties, and facilitates a theoretical foundation for optimizing and developing mung bean-based products. Full article

The APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily is one of the largest transcription factor families in plants, playing diverse roles in development, stress response, and metabolic regulation. Despite their ecological and economic importance, AP2/ERF genes remain uncharacterized in marigold (Tagetes erecta), a valuable ornamental and medicinal plant in the Asteraceae family known for its unique capitulum-type inflorescence with distinct ray and disc florets. Here, we conducted a comprehensive genome-wide analysis of the AP2/ERF superfamily in marigold and identified 177 AP2/ERF genes distributed across 11 of the 12 chromosomes. Phylogenetic analysis revealed their classification into the AP2 (28 genes), ERF (143 genes), RAV (4 genes), and Soloist (2 genes) families based on domain architecture. Gene structure and motif composition analyses demonstrated group-specific patterns that correlated with their evolutionary relationships. Chromosome mapping and synteny analyses revealed that segmental duplications significantly contributed to AP2/ERF superfamily gene expansion in marigold, with extensive collinearity observed between marigold and other species. Expression profiling across different tissues and developmental stages indicated distinct spatio-temporal expression patterns, with several genes exhibiting tissue-specific expression in Asteraceae-specific structures. In floral organs, TeAP2/ERF145 exhibited significantly higher expression in ray floret corollas compared to disc florets, while TeAP2/ERF103 showed stamen-specific expression in disc florets. Protein interaction network analysis revealed AP2 as a central hub with extensive predicted interactions with MADS-box and TCP family proteins. These findings suggest that AP2 family genes may collaborate with MADS-box and CYC2 genes in regulating the characteristic floral architecture of marigold, establishing a foundation for future functional studies and molecular breeding efforts to enhance ornamental and agricultural traits in this economically important plant. Full article

Drought stress is a significant environmental factor that can impede plant growth and ornamental quality. Hemerocallis middendorffii, a drought-tolerant garden plant, has attracted attention for its ornamental value and application prospects. To investigate the molecular mechanism of drought stress resistance of H. middendorffii, this study employed 20% polyethylene glycol (PEG) 6000 to simulate drought stress. Leaves and roots of H. middendorfii were subjected to 24 h treatment and followed by transcriptome sequencing. Analysis revealed 8796 and 3401 differentially expressed genes (DEGs) in leaves and roots. The major biological processes and key molecular pathways activated under drought stress in H. middendorffii were revealed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. The focus of this analysis was on the gene expression changes within plant hormone signal transduction pathway. Additionally, drought-associated transcription factor families such as AP2/ERF, WRKY, MYB, bHLH, NAC, and bZIP were identified among DEGs. Furthermore, potential regulatory relationships of the above transcription factors (TFs) with functional genes in the abscisic acid (ABA) and jasmonic acid (JA) signalling pathways were analysed using correlation network prediction. This research establishes the groundwork for subsequent exploration of drought-responsive gene expression and regulatory patterns in H. middendorfii and provides an importance for the systematic study of its drought-resistant molecular mechanism. Full article

Osmanthus fragrans is a highly valued ornamental tree species in China, but its short flowering period limits its ornamental appeal. Investigating the mechanisms of flower senescence in O. fragrans is therefore of significant importance. Ethylene, a key endogenous hormone, plays a central role in flower senescence, and the AP2/ERF gene family, which includes ethylene response factors, is known to regulate this process in various plants. Transcriptome sequencing and expression analysis identified OfERF17 as a critical gene influencing petal senescence in O. fragrans. Bioinformatics analysis revealed that OfERF17 lacks transmembrane transport structures but contains multiple phosphorylation sites and shares a close phylogenetic relationship with the Olea europaea var. Sylvestris. Subcellular targeting and yeast-based auto-activation tests revealed that OfERF17 resides in the nucleus and possesses a transcriptional self-activation capability. Transient expression studies conducted in O. fragrans petals indicated a decrease in the expressions of two genes associated with senescence, namely, OfSAG21 and OfACO3, when compared to the control group. Additionally, the levels of hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) were markedly reduced. Transgenic Nicotiana tabacum blooms one day more than the wild type, and NtSAG12 and NtACO1 expressions were lower than wild type. These results suggest that OfERF17 functions to delay petal senescence in O. fragrans. This study enhances our knowledge of the molecular mechanisms underlying O. fragrans petal senescence and provides insights into strategies for prolonging its flowering period. Full article

Plants constantly encounter a wide range of biotic and abiotic stresses that adversely affect their growth, development, and productivity. Phytohormones such as abscisic acid, jasmonic acid, salicylic acid, and ethylene serve as crucial regulators, integrating internal and external signals to mediate stress responses while also coordinating key developmental processes, including seed germination, root and shoot growth, flowering, and senescence. Transcription factors (TFs) such as WRKY, NAC, MYB, and AP2/ERF play complementary roles by orchestrating complex transcriptional reprogramming, modulating stress-responsive genes, and facilitating physiological adaptations. Recent advances have deepened our understanding of hormonal networks and transcription factor families, revealing their intricate crosstalk in shaping plant resilience and development. Additionally, the synthesis, transport, and signaling of these molecules, along with their interactions with stress-responsive pathways, have emerged as critical areas of study. The integration of cutting-edge biotechnological tools, such as CRISPR-mediated gene editing and omics approaches, provides new opportunities to fine-tune these regulatory networks for enhanced crop resilience. By leveraging insights into transcriptional regulation and hormone signaling, these advancements provide a foundation for developing stress-tolerant, high-yielding crop varieties tailored to the challenges of climate change. Full article

Malformed coconut fruit occurrence exhibits dual impacts on agricultural productivity and economic returns, primarily through substantial yield reduction and compromised commercial value resulting from morphological defects. To elucidate the molecular determinants underlying this developmental anomaly, we conducted a systematic investigation integrating physiological profiling and transcriptomic sequencing on pulp tissues from malformed (MF) and normal (NF) coconut fruits. Notably, MF specimens displayed marked depletion in carbohydrate reserves, with soluble sugars (SS), reducing sugars (RS), starch (SH), soluble proteins (SP), and fat (FA) declining by 28.57%, 20.43%, 15.51%, 36.78%, and 50.18%, respectively, compared to NF controls. Conversely, a coordinated upregulation of phytohormones was observed, where indole acetic acid (IAA), abscisic acid (ABA), cytokinin (CK), gibberellic acid (GA), brassinosteroid (BR), jasmonic acid (JA), and salicylic acid (SA) levels increased by 31.82–92.97%, while ethylene (ETH) exhibited a paradoxical 30.09% reduction. Transcriptomic dissection revealed 6370 functionally annotated differentially expressed genes (DEGs), comprising 4235 upregulated and 2135 downregulated transcripts. These DEGs were predominantly enriched in critical pathways including plant hormone signal transduction, flavonoid/phenylpropanoid biosynthesis, and carbohydrate metabolic networks. Particularly noteworthy was the enhanced activity of cell wall remodeling enzymes—cellulase (CEL), polygalacturonase (PG), and pectinesterase (PE)—accompanied by differential expression of nine cell wall-associated gene families (CEL, PE, PG, PEL, URG, UTR, VTC2, EXP, XET/XTH) and eight phytohormone-related gene clusters. Functional stratification analysis further identified key transcriptional regulators, with MYB, ERF/AP2, BHLH, WRKY, bZIP, and MADS transcription factors demonstrating significant expression divergence, suggesting their pivotal regulatory roles in MF pathogenesis. This multi-omics integration not only deciphers the molecular choreography of coconut fruit malformation but also establishes a novel conceptual framework for developmental disorder research in perennial crops. Full article

The ethylene response factor (ERF) family is a prominent plant-specific transcription factor family, which plays a crucial role in modulating plant growth and stress tolerance. In this study, a total of 210 ERFs were identified in Populus trichocarpa, comprising 29 AP2 (APETALA2) subfamily members, 176 ERF subfamily members, and 5 RAV (related to ABI3/VP1) subfamily members. The duplication events of the PtERF family members exclusively occurred within the subfamilies. A total of 168 duplication pairs were found among 161 PtERF genes, and all of them were fragment duplications. Gene structure analysis revealed that most ERF subfamily members only had one exon without introns, the AP2 subfamily members had six or more introns and exons, and RAV subfamily members lacked introns except for PtERF102. Considerable cis-acting elements associated with plant growth and development, stress response, hormone response, and light response were detected in the promoters of PtERF genes. The expression levels of PtERFs were highest in roots across tissues and in winter among seasons. Furthermore, the nitrate and urea stimulated the expression of PtERF genes. The co-expression network analysis based on PtERFs indicated their potential roles in hormone signaling, acyltransferase activity, and response to chemicals. This study provides novel insights into investigating the role of PtERFs in environmental stress in poplar species. Full article

Low temperature at the seedling stage adversely affects sorghum growth and development and limits its geographical distribution. APETALA2/Ethylene-Responsive transcription factors (AP2/ERFs), one of the largest transcription factor families in plants, play essential roles in growth, development, and responses to abiotic stresses. However, the roles of AP2/ERF genes in cold tolerance in sorghum and the mechanisms underlying their effects remain largely unknown. Here, transcriptome sequencing (RNA-seq) was performed on the leaves of sorghum seedlings before and after cold treatment. Several candidate genes for cold tolerance and regulation pathways involved in “photosynthesis” under cold stress were identified via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. Additionally, the AP2/ERF family gene SbERF027, a novel regulator of cold tolerance, was functionally identified through a comprehensive analysis. The expression of SbERF027 was high in seedlings and panicles, and its expression was induced by low temperature; the cold-induced expression level of SbERF027 was markedly higher in cold-tolerant accession SZ7 than in cold-sensitive accession Z-5. SbERF027 was detected in the nucleus under both normal and cold stress conditions. In addition, the cold tolerance of SbERF027-overexpressing lines was higher than that of wild-type plants; while the cold tolerance of lines with SbERF027 silenced via virus-induced gene silencing (VIGS) was significantly lower than that of wild-type plants. Further research demonstrated that SNP-911 of the promoter was essential for enhancing cold tolerance by mediating SbERF027 expression. This study lays a theoretical foundation for dissecting the mechanism of cold tolerance in sorghum and has implications for the breeding and genetic improvement of cold-tolerant sorghum. Full article

Feedstock plants for biofuel production can be cultivated on polluted sites that are unsuitable for edible crop production. This approach combines environmental restoration and renewable energy production, therefore enhancing the economic viability of plant-derived biofuels. Previous studies have indicated that exposure to environmental pollutants may elevate lignin levels in exposed plants, potentially impacting the biomass digestibility and the efficiency of bioethanol conversion. In this study, we investigated the impact of the antimicrobial agent chlortetracycline on lignin biosynthesis in the reference organism Arabidopsis thaliana. Toxicity testing showed that exposure to chlortetracycline significantly reduced plant growth at concentrations above 2.5 mg L⁻¹. Using Fourier-transform infrared spectroscopy (FTIR) analysis, we observed a significant increase in the lignin signature, ranging from 16 to 40%, in plants exposed to chlortetracycline as compared to non-exposed control plants. Transcriptomic analysis (RNA sequencing) was conducted to determine the molecular basis of plant response to chlortetracycline, revealing significant enrichment of several genes involved in lignin biosynthesis and the phenylpropanoid pathway, including cinnamyl alcohol dehydrogenase and peroxidases. Exposure to chlortetracycline also resulted in the overexpression of genes involved in the metabolism of xenobiotic compounds, including cytochrome P450 monooxygenases, glutathione S-transferases, and glycosyltransferases. Chlortetracycline also induced several genes involved in plant response to stress and defense mechanisms, including transcription factors (e.g., WRKY, MYB, AP2/ERF families), pathogenesis-related proteins, and genes involved in stress signaling. These results suggest that the antibiotic chlortetracycline triggers multiple stress responses in A. thaliana, which may cause changes in lignin biosynthesis, reductions in plant growth, increases in the lignin content, and induction of defense metabolic pathways. Full article

The AP2/ERF family of transcription factors is one of the most conserved and important transcription factor families, and it is ubiquitous in plants. It plays an essential role in plant morphogenesis, molecular mechanisms of stress responses, hormone signaling pathways, and synthesis of secondary metabolites. FaTINY2 was cloned from the octaploid strawberry Fragaria × ananassa for this investigation. Bioinformatics revealed that the protein possesses a conserved AP2 domain and is localized in the nucleus. When FaTINY2 was expressed in plants, quantitative analysis revealed that the gene was tissue-specific. There are lower contents of reactive oxygen species (ROS) and malondialdehyde (MDA), higher contents of proline, chlorophyll, and higher activities of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) in transgenic Arabidopsis thaliana than wild type (WT) and unload line (UL) plants under cold and salt stress. FaTINY2 plays a role in enhancing stress tolerance by regulating a few genes linked to the stress response. The findings of this study were that FaTINY2 transgenic Arabidopsis thaliana plants were more tolerant to salt and cold than WT and UL plants. In addition to offering a theoretical reference for strawberry production under stress, this research established a groundwork for exploration into the molecular mechanisms in which strawberries respond to cold and high salt stress. Full article

AP2/ERF (APETALA2/Ethylene Responsive Factor) transcription factors, a class of plant-specific transcription factors, play a pivotal role in plant growth, development, metabolism, and stress response. The pineapple (Ananas comosus (L.) Merr.), a perennial fruit, belongs to the Bromeliaceae family. It is an economically important crop worldwide, which is consumed as fresh fruit, canned fruit, a fiber source, and even pharmaceutical raw material. We identified 75 AcoAP2/ERF genes in the pineapple genome, with four manually curated. They were distributed evenly on 23 chromosomes, except on LG20 and LG23. Sequence lengths, molecular weights, and intron numbers were diverse. The majority of pineapple AcoAP2/ERF genes were localized in nuclear while seven AcoERFs were located in mitochondrial or chloroplast. All pineapple AcoAP2/ERF genes possess an AP2 domain and are divided into 10 clades. Most originate from whole-genome or segmental duplication instead of transposon events. Utilizing pineapple calluses as experimental material, qRT–PCR analysis revealed that the expression of the majority of AcoAP2/ERF genes was induced in response to abscisic acid (ABA), gibberellic acid (GA), ethylene (ET), and naphthalene acetic acid (NAA). In this study, we cloned the promoter sequence of the AcoERF24 gene and divided it into three fragments to construct individual vectors. These vectors were subsequently introduced into Arabidopsis thaliana for β-glucuronidase (GUS) activity analysis, revealing variations in activity levels among the different fragments. This study not only deepens our understanding of the AcoAP2/ERF genes family in olives but also provides an important basis for subsequent studies on the regulation of AcoERF24 gene expression and biological functions. Full article

The Apetala2/Ethylene Responsive Factor (AP2/ERF) family represents a critical group of transcription factors in plants, recognized for their roles in growth, development, fruit ripening, and postharvest processes. This study aimed to identify and characterize the AP2/ERF gene family in passion fruit (Passiflora edulis Sims) and investigate their potential roles in flavor enhancement. A total of 91 PeAP2/ERF genes were identified and classified into five subfamilies. Chromosome localization and collinearity analysis demonstrated their distribution across all nine chromosomes of passion fruit, with tandem duplication events identified as a key driver of family expansion. Exon–intron configurations and motif compositions were highly conserved among PeAP2/ERF genes. Promoter cis-acting element analysis indicated potential regulation by environmental signals, including abiotic and biotic stresses, as well as hormonal cues. Postharvest storage induced the expression of 59 PeAP2/ERF genes over time. Notably, PeAP2-10 was found to enhance the expression of PeSTP6, a gene associated with sugar transport, suggesting its potential influence on the flavor profile of passion fruit. These findings provide valuable insights into the functional roles of PeAP2/ERF genes in passion fruit, highlighting their significance in postharvest management and flavor quality enhancement strategies. Full article

M. laxiflora is an endangered plant that grows in the Yangtze River floodplain of China and often suffers from flooding stress. Due to the lack of a reference genome for M. laxiflora, the molecular regulatory mechanism of waterlogging stress in this plant remains unclear. In this study, we report a high-quality reference genome of M. laxiflora with a size of 1.29 Gb. A total of 23,666 gene-encoding proteins and 5457 ncRNAs were predicted in this reference genome. A comparative genome analysis revealed that 902 and 4299 gene families significantly expanded and contracted, respectively, in M. laxiflora. The expansions of the 902 gene families were significantly related to the “response to stress”, “response to abiotic stimulus”, and “response to oxygen-containing compounds” pathways. In the M. laxiflora genome, 101 MylAP2/ERF genes were identified and divided into five subgroups. Several MeJA-, ABA-, and hypoxia-responsive elements were found in the promoter regions of these MylAP2/ERF genes. According to the transcriptome data analysis, 74 MylAP2/ERF genes responded to flooding stress. Moreover, three genes (MylAP2/ERF49/78/91) that belong to the same branch as the RAP2.2 gene exhibited different expression trends under flooding stress. Our results provide valuable information on the molecular regulatory mechanism of flooding stress in M. laxiflora. Full article