Search Results (258)

The cytokinin response regulator (ARR) gene is essential for cytokinin signal transduction, which plays a crucial role in plant growth and development. However, the functional mechanism of ARR genes in cotton leaf abscission remains incompletely understood. In this study, a total of 86 ARR genes were identified within the genome of Gossypium hirsutum. These genes were categorized into four distinct groups based on their phylogenetic characteristics, supported by analyses of gene structures and conserved protein motifs. The GhARR genes exhibited an uneven distribution across 25 chromosomes, with three pairs of tandem duplication events observed. Both segmental and tandem duplication events significantly contributed to the expansion of the ARR gene family. Furthermore, numerous putative cis-elements were identified in the promoter regions, with hormone and stress-related elements being common among all 86 GhARRs. Transcriptome expression profiling screening results demonstrated that GhARRs may play a mediating role in cotton’s response to TDZ (thidiazuron). The functional validation of GhARR16, GhARR43, and GhARR85 using virus-induced gene silencing (VIGS) technology demonstrated that the silencing of these genes led to pronounced leaf wilting and chlorosis in plants, accompanied by a substantial decrease in petiole fracture force. Overall, our study represents a comprehensive analysis of the G. hirsutum ARR gene family, revealing their potential roles in leaf abscission regulation. Full article

WRKY transcription factors play key roles in plant immune responses, including resistance to fungal pathogens. In the present study, we identified a flax resistance-related gene Lus10021999, named LuWRKY39. Here, to identify the role of WRKY transcription factor in resistance of flax against Septoria linicola, we cloned and analyzed the gene LuWRKY39 via homologous cloning using bioinformatics methods and localized the encoded protein. Quantitative real-time PCR (qRT-PCR) was used to explore the response of this gene to S. linicola. The results showed that the gene that is 948 bp long exhibited the closest genetic relationship to WRKY in castor (Ricinus communis), as revealed by phylogenetic analysis, and the encoded protein was localized in the nucleus. The LuWRKY39 gene showed higher expression levels in resistant flax materials than in susceptible ones, and higher in roots and stems than in leaves. Furthermore, gene expression showed an upward trend following treatment with salicylic acid (SA) and methyl jasmonate (MeJA), indicating that LuWRKY39 is involved in the regulation of SA and JA signals. By silencing LuWRKY39 in flax using virus-induced gene silencing (VIGS), the processed plants were more sensitive to S. linicola than untreated plants. Gene expression analysis and disease index statistics confirmed that the silenced plants were more susceptible, highlighting the crucial role of LuWRKY39 in flax disease resistance. This study provides a foundation for functional investigations of WRKY genes in flax and the identification of disease resistance genes. Full article

Background: Verticillium wilt (VW), caused by the fungal pathogen Verticillium dahliae, is a destructive disease that severely compromises cotton yield and fiber quality. Pyrimidine nucleotides, as essential metabolites and nucleic acid components, play critical roles in plant development and stress responses. However, genes involved in pyrimidine metabolism, especially their roles in disease resistance, remain largely uncharacterized in plants. Methods: Ghir_D05G039120, a gene encoding uridine kinase, shown to be associated with VW resistance in our previous study, was cloned and named as GhUKL4. The differential expression of GhUKL4 between the resistant and susceptible cultivars at multiple time points post-inoculation with V. dahliae was analyzed by quantitative real-time PCR (qRT-PCR), and the uracil phosphoribosyl transferase (UPRT) and uridine 5′-monophosphate kinase (UMPK) domains were verified by analyzing the amino acid sequences of GhUKL4. The role of GhUKL4 in the defense against VW infection was estimated by silencing GhUKL4 in the resistant and susceptible cultivars using virus-induced gene silencing (VIGS) analysis. Results: There were significant differences in the expression level of Ghir_D05G039120/ GhUKL4 among resistant and susceptible cotton lines. GhUKL4 contains UPRTase and UMPK domains, and there was one SNP between the resistant and susceptible cultivars in its 3′-UTR region. The silencing of GhUKL4 reduced cotton’s resistance to VW through mediating hormone signaling (JA) and oxidative stress (ROS) pathways. Conclusions: GhUKL4, encoding UMPK and UPRTase domain proteins, is a new regulatory factor associated with VW resistance in Gossypium hirsutum through fine-tuning JA-signalling and ROS bursting. Full article

During fruit ripening in Capsicum species, substantial amounts of carotenoids accumulate in the pericarp. While the carotenoid biosynthesis pathway in Capsicum species has been extensively investigated from various angles, the transcriptional regulation of genes encoding carotenoid biosynthetic enzymes remains less understood in this non-climacteric horticultural crop compared to tomato, a climacteric fruit. In the present study, we investigated the function of the NAM, ATAF1/2 or CUC2 81 (CaNAC81) transcription factor gene. This gene was selected through RNA-Seq co-expression analysis based on the correlation between expressed transcription factor gene profiles and those of carotenoid structural genes. To determine its role in regulating the expression of biosynthetic-related carotenogenic genes, we performed Virus-Induced Gene Silencing (VIGS) assays in the Serrano-type C. annuum ‘Tampiqueño 74’. Fruits from plants infected with a pTRV2:CaNAC81 construct (silenced fruits) exhibited altered carotenoid pigmentation accumulation, manifested as yellow-orange spots, in contrast to fruits from non-agroinfected controls (NTC) and fruits from plants infected with the empty TRV2 construct (red fruits). Quantitative real-time PCR (qPCR) assays confirmed decreased transcript levels of CaNAC81 in fruits displaying altered pigmentation, along with reduced transcription of the PSY gene, which encodes the carotenoid biosynthetic enzyme phytoene synthase (PSY). High-performance liquid chromatography (HPLC) analysis revealed a distinct carotenoid pigment accumulation pattern in fruits from plants showing silencing symptoms, characterized by low concentrations of capsanthin and zeaxanthin and trace amounts of capsorubin, compared to control plants (NTC). These findings suggest the involvement of CaNAC81 in the regulatory network of the carotenoid biosynthetic pathway in chili pepper fruits. Full article

Glucose-6-phosphate dehydrogenase (G6PDH) is a critical enzyme in the pentose phosphate pathway, playing an essential role in plant growth, development, and adaptation to abiotic stress. In this study, we identified four members of the G6PDH gene family in the ‘Zunla-1’ genome, designating them as CaG6PDH1-CaG6PDH4. Multiple sequence alignment revealed that the four protein sequences of pepper contain three unique binding sites characteristic of G6PDH: the substrate binding site, the NADP binding site and the Rossmann fold. The phylogenetic tree, motifs, and gene structure analysis indicate that the CaG6PDH gene sequence is relatively conserved and structurally similar, with a close relationship to the sequence of Solanaceae G6PDH members. The collinearity analysis showed that there were two pairs of collinearity between the CaG6PDH genes and the AtG6PDH genes, as well as the SiG6PDH genes. Additionally, numerous cis-elements associated with stress responses, hormone regulation, development, and light responses were identified in the promoter region of the CaG6PDH gene. Furthermore, the various members of the pepper CaG6PDH gene family exhibit specific expression patterns across different tissues and demonstrate significant variations in response to abiotic stress and phytohormone treatments, particularly the CaG6PDH1 and CaG6PDH2 genes. Subcellular localization studies indicate that CaG6PDH2 is located in chloroplasts. We conducted further investigations into the role of CaG6PDH2 in response to cold stress using Virus-Induced Gene Silencing (VIGS) technology. The tissues of seedlings with silenced CaG6PDH2 exhibited significant damage and displayed a more pronounced cold damage phenotype. This observation is further supported by the accumulation of reactive oxygen species (ROS), the activity of antioxidant enzymes, and a reduction in the expression of cold-responsive genes. In conclusion, the findings of this study indicate that CaG6PDH2 plays an important role in cold stress response and may serve as a potential gene for cultivating cold-tolerant pepper varieties. Full article

Objective: This study aimed to elucidate the regulatory mechanism of an auxin amide hydrolase gene (IAA-Leucine Resistant1-like Hydrolase, RhILL1) in the petal pigmentation of rose (Rosa hybrida), providing theoretical insight into the hormonal regulation of flower coloration at the molecular level. Methods: Using petals at Stage 3 (S3) of the cut rose cultivar ‘Pink Floyd’ as experimental material, we cloned the rose auxin amide hydrolase gene RhILL1 and validated its function via virus-induced gene silencing (VIGS). The expression levels of anthocyanin biosynthetic genes, anthocyanin content, and auxin (IAA) levels were analyzed to assess the role of RhILL1 in petal pigmentation. Results: The full-length open reading frame (ORF) of RhILL1 was cloned, spanning 1326 bp and encoding a 441-amino-acid protein harboring two conserved domains, Peptidase_M20 and M20_dimer, characteristic of the ILL1 protein family. Functional characterization was performed using VIGS. Quantitative real-time PCR (qRT-PCR) revealed that RhILL1 expression progressively increased from the Green (G) stage to S3, correlating with intensified petal coloration. Silencing RhILL1 resulted in visibly lighter petals, the reduced expression of anthocyanin biosynthetic genes, and a significant decrease in endogenous indole-3-acetic acid (IAA) levels compared with controls. Moreover, exogenous application of 10 μM naphthaleneacetic acid (NAA) to petals significantly preserved petal pigmentation. Conclusion: These findings suggest that RhILL1 contributes to the development and maintenance of petal coloration in rose, likely by modulating IAA levels, thereby influencing the expression of anthocyanin biosynthesis-related genes. Full article

The virus-induced gene silencing (VIGS) technique can effectively inhibit systemic viral infection by down-regulating plant endogenous gene expression, and it has become an important tool to study plant gene function. However, few studies have reported that wheat dwarf virus (WDV), which enables high-throughput gene silencing, could be used in a rice VIGS system. In this study, a VIGS vector system was constructed based on WDV, and successfully silenced the Phytoene desaturase gene and the rice blast resistance gene Pi21 in rice. Pi21-silenced plants showed significantly increased resistance to rice blast, significantly reduced lesion area, and did not show high disease symptoms (grade 8–9). In addition, the WDV vector has the advantages of rapid infection, high proliferation, and an unconformity genome, and has little influence on rice growth and development. This study validates the effectiveness of the WDV-VIGS system in rice gene function studies and provides a new gene silencing tool for blast resistance breeding. Full article

Verticillium wilt (VW), induced by the soil-borne fungus Verticillium dahliae, represents a significant threat to global cotton production. Phenylalanine ammonia-lyase (PAL) is an essential enzyme in lignin metabolism that helps plants defend themselves against pathogenic fungal. Nonetheless, its role in imparting resistance to V. dahliae in cotton required further investigation. This study identified the GhPAL9 (GH_D04G1247) as a crucial gene in cotton resistance to V. dahliae via RNA-seq analysis, demonstrating significant upregulation in the resistant variety Xinluzao84. Bioinformatics analysis revealed the conserved evolutionary relationship of GhPAL9 with PAL homologs across various species and highlighted stress-responsive cis-elements in its promoter region. The expression of GhPAL9 was rapidly activated in roots, stems, and leaves following infection with V. dahliae, peaking between 2 and 8 h post inoculation (hpi). Silencing GhPAL9 through virus-induced gene silencing (VIGS) technology intensified disease symptoms, elevated relative fungal biomass, and diminished lignin accumulation, thereby affirming its function in cotton resistance to V. dahliae. The overexpression of GhPAL9 in Arabidopsis improved resistance to V. dahliae, and the OE-GhPAL9 transgenic lines demonstrated reduced disease severity and diminished relative fungal biomass. The results gave us new information about how VW resistance at the molecular level, which established that GhPAL9 acted as a positive regulator to increase resistance to VW via lignin accumulation. Full article

Maize is a vital staple crop significantly affected by climate change, necessitating urgent efforts to enhance its resilience. This review analyzes advanced methodologies for maize improvement, focusing on the identification of genetic determinants through QTL mapping, candidate gene mining, and GWAS. We highlight the transformative potential of CRISPR gene editing for identifying key regulators in maize development and the utility of virus-induced gene silencing (VIGS) for functional genomics. Additionally, we discuss breeding strategies leveraging the genetic diversity of maize wild relatives and innovations such as speed breeding and genomic selection (GS), which accelerate breeding cycles. Marker-assisted selection (MAS) plays a critical role in developing superior maize varieties. The review also encompasses agronomic practices and technological innovations, including GS, aimed at climate mitigation. High-throughput phenotyping and omics-based approaches, including transcriptomics and metabolomics, are essential tools for developing climate-resilient maize. Climate changes have a significant impact on maize production and pose unprecedented challenges to its cultivation. Full article

Soybean (Glycine max L.) is a vital grain and oil crop, serving as a primary source of edible oil, plant-based protein, and livestock feed. Its production is crucial for ensuring global food security. However, soybean yields are severely impacted by various diseases, and the development of disease-resistant cultivars remains the most sustainable strategy for mitigating these losses. While stable genetic transformation is a common approach for studying gene function, virus-induced gene silencing (VIGS) offers a rapid and powerful alternative for functional genomics, enabling efficient screening of candidate genes. Nevertheless, the application of VIGS in soybean has been relatively limited. In this study, we established a tobacco rattle virus (TRV)-based VIGS system for soybean, utilizing Agrobacterium tumefaciens-mediated infection. The TRV vector was delivered through cotyledon nodes, facilitating systemic spread and effective silencing of endogenous genes. Our results demonstrate that this TRV–VIGS system efficiently silences target genes in soybean, inducing significant phenotypic changes with a silencing efficiency ranging from 65% to 95%. Key genes, including phytoene desaturase (GmPDS), the rust resistance gene GmRpp6907, and the defense-related gene GmRPT4, were successfully silenced, confirming the system’s robustness. This work establishes a highly efficient TRV–VIGS platform for rapid gene function validation in soybean, providing a valuable tool for future genetic and disease resistance research. Full article

Drought is one of the major abiotic stresses that inhibits plant growth and development. Therefore, it is critical to explore drought resistance genes in crops to obtain high-quality breeding materials. In this study, the drought-sensitive tomato line “FQ118” and the resistant line “FQ119” were treated with PEG-6000 and, at 0 h (CK), 6 h, 24 h, 36 h and 48 h, the plants were evaluated for growth and physiological indicators, and leaf tissues were collected for RNA-seq. The growth indicators (growth trend, dry and fresh weights above- and below-ground, etc.) and the antioxidant enzyme system reflect that “FQ119” has stronger drought tolerance. Through RNA-seq analysis, a total of 68,316 transcripts (37,908 genes) were obtained. The largest number of significant differentially expressed genes (DEGs) in the comparison of “FQ118” and “FQ119” was observed at 6 h and 48 h. KEGG analysis demonstrated the significant enrichment of certain pathways associated with drought stress, such as glycerolipid metabolism and galactose metabolism. Co-expression analysis revealed that 7 hub DEGs, including genes encoding a photosystem reaction center subunit protein, chlorophyll a-b binding protein, glyceraldehyde-3-phosphate dehydrogenase A (GAPDH), and others, were coenriched in both comparisons. In addition, three hub genes specific to the comparison during the 6-h processing stage, encoding oxygen-evolving enhancer protein 1, receptor-like serine/threonine-protein kinase and calcium-transporting ATPase, were identified. The above hub genes were related to plant resistance to drought stress, and RT‒qPCR verified that the overall magnitudes of the differences in expression between the two lines gradually increased over time. Virus-induced gene silencing (VIGS) experiments have demonstrated that GAPDH plays a relevant role in the drought resistance pathway. In addition, the differences in expression of 7 DEGs encoding transcription factors, including Dofs, WRKYs, MYBs, and MYCs, also tended to increase with increasing duration of drought treatment, as determined via qPCR. In summary, this study identified several valuable genes related to plant drought resistance by screening genes with differential transcription under drought stress. This in-depth gene mining may provide valuable references and resources for future breeding for drought resistance in tomato. Full article

Snapdragon (Antirrhinum majus) serves as a model system for dissecting floral morphogenesis mechanisms. Petal malformation in A. majus impacts ornamental value, but its genetic basis remains poorly understood. We compared transcriptomes of the wild-type (Am11) and a petal-malformed mutant (AmDP2) to identify 2303 differentially expressed genes (DEGs), including E-class MIKC-type MADS-box genes SEP3 (AmMADS25/61/20/26) and SEP2 (AmMADS85). Weighted gene co-expression network (WGCNA), protein-protein interaction (PPI), qRT-PCR and virus-induced gene silencing (VIGS) analyses revealed interactions between SEP2/SEP3 and C/A/B-class MADS-box genes (AG, AP1, AP3), co-regulated MADS transcription factors (MTFs) AGL15 (AmMADS16), and auxin signaling genes (SAUR1, IAA13). qRT-PCR validated upregulation of SEP3 and downregulation of SEP2 in AmDP2. Our results suggest that E-class MADS-box genes are associated with petal malformation through coordinated interactions with hormonal pathways. These findings provide candidate targets for further functional studies in snapdragon. Full article

Tomato fruit ripening is a complex process that determines the formation of fruit quality. Transcription factors (TFs) play key roles in regulating fruit ripening and quality formation. MADS-box genes, a crucial class of genes involved in virtually all aspects of plant development, are regarded as important candidate members among them. In this study, we present a detailed overview of the phylogeny and expression of 32 tomato MIKC-type MADS-box genes. Moreover, 20 genes contained many phytohormone-related elements. In combination with higher expression in fruit, eight genes are suggested to be involved in plant hormone pathways that regulate fruit ripening. A virus-induced gene silencing (VIGS) experiment revealed that TM4, TAGL11, SlMADS6, SlMADS99, TAGL1, SlMADS1, RIN, and MC may positively regulate fruit ripening. Measurements of the endogenous phytohormones in silenced TM4, TAGL11, SlMADS6, SlMADS99, TAGL1, SlMADS1, RIN, or MC fruit suggest that eight MIKC-type MADS-box genes, as well as medicated abscisic acid (ABA), salicylic acid (SA), gibberellin (GA₃), indole-3-acetic acid (IAA), and/or methyl jasmonate (MeJA) pathways, positively regulate fruit ripening in tomatoes. Full article

Despite substantial progress in elucidating the stress-responsive mechanisms of 4-coumarate-CoA ligases (4CL) in various plant species, the maize (Zea mays L.) 4CL gene family remains underexplored, leaving a significant gap in our comprehension of its potential roles in abiotic stress tolerance and adaptive strategies. Through comprehensive genome-wide analysis, we identified and characterized 32 putative 4CL genes in maize, which were phylogenetically classified into seven distinct clades. Members within the same clade exhibited conserved gene structures and motif compositions. Expression profiling across various maize tissues and under multiple abiotic stress conditions revealed specific 4CL genes associated with stress tolerance. Notably, promoter analysis identified numerous stress-responsive cis-regulatory elements in Zm4CL genes. Among the identified genes, six exhibited significant induction under salt stress, while five showed upregulation during drought conditions. Particularly, Zm4CL8, a member of the 4CL clade, demonstrated dual responsiveness to both drought and salt stresses. Functional characterization through virus-induced gene silencing (VIGS) revealed that Zm4CL8-silenced plants displayed enhanced sensitivity to both drought and salt stresses, as evidenced by significantly reduced chlorophyll content and survival rate, which collectively suggests its positive regulatory role in stress adaptation mechanisms. These findings establish Zm4CL8 as a promising molecular target for enhancing drought and salt tolerance in maize, while significantly advancing our understanding of the functional characterization of 4CL genes in this crucial crop species. Full article

Dehydrins (DHNs; late embryogenesis-abundant D11 family) are a class of hydrophilic proteins involved in plant abiotic stress response. However, there is less information regarding DHN gene function in cucurbit crops. Herein, 34 DHN gene family members were identified and characterized in Cucumis sativus, Cucumis melo, Citrullus lanatus, Benincasa hispida, Lagenaria siceraria, and Cucurbita maxima. The DHN genes in the six cucurbit crops exhibited greater collinearity within subfamilies than between different subfamilies. Responses to stress (including low-temperature, salt, cadmium, and aluminum stress) varied among the DHN members, with a significant alteration in the expression of the acidic SnKn-type DHN gene CmDHN3 in response to aluminum stress. Subcellular localization analysis confirmed that CmDHN3 is expressed in the nucleus and cytoplasm. Virus-induced gene silencing (VIGS) revealed a remarkable decrease in CmDHN3 expression, which markedly increased malondialdehyde content, relative conductivity, and proline content in the roots and leaves of plants under aluminum stress. Transcriptome analysis showed that the decreased CmDHN3 expression reduced the expression of water channel protein-encoding genes. Interactions between CmDHN3 and CmAQP1 (MELO3C007188) and between CmDHN3 and CmAQP2 (MELO3C020774) were confirmed using yeast two-hybrid assays. These results clarify the pathway by which dehydrin genes are involved in the transcriptional-level response of melon to aluminum stress and provide a theoretical basis to comprehensively analyze the functions of this gene family in cucurbit crops. Full article