Salicylic acid-related cotton (Gossypium arboreum) ribosomal protein GaRPL18 contributes to resistance to Verticillium dahliae

Suppression of plant immunity by Verticillium dahliae effector Vd6317 through AtNAC53 association

Verticillium dahliae, a soil-borne fungal pathogen, compromises host innate immunity by secreting a plethora of effectors, thereby facilitating host colonization and causing substantial yield and quality losses. The mechanisms underlying the modulation of cotton immunity by V. dahliae effectors are predominantly unexplored. In this study, we identified that the V. dahliae effector Vd6317 inhibits plant cell death triggered by Vd424Y and enhances PVX viral infection in Nicotiana benthamiana. Attenuation of Vd6317 significantly decreased the virulence of V. dahliae, whereas ectopic expression of Vd6317 in Arabidopsis and cotton enhanced susceptibility to V. dahliae infection, underscoring Vd6317's critical role in pathogenicity. We observed that Vd6317 targeted the Arabidopsis immune regulator AtNAC53, thereby impeding its transcriptional activity on the defense-associated gene AtUGT74E2. Arabidopsis nac53 and ugt74e2 mutants exhibited heightened sensitivity to V. dahliae compared to wild-type plants. A mutation at the conserved residue 193L of Vd6317 abrogated its interaction with AtNAC53 and reduced the virulence of V. dahliae, which was partially attributable to a reduction in Vd6317 protein stability. Our findings unveil a hitherto unrecognized regulatory mechanism by which the V. dahliae effector Vd6317 directly inhibits the plant transcription factor AtNAC53 activity to suppress the expression of AtUGT74E2 and plant defense.

GbPP2C80 Interacts with GbWAKL14 to Negatively Co-Regulate Resistance to Fusarium and Verticillium wilt via MPK3 and ROS Signaling in Sea Island Cotton

Fusarium wilt (FW) is widespread in global cotton production, but the mechanism underlying FW resistance in superior-fiber-quality Sea Island cotton is unclear. This study reveals that FW resistance has been the target of genetic improvement of Sea Island cotton in China since the 2010s. The key nonsynonymous single nucleotide polymorphism (SNP, T/C) of gene Gbar_D03G001670 encoding protein phosphatase 2C 80 (PP2C80) results in an amino acid shift (L/S), which is significantly associated with FW resistance of Sea Island cotton. Silencing GbPP2C80 increases FW resistance in Sea Island cotton, whereas overexpressing GbPP2C80 reduces FW resistance in Arabidopsis. GbPP2C80 and GbWAKL14 exist synergistically in Sea Island cotton accessions with haplotype forms "susceptible-susceptible" (TA) and "resistant-resistant" (CC), and interact with each other. CRISPR/Cas9-mediated knockout of GbWAKL14 enhances FW and Verticillium wilt (VW) resistance in upland cotton and overexpression of GbWAKL14 and GbPP2C80 weakens FW and VW resistance in Arabidopsis. GbPP2C80 and GbWAKL14 respond to FW and VW by modulating reactive oxygen species (ROS) content via affecting MPK3 expression. In summary, two tandem genes on chromosome D03, GbPP2C80, and GbWAKL14, functions as cooperative negative regulators in cotton wilt disease defense, providing novel genetic resources and molecular markers for the development of resistant cotton cultivars.

Transcriptional Comparison Reveals Differential Resistance Mechanisms between CMV-Resistant PBC688 and CMV-Susceptible G29

The Cucumber mosaic virus (CMV) presents a significant threat to pepper cultivation worldwide, leading to substantial yield losses. We conducted a transcriptional comparative study between CMV-resistant (PBC688) and -susceptible (G29) pepper accessions to understand the mechanisms of CMV resistance. PBC688 effectively suppressed CMV proliferation and spread, while G29 exhibited higher viral accumulation. A transcriptome analysis revealed substantial differences in gene expressions between the two genotypes, particularly in pathways related to plant-pathogen interactions, MAP kinase, ribosomes, and photosynthesis. In G29, the resistance to CMV involved key genes associated with calcium-binding proteins, pathogenesis-related proteins, and disease resistance. However, in PBC688, the crucial genes contributing to CMV resistance were ribosomal and chlorophyll a-b binding proteins. Hormone signal transduction pathways, such as ethylene (ET) and abscisic acid (ABA), displayed distinct expression patterns, suggesting that CMV resistance in peppers is associated with ET and ABA. These findings deepen our understanding of CMV resistance in peppers, facilitating future research and variety improvement.

Transcriptional Response of Wolfberry to Infestation with the Endophytic Fusarium nematophilum Strain NQ8GII4

Fusarium nematophilum NQ8GII4 is an endophytic fungus isolated from the root of healthy wolfberry (Lycium barbarum). Previous studies have reported that NQ8GII4 could dwell in wolfberry roots and enhance the defense responses in wolfberry against root rot, which is caused by F. oxysporum. To further elucidate the molecular mechanism of wolfberry disease resistance induced by NQ8GII4, in the present study, we adopted RNA sequencing analysis to profile the transcriptome of wolfberry response to NQ8GII4 infestation over a time course of 3 and 7 days postinoculation. Gene ontology enrichment analysis revealed that differentially expressed genes (DEGs) were enriched in biological regulation, response to stimulus, signaling, detoxification, immune system process, transporter activity, electron carrier activity, transcription factor activity, nucleic acid binding transcription factor, and antioxidant activity. Through Kyoto Encyclopedia of Genes and Genomes analysis, it was found that many of these DEGs were enriched in pathways related to plant-pathogen interactions, hormone signal transduction, and the phenylpropanoid biosynthesis pathway in wolfberry. This result suggested that innate immunity, phytohormone signaling, and numerous phenylpropanoid compounds comprise a complex defense network in wolfberry. Chloroplast 50S ribosomal proteins were consistently located at the core position of the response in wolfberry following infestation with NQ8GII4 analyzed by the protein-protein interaction network. This study elucidated the molecular mechanism underlying the interaction between NQ8GII4 and wolfberry, clarified the wolfberry immune response network to endophytic fungi infestation, identified candidate resistance genes in wolfberry, and provided a fundamental date for subsequent work.

Inhibition of Verticillium Wilt in Cotton through the Application of Pseudomonas aeruginosa ZL6 Derived from Fermentation Residue of Kitchen Waste

To isolate and analyze bacteria with Verticillium wilt-resistant properties from the fermentation residue of kitchen wastes, as well as explore their potential for new applications of the residue. A total of six bacterial strains exhibiting Verticillium wilt-resistant capabilities were isolated from the biogas residue of kitchen waste fermentation. Using a polyphasic approach, strain ZL6, which displayed the highest antagonistic activity against cotton Verticillium wilt, was identified as belonging to the Pseudomonas aeruginosa. Bioassay results demonstrated that this strain possessed robust antagonistic abilities, effectively inhibiting V. dahliae spore germination and mycelial growth. Furthermore, P. aeruginosa ZL6 exhibited high temperature resistance (42°C), nitrogen fixation, and phosphorus removal activities. Pot experiments revealed that P. aeruginosa ZL6 fermentation broth treatment achieved a 47.72% biological control effect compared to the control group. Through activity tracking and protein mass spectrometry identification, a neutral metalloproteinase (Nml) was hypothesized as the main virulence factor. The mutant strain ZL6ΔNml exhibited a significant reduction in its ability to inhibit cotton Verticillium wilt compared to the strain P. aeruginosa ZL6. While the inhibitory activities could be partially restored by a complementation of nml gene in the mutant strain ZL6CMΔNml. This research provides a theoretical foundation for the future development and application of biogas residue as biocontrol agents against Verticillium wilt and as biological preservatives for agricultural products. Additionally, this study presents a novel approach for mitigating the substantial amount of biogas residue generated from kitchen waste fermentation.

The crotonylated and succinylated proteins of jujube involved in phytoplasma-stress responses

BACKGROUND

Protein posttranslational modifications (PTMs) are fast and early responses to environmental changes, including pathogen infection. Jujube witches' broom (JWB) is a phytoplasma disease causing great economic loss in jujube production. After phytoplasma infection, the transcriptional, translational, and metabolic levels in jujube were activated, enabling it to survive during phytoplasma invasion. However, no study has yet reported on PTMs in jujube. Lysine crotonylation (Kcr) and lysine succinylation (Ksu) have been popular studies in recent years and their function in plant phytoplasma-stress responses remains unclear.

RESULTS

Here, 1656 crotonylated and 282 succinylated jujube proteins were first identified under phytoplasma-stress, of which 198 were simultaneously crotonylated and succinylated. Comparative analysis revealed that 656 proteins, 137 crotonylated and 43 succinylated proteins in jujube were regulated by phytoplasma infection, suggesting that Kcr was more universal than Ksu. Kcr differentially expressed proteins (DEPs) were related to ribosomes, photosynthetic and carbon metabolism, while Ksu DEPs were mainly involved in carbon metabolism, the TCA cycle and secondary metabolite biosynthesis. The crosstalk network among proteome, crotonylome and succinylome showed that DEPs related to ribosomal, peroxidases and glutathione redox were enriched. Among them, ZjPOD51 and ZjPHGPX2 significantly increased at the protein and Kcr level under phytoplasma-stress. Notably, 7 Kcr sites were identified in ZjPHGPX2, a unique antioxidant enzyme. After inhibitor nicotinamide (NAM) treatment, GPX enzyme activity in jujube seedlings was reduced. Further, site-directed mutagenesis of key Kcr modification sites K130 and/or K135 in ZjPHGPX2 significantly reduced its activity.

CONCLUSIONS

This study firstly provided large-scale datasets of Kcr and Ksu in phytoplasma-infected jujube and revealed that Kcr modification in ZjPHGPX2 positively regulates its activity.

Decoding the molecular mechanism underlying salicylic acid (SA)-mediated plant immunity: an integrated overview from its biosynthesis to the mode of action

Salicylic acid (SA) is an important phytohormone, well-known for its regulatory role in shaping plant immune responses. In recent years, significant progress has been made in unravelling the molecular mechanisms underlying SA biosynthesis, perception, and downstream signalling cascades. Through the concerted efforts employing genetic, biochemical, and omics approaches, our understanding of SA-mediated defence responses has undergone remarkable expansion. In general, following SA biosynthesis through Avr effectors of the pathogens, newly synthesized SA undergoes various biochemical changes to achieve its active/inactive forms (e.g. methyl salicylate). The activated SA subsequently triggers signalling pathways associated with the perception of pathogen-derived signals, expression of defence genes, and induction of systemic acquired resistance (SAR) to tailor the intricate regulatory networks that coordinate plant immune responses. Nonetheless, the mechanistic understanding of SA-mediated plant immune regulation is currently limited because of its crosstalk with other signalling networks, which makes understanding this hormone signalling more challenging. This comprehensive review aims to provide an integrated overview of SA-mediated plant immunity, deriving current knowledge from diverse research outcomes. Through the integration of case studies, experimental evidence, and emerging trends, this review offers insights into the regulatory mechanisms governing SA-mediated immunity and signalling. Additionally, this review discusses the potential applications of SA-mediated defence strategies in crop improvement, disease management, and sustainable agricultural practices.

The role of VdSti1 in Verticillium dahliae: insights into pathogenicity and stress responses

Sti1/Hop, a stress-induced co-chaperone protein, serves as a crucial link between Hsp70 and Hsp90 during cellular stress responses. Despite its importance in stress defense mechanisms, the biological role of Sti1 in Verticillium dahliae, a destructive fungal pathogen, remains largely unexplored. This study focused on identifying and characterizing Sti1 homologues in V. dahliae by comparing them to those found in Saccharomyces cerevisiae. The results indicated that the VdSti1-deficient mutant displayed increased sensitivity to drugs targeting the ergosterol synthesis pathway, leading to a notable inhibition of ergosterol biosynthesis. Moreover, the mutant exhibited reduced production of microsclerotia and melanin, accompanied by decreased expression of microsclerotia and melanin-related genes VDH1, Vayg1, and VaflM. Additionally, the mutant's conidia showed more severe damage under heat shock conditions and displayed growth defects under various stressors such as temperature, SDS, and CR stress, as well as increased sensitivity to H2O2, while osmotic stress did not impact its growth. Importantly, the VdSti1-deficient mutant demonstrated significantly diminished pathogenicity compared to the wild-type strain. This study sheds light on the functional conservation and divergence of Sti1 homologues in fungal biology and underscores the critical role of VdSti1 in microsclerotia development, stress response, and pathogenicity of V. dahliae.

Functional Analysis of the GhIQD1 Gene in Cotton Resistance to Verticillium Wilt

Cotton is a critical crop with massive economic implications worldwide. Verticillium wilt is a soil-borne ailment caused by Verticillium dahliae, which harms the growth and development of cotton. Therefore, investigating the genes associated with resistance to verticillium wilt is of particular significance. In this study, we identified the GhIQD1 gene through transcriptome analysis and experimentally characterized the role of the GhIQD1 gene in cotton against V. dahliae. The findings indicated that GhIQD1 acts as a calmodulin-binding protein. The expression of GhIQD1 was the highest in stems, and the expression level increased significantly following infection with V. dahliae. The expression in resistant cotton varieties was higher than in susceptible cotton varieties. Through overexpression of the GhIQD1 gene in tobacco, these transgenic plants exhibited improved resistance to V. dahliae. In contrast, by silencing the GhIQD1 gene in cotton through VIGS, the resistance to V. dahliae was reduced. Following inoculation, the leaves yellowed, and the disease index was higher. Transcriptome analysis of transgenic tobacco 72 h after inoculation indicated that overexpression of GhIQD1 increased the enrichment of the calmodulin pathway and stimulated the production of plant hormones alongside secondary metabolites. Consequently, we investigated the relationship between the GhIQD1 gene and plant disease-resistant hormones SA, JA, and ABA. In summary, this study uncovered the mechanism by which GhIQD1 conferred resistance to V. dahliae in cotton through positive regulation of JA and ABA, providing crucial information for further research on the adaptation of plants to pathogen invasion.

Cotton GhNAC4 promotes drought tolerance by regulating secondary cell wall biosynthesis and ribosomal protein homeostasis

Drought has a severe impact on the quality and yield of cotton. Deciphering the key genes related to drought tolerance is important for understanding the regulation mechanism of drought stress and breeding drought-tolerant cotton cultivars. Several studies have demonstrated that NAC transcription factors are crucial in the regulation of drought stress, however, the related functional mechanisms are still largely unexplored. Here, we identified that NAC transcription factor GhNAC4 positively regulated drought stress tolerance in cotton. The expression of GhNAC4 was significantly induced by abiotic stress and plant hormones. Silencing of GhNAC4 distinctly impaired the resistance to drought stress and overexpressing GhNAC4 in cotton significantly enhanced the stress tolerance. RNA-seq analysis revealed that overexpression of GhNAC4 enriched the expression of genes associated with the biosynthesis of secondary cell walls and ribosomal proteins. We confirmed that GhNAC4 positively activated the expressions of GhNST1, a master regulator reported previously in secondary cell wall formation, and two ribosomal protein-encoding genes GhRPL12 and GhRPL18p, by directly binding to their promoter regions. Overexpression of GhNAC4 promoted the expression of downstream genes associated with the secondary wall biosynthesis, resulting in enhancing secondary wall deposition in the roots, and silencing of GhRPL12 and GhRPL18p significantly impaired the resistance to drought stress. Taken together, our study reveals a novel pathway mediated by GhNAC4 that promotes secondary cell wall biosynthesis to strengthen secondary wall development and regulates the expression of ribosomal protein-encoding genes to maintain translation stability, which ultimately enhances drought tolerance in cotton.

A novel single nucleotide mutation of TFL1 alters the plant architecture of Gossypium arboreum through changing the pre-mRNA splicing

KEY MESSAGE

A single nucleotide mutation from G to A at the 201st position changed the 5' splice site and deleted 31 amino acids in the first exon of GaTFL1. Growth habit is an important agronomic trait that plays a decisive role in the plant architecture and crop yield. Cotton (Gossypium) tends to indeterminate growth, which is unsuitable for the once-over mechanical harvest system. Here, we identified a determinate growth mutant (dt1) in Gossypium arboreum by EMS mutagenesis, in which the main axis was terminated with the shoot apical meristem (SAM) converted into flowers. The map-based cloning of the dt1 locus showed a single nucleotide mutation from G to A at the 201st positions in TERMINAL FLOWER 1 (GaTFL1), which changed the alternative RNA 5' splice site and resulted in 31 amino acids deletion and loss of function of GaTFL1. Comparative transcriptomic RNA-Seq analysis identified many transporters responsible for the phytohormones, auxin, sugar, and flavonoids, which may function downstream of GaTFL1 to involve the plant architecture regulation. These findings indicate a novel alternative splicing mechanism involved in the post-transcriptional modification and TFL1 may function upstream of the auxin and sugar pathways through mediating their transport to determine the SAM fate and coordinate the vegetative and reproductive development from the SAM of the plant, which provides clues for the TFL1 mechanism in plant development regulation and provide research strategies for plant architecture improvement.

Identification and characterization of the Bicupin domain family and functional analysis of GhBCD11 in response to verticillium wilt in cotton

Bicupin domain protein (BCD) family, an important component of Cupin domain superfamily, plays important roles in oxalic acid (OA) degradation and stress responses in high plants. However, no studies have been reported on the Cupin domain family in cotton up till now. In our study, a total 110 proteins including Cupin domain were identified from the upland cotton (Gossypium hirsutum). Among them, 17 proteins contained Bicupin domain. Subsequently, we found that V. dahliae produces OA leading to cotton leaf wilting. RT-qPCR analysis of GhBCDs revealed that OA and V. dahliae Vd080 significantly enhanced the expression of GhBCD11. The Virus-induced gene silencing and overexpression analysis showed that GhBCD11 positively regulates plant resistance to V. dahliae. Subcellular localization showed GhBCD11 located on the plasma membrane. The analysis of expression pattern showed that GhBCD11 can be induced via hormone-mediated signal pathway including salicylic acid (SA), ethephon (ET), methyl jasmonate (JA) and abscisic acid (ABA). In addition, we identified an interaction between 60 S ribosomal protein GhRPL12-3 and GhBCD11 by yeast double hybridization. Overall, this is the first study, where we identified Cupin domain family in cotton, clarified the role of GhBCD11 in cotton for resistance to V. dahliae and found an interaction between GhRPL12-3 and GhBCD11.

Dynamic characteristics and functional analysis provide new insights into the role of GauERF105 for resistance against Verticillium dahliae in cotton

BACKGROUND

The cotton industry suffers significant yield losses annually due to Verticillium wilt, which is considered the most destructive disease affecting the crop. However, the precise mechanisms behind this disease in cotton remain largely unexplored.

METHODS

Our approach involved utilizing transcriptome data from G. australe which was exposed to Verticillium dahliae infection. From this data, we identified ethylene-responsive factors and further investigated their potential role in resistance through functional validations via Virus-induced gene silencing (VIGS) in cotton and overexpression in Arabidopsis.

RESULTS

A total of 23 ethylene response factors (ERFs) were identified and their expression was analyzed at different time intervals (24 h, 48 h, and 72 h post-inoculation). Among them, GauERF105 was selected based on qRT-PCR expression analysis for further investigation. To demonstrate the significance of GauERF105, VIGS was utilized, revealing that suppressing GauERF105 leads to more severe infections in cotton plants compared to the wild-type. Additionally, the silenced plants exhibited reduced lignin deposition in the stems compared to the WT plants, indicating that the silencing of GauERF105 also impacts lignin content. The overexpression of GauERF105 in Arabidopsis confirmed its pivotal role in conferring resistance against Verticillium dahliae infection. Our results suggest that WT possesses higher levels of the oxidative stress markers MDA and H2O2 as compared to the overexpressed lines. In contrast, the activities of the antioxidant enzymes SOD and POD were higher in the overexpressed lines compared to the WT. Furthermore, DAB and trypan staining of the overexpressed lines suggested a greater impact of the disease in the wild-type compared to the transgenic lines.

CONCLUSIONS

Our findings provide confirmation that GauERF105 is a crucial candidate in the defense mechanism of cotton against Verticillium dahliae invasion, and plays a pivotal role in this process. These results have the potential to facilitate the development of germplasm resistance in cotton.

Insights to Gossypium defense response against Verticillium dahliae: the Cotton Cancer

The soil-borne pathogen Verticillium dahliae, also referred as "The Cotton Cancer," is responsible for causing Verticillium wilt in cotton crops, a destructive disease with a global impact. To infect cotton plants, the pathogen employs multiple virulence mechanisms such as releasing enzymes that degrade cell walls, activating genes that contribute to virulence, and using protein effectors. Conversely, cotton plants have developed numerous defense mechanisms to combat the impact of V. dahliae. These include strengthening the cell wall by producing lignin and depositing callose, discharging reactive oxygen species, and amassing hormones related to defense. Despite the efforts to develop resistant cultivars, there is still no permanent solution to Verticillium wilt due to a limited understanding of the underlying molecular mechanisms that drive both resistance and pathogenesis is currently prevalent. To address this challenge, cutting-edge technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), host-induced gene silencing (HIGS), and gene delivery via nano-carriers could be employed as effective alternatives to control the disease. This article intends to present an overview of V. dahliae virulence mechanisms and discuss the different cotton defense mechanisms against Verticillium wilt, including morphophysiological and biochemical responses and signaling pathways including jasmonic acid (JA), salicylic acid (SA), ethylene (ET), and strigolactones (SLs). Additionally, the article highlights the significance of microRNAs (miRNAs), circular RNAs (circRNAs), and long non-coding RNAs (lncRNAs) in gene expression regulation, as well as the different methods employed to identify and functionally validate genes to achieve resistance against this disease. Gaining a more profound understanding of these mechanisms could potentially result in the creation of more efficient strategies for combating Verticillium wilt in cotton crops.

VdERG2 was involved in ergosterol biosynthesis, nutritional differentiation and virulence of Verticillium dahliae

The ergosterol biosynthesis pathway plays an important role in model pathogenic bacteria Saccharomyces cerevisiae, but little is known about the biosynthesis of ergosterol in the pathogenic fungus Verticillium dahliae. In this study, we identified the VdERG2 gene encoding sterol C-8 isomerase from V. dahliae and investigated its function in virulence by generating gene deletion mutants (ΔVdERG2) and complemented mutants (C-ΔVdERG2). Knockout of VdERG2 reduced ergosterol content. The conidial germination rate and conidial yield of ΔVdERG2 significantly decreased and abnormal conidia were produced. In spite of VdERG2 did not affect the utilization of carbon sources by V. dahliae, but the melanin production of ΔVdERG2 was decreased in cellulose and pectin were used as the sole carbon sources. Furthermore, the ΔVdERG2 mutants produced less microsclerotia and melanin with a significant decrease in the expression of microsclerotia and melanin-related genes VaflM, Vayg1, VDH1, VdLAC, VdSCD and VT4HR. In addition, mutants ΔVdERG2 were very sensitive to congo red (CR), sodium dodecyl sulfate (SDS) and hydrogen peroxide (H₂O₂) stresses, indicating that VdERG2 was involved in the cell wall and oxidative stress response. The absence of VdERG2 weakened the penetration ability of mycelium on cellophane and affected the growth of mycelium. Although ΔVdERG2 could infect cotton, its pathogenicity was significantly impaired. These phenotypic defects in ΔVdERG2 could be complemented by the reintroduction of a full-length VdERG2 gene. In summary, as a single conservative secretory protein, VdERG2 played a crucial role in ergosterol biosynthesis, nutritional differentiation and virulence in V. dahliae.

Recent progression and future perspectives in cotton genomic breeding

Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content. Progress in cotton genomics promotes the advancement of cotton genetics, evolutionary studies, functional genetics, and breeding, and has ushered cotton research and breeding into a new era. Here, we summarize high-impact genomics studies for cotton from the last 10 years. The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studies. We next review recent progress in cotton molecular biology and genetics, which builds on cotton genome sequencing efforts, population studies, and functional genomics, to provide insights into the mechanisms shaping abiotic and biotic stress tolerance, plant architecture, seed oil content, and fiber development. We also suggest the application of novel technologies and strategies to facilitate genome-based crop breeding. Explosive growth in the amount of novel genomic data, identified genes, gene modules, and pathways is now enabling researchers to utilize multidisciplinary genomics-enabled breeding strategies to cultivate "super cotton", synergistically improving multiple traits. These strategies must rise to meet urgent demands for a sustainable cotton industry.

A Novel Intelligent System for Dynamic Observation of Cotton Verticillium Wilt

Verticillium wilt is one of the most critical cotton diseases, which is widely distributed in cotton-producing countries. However, the conventional method of verticillium wilt investigation is still manual, which has the disadvantages of subjectivity and low efficiency. In this research, an intelligent vision-based system was proposed to dynamically observe cotton verticillium wilt with high accuracy and high throughput. Firstly, a 3-coordinate motion platform was designed with the movement range 6,100 mm × 950 mm × 500 mm, and a specific control unit was adopted to achieve accurate movement and automatic imaging. Secondly, the verticillium wilt recognition was established based on 6 deep learning models, in which the VarifocalNet (VFNet) model had the best performance with a mean average precision (mAP) of 0.932. Meanwhile, deformable convolution, deformable region of interest pooling, and soft non-maximum suppression optimization methods were adopted to improve VFNet, and the mAP of the VFNet-Improved model improved by 1.8%. The precision-recall curves showed that VFNet-Improved was superior to VFNet for each category and had a better improvement effect on the ill leaf category than fine leaf. The regression results showed that the system measurement based on VFNet-Improved achieved high consistency with manual measurements. Finally, the user software was designed based on VFNet-Improved, and the dynamic observation results proved that this system was able to accurately investigate cotton verticillium wilt and quantify the prevalence rate of different resistant varieties. In conclusion, this study has demonstrated a novel intelligent system for the dynamic observation of cotton verticillium wilt on the seedbed, which provides a feasible and effective tool for cotton breeding and disease resistance research.

Two Metalloproteases VdM35-1 and VdASPF2 from Verticillium dahliae Are Required for Fungal Pathogenicity, Stress Adaptation, and Activating Immune Response of Host

Verticillium dahliae is a soilborne fungus that causes destructive vascular wilt diseases in a wide range of plant hosts. In this study, we identified two M35 family metalloproteinases: VdM35-1 and VdASPF2, and investigated their function in vitro and in vivo. The results showed that VdM35-1 and VdASPF2 were located in the cell membrane, as secreted proteins depended on signal peptide, and two histidine residues (H) induced cell death and activated plant immune response. VdM35-1 depended on membrane receptor proteins NbBAK1 and NbSOBIR1 in the process of inducing cell death, while VdASPF2 did not depend on them. The deletion of VdM35-1 and VdASPF2 led to the decrease of sporulation and the slow shortening of mycelial branch growth, and the spore morphology of VdM35-1-deficient strain became malformed. In addition, ΔVdM35-1 and ΔVdASPF2 showed more sensitive to osmotic stress, SDS, Congo red (CR), and high temperature. In terms of the utilization of carbon sources, the knockout mutants exhibited decreased utilization of carbon sources, and the growth rates on the medium containing sucrose, starch, and pectin were lower than the wild type strain, with significantly limited growth, especially on galactose-containing medium. Furthermore, ΔVdM35-1 and ΔVdASPF2 showed a significant reduction in pathogenicity. Collectively, these results suggested that VdM35-1 and VdASPF2 were important multifunction factors in the pathogenicity of V. dahliae and relative to stress adaptation and activated plant immune response. IMPORTANCE Verticillium wilt, caused by the notorious fungal pathogen V. dahliae, is one of the main limiting factors for agricultural production. Metalloproteases played an important role in the pathogenic mechanism of pathogens. Our research found that M35 family metalloproteases VdM35-1 and VdASPF2 played an important role in the development, adaptability, and pathogenicity of V. dahliae, providing a new perspective for further understanding the molecular mechanism of virulence of fungal pathogens.

Functional divergence of GLP genes between G. barbadense and G. hirsutum in response to Verticillium dahliae infection

Germin-like proteins (GLPs) play important roles in plant disease resistance but are rarely reported in cotton. We compared the expression of GLPs in Verticillium dahliae inoculate G. hirsutum (susceptible) and G. barbadense (resistant) and enriched 11 differentially expressed GLPs. 2741 GLP proteins identified from 53 species determined that GLP probably originated from algae and could be classified into 7 clades according to phylogenetic analysis, among which Clade I is likely the most ancient. Cotton GLP (two allopolyploids and two diploids) genes within a shared clade were highly conserved. Intriguingly, clade VII genes were mainly located in gene clusters that derived from the expansion of LTR transposons. Clade VII members expressed mainly in root which is the first battle against Verticillium dahlia and could be induced more intensely in G. barbadense than G. hirsutum. The GLP genes are resistant to Verticillium dahliae, which can be further investigated against Verticillium wilt.

The Effect of Some Bio-Agents and Organic Substances Against Verticillium dahliae, A Problem in Lettuce (Lactuca sativa) Plant

Bu çalışmada, Verticillium dahliae’nın gelişimi üzerine bazı fungal (Trichoderma harzianum, Trichoderma virens, Trichoderma asperellum, Trichoderma viride) ve maya (Saccharomyces cerevisiae) biyolojik kontrol etmenleri ile vermikompost ve salisilik asit organik maddelerin etkisi araştırılmıştır. Çalışma in vitro ve in vivo koşullarda yürüyülmüş ve in vitro’da antagonizmin derecesi ve yüzde olarak engelleme oranı belirlenmiştir. In vitro’da inhibisyon oranı en yüksek olarak belirlenen T. asperellum ve S. cerevisiae ile vermikompost ve salisilik asit organik maddelerin, in vivo’da marul (Lactuca sativa) bitkisinde sorun teşkil eden V. dahliae’nın gelişimine etkisi incelenmiştir. Ayrıca organik maddelerden salisilik asitin V. dahliae’ nın gelişimini tamamen engellediği belirlenmiştir. S. cerevisiae ve salisilik asit, V. dahliae patojeninin olduğu uygulamalarda kontrol grubuna oranla bitkilerin sürgün boyunu ve kök uzunluğunu arttırmıştır. Gerek yeşil aksam gerek gövde kesiti skala değerlerinde salisilik asit ve T. asperellum, V. dahliae patojeninin etkinliğini azaltmıştır.

Loss of function of VdDrs2, a P4-ATPase, impairs the toxin secretion and microsclerotia formation, and decreases the pathogenicity of Verticillium dahliae

Four P4-ATPase flippase genes, VdDrs2, VdNeo1, VdP4-4, and VdDnf1 were identified in Verticillium dahliae, one of the most devastating phytopathogenic fungi in the world. Knock out of VdDrs2, VdNeo1, and VdP4-4, or knock down of VdDnf1 significantly decreased the pathogenicity of the mutants in cotton. Among the mutants, the greatest decrease in pathogenicity was observed in ΔVdDrs2. VdDrs2 was localized to plasma membrane, vacuoles, and trans-Golgi network (TGN). In vivo observation showed that the infection of the cotton by ΔVdDrs2 was significantly delayed. The amount of two known Verticillium toxins, sulfacetamide, and fumonisin B1 in the fermentation broth produced by the ΔVdDrs2 strain was significantly reduced, and the toxicity of the crude Verticillium wilt toxins to cotton cells was attenuated. In addition, the defect of VdDrs2 impaired the synthesis of melanin and the formation of microsclerotia, and decreased the sporulation of V. dahliae. Our data indicate a key role of P4 ATPases-associated vesicle transport in toxin secretion of disease fungi and support the importance of mycotoxins in the pathogenicity of V. dahliae.

Comparative Proteomic Analysis Reveals the Ascorbate Peroxidase-Mediated Plant Resistance to Verticillium dahliae in Gossypium barbadense

In previous research on the resistance of cotton to Verticillium wilt (VW), Gossypium hirsutum and G. barbadense were usually used as the susceptible and resistant cotton species, despite their different genetic backgrounds. Herein, we present data independent acquisition (DIA)-based comparative proteomic analysis of two G. barbadense cultivars differing in VW tolerance, susceptible XH7 and resistant XH21. A total of 4,118 proteins were identified, and 885 of them were differentially abundant proteins (DAPs). Eight co-expressed modules were identified through weighted gene co-expression network analysis. GO enrichment analysis of the module that significantly correlated with V. dahliae infection time revealed that oxidoreductase and peroxidase were the most significantly enriched GO terms. The last-step rate-limiting enzyme for ascorbate acid (AsA) biosynthesis was further uncovered in the significantly enriched GO terms of the 184 XH21-specific DAPs. Additionally, the expression of ascorbate peroxidase (APX) members showed quick accumulation after inoculation. Compared to XH7, XH21 contained consistently higher AsA contents and rapidly increased levels of APX expression, suggesting their potential importance for the resistance to V. dahliae. Silencing GbAPX1/12 in both XH7 and XH 21 resulted in a dramatic reduction in VW resistance. Our data indicate that APX-mediated oxidoreductive metabolism is important for VW resistance in cotton.

Analysis of the PRA1 Genes in Cotton Identifies the Role of GhPRA1.B1-1A in Verticillium dahliae Resistance

Verticillium wilt in cotton (Gossypium hirsutum) is primarily caused by Verticillium dahliae. Previous data suggest that prenylated RAB acceptors (PRAs) play essential roles in environmental plant adaptation, although the potential roles of PRA1 in cotton are unclear. Therefore, in this study, PRA1 family members were identified in G. hirsutum, and their roles in biotic and abiotic stresses were analyzed. Thirty-seven GhPRA1 family members were identified in upland cotton, which were divided into eight groups. Gene structure and domain analyses revealed that the sequences of GhPRA1 members in each group were highly conserved. Many environmental stress-related and hormone-response cis-acting elements were identified in the GhPRA1 promoter regions, indicating that they may respond to biotic and abiotic stresses. Expression analysis revealed that GhPRA1 members were widely expressed in upland cotton. The GhPRA1 genes responded to abiotic stress: drought, cold, salt, and heat stress. GhPRA1.B1-1A expression increased after V. dahliae infection. Furthermore, the functional role of GhPRA1.B1-1A was confirmed by overexpression in Arabidopsis thaliana, which enhanced the resistance to V. dahliae. In contrast, V. dahliae resistance was significantly weakened via virus-induced gene silencing of GhPRA1.B1-1A in upland cotton. Simultaneously, reactive oxygen species accumulation; the H2O2, salicylic acid, and jasmonic acid contents; and callose deposition were significantly decreased in cotton plants with GhPRA1.B1-1A silencing. These findings contribute to a better understanding of the biological roles of GhPRA1 proteins and provide candidate genes for cotton breeders for breeding V. dahliae-resistant cultivars.

Plant cytoplasmic ribosomal proteins: an update on classification, nomenclature, evolution and resources

Standardized naming systems are essential to integrate and unify distinct research fields, and to link multi-species data within and across kingdoms. We conducted a comprehensive survey of cytoplasmic ribosomal proteins (CRPs) in the dicot model Arabidopsis thaliana and the monocot model rice, noting that the standardized naming system has not been widely adopted in the plant community. We generated a database linking the old classical names to their updated and compliant names. We also explored the sequences, molecular evolution, and structural and functional characteristics of all plant CRP families, emphasizing evolutionarily conserved and plant-specific features through cross-kingdom comparisons. Unlike fungal CRP paralogs that were mainly created by whole-genome duplication (WGD) or retroposition under a concerted evolution mode, plant CRP genes evolved primarily through both WGD and tandem duplications in a rapid birth-and-death process. We also provide a web-based resource (http://www.plantcrp.cn/) with the aim of sharing the latest knowledge on plant CRPs and facilitating the continued development of a standardized framework across the entire community.

RAD gene family analysis in cotton provides some key genes for flowering and stress tolerance in upland cotton G. hirsutum

Background

RADIALIS (RAD), belongs to the MYB gene family and regulates a variety of functions including floral dorsoventral asymmetry in Antirrhinum majus and development of fruit proteins in Solanum lycopersicum. RAD genes contain an SNF2_N superfamily domain. Here, we comprehensively identified 68 RAD genes from six different species including Arabidopsis and five species of cotton.

Results

Phylogenetic analysis classified RAD genes into five groups. Gene structure, protein motifs and conserved amino acid residues indicated that GhRAD genes were highly conserved during the evolutionary process. Chromosomal location information showed that GhRAD genes were distributed unevenly on different chromosomes. Collinearity and selection pressure analysis indicated RAD gene family expansion in G. hirsutum and G. barbadense with purifying selection pressure. Further, various growth and stress related promotor cis-acting elements were observed. Tissue specific expression level indicated that most GhRAD genes were highly expressed in roots and flowers (GhRAD2, GhRAD3, GhRAD4 and GhRAD11). Next, GhRAD genes were regulated by phytohormonal stresses (JA, BL and IAA). Moreover, Ghi-miRN1496, Ghi-miR1440, Ghi-miR2111b, Ghi-miR2950a, Ghi-miR390a, Ghi-miR390b and Ghi-miR7495 were the miRNAs targeting most of GhRAD genes.

Conclusions

Our study revealed that RAD genes are evolutionary conserved and might be involved in different developmental processes and hormonal stress response. Data presented in our study could be used as the basis for future studies of RAD genes in cotton.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08248-z.

The heat shock factor GhHSFA4a positively regulates cotton resistance to Verticillium dahliae

Heat shock factors (HSFs) play a crucial role in the environmental stress responses of numerous plant species, including defense responses to pathogens; however, their role in cotton resistance to Verticillium dahliae remains unclear. We have previously identified several differentially expressed genes (DEGs) in Arabidopsis thaliana after inoculation with V. dahliae. Here, we discovered that GhHSFA4a in Gossypium hirsutum (cotton) after inoculation with V. dahliae shares a high identity with a DEG in A. thaliana in response to V. dahliae infection. Quantitative real-time PCR (qRT-PCR) analysis indicated that GhHSFA4a expression was rapidly induced by V. dahliae and ubiquitous in cotton roots, stems, and leaves. In a localization analysis using transient expression, GhHSFA4a was shown to be localized to the nucleus. Virus-induced gene silencing (VIGS) revealed that downregulation of GhHSFA4a significantly increased cotton susceptibility to V. dahliae. To investigate GhHSFA4a-mediated defense, 814 DEGs were identified between GhHSFA4a-silenced plants and controls using comparative RNA-seq analysis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that DEGs were enriched in "flavonoid biosynthesis", "sesquiterpenoid and triterpenoid biosynthesis", "linoleic acid metabolism" and "alpha-linolenic acid metabolism". The expression levels of marker genes for these four pathways were triggered after inoculation with V. dahliae. Moreover, GhHSFA4a-overexpressing lines of A. thaliana displayed enhanced resistance against V. dahliae compared to that of the wild type. These results indicate that GhHSFA4a is involved in the synthesis of secondary metabolites and signal transduction, which are indispensable for innate immunity against V. dahliae in cotton.

The Respiratory Burst Oxidase Homolog Protein D (GhRbohD) Positively Regulates the Cotton Resistance to Verticillium dahliae

Verticillium wilt, mainly caused by a soil-inhabiting fungus Verticillium dahliae, can seriously reduce the yield and quality of cotton. The complex mechanism underlying cotton resistance to Verticillium wilt remains largely unknown. In plants, reactive oxygen species (ROS) mediated by Rbohs is one of the earliest responses of plants to biotic and abiotic stresses. In our previous study, we performed a time-course phospho-proteomic analysis of roots of resistant and susceptible cotton varieties in response to V. dahliae, and found early differentially expressed protein burst oxidase homolog protein D (GhRbohD). However, the role of GhRbohD-mediated ROS in cotton defense against V. dahliae needs further investigation. In this study, we analyzed the function of GhRbohD-mediated resistance of cotton against V. dahliae in vitro and in vivo. Bioinformatics analysis showed that GhRbohD possessed the conservative structural attributes of Rbohs family, 12 members of RbohD out of 57 Rbohs in cotton. The expression of GhRbohD was significantly upregulated after V. dahliae inoculation, peaking at 6 hpi, and the phosphorylation level was also increased. A VIGS test demonstrated that ROS production, NO, H₂O₂ and Ca²⁺ contents of GhRbohD-silenced cotton plants were significantly reduced, and lignin synthesis and callose accumulation were damaged, important reasons for the impairment of GhRbohD-silenced cotton’s defense against V. dahliae. The expression levels of resistance-related genes were downregulated in GhRbohD-silenced cotton by qRT-PCR, mainly involving the lignin metabolism pathway and the jasmonic acid signaling pathway. However, overexpression of GhRbohD enhanced resistance of transgenic Arabidopsis to V. dahliae challenge. Furthermore, Y2H assays were applied to find that GhPBL9 and GhRPL12C may interact with GhRbohD. These results strongly support that GhRbohD activates ROS production to positively regulate the resistance of plants against V. dahliae.

GhPLP2 Positively Regulates Cotton Resistance to Verticillium Wilt by Modulating Fatty Acid Accumulation and Jasmonic Acid Signaling Pathway

Patatin-like proteins (PLPs) have non-specific lipid acyl hydrolysis (LAH) activity, which can hydrolyze membrane lipids into fatty acids and lysophospholipids. The vital role of PLPs in plant growth and abiotic stress has been well documented. However, the function of PLPs in plant defense responses against pathogens is still poorly understood. Here, we isolated and identified a novel cotton (Gossypium hirsutum) PLP gene GhPLP2. The expression of GhPLP2 was induced upon treatment with Verticillium dahliae, the signaling molecules jasmonic acid (JA) and ethylene (ETH) in cotton plants. Subcellular localization revealed that GhPLP2 was localized to the plasma membrane. GhPLP2-silenced cotton plants were more susceptible to infection by V. dahliae, while the overexpression of GhPLP2 in Arabidopsis enhanced its resistance to V. dahliae, which was apparent as mild symptoms, and a decrease in the disease index and fungal biomass. The hypersensitive response, deposition of callose, and H₂O₂ accumulation triggered by V. dahliae elicitor were reduced in GhPLP2-silenced cotton plants. The overexpression of GhPLP2 in Arabidopsis resulted in the accumulation of linoleic acid (LA, 18:2) and α-linolenic acid (ALA, 18:3) and facilitated the biosynthesis of JA and JA-mediated defensive responses. GhPLP2 silencing in cotton plants consistently reduced the accumulation of linoleic acid (LA, 18:2) and α-linolenic acid (ALA, 18:3) and suppressed the biosynthesis of JA and the defensive responses mediated by JA. These results indicate that GhPLP2 is involved in the resistance of cotton to V. dahliae by maintaining fatty acid metabolism pools for JA biosynthesis and activating the JA signaling pathway.

GhPLP2 Positively Regulates Cotton Resistance to Verticillium Wilt by Modulating Fatty Acid Accumulation and Jasmonic Acid Signaling Pathway

Patatin-like proteins (PLPs) have non-specific lipid acyl hydrolysis (LAH) activity, which can hydrolyze membrane lipids into fatty acids and lysophospholipids. The vital role of PLPs in plant growth and abiotic stress has been well documented. However, the function of PLPs in plant defense responses against pathogens is still poorly understood. Here, we isolated and identified a novel cotton (Gossypium hirsutum) PLP gene GhPLP2. The expression of GhPLP2 was induced upon treatment with Verticillium dahliae, the signaling molecules jasmonic acid (JA) and ethylene (ETH) in cotton plants. Subcellular localization revealed that GhPLP2 was localized to the plasma membrane. GhPLP2-silenced cotton plants were more susceptible to infection by V. dahliae, while the overexpression of GhPLP2 in Arabidopsis enhanced its resistance to V. dahliae, which was apparent as mild symptoms, and a decrease in the disease index and fungal biomass. The hypersensitive response, deposition of callose, and H₂O₂ accumulation triggered by V. dahliae elicitor were reduced in GhPLP2-silenced cotton plants. The overexpression of GhPLP2 in Arabidopsis resulted in the accumulation of linoleic acid (LA, 18:2) and α-linolenic acid (ALA, 18:3) and facilitated the biosynthesis of JA and JA-mediated defensive responses. GhPLP2 silencing in cotton plants consistently reduced the accumulation of linoleic acid (LA, 18:2) and α-linolenic acid (ALA, 18:3) and suppressed the biosynthesis of JA and the defensive responses mediated by JA. These results indicate that GhPLP2 is involved in the resistance of cotton to V. dahliae by maintaining fatty acid metabolism pools for JA biosynthesis and activating the JA signaling pathway.

ZmmiR190 and its target regulate plant responses to drought stress through an ABA-dependent pathway

MicroRNAs (miRNAs) are small, non-coding regulatory RNAs that regulate gene expression by facilitating target mRNA cleavage in plants. They are crucial for responses to diverse stresses. The novel drought-responsive miRNA ZmmiR190 was previously identified during an analysis of the maize transcriptome. In this study, we revealed that transgenic Arabidopsis thaliana overexpressing ZmmiR190 is more sensitive to drought than the wild-type control. The transcript of a nuclear-localized gene, ZmCRP04, was identified as a likely target of ZmmiR190. Moreover, ZmmiR190 and ZmCRP04 had the opposite expression profiles following drought and salt treatments. Additionally, 5' RACE and coexpression analyses in A. thaliana provided evidence of the in vivo targeting of the ZmCRP04 transcript by ZmmiR190. Furthermore, the overexpression of ZmCRP04 in A. thaliana and rice significantly enhanced drought tolerance, with lower malonaldehyde contents and relative electrolyte leakage in the transgenic A. thaliana and rice plants than in the wild-type control. Transgenic plants overexpressing ZmmiR190 or ZmCRP04 were hypersensitive to abscisic acid. These results suggest that the ZmCRP04 transcript is targeted by ZmmiR190 and may encode a protein that positively regulates drought stress tolerance via an abscisic acid-dependent pathway. These findings may be relevant for future molecular breeding aimed at improving crop drought tolerance.

Verticillium dahliae secreted protein Vd424Y is required for full virulence, targets the nucleus of plant cells, and induces cell death

Fungal pathogens secrete effector proteins that regulate host immunity and can suppress basal defence mechanisms against colonization in plants. Verticillium dahliae is a widespread and destructive soilborne fungus that can cause vascular wilt disease and reduces plant yields. However, little is currently known about how the effectors secreted by V. dahliae function. In this study, we analysed and identified 34 candidate effectors in the V. dahliae secretome and found that Vd424Y, a glycoside hydrolase family 11 protein, was highly upregulated during the early stages of V. dahliae infection in cotton plants. This protein was located in the nucleus and its deletion compromised the virulence of the fungus. The transient expression of Vd424Y in Nicotiana benthamiana induced BAK1- and SOBIR1-dependent cell death and activated both salicylic acid and jasmonic acid signalling. This enhanced its resistance to the oomycetes Phytophthora capsici in a way that depended on its nuclear localization signal and signal peptides. Our results demonstrate that Vd424Y is an important effector protein targeting the host nucleus to regulate and activate effector-triggered immunity in plants.

A 13-Lipoxygenase, GhLOX2, positively regulates cotton tolerance against Verticillium dahliae through JA-mediated pathway

Verticillium wilt is a major limiting factor for sustainable production of cotton but the mechanism of controlling this disease is still poorly understood. Lipoxygenase (LOX)-derived oxylipins have been implicated in defense responses against diverse pathogens; however there is limited information about the functional characterization of LOXs in response to Verticillium dahliae infection. In this study, we report the characterization of a cotton LOX gene, GhLOX2, which phylogenetically clustered into 13-LOX subfamily and is closely related to Arabidopsis LOX2 gene. GhLOX2 was predominantly expressed in leaves and strongly induced following V. dahliae inoculation and treatment of methyl jasmonate (MeJA). RNAi-mediated knock-down of GhLOX2 enhanced cotton susceptibility to V. dahliae and was coupled with suppression of jasmonic acid (JA)-related genes both after inoculation with the cotton defoliating strain V991 or MeJA treatment. Interestingly, lignin contents, transcripts of lignin synthesis genes and H₂O₂ contents were also decreased in GhLOX2-silenced plants. This study suggests that GhLOX2 is involved in defense responses against infection of V. dahliae in cotton and supports that JA is one of the major defense hormones against this pathogen.

Proteomic analysis of early-stage incompatible and compatible interactions between grapevine and P. viticola

Wild grapevines can show strong resistance to the downy mildew pathogen P. viticola, but the associated mechanisms are poorly described, especially at early stages of infection. Here, we performed comparative proteomic analyses of grapevine leaves from the resistant genotype V. davidii "LiuBa-8" (LB) and susceptible V. vinifera "Pinot Noir" (PN) 12 h after inoculation with P. viticola. By employing the iTRAQ technique, a total of 444 and 349 differentially expressed proteins (DEPs) were identified in LB and PN, respectively. The majority of these DEPs were related to photosynthesis, respiration, cell wall modification, protein metabolism, stress, and redox homeostasis. Compared with PN, LB showed fewer downregulated proteins associated with photosynthesis and more upregulated proteins associated with metabolism. At least a subset of PR proteins (PR10.2 and PR10.3) was upregulated upon inoculation in both genotypes, whereas HSP (HSP70.2 and HSP90.6) and cell wall-related XTH and BXL1 proteins were specifically upregulated in LB and PN, respectively. In the incompatible interaction, ROS signaling was evident by the accumulation of H₂O₂, and multiple APX and GST proteins were upregulated. These DEPs may play crucial roles in the grapevine response to downy mildew. Our results provide new insights into molecular events associated with downy mildew resistance in grapevine, which may be exploited to develop novel protection strategies against this disease.

Ergosterol-targeting fusion antifungal peptide significantly increases the Verticillium wilt resistance of cotton

Increasing the targeting ability of antifungal proteins towards specific components of fungal cells has the potential to improve their antifungal activity and reduce harmful effects to nontarget cells. To obtain effective disease resistance genes against cotton Verticillium wilt, we constructed several fusion genes, in which binding domains targeting chitin, sphingolipid or ergosterol in the fungal cell wall or cell membrane were individually fused to the antifungal peptide BbAFP1 from entomopathogenic fungus Beauveria bassiana. Transient expression of fusion genes in cotton cotyledons indicated that the BbAFP1::ErBD fusion peptide with an ergosterol binding domain exhibited better disease resistance against V. dahliae than wild-type BbAFP1 and other fusion genes. BbAFP1::ErBD and BbAFP1 transgenic cotton were obtained and verified by Southern and Western blotting. Compared with BbAFP1-expressing cotton, BbAFP1::ErBD-expressing cotton showed higher disease resistance against V. dahliae, with smaller lesion areas (0.07 cm2 vs. 0.16 cm2 ) on the leaves and a lower disease index (23.9 vs. 34.5). Overexpression of BbAFP1::ErBD by transgenic tobacco also showed enhanced disease resistance against V. dahliae compared with that of the wild-type gene. These results indicated that construction of fusion antifungal peptides that target fungal cells is a powerful strategy to obtain new anti-disease genes, and the obtained fusion gene BbAFP1::ErBD has the potential to defend against plant fungal diseases.

Genome-Wide Analysis of Ribosomal Protein GhRPS6 and Its Role in Cotton Verticillium Wilt Resistance

Verticillium wilt is threatening the world’s cotton production. The pathogenic fungus Verticillium dahliae can survive in the soil in the form of microsclerotia for a long time, colonize through the root of cotton, and invade into vascular bundles, causing yellowing and wilting of cotton leaves, and in serious cases, leading to plant death. Breeding resistant varieties is the most economical and effective method to control Verticillium wilt. In previous studies, proteomic analysis was carried out on different cotton varieties inoculated with V. dahliae strain Vd080. It was found that GhRPS6 was phosphorylated after inoculation, and the phosphorylation level in resistant cultivars was 1.5 times than that in susceptible cultivars. In this study, knockdown of GhRPS6 expression results in the reduction of SA and JA content, and suppresses a series of defensive response, enhancing cotton plants susceptibility to V. dahliae. Overexpression in Arabidopsis thaliana transgenic plants was found to be more resistant to V. dahliae. Further, serines at 237 and 240 were mutated to phenylalanine, respectively and jointly. The transgenic Arabidopsis plants demonstrated that seri-237 compromised the plant resistance to V. dahliae. Subcellular localization in Nicotiana benthamiana showed that GhRPS6 was localized in the nucleus. Additionally, the pathogen inoculation and phosphorylation site mutation did not change its localization. These results indicate that GhRPS6 is a potential molecular target for improving resistance to Verticillium wilt in cotton. This lays a foundation for breeding disease-resistant varieties.

Regulatory Network of Cotton Genes in Response to Salt, Drought and Wilt Diseases (Verticillium and Fusarium): Progress and Perspective

In environmental conditions, crop plants are extremely affected by multiple abiotic stresses including salinity, drought, heat, and cold, as well as several biotic stresses such as pests and pathogens. However, salinity, drought, and wilt diseases (e.g., Fusarium and Verticillium) are considered the most destructive environmental stresses to cotton plants. These cause severe growth interruption and yield loss of cotton. Since cotton crops are central contributors to total worldwide fiber production, and also important for oilseed crops, it is essential to improve stress tolerant cultivars to secure future sustainable crop production under adverse environments. Plants have evolved complex mechanisms to respond and acclimate to adverse stress conditions at both physiological and molecular levels. Recent progresses in molecular genetics have delivered new insights into the regulatory network system of plant genes, which generally includes defense of cell membranes and proteins, signaling cascades and transcriptional control, and ion uptake and transport and their relevant biochemical pathways and signal factors. In this review, we mainly summarize recent progress concerning several resistance-related genes of cotton plants in response to abiotic (salt and drought) and biotic (Fusarium and Verticillium wilt) stresses and classify them according to their molecular functions to better understand the genetic network. Moreover, this review proposes that studies of stress related genes will advance the security of cotton yield and production under a changing climate and that these genes should be incorporated in the development of cotton tolerant to salt, drought, and fungal wilt diseases (Verticillium and Fusarium).

The Lethal Effect of Bacillus subtilis Z15 Secondary Metabolites on Verticillium dahliae

Bacillus subtilis Z15 (BS-Z15), isolated from cotton rhizosphere soil, inhibits Verticillium dahliae and suppresses cotton Verticillium wilt in pot experiments. We investigated the influence of environmental factors, pH, temperature, ultraviolet light, protease, and incubation time on the stability of BS-Z15 secondary metabolites (SMs), and the mechanism underlying the cytotoxicity of BS-Z15 SMs on V. dahliae. BS-Z15 and its fermentation broth inhibited V. dahliae, and this effect was mediated by its SMs. These were shown to be stable to the influence of the above environmental factors. BS-Z15 SMs decreased the viability of V. dahliae conidia in a time-dependent manner. Scanning electron microscopy showed that BS-Z15 and its SMs resulted in flattened and depressed conidia. BS-Z15 SMs induced morphological abnormalities in the hyphae, which showed rough aberrant structures, reduced conidiophore production, and accelerated aging. Flow cytometry using Hoechst/propidium iodide double staining revealed that BS-Z15 SMs induced necrosis in V. dahliae in a time-dependent manner. Fluorescence microscopy showed that BS-Z15 SMs did not induce apoptotic bodies in the conidia of V. dahliae but caused significant changes in karyotypes, accompanied by nuclear lysis and nucleic-acid diffusion, which may play important roles in necrosis. In addition, 0.3 mg/mL BS-Z15 SMs had no effect on either the mitochondrial membrane potential or the synthesis of proapoptotic proteins, indicating that the SMs did not induce apoptosis in V. dahliae. Their lethal effect on V. dahliae was by inducing necrosis in its conidia and hyphae. BS-Z15 SMs thus have potential as biological pesticides to control Verticillium wilt in cotton.

Rapid Mining of Candidate Genes for Verticillium Wilt Resistance in Cotton Based on BSA-Seq Analysis

Cotton is a globally important cash crop. Verticillium wilt (VW) is commonly known as "cancer" of cotton and causes serious loss of yield and fiber quality in cotton production around the world. Here, we performed a BSA-seq analysis using an F_2:3 segregation population to identify the candidate loci involved in VW resistance. Two QTLs (qvw-D05-1 and qvw-D05-2) related to VW resistance in cotton were identified using two resistant/susceptible bulks from the F₂ segregation population constructed by crossing the resistant cultivar ZZM2 with the susceptible cultivar J11. A total of 30stop-lost SNPs and 42 stop-gained SNPs, which included 17 genes, were screened in the qvw-D05-2 region by SnpEff analysis. Further analysis of the transcriptome data and qRT-PCR revealed that the expression level of Ghir_D05G037630 (designated as GhDRP) varied significantly at certain time points after infection with V. dahliae. The virus-induced gene silencing of GhDRP resulted in higher susceptibility of the plants to V. dahliae than the control, suggesting that GhDRP is involved in the resistance to V. dahlia infection. This study provides a method for rapid mining of quantitative trait loci and screening of candidate genes, as well as enriches the genomic information and gene resources for the molecular breeding of disease resistance in cotton.

Cotton CC-NBS-LRR Gene GbCNL130 Confers Resistance to Verticillium Wilt Across Different Species

Verticillium wilt (VW) is a destructive disease in cotton caused by Verticillium dahliae and has a significant impact on yield and quality. In the absence of safe and effective chemical control, VW is difficult to manage. Thus, at present, developing resistant varieties is the most economical and effective method of controlling Verticillium wilt of cotton. The CC-NBS-LRR (CNL) gene family is an important class of plant genes involved in disease resistance. This study identified 141 GbCNLs in Gossypium barbadense genome, with 37.5% (53 genes) GbCNLs enriched in 12 gene clusters (GC01-GC12) based on gene distribution in the chromosomes. Especially, seven GbCNLs from two largest clusters (GC11 and GC12) were significantly upregulated in the resistant cultivar (Hai No. 7124) and the susceptible (Giza No. 57). Virus-induced gene silencing of GbCNL130 in G. barbadense, one typical gene in the gene cluster 12 (GC12), significantly altered the response to VW, compromising plant resistance to V. dahliae. In contrast, GbCNL130 overexpression significantly increased the resistance to VW in the wild-type Arabidopsis thaliana. Based on our research findings presented here, we conclude that GbCNL130 promotes resistance to VW by activating the salicylic acid (SA)-dependent defense response pathway resulting in strong accumulation of reactive oxygen species and upregulation of pathogenesis-related (PR) genes. In conclusion, our study resulted in the discovery of a new CNL resistance gene in cotton, GbCNL130, that confers resistance to VW across different hosts.

A cotton WAKL protein interacted with a DnaJ protein and was involved in defense against Verticillium dahliae

Accumulating evidence indicates that plant cell wall-associated receptor-like kinases (WAKs) involve in defense against pathogen attack, but their related signaling processes and regulatory mechanism remain largely unknown. We identified a WAK-like kinase (GhWAKL) from upland cotton (Gossypium hirsutum) and characterized its functional mechanism. Expression of GhWAKL in cotton plants was induced by Verticillium dahliae infection and responded to the application of salicylic acid (SA). Knockdown of GhWAKL expression results in the reduction of SA content and suppresses the SA-mediated defense response, enhancing cotton plants susceptibility to V. dahliae. And, ecotopic overexpression of GhWAKL in Arabidopsis thaliana conferred plant resistance to the pathogen. Further analysis demonstrated that GhWAKL interacted with a cotton DnaJ protein (GhDNAJ1) on the cell membrane. Silencing GhDNAJ1 also enhanced cotton susceptibility to V. dahliae. Moreover, the mutation of GhWAKL at site Ser628 with the phosphorylation decreased the interaction with GhDNAJ1 and compromised the plant resistance to V. dahliae. We propose that GhWAKL is a potential molecular target for improving resistance to Verticillium wilt in cotton.

Comprehensive Genome-Wide Analysis of Thaumatin-Like Gene Family in Four Cotton Species and Functional Identification of GhTLP19 Involved in Regulating Tolerance to Verticillium dahlia and Drought

Thaumatin-like proteins (TLPs) present in the form of large multigene families play important roles in biotic stress and abiotic stress. However, there has been no systematic analysis of the TLPs in cotton. In this study, comprehensive identification and evolutionary analysis of TLPs in four species of cotton were conducted. In total, 50, 48, 91, and 90 homologous sequences were identified in Gossypium raimondii, G. arboreum, G. barbadense, and G. hirsutum, respectively. Gene structure, protein motifs, and gene expression were further investigated. Transcriptome and quantitative real-time PCR analysis indicated that GhTLPs participate in abiotic, biotic stress and cotton fiber development. GhTLP19 on chromosome At05 was selected as a candidate gene for further study. When GhTLP19 was silenced by virus-induced gene silencing (VIGS) in cotton, with the increase of malondialdehyde (MDA) content and the decrease of catalase (CAT) content, and as the increase of disease index (DI) and hyphae accumulation, the plants were more sensitive to drought and Verticillium dahliae. Furthermore, the GhTLP19 overexpressing Arabidopsis transgenic lines exhibited higher proline content, thicker and longer trichomes and more tolerance to drought when compared to wild type. This study will provide a basis and reference for future research on their roles in stress tolerance and fiber development.

Genetic and evolution analysis of extrafloral nectary in cotton

Extrafloral nectaries are a defence trait that plays important roles in plant-animal interactions. Gossypium species are characterized by cellular grooves in leaf midribs that secret large amounts of nectar. Here, with a panel of 215 G. arboreum accessions, we compared extrafloral nectaries to nectariless accessions to identify a region of Chr12 that showed strong differentiation and overlapped with signals from GWAS of nectaries. Fine mapping of an F2 population identified GaNEC1, encoding a PB1 domain-containing protein, as a positive regulator of nectary formation. An InDel, encoding a five amino acid deletion, together with a nonsynonymous substitution, was predicted to cause 3D structural changes in GaNEC1 protein that could confer the nectariless phenotype. mRNA-Seq analysis showed that JA-related genes are up-regulated and cell wall-related genes are down-regulated in the nectary. Silencing of GaNEC1 led to a smaller size of foliar nectary phenotype. Metabolomics analysis identified more than 400 metabolites in nectar, including expected saccharides and amino acids. The identification of GaNEC1 helps establish the network regulating nectary formation and nectar secretion, and has implications for understanding the production of secondary metabolites in nectar. Our results will deepen our understanding of plant-mutualism co-evolution and interactions, and will enable utilization of a plant defence trait in cotton breeding efforts.

The Cotton BEL1-Like Transcription Factor GhBLH7-D06 Negatively Regulates the Defense Response against Verticillium dahliae

Verticillium wilt will seriously affect cotton yield and fiber quality. BEL1-Like transcription factors are involved in the regulation of secondary cell wall (SCW) formation, especially the biosynthesis of lignin that also plays a key role in cotton disease resistance. However, there is no report on the role of BEL1-Like transcription factor in the regulation of plant biological stress. In this study, tissue expression pattern analysis showed that a BEL1-Like transcription factor GhBLH7-D06 was predominantly expressed in vascular tissues and the SCW thickening stage of fiber development, while its expression could also respond to Verticillium dahliae infection and the phytohormone MeJA treatment, which indicated that GhBLH7-D06 might be involved in the defense response of Verticillium wilt. Using virus-induced gene silencing (VIGS) technology, we found silencing the expression of GhBLH7-D06 could enhance the resistance of cotton plants to Verticillium wilt, and the acquisition of resistance might be mainly due to the significant overexpression of genes related to lignin biosynthesis and JA signaling pathway, which also proves that GhBLH7-D06 negatively regulates the resistance of cotton to Verticillium wilt. Based on the results of yeast two-hybrid (Y2H) library screening and confirmation by bimolecular fluorescence complementary (BiFC) experiment, we found an Ovate Family Protein (OFP) transcription factor GhOFP3-D13 which was also a negative regulator of cotton Verticillium wilt resistance could that interacts with GhBLH7-D06. Furthermore, the dual-luciferase reporter assay and yeast one-hybrid (Y1H) experiment indicated that GhBLH7-D06 could target binding to the promoter region of GhPAL-A06 to suppress its expression and eventually lead to the inhibition of lignin biosynthesis. In general, the GhBLH7-D06/GhOFP3-D13 complex can negatively regulate resistance to Verticillium wilt of cotton by inhibiting lignin biosynthesis and JA signaling pathway.

Complementary analyses of the transcriptome and iTRAQ proteome revealed mechanism of ethylene dependent salt response in bread wheat (Triticum aestivum L.)

In order to clarify the ethylene dependent salt response mechanism in wheat, 2-week-old wheat seedlings of cultivar 'Qingmai 6' treated with water, sodium chloride (NaCl), NaCl and ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC), and NaCl and ethylene signaling inhibitor 1-methylcyclopropene (1-MCP) were collected and analyzed by transcriptional sequencing and isobaric tags for relative and absolute quantitation (iTRAQ) proteomics. At least 1140 proteins and 73,401 genes were identified, and proteins including ribosomal proteins (RPs), nucleoside diphosphate kinases (CDPKs), transaldolases (TALs), beta-glucosidases (BGLUs), phosphoenlpyruvate carboxylases (PEPCs), superoxide dismutases (SODs), and 6-phosphogluconate dehydrogenases (6-PGDHs) were significantly differently expressed. These genes and proteins revealed that ethylene dependent salt response through RPs activation, chaperones synthesis, the reactive oxygen species (ROS) scavenging, and carbohydrate metabolites pathway. Our results provided transcriptomics and proteomics information with respect to the molecular mechanisms of ethylene regualted salt response.

GbMPK3 overexpression increases cotton sensitivity to Verticillium dahliae by regulating salicylic acid signaling

The soil-born vascular disease Verticillium wilt, which is caused by fungal pathogen Verticillium dahliae, is a devastating disease of cotton worldwide. In the last decade, a large number of genes have been found to participate in cotton-V. dahliae interactions, but the detailed mechanisms of cotton resistance to V. dahliae remain unclear. Here, we functionally characterized MPK3, a MAPK gene from cotton. MPK3 was induced in the roots of both resistant and susceptible cotton cultivars by V. dahliae inoculation. Transgenic cotton and tobacco with constitutively higher GbMPK3 expression conferred higher V. dahliae susceptibility, while MPK3 knockdown in cotton has limited effect on cotton resistance to V. dahliae. Expression profiling revealed that SA-mediated defense pathway genes (WRKY70, PR1, and PR5) accumulated after V. dahliae inoculation in roots of both wild-type and transgenic cotton, and the expression levels of these genes were higher in GbMPK3-overexpressing plants than in wild-type plants, indicating that GbMPK3 upregulation may reduce plant resistance to V. dahliae through regulating salicylic acid signaling transduction.

An Overview of the Molecular Genetics of Plant Resistance to the Verticillium Wilt Pathogen Verticillium dahliae

Verticillium dahliae is a soil-borne hemibiotrophic fungus that can lead to plant vascular disease and significant economic loss worldwide. Its hosts include over 400 dicotyledon plant species, such as annual herbs, perennials, and woody plants. The average yield loss of cotton crop caused by Verticillium wilt is approximately 10–35%. As the control of this disease is an urgent task for many countries, further understanding of the interaction between plants and V. dahliae is essential. Fungi can promote or inhibit plant growth, which is important; however, the most important relationship between plants and fungi is the host–pathogen relationship. Plants can become resistant to V. dahliae through diverse mechanisms such as cell wall modifications, extracellular enzymes, pattern recognition receptors, transcription factors, and salicylic acid (SA)/jasmonic acid (JA)/ethylene (ET)-related signal transduction pathways. Over the last decade, several studies on the physiological and molecular mechanisms of plant resistance to V. dahliae have been undertaken. In this review, many resistance-related genes are summarised to provide a theoretical basis for better understanding of the molecular genetic mechanisms of plant resistance to V. dahliae. Moreover, it is intended to serve as a resource for research focused on the development of genetic resistance mechanisms to combat Verticillium wilt.

Heterologous Expression of the AtNPR1 Gene in Olive and Its Effects on Fungal Tolerance

The NPR1 gene encodes a key component of systemic acquired resistance (SAR) signaling mediated by salicylic acid (SA). Overexpression of NPR1 confers resistance to biotrophic and hemibiotrophic fungi in several plant species. The NPR1 gene has also been shown to be involved in the crosstalk between SAR signaling and the jasmonic acid-ethylene (JA/Et) pathway, which is involved in the response to necrotrophic fungi. The aim of this research was to generate transgenic olive plants expressing the NPR1 gene from Arabidopsis thaliana to evaluate their differential response to the hemibiotrophic fungus Verticillium dahliae and the necrotroph Rosellinia necatrix. Three transgenic lines expressing the AtNPR1 gene under the control of the constitutive promoter CaMV35S were obtained using an embryogenic line derived from a seed of cv. Picual. After maturation and germination of the transgenic somatic embryos, the plants were micropropagated and acclimated to ex vitro conditions. The level of AtNPR1 expression in the transgenic materials varied greatly among the different lines and was higher in the NPR1-780 line. The expression of AtNPR1 did not alter the growth of transgenic plants either in vitro or in the greenhouse. Different levels of transgene expression also did not affect basal endochitinase activity in the leaves, which was similar to that of control plants. Response to the hemibiotrophic pathogen V. dahliae varied with pathotype. All plants died by 50 days after inoculation with defoliating (D) pathotype V-138, but the response to non-defoliating (ND) strains differed by race: following inoculation with the V-1242 strain (ND, race 2), symptoms appeared after 44-55 days, with line NPR1-780 showing the lowest disease severity index. This line also showed good performance when inoculated with the V-1558 strain (ND, race 1), although the differences from the control were not statistically significant. In response to the necrotroph R. necatrix, all the transgenic lines showed a slight delay in disease development, with mean area under the disease progress curve (AUDPC) values 7-15% lower than that of the control.

Dynamic infection of Verticillium dahliae in upland cotton

Verticillium wilt, an infection caused by the soilborne fungus Verticillium dahliae, is one of the most serious diseases in cotton. No effective control method against V. dahliae has been established, and the infection mechanism of V. dahliae in upland cotton remains unknown. GFP-tagged V. dahliae isolates with different pathogenic abilities were used to analyse the colonisation and infection of V. dahliae in the roots and leaves of different upland cotton cultivars, the relationships among infection processes, the immune responses and the resistance ability of different cultivars against V. dahliae. Here, we report a new infection model for V. dahliae in upland cotton plants. V. dahliae can colonise and infect any organ of upland cotton plants and then spread to the entire plant from the infected organ through the surface and interior of the organ. Vascular tissue was found to not be the sole transmission route of V. dahliae in cotton plants. In addition, the rate of infection of a V. dahliae isolate with strong pathogenicity was notably faster than that of an isolate with weak pathogenicity. The resistance of upland cotton to Verticillium wilt was related to the degree of the immune response induced in plants infected with V. dahliae. These results provide a theoretical basis for studying the mechanism underlying the interaction between V. dahliae and upland cotton. These results provide a theoretical basis for studying the mechanism underlying the interaction between V. dahliae and upland cotton.

GhWRKY70D13 Regulates Resistance to Verticillium dahliae in Cotton Through the Ethylene and Jasmonic Acid Signaling Pathways

Verticillium wilt caused by Verticillium dahliae is a destructive cotton disease causing severe yield and quality losses worldwide. WRKY transcription factors play important roles in plant defense against pathogen infection. However, little has been reported on the functions of WRKYs in cotton's resistance to V. dahliae. Here, we identified 5, 5, and 10 WRKY70 genes in Gossypium arboreum, Gossypium raimondii, and Gossypium hirsutum, respectively, and investigated the expression profiles of all GhWRKY70 genes in various cotton tissues and in response to hormone treatment or V. dahliae infection. Reverse transcription-quantitative PCR analysis showed that GhWRKY70D13 was expressed higher in roots and stems than in other tissues, and up-regulated after V. dahliae inoculation. Knock-down of GhWRKY70D13 improved resistance to V. dahliae in both resistant and susceptible cotton cultivars. Comparative analysis of transcriptomes generated from wild-type and stable RNAi (RNA interference) plant with down-regulated GhWRKY70D13 showed that genes involved in ethylene (ET) and jasmonic acid (JA) biosynthesis and signaling were significantly upregulated in the GhWRKY70D13 RNAi plants. Consistently, the contents of 1-aminocyclopropane-1-carboxylic (ACC), JA, and JA-isoleucine levels were significantly higher in the GhWRKY70D13 RNAi plants than in wild-type. Following V. dahliae infection, the levels of ACC and JA decreased in the GhWRKY70D13 RNAi plants but still significantly higher (for ACC) than that in wild-type or at the same level (for JA) as in non-infected wild-type plants. Collectively, our results suggested that GhWRKY70D13 negatively regulates cotton's resistance to V. dahliae mainly through its effect on ET and JA biosynthesis and signaling pathways.

Hormone Signaling and Its Interplay With Development and Defense Responses in Verticillium-Plant Interactions

Soilborne plant pathogenic species in the fungal genus Verticillium cause destructive Verticillium wilt disease on economically important crops worldwide. Since R gene-mediated resistance is only effective against race 1 of V. dahliae, fortification of plant basal resistance along with cultural practices are essential to combat Verticillium wilts. Plant hormones involved in cell signaling impact defense responses and development, an understanding of which may provide useful solutions incorporating aspects of basal defense. In this review, we examine the current knowledge of the interplay between plant hormones, salicylic acid, jasmonic acid, ethylene, brassinosteroids, cytokinin, gibberellic acid, auxin, and nitric oxide, and the defense responses and signaling pathways that contribute to resistance and susceptibility in Verticillium-host interactions. Though we make connections where possible to non-model systems, the emphasis is placed on Arabidopsis-V. dahliae and V. longisporum interactions since much of the research on this interplay is focused on these systems. An understanding of hormone signaling in Verticillium-host interactions will help to determine the molecular basis of Verticillium wilt progression in the host and potentially provide insight on alternative approaches for disease management.