Return of old foes - recurrence of bacterial blight and Fusarium wilt of cotton

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.

Endophytic Fungi Inoculation Reduces Ramulosis Severity in Gossypium hirsutum Plants

Biotic stress in cotton plants caused by the phytopathogenic fungus Colletotrichum gossypii var. cephalosporioides triggers symptoms of ramulosis, a disease characterized by necrotic spots on young leaves, followed by death of the affected branch's apical meristem, plant growth paralysis, and stimulation of lateral bud production. Severe cases of ramulosis can cause up to 85% yield losses in cotton plantations. Currently, this disease is controlled exclusively by using fungicides. However, few studies have focused on biological alternatives for mitigating the effects of contamination by C. gossypii var. cephalosporioides on cotton plants. Thus, the hypothesis raised is that endophytic fungi isolated from an Arecaceae species (Butia purpurascens), endemic to the Cerrado biome, have the potential to reduce physiological damage caused by ramulosis, decreasing its severity in these plants. This hypothesis was tested using plants grown from seeds contaminated with the pathogen and inoculated with strains of Gibberella moniliformis (BP10EF), Hamigera insecticola (BP33EF), Codinaeopsis sp. (BP328EF), G. moniliformis (BP335EF), and Aspergillus sp. (BP340EF). C. gossypii var. cephalosporioides is a leaf pathogen; thus, the evaluations were focused on leaf parameters: gas exchange, chlorophyll a fluorescence, and oxidative metabolism. The hypothesis that inoculation with endophytic strains can mitigate physiological and photochemical damage caused by ramulosis in cotton was confirmed, as the fungi improved plant growth and stomatal index and density, increased net photosynthetic rate (A) and carboxylation efficiency (A/Ci), and decreased photochemical stress (ABS/RC and DI0/RC) and oxidative stress by reducing enzyme activity (CAT, SOD, and APX) and the synthesis of malondialdehyde (MDA). Control plants developed leaves with a low adaxial stomatal index and density to reduce colonization of leaf tissues by C. gossypii var. cephalosporioides due to the absence of fungal antagonism. The Codinaeopsis sp. strain BP328EF can efficiently inhibit C. gossypii var. cephalosporioides in vitro (81.11% relative inhibition), improve gas exchange parameters, reduce photochemical stress of chlorophyll-a, and decrease lipid peroxidation in attacked leaves. Thus, BP328EF should be further evaluated for its potential effect as a biological alternative for enhancing the resistance of G. hirsutum plants and minimizing yield losses caused by C. gossypii var. cephalosporioides.

Characterization of the High-Quality Genome Sequence and Virulence Factors of Fusarium oxysporum f. sp. vasinfectum Race 7

Fusarium oxysporum f. sp. vasinfectum (Fov) is a common soilborne fungal pathogen that causes Fusarium wilt (FW) disease in cotton. Although considerable progress has been made in cotton disease-resistance breeding against FW in China, and the R gene conferring resistance to Fov race 7 (FOV) in Upland cotton (Gossypium hirsutum) has been identified, knowledge regarding the evolution of fungal pathogenicity and virulence factors in Fov remains limited. In this study, we present a reference-scale genome assembly and annotation for FOV7, created through the integration of single-molecule real-time sequencing (PacBio) and high-throughput chromosome conformation capture (Hi-C) techniques. Comparative genomics analysis revealed the presence of six supernumerary scaffolds specific to FOV7. The genes or sequences within this region can potentially serve as reliable diagnostic markers for distinguishing Fov race 7. Furthermore, we conducted an analysis of the xylem sap proteome of FOV7-infected cotton plants, leading to the identification of 19 proteins that are secreted in xylem (FovSIX). Through a pathogenicity test involving knockout mutants, we demonstrated that FovSIX16 is crucial for the full virulence of FOV7. Overall, this study sheds light on the underlying mechanisms of Fov's pathogenicity and provides valuable insights into potential management strategies for controlling FW.

Genetic Channelization Mechanism of Four Chalcone Isomerase Homologous Genes for Synergistic Resistance to Fusarium wilt in Gossypium barbadense L

Duplication events occur very frequently during plant evolution. The genes in the duplicated pathway or network can evolve new functions through neofunctionalization and subfunctionalization. Flavonoids are secondary metabolites involved in plant development and defense. Our previous transcriptomic analysis of F6 recombinant inbred lines (RILs) and the parent lines after Fusarium oxysporum f. sp. vasinfectum (Fov) infection showed that CHI genes have important functions in cotton. However, there are few reports on the possible neofunctionalization differences of CHI family paralogous genes involved in Fusarium wilt resistance in cotton. In this study, the resistance to Fusarium wilt, expression of metabolic pathway-related genes, metabolite content, endogenous hormone content, reactive oxygen species (ROS) content and subcellular localization of four paralogous CHI family genes in cotton were investigated. The results show that the four paralogous CHI family genes may play a synergistic role in Fusarium wilt resistance. These results revealed a genetic channelization mechanism that can regulate the metabolic flux homeostasis of flavonoids under the mediation of endogenous salicylic acid (SA) and methyl jasmonate (MeJA) via the four paralogous CHI genes, thereby achieving disease resistance. Our study provides a theoretical basis for studying the evolutionary patterns of homologous plant genes and using homologous genes for molecular breeding.

Comparative Genomics Identifies Conserved and Variable TAL Effectors in African Strains of the Cotton Pathogen Xanthomonas citri pv. malvacearum

Strains of Xanthomonas citri pv. malvacearum cause bacterial blight of cotton, a potentially serious threat to cotton production worldwide, including in sub-Saharan countries. Development of disease symptoms, such as water soaking, has been linked to the activity of a class of type 3 effectors, called transcription activator-like (TAL) effectors, which induce susceptibility genes in the host's cells. To gain further insight into the global diversity of the pathogen, to elucidate their repertoires of TAL effector genes, and to better understand the evolution of these genes in the cotton-pathogenic xanthomonads, we sequenced the genomes of three African strains of X. citri pv. malvacearum using nanopore technology. We show that the cotton-pathogenic pathovar of X. citri is a monophyletic lineage containing at least three distinct genetic subclades, which appear to be mirrored by their repertoires of TAL effectors. We observed an atypical level of TAL effector gene pseudogenization, which might be related to resistance genes that are deployed to control the disease. Our work thus contributes to a better understanding of the conservation and importance of TAL effectors in the interaction with the host plant, which can inform strategies for improving resistance against bacterial blight in cotton.

Gene B5 in Cotton Confers High and Broad Resistance to Bacterial Blight and Conditions High Amounts of Sesquiterpenoid Phytoalexins

Bacterial blight resistance gene B₅ has received little attention since it was first described in 1950. A near-isogenic line (NIL) of Gossypium hirsutum cotton, AcB₅, was generated in an otherwise bacterial-blight-susceptible 'Acala 44' background. The introgressed locus B₅ in AcB₅ conferred strong and broad-spectrum resistance to bacterial blight. Segregation patterns of test crosses under Oklahoma field conditions indicated that AcB₅ is likely homozygous for resistance at two loci with partial dominance gene action. In controlled-environment conditions, two of the four copies of B₅ were required for effective resistance. Contrary to expectations of gene-for-gene theory, AcB₅ conferred high resistance toward isogenic strains of Xanthomonas citri subsp. malvacearum carrying cloned avirulence genes avrB4, avrb7, avrBIn, avrB101, and avrB102, respectively, and weaker resistance toward the strain carrying cloned avrb6. The hypothesis that each B gene, in the absence of a polygenic complex, triggers sesquiterpenoid phytoalexin production was tested by measurement of cadalene and lacinilene phytoalexins during resistant responses in five NILs carrying different B genes, four other lines carrying multiple resistance genes, as well as susceptible Ac44E. Phytoalexin production was an obvious, but variable, response in all nine resistant lines. AcB₅ accumulated an order of magnitude more of all four phytoalexins than any of the other resistant NILs. Its total levels were comparable to those detected in OK1.2, a highly resistant line that possesses several B genes in a polygenic background.

The Arabidopsis thaliana-Fusarium oxysporum strain 5176 pathosystem: an overview

Fusarium oxysporum is a soil-borne fungal pathogen of several major food crops. Research on understanding the molecular details of fungal infection and the plant's defense mechanisms against this pathogen has long focused mainly on the tomato-infecting F. oxysporum strains and their specific host plant. However, in recent years, the Arabidopsis thaliana-Fusarium oxysporum strain 5176 (Fo5176) pathosystem has additionally been established to study this plant-pathogen interaction with all the molecular biology, genetic, and genomic tools available for the A. thaliana model system. Work on this system has since produced several new insights, especially with regards to the role of phytohormones involved in the plant's defense response, and the receptor proteins and peptide ligands involved in pathogen detection. Furthermore, work with the pathogenic strain Fo5176 and the related endophytic strain Fo47 has demonstrated the suitability of this system for comparative studies of the plant's specific responses to general microbe- or pathogen-associated molecular patterns. In this review, we highlight the advantages of this specific pathosystem, summarize the advances made in studying the molecular details of this plant-fungus interaction, and point out open questions that remain to be answered.

Group IIc WRKY transcription factors regulate cotton resistance to Fusarium oxysporum by promoting GhMKK2-mediated flavonoid biosynthesis

WRKY transcription factors (TFs) are crucial regulators in response to pathogen infection. However, the regulatory mechanisms of WRKY TFs in response to Fusarium oxysporum f. sp. vasinfectum (Fov), the most devastating pathogen of cotton, remain unclear. Here, transcriptome sequencing indicated that the group IIc WRKY TF subfamily was the most important TF subfamily in response to Fov. Gain-of-function and loss-of-function analyses showed that group IIc WRKY TFs positively regulated cotton resistance to Fov. A series of chromatin immunoprecipitation sequencing, yeast one-hybrid assay and electrophoresis mobility shift assay experiments indicated that group IIc WRKY TFs directly bound to the promoter of GhMKK2 and regulated its expression. Importantly, a novel mitogen-activated protein kinase (MAPK) cascade composed of GhMKK2, GhNTF6 and GhMYC2 was identified. The functional analysis indicated that group IIc WRKY TFs induced the GhMKK2-GhNTF6 pathway to increase resistance to Fov by upregulating the GhMYC2-mediated expression of several flavonoid biosynthesis-related genes, which led to flavonoid accumulation. In conclusion, our study demonstrated a novel disease defense mechanism by which the WRKY-MAPK pathway promotes flavonoid biosynthesis to defend against pathogen infection. This pathway improves our understanding of the interaction mode between WRKY TFs and MAPK cascades in plant immunity and the vital role of plant flavonoids in pathogen defense.

DNA-Based Quantification of Fusarium oxysporum f. sp. vasinfectum in Environmental Soils to Describe Spatial Variation in Inoculum Density

Fusarium wilt of cotton, caused by the soilborne fungal pathogen Fusarium oxysporum f. sp. vasinfectum (FOV), occurs in regions of the United States where cotton (Gossypium spp.) is grown. Race 4 of this pathogen (FOV4) is especially aggressive, and does not require the co-occurrence of the root knot nematode (Meloidogyne incognita) to infect cotton. Its sudden appearance in far-west Texas in 2016 after many years of being restricted to California is of great concern, as is the threat of its continued spread through the cotton-producing regions of the United States. The aim of this research was to analyze the spatial variability of FOV4 inoculum density in the location where FOV4 is locally emerging, using quantitative and droplet digital PCR methods. Soil samples collected from a field with known FOV4 incidence in Fabens, Texas, were analyzed. Appreciable variation in inoculum density was found to occur at spatial scales smaller than the size of plots involved in cultivar trial research, and was spatially autocorrelated (Moran's I, Z = 17.73, P < 0.0001). These findings indicate that, for cultivar trials, accounting for the spatial distribution of inoculum, either by directly quantifying it or through the use of densely distributed calibration checks, is important to the interpretation of results.

Soil Microbial Communities Altered by Titanium Ions in Different Agroecosystems of Pitaya and Grape

Titanium (Ti) is an element beneficial to plant growth. Application of titanium to roots or leaves at low concentrations can improve crop yield and performance. However, the effect of titanium ions on the bulk soil microbial community of planted crops remains unclear. This study aimed to explore the effects of titanium on soil bacterial and fungal communities. Field surveys were conducted to determine the effect of titanium ions on bulk soil microbial communities in pitaya and grape plantations of Panzhihua and Xichang areas, respectively. Full-length 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing were performed using PacBio Sequel to further explore the composition and structure of soil microbiota. The application of titanium ions significantly altered the composition and structure of soil microbiota. Root irrigation with titanium ions in pitaya gardens reduced the diversity of soil fungi and bacteria. However, the decline in bacterial diversity was not statistically significant. Meanwhile, foliar spray of titanium ions on grapes greatly reduced the soil microbial diversity. The bulk soil microbiota had a core of conserved taxa, and titanium ions significantly altered their relative abundances. Furthermore, the application of titanium increased the interaction network of soil fungi and bacteria compared with the control group. Thus, titanium ions potentially improve the stability of the soil microbial community.

IMPORTANCE Pitaya and grape are important cash crops in the Panzhihua and Xichang areas, respectively, where they are well adapted. Titanium is a plant growth-promoting element, but the interaction between titanium and soil microorganisms is poorly understood. Titanium ions are still not widely used for growing pitaya and grape in the two regions. Thus, we investigated the effects of titanium ions on soil microbial communities of the two fruit crops in these two regions. Microbial diversity decreased, and the community structure changed; however, the addition of titanium ions enhanced cooccurrence relationships and improved the stability of the community. This study provides a basis for the importance of titanium ion application in crop cultivation.

Patterns of Seed-to-Seedling Transmission of Xanthomonas citri pv. malvacearum, the Causal Agent of Cotton Bacterial Blight

Cotton bacterial blight (CBB), caused by Xanthomonas citri pv. malvacearum, was a major disease of cotton in the United States in the early part of the twentieth century. The reemergence of CBB revealed many gaps in our understanding of this important disease. In this study, we employed a wild-type (WT) field isolate of X. citri pv. malvacearum from Georgia (U.S.A.) to generate a nonpathogenic hrcV mutant lacking a functional type-III secretion system (T3SS-). We tagged the WT and T3SS- strains with an auto-bioluminescent Tn7 reporter and compared colonization patterns of CBB-susceptible and CBB-resistant cotton seedlings using macroscopic image analysis and bacterial load enumeration. WT and T3SS- X. citri pv. malvacearum strains colonized cotton cotyledons of CBB-resistant and CBB-susceptible cotton cultivars. However, X. citri pv. malvacearum populations were significantly higher in CBB-susceptible seedlings inoculated with the WT strain. Additionally, WT and T3SS- X. citri pv. malvacearum strains systemically colonized true leaves, although at different rates. Finally, we observed that seed-to-seedling transmission of X. citri pv. malvacearum may involve systemic spread through the vascular tissue of cotton plants. These findings yield novel insights into potential X. citri pv. malvacearum reservoirs for CBB outbreaks.

The Biocontrol and Plant Growth-Promoting Properties of Streptomyces alfalfae XN-04 Revealed by Functional and Genomic Analysis

Fusarium wilt of cotton, caused by the pathogenic fungal Fusarium oxysporum f. sp. vasinfectum (Fov), is a devastating disease of cotton, dramatically affecting cotton production and quality. With the increase of pathogen resistance, controlling Fusarium wilt disease has become a significant challenge. Biocontrol agents (BCAs) can be used as an additional solution to traditional crop breeding and chemical control. In this study, an actinomycete with high inhibitory activity against Fov was isolated from rhizosphere soil and identified as Streptomyces alfalfae based on phylogenetic analyses. Next, an integrative approach combining genome mining and metabolites detection was applied to decipher the significant biocontrol and plant growth-promoting properties of XN-04. Bioinformatic analysis and bioassays revealed that the antagonistic activity of XN-04 against Fov was associated with the production of various extracellular hydrolytic enzymes and diffusible antifungal metabolites. Genome analysis revealed that XN-04 harbors 34 secondary metabolite biosynthesis gene clusters. The ability of XN-04 to promote plant growth was correlated with an extensive set of genes involved in indoleacetic acid biosynthesis, 1-aminocyclopropane-1-carboxylic acid deaminase activity, phosphate solubilization, and iron metabolism. Colonization experiments indicated that EGFP-labeled XN-04 had accumulated on the maturation zones of cotton roots. These results suggest that S. alfalfae XN-04 could be a multifunctional BCA and biofertilizer used in agriculture.

A nonproteinaceous Fusarium cell wall extract triggers receptor-like protein-dependent immune responses in Arabidopsis and cotton

Fusarium wilt caused by the ascomycete fungus Fusarium oxysporum is a devastating disease of many economically important crops. The mechanisms underlying plant responses to F. oxysporum infections remain largely unknown. We demonstrate here that a water-soluble, heat-resistant and nonproteinaceous F. oxysporum cell wall extract (FoCWE) component from multiple F. oxysporum isolates functions as a race-nonspecific elicitor, also termed pathogen-associated molecular pattern (PAMP). FoCWE triggers several demonstrated immune responses, including mitogen-activated protein (MAP) kinase phosphorylation, reactive oxygen species (ROS) burst, ethylene production, and stomatal closure, in cotton and Arabidopsis. Pretreated FoCWE protects cotton seeds against infections by virulent F. oxysporum f. sp. vasinfectum (Fov), and Arabidopsis plants against the virulent bacterium, Pseudomonas syringae, suggesting the potential application of FoCWEs in crop protection. Host-mediated responses to FoCWE do not appear to require LYKs/CERK1, BAK1 or SOBIR1, which are commonly involved in PAMP perception and/or signalling. However, FoCWE responses and Fusarium resistance in cotton partially require two receptor-like proteins, GhRLP20 and GhRLP31. Transcriptome analysis suggests that FoCWE preferentially activates cell wall-mediated defence, and Fov has evolved virulence mechanisms to suppress FoCWE-induced defence. These findings suggest that FoCWE is a classical PAMP that is potentially recognised by a novel pattern-recognition receptor to regulate cotton resistance to Fusarium infections.

SEVEN IN ABSENTIA Ubiquitin Ligases Positively Regulate Defense Against Verticillium dahliae in Gossypium hirsutum

Ubiquitination is a post-translational regulatory mechanism that controls a variety of biological processes in plants. The E3 ligases confer specificity by recognizing target proteins for ubiquitination. Here, we identified SEVEN IN ABSENTIA (SINA) ubiquitin ligases, which belong to the RING-type E3 ligase family, in upland cotton (Gossypium hirsutum). Twenty-four GhSINAs were characterized, and the expression levels of GhSINA7, GhSINA8, and GhSINA9 were upregulated at 24 h after inoculation with Verticillium dahliae. In vitro ubiquitination assays indicated that the three GhSINAs possessed E3 ubiquitin ligase activities. Transient expression in Nicotiana benthamiana leaves showed that they localized to the nucleus. And yeast two-hybrid (Y2H) screening revealed that they could interact with each other. The ectopic overexpression of GhSINA7, GhSINA8, and GhSINA9 independently in Arabidopsis thaliana resulted in increased tolerance to V. dahliae, while individual knockdowns of GhSINA7, GhSINA8, and GhSINA9 compromised cotton resistance to the pathogen. Thus, GhSINA7, GhSINA8, and GhSINA9 act as positive regulators of defense responses against V. dahliae in cotton plants.

A review of plant leaf fungal diseases and its environment speciation

There is increasing difficulty in identifying new plant leaf diseases as a result of environmental change. There is a need to identify the factors influencing the emergence and the increasing incidences of these diseases. Here, we present emerging fungal plant leaf diseases and describe their environmental speciation. We considered the factors controlling for local adaptation associated with environmental speciation. We determined that the advent of emergent fungal leaf diseases is closely connected to environmental speciation. Fungal pathogens targeting the leaves may adversely affect the entire plant body. To mitigate the injury caused by these pathogens, it is necessary to be able to detect and identify them early in the infection process. In this way, their distribution, virulence, incidence, and severity could be attenuated.