Phytopathology最新文献

Fusarium crown rot (FCR) has become increasingly prevalent in China's Huanghuai wheat-growing region, with Fusarium pseudograminearum emerging as the predominant causal pathogen. In this study, we developed a TaqMan qPCR assay targeting the conserved FpAH1 gene to specifically detect F. pseudograminearum. The assay's specificity was verified against 12 Fusarium species and 10 other wheat pathogenic fungi, achieving an amplification efficiency of 105.3% (R² = 0.997) and a limit of detection (LOD) of 1 × 10² copies/μL. Using this assay, we monitored the monthly dynamics of F. pseudograminearum in wheat basal stems and top soil throughout two entire growing seasons (2023-2024 and 2024-2025) under three seed treatments: untreated control, tebuconazole-coated, and cyclobutrifluram-coated. Field dynamics showed that cyclobutrifluram treatment significantly suppressed F. pseudograminearum biomass in wheat plants, while tebuconazole-coated seeds exhibited no significant difference from the untreated control. Notably, F. pseudograminearum biomass surged sharply in the late growing stage across all three treatments. Top soil maintained relatively stable F. pseudograminearum biomass, comparable to the early-stage level in wheat basal stems, across all seasons. This study established a rapid and robust TaqMan qPCR assay for specific detection of F. pseudograminearum, with broad utility in related research and practice, and documented the pathogen's cross-seasonal dynamics in both wheat plants and top soil. These characterized dynamics provide a theoretical foundation for refining Fusarium crown rot (FCR) control measures, exemplifying the assay's practical value while highlighting its potential for broader applications.

Pantoea stewartii subsp. indologenes (Psi) isolates can cause disease in several Poaceae hosts, including millets and rice, and were recently known to cause foliar and bulb symptoms characteristic of center rot in onions. Cover crops such as millet and cash crops such as corn are commonly grown in the summer after onion harvest in Vidalia, Georgia, United States. However, the risk of pathogen transmission to onions in the cropping systems in which summer crops precede onion planting is largely understudied. We evaluated the survivability of Psi in corn and pearl millet residues and assessed its ability to colonize onions transplanted into the infested soil. Our microplot study showed that millet and corn residues support the transient survival of Psi. The presence of the pathogen in the soil also overlapped with the presence of onion transplants. However, despite planting onion seedlings in Psi-infested soil, no bacterial colonization was observed in their rhizosphere and foliar surfaces. Moreover, no visible symptoms of center rot were observed in onion foliage and bulbs, indicating a lesser risk of vertical transmission in the Poaceae-Allium cropping system. We further investigated genetic determinants for bacterial survival in millet residue and bare soil by creating deletion mutants of the genes responsible for exopolysaccharides, flagellar motility, quorum sensing, and pathogenicity in a Psi pathovar cepacicola strain PNA 14-12. All mutant strains persisted for at least 24 days in millet residue at high population levels, and colonies of all the strains remained detectable in bare soil until 44 days. Exopolysaccharide production played a minor role in Psi survival, whereas none of the other targeted genes contributed to bacterial persistence in millet residue or bare soil. Overall, our findings suggest that summer crop residues play an important role in the survival of Psi in fields under an onion-millet/corn cropping scheme; however, the risk of Psi transmission from millet or corn residue to onions appears minimal. Despite this observation, crop residues should be incorporated into the soil to facilitate decomposition before onion transplanting.

Insect vectors are increasingly recognized as overlooked drivers of postharvest disease spread. Ceratocystis fimbriata, the causal agent of sweetpotato black rot, can spread rapidly in postharvest environments. Previous work established that Drosophila hydei can acquire viable C. fimbriata propagules both externally and internally, identifying this fly as a potential vector in storage facilities. Here, we expand on that finding by testing whether vector density influences disease transmission and by developing molecular diagnostic assays to improve pathogen detection. Transmission assays were conducted with four fly densities (10, 30, 50, and 80 flies) exposed to inoculum sources and then transferred to clean targets (sterile agar and uninfected sweetpotatoes, with and without wounds). Transmission occurred regardless of fly density, indicating that even small populations are sufficient to spread the inoculum, although incidence was significantly higher in wounded roots. To complement these assays, we standardized qPCR assays using dual-quencher probes targeting two C. fimbriata-specific markers (T3G9 and T5G26). Pathogen DNA was detected in both flies and asymptomatic roots, with the more sensitive marker identifying latent infections that were not visible through symptoms. Together, these results demonstrate that D. hydei vectors C. fimbriata in a density-independent manner, that wounding increases the success of infection, and that qPCR diagnostics can detect transmission events that are overlooked by visual assessment. These findings provide new epidemiological insight into postharvest black rot and support integrated management strategies that combine vector suppression with molecular surveillance.

Osthole exhibits strong inhibitory activity against phytopathogenic fungi; however, its antifungal mechanism remains unclear. This study assessed osthole's inhibitory effects on several phytopathogenic fungi, revealing a half-maximal effective concentration of 73.03 μg/ml against the hyphal growth of Botrytis cinerea. Micromorphological analysis showed that osthole caused abnormalities in the hyphae, including unclear organelle boundaries and organelle dissolution. Integrated transcriptomic and metabolomic assays and correlation analysis indicated that osthole induced differentially expressed genes and differentially abundant metabolites, which were enriched particularly in the pathways of glyoxylate and dicarboxylate metabolism, tyrosine metabolism, glycerophospholipid metabolism, fructose and mannose metabolism, citrate cycle, biosynthesis of unsaturated fatty acids, and ABC transporters. Molecular docking and molecular dynamics simulation assays demonstrated that osthole binds stably to amidase, a key enzyme in energy metabolism, with a relatively lower binding energy of -8.5 kcal/mol compared with osthole's analogs, suggesting that amidase may be a potential target protein in the fungus. A microscale thermophoresis assay indicated that the dissociation constant (Kd) value for osthole binding to amidase was significantly lower compared with that of osthole's analog 7-methoxycoumarin. Overall, this study demonstrates that osthole disrupts energy metabolism, nitrogen metabolism, substance transport, and the metabolism of the hyphal cell wall and cell membrane, potentially targeting the amidase of B. cinerea. These findings highlight the potential of osthole for controlling gray mold.

How host genotype shapes pathogen tissue tropism remains poorly understood. Vascular and nonvascular tissues represent distinct habitats within a plant for bacteria to colonize. Host plants often utilize different mechanisms to defend themselves against vascular and nonvascular pathogens, and mechanisms of resistance employed by the host can vary by organ. Xanthomonas vasicola pv. vasculorum (Xvv) is an emerging bacterial maize pathogen, and this pathosystem offers an opportunity to study how host resistance differs in response to the vascular and nonvascular lifestyles exhibited by a single bacterial phytopathogen. We used different inoculation techniques to induce vascular and nonvascular disease and evaluated maize populations using both techniques to map resistance to vascular and nonvascular disease caused by Xvv. Xvv can colonize both vascular and nonvascular tissues, depending on the genotype. Different inoculation techniques can be used to induce vascular or nonvascular colonization. Independent loci control variation in resistance to Xvv during vascular and nonvascular pathogenesis. We confirmed the role of those regions in resistance to vascular and nonvascular infection. This study offers insights into how host resistance shapes how bacterial pathogens adapt to both vascular and nonvascular lifestyles. We show that host genotype can dictate which tissues a pathogen can infect. This system can serve as a model to understand tissue-specific host resistance to plant pathogens and tissue specificity in pathogens.

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial leaf blight (BLB), a major rice disease causing up to 70% yield loss in Asia and West Africa. First described in Japan in 1884 and later reported in West Africa in the 1970s, BLB recently emerged in East Africa, with an epidemic reported in Tanzania in 2019. Remarkably, the disease was detected for the first time in Madagascar the same year, representing a serious threat to food security. To investigate the origin of BLB in Madagascar, we isolated 73 Xoo strains from symptomatic rice leaves collected between 2019 and 2023. MLVA genotyping revealed 19 haplotypes forming a single clonal complex, indicating low diversity and a likely recent introduction. In order to come up with disease control strategies, IRBB-based race-typing was achieved and identified four resistance genes (Xa8, xa13, Xa21, Xa23) that confer resistance to all Malagasy strains tested, while the 19 Malagasy varieties assessed were susceptible. The analysis of SWEET knock-out lines confirmed that Malagasy strains rely on the susceptibility gene OsSWEET11 for full virulence. Whole-genome sequencing and TALEs repertoire analyses of two strains allowed the identification of a PthXo1 ortholog predicted to induce OsSWEET11. SNP-based phylogenetic analyses clustered Malagasy strains within Asian lineages, most closely related to strains originated from India. Malagasy strains did not cluster with recently reported Tanzanian Xoo, suggesting independent introductions. Overall, our study demonstrates that BLB in Madagascar results from a recent and single introduction from Asia and identifies effective resistance genes for deployment.

Trichoderma Gene Prediction Web server (TGP-WEB) is designed for accurate gene prediction in genomes of Trichoderma species, the biological control agents and the plant-beneficial microorganisms. It employs a hybrid gene prediction strategy, combining ab initio (Augustus and GeneMark) and homology-based (Braker utilizing fungal protein sequences from NCBI Refseq database) methods. Predictions are integrated and prioritized using a ranking framework, followed by functional assessment via domain annotation. After uploading a single-genome FASTA file, users can download TGP-WEB prediction results (including GFF3 files with gene locations, and FASTA files for both the predicted nucleotide and amino acid sequences) within ~4 hours. TGP-WEB demonstrates high accuracy in gene prediction across 177 genomes. When benchmarked against 42 published genomes with annotated gene sets available on NCBI, it recovers more than 90.00% of reported genes in 37 (88.00%) genomes. For 135 previously unannotated genomes, TGP-WEB generates complete gene sets, now available on the web server. BUSCO evaluation shows greater than 97.00% completeness for 94.92% (168/177) of genomes. TGP-WEB predictions enable the identification of 2100 single-copy genes from Trichoderma genomes. These genes are used to construct a robust phylogenetic tree, which clarifies the taxonomy of 49 strains. The robust performance of TGP-WEB prediction will contribute to the increasing studies of Trichoderma genomes, and it is freely available from www.fungalgenomics.cn/geneprediction.

The family Caulimoviridae comprises plant-infecting pararetroviruses that replicate by reverse transcription and encapsidate a circular double-stranded DNA genome. They can occur as episomal (encapsidated and replicative forms) and endogenous forms integrated into the host genome. Some endogenous sequences can give rise to episomal forms. In this study, we report and characterize a new badnavirus infecting Pelargonium × hortorum. We propose the name Pelargonium vein banding virus (PVBV). The episomal genome is 7,586 bp in length. Endogenous PVBV (ePVBV) DNA was identified in healthy plants and characterized. Southern blotting and PCR suggest that in many cultivars, the ePVBV consists of a tandem array of the complete PVBV genome. The ePVBV tandem array was not detected in 'Maverick White'. The major parents of P. × hortorum hybrids are P. zonale and P. inquinans. P. zonale contained ePVBV, but P. inquinans did not. The sequence of ePVBV recovered from the cultivar 'BullsEye Salmon' was >99% identical to the episomal sequence. Agroinoculation experiments demonstrated that ePVBV is infectious. Bacilliform-shaped virions with a modal particle length of 144 nm and 33 nm in diameter were recovered from leaves of agroinfected Maverick White exhibiting mosaic symptoms and chlorosis surrounding the veins. P. zonale and P. × hortorum varieties with full ePVBV genomes were not infected. Interestingly, P. inquinans, which does not contain ePVBV, was also not infected.

Plant-pathogenic bacteria cause great damage to global agriculture by infecting economically important crops and reducing yield. Among them, Xanthomonas spp. are a particularly important group of plant pathogens, as they have the ability to colonize hundreds of plant species. These pathogens exhibit a dual lifestyle, existing both epiphytically on plant surfaces and endophytically within host tissues. To establish infection, Xanthomonas must adapt to a range of abiotic and biotic stresses, including temperature, light, osmotic changes, oxidative stress, and host immune responses. The bacteria rely on sophisticated environmental sensing mechanisms, including chemotaxis mediated by methyl-accepting chemotaxis proteins, which help them detect host-derived chemical signals and navigate toward infection sites. Limited availability of nutrients, such as iron and magnesium within host tissues, acts as a cue that further modulates bacterial physiology and virulence. Xanthomonas has evolved efficient strategies to scavenge and store these nutrients, integrating these signals through tightly regulated gene networks. A central regulatory system involves diffusible signal factor (DSF)-mediated quorum sensing, which coordinates community-level behaviors such as motility, extracellular polysaccharide production, and secretion of virulence effectors. This review discusses recent advances in understanding how Xanthomonas integrates environmental and host-derived signals to regulate its pathogenicity. It emphasizes the role of DSF signaling, chemotaxis, and micronutrient acquisition in disease progression and host-pathogen interactions. Insights into these adaptive and regulatory mechanisms offer promising avenues for developing targeted strategies to control Xanthomonas-induced plant diseases and improve crop protection. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Syndrome "Basses Richesses" (SBR) is a rapidly emerging sugar beet disease in central Europe that has a severe economic impact on the sugar beet industry and thus requires control. The cultivation of tolerant varieties is a promising method to reduce SBR. Digital plant phenotyping can support the screening process for tolerant varieties by characterizing traits of interest and quantifying tolerance. This research provides foundational work for digitally phenotyping SBR. Morphological and spectral traits were analyzed with machine learning, supporting disease monitoring and screening for tolerant varieties under controlled conditions. A susceptible sugar beet variety was infected with the dominant causal agent of SBR, 'Candidatus Arsenophonus phytopathogenicus' (ARSEPH). Hyperspectral images of the canopy were recorded weekly between 20 and 62 days after inoculation and segmented by leaves and petioles. Sixty-seven days after inoculation, each leaf was two-dimensionally (2D) and each taproot three-dimensionally (3D) imaged by angle-corrected 2D imaging and structured-light 3D scans, respectively. The results indicated substantial decreases in leaf area (19.7%), leaf length (6.9%), leaf blade length (13.1%), and leaf blade width (12.1%) resulting from ARSEPH infection. The most important wavelengths for machine learning classification of ARSEPH-infected sugar beet were from the petioles (97% accuracy) in the range 623 to 659 nm and 421 to 432 nm. The 22 most relevant taproot 3D parameters were evaluated with Boruta-SHAP based on their importance to characterize SBR-induced taproot deformation. Certain value and spatial regions were characteristic, indicating thresholds for 3D parameters and taproot regions to analyze when comparing varieties. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.