Phytopathology最新文献

Infection by aphid-transmitted poleroviruses modulates gene expression associated with plant development and defense. This study assessed the gene expression patterns following cotton leafroll dwarf virus (CLRDV) infection in primary and alternate hosts. Two comparisons (CLRDV-infected vs. non-infested and mock-inoculated vs. non-infested) were evaluated to identify differentially expressed genes (DEGs), and to tease out differences in gene expression profiles between aphid feeding and aphid-mediated CLRDV infection in each host. CLRDV infection was characterized by 2079, 1238, 1484, and 1773 DEGs in the primary host cotton, and in alternate hosts hibiscus, okra, and prickly sida, respectively. The number of DEGs upon aphid feeding was less than CLRDV infection in all hosts except okra. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms identified DEGs associated with development, defense, and vector fitness influencing compounds (VFICs) in CLRDV-infected plants. Genes associated with phytohormones, photosynthesis, salicylic acid, jasmonic acid, pathogenesis related proteins, heat shock proteins, transcription factors, membrane transporters, terpenoids, carbohydrates, and amino acids were differentially expressed in CLRDV-infected plants and varied between hosts. Few overlapping and numerous unique genes in the above-stated categories were differentially expressed upon aphid feeding and varied between hosts. DEGs associated with signaling pathways, transcription factors, systemic resistance, pathogenesis related proteins, and carbohydrate and amino acid biosynthesis were common between aphid-mediated CLRDV infection and aphid feeding alone. The observed gene expression patterns reiterate that differences in host susceptibility to the virus and/or the vector could differentially influence host defense and development, and vector fitness.

Sweet cherry (Prunus avium L.) is a commercially vital fruit crop in China. The hop stunt viroid (HSVd) infection in sweet cherry causes dappled fruit. This study investigated the mechanism of dappled fruit formation in HSVd-infected sweet cherry using integrated metabolomics and transcriptomics. Dappled and non-dappled peel tissues were sampled at the color change and ripening stages. UPLC-MS/MS identified 181 flavonoid metabolites, with peonidin-3-O-rutinoside, cyanidin-3-O-glucoside, peonidin-3-O-glucoside, cyanidin-3-O-arabinoside, cyanidin 3-xyloside and cinchonain Ic being significantly enriched in dappled areas. RNA-seq revealed 3,287 differentially expressed genes, with PaCHS, PaCHI, PaDFR, and PaANS up-regulated in dappled areas at the early stage, correlating with anthocyanin accumulation. KEGG enrichment highlighted anthocyanin and flavonoid biosynthesis pathways as central to pigmentation. This study suggests that HSVd disrupts anthocyanin biosynthesis to induce dappled pigmentation, offering novel insights into viroid-host interactions affecting fruit color in sweet cherry.

The spread of Phytophthora ramorum, the causal agent of Sudden Oak Death and Sudden Larch Death, has resulted in a destructive loss of trees, woody shrubs, and ornamentals in nurseries and forests in the US, Canada, and Europe since the late 1990s. Twelve lineages of P. ramorum are described that vary in global distribution and virulence. Herein, we present a maximum likelihood phylogeny for P. ramorum inferred using IQ-TREE and Tree-Based Alignment Selector Toolkit (T-BAS). The phylogeny was generated based on six loci (avh120, avh121, btub, gweuk.30.30.1, hsp90, and trp1). This phylogeny of P. ramorum improves on previous phylogenies since it is dynamic and interactive and incorporates a diverse set of all known global lineages from the US, Europe (NA1, NA2, EU1, and EU2), and ancestral lineages from the putative native range in East Asia. The phylogenetic relationships inferred in the T-BAS tree support lineages NP1 and NP2 of P. ramorum as ancestral to NA1 and NA2 lineages found in North America. In addition, East Asian IC1, IC2, IC3, and IC4 lineages are ancestral to EU1 and EU2 lineages found in Europe. We used sequence data generated from isolates of P. ramorum collected from Ireland and Northern Ireland and placed them accurately in the tree. The P. ramorum phylogeny is available through T-BAS within the DeCIFR platform. This "interactive phylogeny" can be used by the research community to rapidly update and better reflect the evolutionary relationships of new lineages of P. ramorum.

Sclerotinia sclerotiorum causes Sclerotinia stem rot, or white mold, on multiple economically important crops in Michigan. Soybean farmers and crop consultants in the Midwestern U.S. currently use S. sclerotiorum apothecia prediction models to inform fungicide application timing to optimize disease control and economic return. However, current models have not been validated for use in dry bean or potato and do not account for the effects of irrigation on apothecia development. To improve S. sclerotiorum apothecia prediction, on-site weather data were collected and used to generate new binomial logistic regression (LR) and supervised machine learning (ML) models for irrigated soybean, dry bean and potato fields. The ML algorithms investigated included decision trees, random forests and support vectors machines. Decision tree classification models outperformed LR and other ML models, achieving 77% accuracy on testing data. Accuracy increased to 89% when on-site weather data were included, indicating that on-site weather monitoring may be required to reliably predict apothecia presence in irrigated environments. Feature importance analysis identified row shading (the distance the plant canopy extends into the row) as critical for prediction accuracy. The minimum row shading required to trigger apothecia development varied slightly between crop types and row spacings, from 0.15 to 0.21m. Apothecia density peaked when soil temperatures were 21.51°C and volumetric water content were 11.43% and 19.58%. Additionally, a rapid increase in apothecia presence was observed after canopy closure reached 87%. Future model testing and validation will be required prior to deployment as a decision aid for farmers and crop consultants.

Citrus canker, caused by Xanthomonas citri pv. citri, is one of the most devastating bacterial diseases of citrus species. The global population of Xanthomonas citri pv. citri includes three lineages designated as pathotypes A, A* and A^w. While pathotype A is the most prevalent lineage around the world, the citrus canker pathogen in Iran includes only pathotype A* strains. Previous work on the Xanthomonas citri pv. citri strains collected before 2013 showed that two lineages of the pathogen presented in Iran, i.e., 4.1 and 4.4, with 4.4 not present anywhere else at that time. In this study, using a new set of strains collected in 2021-2022, we re-assessed the population structure of the pathogen in Iran using a phylogeographic approach. All strains isolated in Iran still belonged to pathotype A*. Multilocus variable number tandem repeat analysis (MLVA) revealed that 62 Iranian strains collected between 1991-2022 were distributed among 22 haplotypes. Four new haplotypes were identified within the strains isolated in this study which have not previously been reported elsewhere in the world. Although all pre-2013 strains isolated in Sistan-Baluchestan Province of Iran were grouped in subcluster 4.4, all post-2020 strains isolated in the same area were identified as members of subcluster 4.1. None of the post-2020 strains isolated in Iran belonged to subcluster 4.4, which suggests a shift in population structure of the pathogen over the past two decades. Our data would pave the way of research on the population structure of citrus canker pathogen in the area.

Tea disease caused by Lasiodiplodia theobromae is an emerging fungal disease that significantly reduces the yield and quality of tea in tea-producing regions owing to the lack of effective control methods. In this study, we evaluated the antifungal activity of azithromycin, a macrolide antibiotic, against L. theobromae. In vitro assays demonstrated strong inhibitory activity, with a half-maximal effective concentration (EC₅₀) of 140.61 μg/ml, and in vivo application resulted in a 54.30% lesion inhibition rate at 800 μg/ml against tea leaf spot. Morphological and ultrastructural analyses using optical and transmission electron microscopy revealed that azithromycin induced pronounced hyphal abnormalities, including cytoplasmic disorganization and membrane disruption. Integrated transcriptomic, proteomic, and metabolomic analyses indicated that azithromycin treatment led to systemic disruptions in L. theobromae, including dysregulation of genes involved in carbohydrate metabolism, protein degradation, glycoprotein and cell wall biosynthesis, ergosterol biosynthesis, mitochondrial function, and stress response pathways. Molecular docking and bioinformatic analyses identified glycoside hydrolase family 35 (GH35), a key protein in carbohydrate metabolism, as the principal target of azithromycin, exhibiting the most favorable binding energy of -7.9 kcal/mol. These findings demonstrate that azithromycin disrupts multiple metabolic and cellular processes in L. theobromae, primarily by targeting GH35, providing a robust multitarget approach for fungal inhibition and sustainable disease control strategies for tea cultivation.

Thanatephorus cucumeris anastomosis subgroup 3-TB (AG-3-TB) is the primary pathogen causing tobacco target spot disease, which has resulted in substantial economic losses in tobacco production worldwide. Traditionally, soilborne sclerotia have been considered to be the main primary infection source, whereas the role of airborne basidiospores has long been underestimated; particularly, they serve as the inoculum of primary and secondary infection developing on the hymenia of infected alternate host plants. This study investigated the influence of different host plants on T. cucumeris AG-3 sporulation. The results showed that in the natural environment, T. cucumeris AG-3-TB could develop hymenia on Solanaceae (tobacco, tomato, eggplant, pepper, and potato), Gramineae (rice), Cruciferae (cabbage), weeds (shamrock, dandelion, and Tartary buckwheat), and the soil surface surrounding tomato stems, and the fungal hymenium formation capacity differed among plant host species. Furthermore, this sporulation phenomenon was widely prevalent across the AG-3-TB subgroup, and urea as a nitrogen fertilizer and 18% albendazole-moroxydine hydrochloride wettable powder as a virucide significantly promoted AG-3-TB strain sporulation on tomato hosts. Our findings indicate that host plant species, strain differences, urea, and fungistatic stress significantly influence the fungal sporulation, revealing the pivotal role of spore production in the disease development.

Macrophomina phaseolina (MP), a fungal phytopathogen, causes charcoal rot disease in soybean. This pathogen's ability to form microsclerotia makes it difficult to control and thus poses a major threat to soybean production. The present study focused on effective charcoal rot disease management using Bacillus subtilis M-4, which exhibits strong biocontrol potential against MP. This study evaluated the antifungal efficacy of B. subtilis M-4 cell-free filtrate (BS-CFF) and bacterial pellet (BS-BP) against MP under in vitro conditions. The results showed that BS-CFF exhibited significantly greater inhibition of MP growth, with higher concentrations yielding stronger mycelial suppression and reduced host plant infection. Moreover, an RT-qPCR assay was performed to evaluate the gene expression in MP after BS-CFF and BS-BP treatment. The results indicated that treatment of BS-CFF downregulated essential fungal mitochondrial genes (nad5, atp6, cob, rps3, and rnl) that are involved in the growth and pathogenicity of MP. Proteomic analysis further revealed substantial downregulation of fungal proteins associated with genetic information processing (26.34%), energy/carbohydrate metabolism (19.16%), signaling pathways (14.11%), and defense/stress responses (12%) after BS-CFF treatment, compared with BS-BP. Additionally, a phenotype microarray assay confirmed that BS-CFF suppresses the utilization of 18 crucial substrates by 100%. These substrates belong to amino acid and nitrogen categories that are essential for fungal metabolism. These findings elucidate the molecular, proteomic, and metabolic mechanisms underlying BS-CFF's biocontrol efficacy, providing valuable insights for effective fungal disease management in agriculture.

Measuring individual components of pathogen reproduction is key to understanding the mechanisms underlying rate-reducing quantitative resistance (QR). Simulation models predict that lesion expansion plays a key role in seasonal epidemics of foliar diseases, but measuring lesion growth with sufficient precision and scale to test these predictions under field conditions has remained impractical. We used deep learning-based image analysis to track 6,889 individual lesions caused by Zymoseptoria tritici on 14 wheat cultivars across two field seasons, enabling 27,218 precise and objective measurements of lesion growth in the field. Lesion appearance traits reflecting specific interactions between particular host and pathogen genotypes were consistently associated with lesion growth, whereas overall effects of host genotype and environment were modest. Both host cultivar and cultivar-by-environment interaction effects on lesion growth were highly significant and moderately heritable (h² ≥ 0.40). After excluding a single outlier cultivar, a strong and statistically significant association between lesion growth and overall QR was found. Lesion expansion appears to be an important component of QR to Septoria tritici blotch in most-but not all-wheat cultivars, underscoring its potential as a selection target. By facilitating the dissection of individual resistance components, our approach can support more targeted, knowledge-based breeding for durable QR. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Viruses of cultivated apple (Malus × domestica) are believed to be transmitted nearly exclusively via vegetative propagation, with few known biotic vectors and limited evidence of vertical transmission. To evaluate the seed transmission capabilities of six viruses and one viroid of apple, a large-scale seedling grow-out experiment was conducted using seeds harvested from 51 trees infected by several combinations of six viruses and one viroid. Virus detection via multiplex PCR-based amplicon sequencing followed by RT-qPCR validation demonstrated that citrus concave gum-associated virus and apple stem grooving virus were transmitted to seedlings at rates of 4.0% (32/792) and 0.3% (3/908), respectively. No evidence of seed transmission was obtained for apple chlorotic leaf spot virus, apple green crinkle-associated virus, apple hammerhead viroid, apple rubbery wood virus 2, or apple stem pitting virus. These findings document a previously unknown mode of transmission for two widely distributed apple viruses with direct implications for breeding programs, the selection of virus-free trees, and the exchange of germplasm.