Phytopathology最新文献

Puccinia striiformis f. sp. tritici, causing stripe rust, is one of the most prominent pathogens of wheat worldwide. The biotrophic and obligate fungus is capable of rapidly developing new virulent races that can overcome race-specific resistance in host plants. The traditional virulence characterization of the pathogen requires strict conditions for testing isolates on wheat differentials with specific resistance genes, which is time-consuming. Developing molecular markers for avirulence genes could provide an efficient method for monitoring virulence changes in the pathogen population. In this study, secreted protein gene-based single-nucleotide polymorphism markers previously identified to be associated with avirulence genes of the pathogen were converted to kompetitive allele-specific PCR (KASP) markers. The KASP markers were screened with a diverse panel of 192 isolates selected from various countries based on their virulent races and molecular genotypes. The markers significantly correlated with the avirulence/virulence phenotypic data of the 192 isolates were further validated with 845 isolates collected from the United States in 2019 to 2021. Based on the results of both the screening and validation data, 21 KASP markers significantly associated with different avirulence genes were developed. Seventeen of the 21 markers were significantly associated with two or more avirulence genes, and except AvrYr10, and the remaining 15 avirulence genes had two or more markers. Different combinations of up to three markers could be used for specific detection of 16 avirulence genes in monitoring the pathogen population.

Highbush blueberries (Vaccinium corymbosum) are an important fruit crop worldwide, and Michigan is one of the largest producers within the United States. Botrytis blossom blight and fruit rot are major diseases in this region. Although Botrytis cinerea has long been considered the primary causal agent, a recent study identified a novel species in Michigan. In this article, we describe a new species, B. michiganensis, as an additional pathogen causing blossom blight. This study aimed to characterize B. michiganensis through multilocus phylogenetic analysis (G3PDH, HSP60, RPB2, NEP1, and NEP2), morpho-cultural traits, and fungicide sensitivity. Phylogenetic analyses, using both individual and concatenated gene sequences, placed B. michiganensis in a distinct clade closely related to B. fabiopsis, B. caroliniana, and B. galanthina. The isolates exhibited diverse cultural and morphological characteristics on potato dextrose agar, ranging from white to gray fluffy/cottony mycelia. None of the isolates produced conidia on artificial media but developed typical Botrytis-like conidiophores and conidia on inoculated plant tissues, characterized by hyaline to pale brown, elliptical to ovoid conidia and branching conidiophores. Pathogenicity tests on blueberry tissues, green grapes, and white rose petals confirmed its ability to cause Botrytis blossom blight and fruit rot, with disease severity comparable to B. cinerea. Fungicide sensitivity assays revealed that B. michiganensis isolates were sensitive to all tested fungicides except cyprodinil. These findings provide new insights into the Botrytis species complex affecting blueberries and highlight the need for further diversity studies.

The economic value of cultivars resistant to disease is of great interest, but how growers change their fungicide use in response to host resistance may be nuanced. We draw upon a well-described data set of the incidence of hop plants with powdery mildew and associated production metadata and demonstrate the utility of Bayesian networks as a framework for quantifying causal relationships for fungicide use and cost in response to host resistance. Conditional Gaussian Bayesian network models applied to cultivars differing in race-specific resistance to powdery mildew revealed cultivar resistance to powdery mildew influenced disease levels in early spring, which had a causal effect on how often and what fungicides growers later applied. Annual costs depended on not only the number of applications made but also the specific types of fungicides growers selected. Fungicide costs were little changed on cultivars that possessed race-specific resistance to only one of two extant strains of the pathogen. For cultivars with resistance to both pathogen strains, annual costs of fungicides were reduced commensurate with the level of resistance. Predicted values from the Bayesian networks and simulation indicate that growers apply a baseline level of fungicide, independent of cultivar resistance. Fungicide cost savings result from how fungicide inputs differentially scale with the incidence of powdery mildew and the type of fungicides used. Our analyses indicate that for a high-value crop, deployment of disease resistance may cause complex and unexpected changes in growers' fungicide use patterns that may not be obvious in simplified randomized controlled trials.

Wheat blast caused by the fungus Magnaporthe oryzae Triticum (MoT) pathotype is a catastrophic disease that threatens global food security. Recently, Rmg8 was discovered as a blast resistance gene in wheat genotype S615. However, although Rmg8 has recently been cloned, the precise underlying biochemical and molecular mechanisms by which this gene confers resistance against MoT remain to be fully elucidated. This study investigated the antioxidant defense mechanisms in the wheat genotype S615, which carries the blast resistance gene Rmg8 against MoT infection, compared with the blast-susceptible wheat variety BARI Gom-26 (BG26). Artificial inoculation of wheat heads with MoT followed by biochemical analyses revealed that the levels of hydrogen peroxide (H₂O₂), lipoxygenases (LOXs), and malondialdehyde (MDA) in rachis tissues increased significantly until 48 h after inoculation in both S615 and BG26. However, LOX and MDA concentrations were substantially lower in S615 than in BG26. These biochemical alterations may have contributed to less damage to photosynthetic pigments, such as chlorophyll a, chlorophyll b, total chlorophyll, and carotenoids in the rachis of S615. The S615 genotype exhibited significantly higher levels of several enzymatic (superoxide dismutase, catalase, ascorbate peroxidase, glutathione peroxidase, glutathione reductase, dehydroascorbate reductase, and monodehydroascorbate reductase) and non-enzymatic (e.g., proline) antioxidants in the MoT-inoculated rachis tissues than in those of BG26. To the best of our knowledge, this study biochemically demonstrates for the first time that the blast resistance in S615 is, in part, correlated with its strong antioxidant defense responses to MoT infection, providing a physiological basis for this resistance mechanism.

Early and accurate identification and quantification of plant-parasitic nematodes (PPN) is crucial for their effective control. Although valuable, the current techniques for identifying PPN, such as morphology and molecular marker-based methods, can be time and resource-intensive. This study aims to develop and validate cutting-edge computer vision tools for automated, accurate, and reproducible PPN detection. To achieve this goal, we captured microscopic images of the three economically-important PPN genera associated with potato crop: root lesion (RLN; Pratylenchus spp.), root-knot (RKN; Meloidogyne spp.), and stubby root (SRN; Paratrichodorus and Trichodorus spp.), additional plant-parasitic nematodes (PPN-OTHERS) and non-parasitic (NON-PARASITIC) nematodes, for a total of five groups. The captured images (total instances = 8,654) were preprocessed, annotated, and randomly split into three datasets: 75% for training, 15% for validation, and 10% for testing. An object segmentation algorithm, YOLOv11-seg, which predicts each pixel in the image, was trained and evaluated on previously unseen images. The model achieved high accuracy in validation (92.4%) and test: (88.6%) datasets with strong performance for key PPN genera (RKN, RLN, SRN; F1-scores >0.92; AUC >0.93 in the test set). While the NON-PARASITIC showed strong performance (F1-score > 0.846 and AUC >0.91), the PPN-OTHERS group performed poorly (test accuracy: 43.9%), frequently misclassified as RLN and NON-PARASITIC nematodes. The results highlight the potential of artificial intelligence-based tools in identifying PPN, paving the way for the long-term goal of developing automated detection and quantification systems for plant pathogens.

In this study, we present novel genomic data for Xanthomonas citri pv. bilvae (Xcb), the causal agent of bacterial shot-hole disease in bael trees. Using a hybrid sequencing approach that combines short- and long-read technologies, we assembled high-quality genomes of the only two available contemporary Xcb strains. Furthermore, we reconstructed the first historical genome of Xcb from a herbarium specimen collected in 1848, thereby extending the documented presence of this overlooked disease in India by nearly 100 years. We then characterized the genomic features of these strains, with a particular emphasis on virulence factors and plasmid content, using a suite of specialized bioinformatics tools. The contemporary Xcb strains were found to carry between one and four plasmids, which varied in their mobility potential (conjugative, mobilizable, or non-mobile). A total of 30 to 32 type III effector genes were identified across chromosomes and plasmids. Notably, one of the contemporary strains harbored four plasmid-borne transcription activator-like effectors (TALEs), which showed only distant similarity to TALEs found in X. citri pv. citri, a globally major pathogen with a partially overlapping host range. Comparative genomic analysis between the contemporary and historical strains revealed a remarkable conservation of effector gene content, indicating that key pathogenic traits may have been acquired early in Xcb's evolutionary history. Collectively, these new genomic resources provide valuable insights into the biology and evolution of this underexplored bacterial pathogen.

Rice blast, caused by the ascomycete fungus Magnaporthe oryzae, is one of the most problematic diseases for rice production, threatening global food security. Genetic resistance to some M. oryzae races can be achieved using major resistance genes that recognize their corresponding fungal avirulence genes. Weedy rice, a close relative of cultivated rice that competes with the crop, has evolved unique genetic mechanisms to resist M. oryzae infections; thus, weedy rice can serve as an excellent resource for blast control. In this study, we assessed disease scores of 183 F₅ and F₆ recombinant inbred lines (RILs) derived from a weedy rice × crop biparental mapping population and their parental lines, a Black Hull Awn weedy rice strain (PI 653413, RR14) and the aus-196 rice variety, using four distinct common U.S. blast races (IB33, IG1, IE1K, and IC17) under greenhouse conditions. All the parental lines were resistant to all blast races; however, RILs showed a wide degree of variation in resistance. Genotyping-by-sequencing of the RIL population and parents generated 1,498 single-nucleotide polymorphisms, which were used to construct a linkage map, and quantitative trait locus (QTL) mapping of blast resistance was performed using r/qtl. A single major blast resistance QTL on chromosome 12 was mapped to the Pi-ta/Pi39(t)/Ptr locus. Identification of Pi-ta/Pi-39(t)/Ptr as the key contributor to blast resistance in weedy rice provides insight into the evolution and adaptation of weedy rice and can aid in the development of blast-resistant rice varieties through marker-assisted selection.

Chemical modifications are prevalent on the genomic and messenger RNAs of RNA viruses. The AlkB family proteins are a class of demethylases that have the capacity to modulate the abundance and distribution of chemical modifications on nucleic acids in a dynamic manner, thereby dictating the functional competence of viral RNAs and, ultimately, affecting viral infectivity and replication. A subset of positive-sense RNA viruses harbour an AlkB domain within their polyproteins; however, whether this domain displays enzymatic activity equivalent to that of canonical AlkB enzymes, and thus participates in virus-host interactions, remains unresolved. Here, we characterized the biological role of the AlkB domain embedded in ORF1 of citrus leaf blotch virus (CLBV). Site-directed mutagenesis of catalytic core residues within the domain did not abolish infectivity in Nicotiana benthamiana, but markedly delayed cell-to-cell movement, reduced viral accumulation in emerging leaves, and attenuated plant stunting. Moreover, m⁶A peaks in total RNA were significantly more abundant, and their distribution patterns on both host mRNAs and the viral genomic RNA were altered, in plants inoculated with the AlkB-mutated infectious clone. Collectively, these data suggest that the CLBV-encoded AlkB domain likely possesses m⁶A demethylase activity that is analogous to that of cellular AlkB proteins. The results of the present study provide the first functional characterisation of a viral AlkB domain and provide a critical reference for future mechanistic interrogation of AlkB-domain function across viral systems.

Pantoea ananatis was first reported infecting rice in the United States in 2021, causing leaf blight in research plots in Arkansas. In 2024, two breeding lines exhibited leaf blight symptoms in research plots at the Rice Research and Extension Center, Stuttgart, AR. This study aimed to recover new P. ananatis isolates and characterize their pathogenicity in rice, as well as their ability to induce plant responses in rice, tobacco, and onion. Isolates were obtained from seeds of symptomatic plants using a Pantoea genus-specific agar protocol and confirmed by PCR and sequencing of 16S rRNA and gyrB genes. P. ananatis isolates were infiltrated into tobacco and rice plants and inoculated in onion to determine their ability to elicit hypersensitive or necrotic responses. Notably, isolate PP105 consistently triggered a necrotic response in rice, tobacco and onion, suggesting distinct pathogenicity mechanisms compared with the other isolates. Overall, this study enhanced the understanding of P. ananatis characterization in rice and alternative model hosts, while highlighting challenges and raising new questions for future research.

Colletotrichum fructicola is a significant phytopathogen in both pre- and postharvest stages of fruit development and storage. The development of environmentally friendly biological control agents has attracted increasing research interest. In this study, we characterized a fungal strain (Epicoccum layuense LQ) that strongly inhibits C. fructicola. A potato dextrose broth culture filtrate of strain LQ inhibited the vegetative growth of C. fructicola by approximately 80% at a 1:10 (vol/vol) dilution. Cytological observations revealed that the filtrate disrupted mitosis and cellular polarity during conidial germination. Furthermore, the culture filtrate effectively suppressed C. fructicola infection on both apple leaves and fruits. The fungal strain LQ was identified as E. layuense through integrated morphological characterization and multilocus phylogenetic analysis. Whole-genome sequencing of strain LQ identified 36 biosynthetic gene clusters (BGCs), and subsequent gene synteny analysis demonstrated structural conservation in three BGCs homologous to known antifungal clusters. Notably, substitution of NaNO₃ with yeast extract in a Czapek-Dox medium enhanced the antifungal activity of the strain LQ filtrate by 14.2-fold. Consistent with this finding, transcriptomic profiling revealed significant upregulation of BGCs associated with epipyrone A and burnettramic acid A biosynthesis under a yeast extract supplementation condition. In sum, our results demonstrate the antagonistic potential of E. layuense LQ and identify two candidate BGCs that may mediate this biocontrol activity, which lays a foundation for further mechanism dissection.