Fusarium oxysporum f. sp. conglutinans, F. oxysporum f. sp. rapae, F. oxysporum f. sp. raphani, and F. oxysporum f. sp. matthiolae can cause yellows disease of economically important species in the Brassicaceae family. Among these, F. oxysporum f. sp. rapae induces yellows in leaf mustard and Chinese cabbage. SGE1 (secreted-in-xylem [SIX] gene expression 1) is a transcription factor characterized by the presence of the WOPR box domain. Homologs of SGE1 in other Fusarium species play a crucial role in virulence and regulate the expression of SIX effector genes. However, the role of the SGE1 homolog in F. oxysporum f. sp. rapae (FoRP-SGE1) in pathogenesis and fungal development remains unexplored. To investigate its function in regulating pathogenicity and fungal development, gene knockout mutants of FoRP-SGE1 (ΔFoRP-SGE1) were generated and validated. ΔFoRP-SGE1 showed a reduction in conidiation but normal colony growth and conidial germination. Notably, ΔFoRP-SGE1 completely lost pathogenicity in both leaf mustard and Arabidopsis thaliana, but it retained the ability to colonize leaf mustard plants, indicating that FoRP-SGE1 is a key pathogenicity factor. Expression of SIX9 and SIX14 was significantly diminished in ΔFoRP-SGE1. Furthermore, most chlamydospores of ΔFoRP-SGE1 lacked the outermost fibrillose coat. Germination of ΔFoRP-SGE1 chlamydospores was also impaired under various stress conditions, including osmotic stress, drought, UV exposure, and fluazinam toxicity. This study presents, for the first time, the role of a Fusarium SGE1 homolog in the morphology and persistence of chlamydospores. Collectively, our findings suggest that FoRP-SGE1 is a critical pathogenicity factor in the leaf mustard-F. oxysporum f. sp. rapae and Arabidopsis-F. oxysporum f. sp. rapae pathosystems and is involved in the development of the fibrillose coat of chlamydospores and their resistance to environmental stresses.

Maize stalk rot, primarily caused by Fusarium spp., is a significant disease in many maize-growing areas worldwide, often leading to considerable yield losses under favorable conditions for infection. In this study, a genome-wide association study (GWAS) for Fusarium stalk rot resistance was carried out using 230,506 single nucleotide polymorphism (SNP) markers on phenotypic data from 178 maize inbred lines. Four SNPs were significantly associated with stalk rot resistance, with three located within previously reported QTL regions and one novel locus identified on chromosome 9 (9_149289012). Candidate genes within a 600-kb window around each SNP were retrieved from the MaizeGDB database, revealing 174 candidate genes in the B73_RefGen_v5 reference genome, including 8 R genes and 8 differentially expressed genes (DEGs). Notably, three potential candidate genes were identified around the novel SNP 9_149289012 on chromosome 9. Additionally, transcriptome analysis identified 1,597 genes related to disease resistance, associated with GO terms involved in resistance responses, nutrient metabolism, and toxin metabolism. Overall, this study provides valuable insights into the genetic basis of Fusarium stalk rot resistance in maize, highlighting both known and novel loci along with candidate genes for further functional characterization.

Plant pathology has a long history of categorizing fungal pathogens according to discrete nutritional lifestyles. While this is expedient for practical management efforts, this categorization often implies that disease is a defining property of the microbe, despite increasing ecological, genomic, and experimental evidence which challenges this implication. To describe the many plant-associated fungi that break this mold, we suggest adopting an encompassing term. Here, we hypothesize that facultative pathogenicity, where fungi colonize plants asymptomatically and induce disease only under specific conditions, is not an exception but the dominant state of many plant-pathogenic fungi. We further suggest that an overreliance on obligate biotrophs and other model organisms has biased conceptual frameworks and prevented our recognition of the ecological flexibility of many fungal plant pathogens. Drawing on phylogenetic, genomic, and ecological data, we show that many plant-associated fungi shift dynamically along a continuum from endophytism to necrotrophy. This evidence is synthesized across diverse fungal taxa demonstrating widespread asymptomatic colonization of hosts and highlights how environmental, developmental, genetic, and biochemical cues catalyze transitions to disease. Reframing our thinking about many of these fungi as facultative pathogens challenges prevailing concepts of pathogenic lifestyle classification, nonhost resistance, and experimental design in plant pathology. Recognizing disease as one possible outcome, rather than a defining trait, of plant-fungal interactions invites a conceptual shift towards studying the ecological and physiological conditions that govern these associations, with diverse implications for the study of these fungi and the management of their resulting diseases.

Wheat blast, caused by Pyricularia oryzae Triticum lineage, is a major constraint to wheat expansion in the Brazilian Cerrado. Delayed sowing is often recommended for disease avoidance; however, late sowing can increase the risk of water deficit. This study quantifies the joint risks from head blast and water deficit in the Brazilian Cerrado to inform sowing-date recommendations. Using daily weather data from a 62-year period (1961-2023), crop phenology was simulated based on an accumulated growing degree day approach. Heading and maturity dates were estimated for six sowing dates defined at 10-day intervals across the sowing window, starting on February 25. Epidemic probability was calculated using a logistic model, while water-deficit events were identified based on an accumulated effective precipitation threshold (150 mm) during crop growth. For each pixel within the potential wheat area in the Cerrado and for each sowing date, we empirically estimated the probability of at least one hazard, fitted smooth pixel-wise probability curves, and identified the optimal sowing date. A spatially smoothed 7-day bin classification was used to generate a practical sowing-recommendation map. In addition, we assessed the effects of the El Niño-Southern Oscillation on epidemic probability. Results showed that mid- to late-March sowings generally minimize joint risk. Spatial heterogeneity highlighted regions suitable for earlier sowing and potential expansion. El Niño/La Niña events amplified/suppressed epidemic probability, particularly for intermediate sowing dates where sensitivity was greatest. These findings support region-specific, multi-hazard sowing recommendations and the incorporation of climate-variability signals into decision support for tropical rainfed wheat.

Mixed viral infections are common in the field but are rarely studied due to their inherent complexity. Here, we observed a mixed infection of brassica yellows virus (BrYV) and turnip mosaic virus (TuMV) in oilseed rape (Brassica napus L.). Therefore, this study explores the relationships between two viruses based on newly constructed infectious clones of BrYV-GZA, BrYV-GZB, and a previously reported TuMV-GFP clone. Our results demonstrate that BrYV-GZA significantly inhibited TuMV in Nicotiana benthamiana (N. benthamiana). In contrast, BrYV-GZB was a mild strain, which exhibited a delayed onset time and less influence on TuMV. In oilseed rape, the incidence of TuMV was significantly lower in plants co-infected with BrYV-GZA and TuMV (AT) than in those infected with TuMV alone (p = 0.015). Besides, TuMV failed to infect oilseed rape plants pre-inoculated with BrYV-GZA. Furthermore, RNA silencing suppressors of HC-Pro and P0 were found promote the accumulation of BrYV-GZA and TuMV accumulation, respectively. Symptom analysis showed that both BrYV-GZA single infection and AT double infection significantly reduced the plant height of oilseed rape. Additionally, these infections led to a 3% and 7% decrease in oil content of rapeseed, respectively. AT double infection also altered fatty acid composition, resulting in significant decreases in both oleic acid and stearic acid, and an increase in linoleic acid. Overall, our findings reveal an asymmetric interaction between BrYV-GZA and TuMV in both N. benthamiana and oilseed rape, highlighting the effects of mixed infections on agronomic traits of oilseed rape.

Wheat stripe rust, caused by the biotrophic fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is among the top crop diseases incurring huge economic losses worldwide. Identification of new stripe rust-resistant sources that can be easily used in wheat cultivar development is essential for food security. PI 622129, an Iranian wheat landrace, exhibits high resistance to the predominant U.S. Pst races. A recombinant inbred line (RIL) population from the cross PI 622129 × Stardust was genotyped using single-nucleotide polymorphisms generated by genotyping-by-sequencing. The RIL population was evaluated for responses to the Pst race PSTv-37 at the seedling stage in three environments, and quantitative trait loci (QTLs) analysis revealed four QTLs for stripe rust resistance on chromosome arms 2DS, 5BS, 2AL, and 7BL. Of these, QYr.stars-2DS and QYr.stars-5BS are major QTLs that explained 21 to 38% and 11.6 to 27.2% of the total phenotypic variance, respectively, in three experiments. QYr.stars-2DS is a new stripe rust resistance locus that was identified in the interval of 2.58 to 5.54 Mb on chromosome arm 2DS based on the Chinese Spring IWGSC RefSeq v.2.1 reference genome. Another QTL, QYr.stars-5BS, is close to Yr47 and was delimited to the interval 8.1 to 9.0 Mb in the reference genome. QYr.stars-2AL and QYr.stars-7BL were mapped to the terminal and QTL-rich regions on chromosome arms 2AL (750.8 to 752.5 Mb) and 7BL (718.1 to 721.2 Mb), respectively. KASP markers were developed to facilitate rapid introgression of these QTLs into locally adapted lines via marker-assisted selection.

Xylella fastidiosa (Xf) is the etiological agent of Pierce's disease (PD), a major threat to viticulture worldwide. The Xf prtA- mutant, characterized by its planktonic phenotype and absence of biofilm formation, has been previously labeled as hypervirulent due to its aggressive symptomatology in the PD-susceptible Vitis vinifera 'Thompson Seedless'. This study challenges the hypervirulent concept by demonstrating that a diverse range of grapevine accessions, especially the PD line U0505, exhibited resistance to Xf prtA-. Our findings suggest that different resistance mechanisms are present against the planktonic and biofilm phenotypes of Xf, as represented by the prtA- Xf mutant and the wild-type Temecula1 Xf strain, respectively. This study underscores the complexity of host-pathogen interactions and highlights the importance of multiple host defense mechanisms in countering specific virulence strategies of Xf. The resistance assessed in the U0505 line against Xf prtA- infection provides valuable insights into potential genetic and molecular targets for breeding PD-resistant grapevine cultivars and developing effective disease management strategies.

Root-knot nematodes (Meloidogyne spp.) are obligate endoparasites among the most ‎destructive agricultural worldwide causing substantial yield losses across numerous crops. ‎Current management options are limited, and the overuse of chemical nematicides poses ‎serious risks to human health and the environmental. In this study, a bacterial isolate ‎obtained was investigated as a biocontrol agent against Meloidogyne incognita, identified as ‎Pantoea conspicua strain PC (GeneBank accession no.ON203125) based on 16S rRNA gene ‎sequencing. Exposure of second-stage juveniles (J2s) caused mortality rates of 67.9%, ‎‎94.7%, 97.7%, and 99.3% in M. incognita at 12, 24, 48, and 96 hours after exposure to a ‎‎100% concentration of bacterial filtrate, respectively. In comparison, bacterial pellets ‎resulted in 18.5%, 51.8%, 62.9%, and 82.9% mortality at the same time intervals. Both, the ‎bacterial filtrate and pellets significantly inhibited egg hatchability in vitro. Greenhouse ‎experiment demonstrated that tomato plant treated with the bacterial filtrate or pellets ‎exhibited marked improvements in root and shoot growth parameters. Specifically, the ‎bacterial filtrate caused reduced the number of galls, eggs, and eggmasses per gram of root ‎by 93.12%, 97.9%, and 79.9% respectively, along with a 92.7% decrease in J2s per 250 ‎grams of soil. Overall, P. conspicua strain PC demonstrated high potential as a biocontrol ‎agent, offering advantages in its mode of action, efficacy, and contribution to ongoing ‎nematode management, while also reducing environmental impact and supporting integrated ‎pest management strategies.

Early and accurate identification and quantification of plant-parasitic nematodes (PPNs) is crucial for their effective control. Although valuable, the current techniques for identifying PPNs, such as morphology and molecular marker-based methods, can be time- and resource-intensive. This study aimed 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 nematode (RLN; Pratylenchus spp.), root-knot nematode(RKN; Meloidogyne spp.), and stubby root nematode (SRN; Paratrichodorus and Trichodorus spp.), as well as additional PPNs (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 an image, was trained and evaluated onpreviously 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, and SRN; F1 scores > 0.92; AUC > 0.93 in the test set). Whereas the NON-PARASITIC group showed strong performance (F1 score > 0.846 and AUC > 0.91), the PPN-OTHERS group performed poorly (test accuracy: 43.9%), frequently misclassified as RLNs and NON-PARASITIC nematodes. The results highlight the potential of artificial intelligence-based tools for identifying PPNs, paving the way for the long-term goal of developing automated detection and quantification systems for plant pathogens.

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.