Phytopathology最新文献

Diseases that affect the vascular system or the pith are of great economic impact since they can rapidly destroy the affected plants, leading to complete loss in production. Fast and precise identification is thus important to inform containment and management, but many identification methods are slow because they are culture-dependent and they do not reach strain resolution. Here we used culture-independent long-read metagenomic sequencing of DNA extracted directly from stems of two tomato samples that displayed wilt symptoms. We obtained enough sequencing reads to assemble high quality metagenome-assembled genomes (MAGs) of Ralstonia solanacearum from one sample and of Pseudomonas corrugata from the other. The genome sequences allowed us to identify both pathogens to strain level using the genomerxiv platform, perform phylogenetic analyses, predict virulence genes, and infer antibiotic and copper resistance. In the case of R. solanacearum, it was straightforward to exclude the pathogen from being the Select Agent Race 3 biovar 2. Using the Branchwater tool, it was also possible to determine the world-wide distribution of both pathogen strains based on public metagenomic sequences. The entire analysis could have been completed within two days starting with sample acquisition. Steps necessary towards establishing metagenomic sequencing as a more routine approach in plant diseases clinics are discussed.

Meloidogyne enterolobii and M. incognita are major pests of sweetpotato. The ability of M. enterolobii to cause symptoms and reproduce on nematode-resistant cultivars threatens the sweetpotato industry. To evaluate the penetration, development, and reproduction of M. enterolobii and M. incognita on sweetpotato, a time-course study was conducted using the genotypes 'LA14-31' (resistant to M. enterolobii and intermediate-resistant to M. incognita), 'LA18-100' (susceptible to M. enterolobii and resistant to M. incognita), and 'LA19-65' (resistant to M. enterolobii and susceptible to M. incognita), with 'Beauregard' (susceptible to both species) and 'Jewel' (resistant to M. enterolobii and intermediate-resistant to M. incognita) as controls. Sweetpotato roots were collected at 7-, 9-, 11-, 13-, 21-, and 35-days post-inoculation (DPI), stained with acid fuchsin, and analyzed for nematode developmental stages. Nematode reproduction was evaluated by examining egg production at 42 DPI. Results showed that M. enterolobii developed and reproduced only in 'Beauregard' and 'LA18-100'. In resistant genotypes such as 'Jewel', 'LA14-31', and 'LA19-65', M. enterolobii remained at the pre-parasitic J2-stage, with halted development linked to localized cell death in response to M. enterolobii penetration. For M. incognita, the defense response was most notable in 'LA18-100', where infective juveniles either died, matured as males, or experienced delayed development into adult females, with a marked reduction in M. incognita reproduction. These findings suggest that resistance to M. enterolobii likely involves a hypersensitive-like response that prevents feeding site establishment, whereas resistance to M. incognita appears quantitative, as evidenced by delayed nematode development and reduced reproduction in resistant genotypes.

Transglutaminases (TGases) are enzymes highly conserved among prokaryotic and eukaryotic organisms, where their role is to catalyze protein cross-linking. One of the putative TGases of Phytophthora infestans has previously been shown to be localized to the cell wall. Based on sequence similarity we were able to identify six more genes annotated as putative TGases and show that these seven genes group together in phylogenetic analysis. These seven proteins are predicted to contain both a TGase domain and a MANSC domain, the latter of which was previously shown to play a role in protein stability. Chemical inhibition of transglutaminase activity and silencing of the entire family of the putative cell wall TGases are both lethal to P. infestans indicating the importance of these proteins in cell wall formation and stability. The intermediate phenotype obtained with lower drug concentrations and less efficient silencing displays a number of deformations to germ tubes and appressoria. Both chemically treated and silenced lines show lower virulence than the wild type in leaf infection assays. Finally, we show that appressoria of P. infestans possess the ability to build up turgor pressure and that this ability is decreased by chemical inhibition of TGases.

Brown rot is a disease that affects stone and pome fruit crops worldwide. It is caused by fungal members of the genus Monilinia, mainly M. fructicola, M. laxa and M. fructigena. This study presents evidence that, despite having a very similar battery of Cell Wall Degrading Enzymes (CWDEs), the three species behave differently during the early stages of infection, suggesting differences at the regulatory level, which could also explain the differences in host preference among the three species. We have shown that M. fructicola infection is accelerated by red light, and the first symptoms appear much earlier than in darkness or in the other two species. The overexpression of genes encoding for CAZymes such as pme3, pme2, pg1, cel1, pnl1 and pnl2, as well as the necrosis factor nep2, can be associated with the etiology of Monilinia spp. In addition, we found that nep2 in M. fructigena lacks binding sites in its promoter sequence for the White-Collar Complex (WCC), which is the major transcription factor responsible for regulating photo-reception processes in fungi. Finally, we found that AlphaFold models of the NEP1-like proteins (NLPs) present on the three Monilinia species predict proteins with a very high degree of similarity.

Pine wilt disease has caused significant damage to China's ecological and financial resources. To prevent its further spread across the country, proactive control measures are necessary. Given the low accuracy of traditional models, we have employed an enhanced LightGBM model to predict the development trend of pine wilt disease in China. By incorporating anthropogenic factors such as the volume of pine wood imports from 2017 to 2022, the density of graded roads, the number of adjacent counties, and the presence of wood processing factories, as well as natural factors like temperature, humidity, and wind speed, we employed Pearson correlation and LightGBM model's feature importance analysis to select the 17 most significant influencing factors. Spatial analysis was conducted on the epidemic sub-compartments (A divisional unit smaller than a township) of pine wilt disease for 2022 and 2023, revealing the distribution patterns of epidemic sub-compartments within 2 km of roads and the spatial relationships between new and old epidemic sub-compartments. We improved the LightGBM model using Bayesian algorithm, SSA, and HPO. By comparison, the enhanced model was validated to outperform in terms of accuracy, precision, recall, sensitivity, and specificity. Based on the results of correlation analysis and spatial analysis, an enhanced model was used to predict the emergence of pine wilt disease in new counties and districts in the future. Currently, pine wilt disease is primarily concentrated in the central-southern and northeastern provinces of China. Predictions indicate that the disease will further spread to the northeastern and southern regions of the country in the future.

Traditional assessments of grapevine susceptibility to grapevine downy mildew (GDM) caused by Plasmopara viticola rely on the visual evaluation of leaf symptoms. In this study, we used a well-established quantitative real-time PCR TaqMan assay (real-time PCR) to quantify the number of P. viticola infecting 12 grapevine cultivars under controlled conditions. The molecular disease index (MDI), derived from molecular detection methods, reflects the relative abundance of pathogens in plant tissues during the latent infection phase. Our application of MDI revealed a progressive increase in latent P. viticola levels over time, indicating dynamic levels of latent P. viticola infection across the inoculation processes. We calculated the area under the disease progression curve in terms of MDI (AUDPCMDI) to evaluate the susceptibility of each cultivar to GDM. Cultivars with lower AUDPCMDI values consistently exhibited reduced pathogen establishment, suggesting higher levels of innate resistance. Correlation analysis revealed a significant correlation between the visual disease index (DI) and the AUDPCMDI values (r = 0.790, P = 0.002), indicating that higher levels of latent P. viticola infections were associated with higher disease severity. Grapevine cultivars were clustered into distinct groupings, indicating variability in their susceptibility to the pathogen. Cultivars with similar levels of susceptibility were grouped, highlighting that the real-time PCR assay used in this study represents a robust, rapid, and standardized method for quantifying pathogens, which significantly improves the efficiency of evaluating the susceptibility of grapevine cultivars to GDM This quantitative protocol provides practical guidelines for selecting resistant cultivars and implementing effective disease management strategies.

Wheat leaf rust, caused by Puccinia triticina Erikss. (Pt), is one of the most devastating diseases in common wheat (Triticum aestivum L.) globally. Using resistant lines is the most cost-effective and safe disease control method. Eighty-three wheat lines from China and 36 differential lines, mainly near-isogenic lines (NILs) with known leaf rust resistance (Lr) genes in the Thatcher background, were inoculated with 17 Pt races at the seedling stage to postulate Lr gene(s) in the greenhouse. Field tests conducted during the 2020-2021 and 2021-2022 cropping seasons assessed adult-plant resistance to leaf rust. Moreover, we developed a graphical user interface (GUI) bioinformatics toolkit platform called WEKits v1.0, which integrates a gene postulation submodule based on the gene-for-gene hypothesis, providing accurate and efficient analysis. Through gene postulation, molecular marker detection, and pedigree analysis, we identified the presence of nine Lr genes Lr1, Lr10, Lr14a, Lr21, Lr26, Lr34, Lr37, Lr44, and Lr13/LrZH22, either individually or in combination in 30 wheat lines. Furthermore, 19 lines exhibited slow rusting resistance in both growing seasons. The development of the WEKits software significantly enhanced the efficiency and accuracy of the gene postulation process, providing a valuable tool for rapid identification of known resistance genes in the wheat lines. This could create a vital input to wheat rust resistance breeding. The results identified in this study and the WEKits platform are valuable for selecting lines with effective Lr genes and breeding rust-resistant wheat.

Xanthomonas spp. are plant pathogens known for significantly impacting crop yields. Among them, Xanthomonas albilineans (Xal) is notable for colonizing the xylem and causing sugarcane leaf scald disease. This study employed homologous recombination to mutate quorum sensing regulatory genes (rpf) to investigate their role in Xal pathogenicity. Deletions of rpfF (ΔrpfF), rpfC (ΔrpfC), and rpfG (ΔrpfG) led to reduced swarming, growth, and virulence. However, diffusible signal factor (DSF) supplementation restored swarming and growth in the ΔrpfF mutant. Deleting rpfC, rpfG, and rpfF also reduced twitching motility and affected type IV pilus expression. Transcriptomic analysis revealed that ΔrpfF positively regulates flagellar genes. DSF supplementation in ΔrpfF (ΔrpfF-DSF) modulated the expression of flagellar, chemotaxis, and type IV pilus genes. These findings elucidate the DSF-mediated swarming pathway in Xal and provide valuable insights into its regulatory mechanisms.

Plant diseases impact the production of all kinds of crops, resulting in significant economic losses worldwide. Timely and accurate detection of plant pathogens is crucial for surveillance and management of plant diseases. In recent years, loop-mediated isothermal amplification (LAMP) has become a popular method for pathogen detection and disease diagnosis due to the advantages of its simple instrument requirement and constant reaction temperature. In this review, we provide an overview of current research on LAMP, including the reaction system, design of primers, selection of target regions, visualization of amplicons, and application of LAMP on the detection of all major groups of plant pathogens. We also discuss plant pathogens for which LAMP is yet to be developed, potential improvements of plant disease diagnosis, and disadvantages that need to be considered.

The effectiveness of fungicides to control foliar fungal crop diseases is being diminished by the increasing spread of resistance to fungicides. One approach that may help to maintain efficacy is remediation of resistant populations by sensitive ones. However, the success of such approaches can be compromised by re-incursion of resistance through aerial spore dispersal, although knowledge of localized gene flow is lacking. Here, we report on a replicated mark-release-recapture field experiment with several treatments set up to study spore-dispersal-mediated gene flow of a mutated allele that confers demethylase inhibitor resistance in Pyrenophora teres f. teres (Ptt). Artificial inoculation of the host, barley (Hordeum vulgare), was successful across the 12-ha trial, where the introduced sensitive and resistant populations were, respectively, 6- and 13-fold the DNA concentration of the native Ptt population. Subsequent disease pressure remained low, which hampered spread of the epidemic to such an extent that gene flow was not detected at, or beyond, 2.5 m from source points. In the absence of gene flow, plots were assessed for treatment effects; fungicide applied to populations that contained 14.3% of allele mutation increased in frequency to 24.5%, whereas sensitive populations had no change in structure. Untreated controls of the native Ptt population remained genetically stable, yet untreated controls that were inoculated with sensitive Ptt had half the resistance frequency of the native population structure. The trial demonstrates the potential for management to remediate fungicide-resistant pathogen populations, where localized gene flow is minimal, to safeguard chemical crop protection into the future.