Early molecular diagnosis and detection of Puccinia striiformis f. sp. tritici in China

Development and Validation of a Multiplex TaqMan Probe qPCR Assay Specific for Three Rust Fungi Infecting Meliosma myriantha

Rust fungi are the largest group of obligate plant pathogens and cause severe damage to global forests and agricultural security. Meliosma myriantha, a tree species native to East Asia (China, Japan, and Korea), is vulnerable to three rust species: Neophysopella meliosmae, N. meliosmae-myrianthae, and N. vitis. The early symptoms of infection are indistinguishable between these species, making an accurate and rapid diagnosis challenging. The urediniospores of N. meliosmae-myrianthae and N. vitis are also known to infect economically relevant grapevines (Vitis spp.) and ivies (Parthenocissus spp.), respectively, rendering early detection and identification even more important. To address this issue, we developed a multiplex quantitative polymerase chain reaction assay equipped with TaqMan probes targeting the internal transcribed spacer rDNA sequences specific to the three rust pathogens. This assay successfully detected minute quantities (5 fg for N. meliosmae-myrianthae and 50 fg for N. meliosmae and N. vitis) of DNA from the three Neophysopella species and demonstrated consistent reliability when applied to fresh and herbarium samples collected from M. myriantha, grapevines, and ivies. In conclusion, this novel assay is a rapid and robust diagnostic tool for the three rust pathogens, N. meliosmae, N. meliosmae-myrianthae, and N. vitis, and offers the potential to identify and detect their global movement and spread to grapevines, ivies, and trees.

A Novel Mitovirus PsMV2 Facilitates the Virulence of Wheat Stripe Rust Fungus

Wheat stripe rust, caused by the obligate biotrophic fungus Puccinia striiformis f. sp. tritici (Pst), seriously affects wheat production. Here, we report the complete genome sequence and biological characterization of a new mitovirus from P. striiformis strain GS-1, which was designated as "Puccinia striiformis mitovirus 2" (PsMV2). Genome sequence analysis showed that PsMV2 is 2658 nt in length with an AU-rich of 52.3% and comprises a single ORF of 2348 nt encoding an RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis indicated that PsMV2 is a new member of the genus Unuamitovirus within the family Mitoviridae. In addition, PsMV2 multiplied highly during Pst infection and it suppresses programmed cell death (PCD) triggered by Bax. Silencing of PsMV2 in Pst by barley stripe mosaic virus (BSMV)-mediated Host Induced Gene Silencing (HIGS) reduced fungal growth and decreased pathogenicity of Pst. These results indicate PsMV2 promotes host pathogenicity in Pst. Interestingly, PsMV2 was detected among a wide range of field isolates of Pst and may have coevolved with Pst in earlier times. Taken together, our results characterized a novel mitovirus PsMV2 in wheat stripe rust fungus, which promotes the virulence of its fungal host and wide distribution in Pst which may offer new strategies for disease control.

A novel ambigrammatic mycovirus, PsV5, works hand in glove with wheat stripe rust fungus to facilitate infection

Here we describe a novel narnavirus, Puccinia striiformis virus 5 (PsV5), from the devastating wheat stripe rust fungus P. striiformis f. sp. tritici (Pst). The genome of PsV5 contains two predicted open reading frames (ORFs) that largely overlap on reverse strands: an RNA-dependent RNA polymerase (RdRp) and a reverse-frame ORF (rORF) with unknown function. Protein translations of both ORFs were demonstrated by immune technology. Transgenic wheat lines overexpressing PsV5 (RdRp-rORF), RdRp ORF, or rORF were more susceptible to Pst infection, whereas PsV5-RNA interference (RNAi) lines were more resistant. Overexpression of PsV5 (RdRp-rORF), RdRp ORF, or rORF in Fusarium graminearum also boosted fungal virulence. We thus report a novel ambigrammatic mycovirus that promotes the virulence of its fungal host. The results are a significant addition to our understanding of virosphere diversity and offer insights for sustainable wheat rust disease control.

A CRISPR-based lateral flow assay for plant genotyping and pathogen diagnostics

Efficient pathogen diagnostics and genotyping methods enable effective disease management and breeding, improve crop productivity and ensure food security. However, current germplasm selection and pathogen detection techniques are laborious, time-consuming, expensive and not easy to mass-scale application in the field. Here, we optimized a field-deployable lateral flow assay, Bio-SCAN, as a highly sensitive tool to precisely identify elite germplasm and detect mutations, transgenes and phytopathogens in <1 h, starting from sample isolation to result output using lateral flow strips. As a proof of concept, we genotyped various wheat germplasms for the Lr34 and Lr67 alleles conferring broad-spectrum resistance to stripe rust, confirmed the presence of synthetically produced herbicide-resistant alleles in the rice genome and screened for the presence of transgenic elements in the genome of transgenic tobacco and rice plants with 100% specificity. We also successfully applied this new assay to the detection of phytopathogens, including viruses and bacterial pathogens in Nicotiana benthamiana, and two destructive fungal pathogens (Puccinia striiformis f. sp. tritici and Magnaporthe oryzae Triticum) in wheat. Our results illustrate the power of Bio-SCAN in crop breeding, genetic engineering and pathogen diagnostics to enhance food security. The high sensitivity, simplicity, versatility and in-field deployability make the Bio-SCAN as an attractive molecular diagnostic tool for diverse applications in agriculture.

Remote Sensing Monitoring of Winter Wheat Stripe Rust Based on mRMR-XGBoost Algorithm

For the problem of multi-dimensional feature redundancy in remote sensing detection of wheat stripe rust using reflectance spectrum and solar-induced chlorophyll fluorescence (SIF), a feature selection and disease index (DI) monitoring model combining mRMR and XGBoost algorithm was proposed in this study. Firstly, characteristic wavelengths selected by successive projections algorithm (SPA) were combined with the vegetation indices, trilateral parameters, and canopy SIF parameters to constitute the initial feature set. Then, the max-relevance and min-redundancy (mRMR) algorithm and correlation coefficient (CC) analysis were used to reduce the dimensionality of the initial feature set, respectively. Features selected by mRMR and CC were input as independent variables into the extreme gradient boosting regression (XGBoost) and gradient boosting regression tree (GBRT) to monitor the severity of stripe rust. The experimental results show that, compared with CC analysis, the monitoring accuracy of the features selected by mRMR in the XGBoost and GBRT models increased by 12% and 17% on average, respectively. Meanwhile, the mRMR-XGBoost model achieved the best monitoring accuracy (R2 = 0.8894, RMSE = 0.1135). The R2 between the measured DI and predicted DI of mRMR-XGBoost was improved by an average of 5%, 12%, and 22% compared with mRMR-GBRT, CC-XGBoost, and CC-GBRT models. These results suggested that XGBoost is more suitable for the remote sensing monitoring of wheat stripe rust, and mRMR has more advantages than the commonly used CC analysis in feature selection. Field survey data validation results also confirm that the mRMR-XGBoost algorithm has excellent monitoring applicability and scalability. The proposed model could provide a reference for data dimensionality reduction and crop disease index monitoring based on hyperspectral data.

Rapid detection of Puccinia triticina causing leaf rust of wheat by PCR and loop mediated isothermal amplification

Leaf rust of wheat caused by Puccinia triticina has significant impact on wheat production worldwide. Effective and quick detection methodologies are required to mitigate yield loss and time constraints associated with monitoring and management of leaf rust of wheat. In the present study, detection of P. triticina has been simplified by developing a rapid, reliable, efficient and visual colorimetric method i.e., loop mediated isothermal amplification of DNA (LAMP). Based on in silico analysis of P. triticina genome, PTS68, a simple sequence repeat was found highly specific to leaf rust fungus. A marker (PtRA68) was developed and its specificity was validated through PCR technique which gave a unique and sharp band of 919 bp in P. triticina pathotypes only. A novel gene amplification method LAMP which enables visual detection of pathogen by naked eye was developed for leaf rust pathogen. A set of six primers was designed from specific region of P. triticina and conditions were optimised to complete the observation process in 60 minutes at 65o C. The assay developed in the study could detect presence of P. triticina on wheat at 24 hpi (pre-symptomatic stage) which was much earlier than PCR without requiring thermal cycler. Sensitivity of LAMP assay developed in the study was 100 fg which was more sensitive than conventional PCR (50 pg) and equivalent to qPCR (100 fg). The protocol developed in the study was utilized for detection of leaf rust infected samples collected from different wheat fields. LAMP based colorimetric detection assay showed sky blue color in positive reaction and violet color in negative reaction after addition of 120 μM hydroxyl napthol blue (HNB) solution to reaction mixture. Similarly, 0.6 mg Ethidium bromide/ml was added to LAMP products, placed on transilluminator to witness full brightness in positive reaction and no such brightness could be seen in negative reaction mixture. Further, LAMP products spread in a ladder like banding pattern in gel electrophoresis. Our assay is significantly faster than the conventional methods used in the identification of P. triticina. The assay developed in the study shall be very much useful in the development of diagnostic kit for monitoring disease, creation of prediction model and efficient management of disease.

Novel PCR Assays for the Detection of Biological Agents Responsible for Wheat Rust Diseases: Puccinia triticina and Puccinia striiformis f. sp. tritici

The species Puccinia triticina (Pt) and Puccinia striiformis f. sp. tritici (Pst) are devastating cereal pathogens that cause leaf and stripe rust diseases. We developed PCR assays for the species-specific detection of Pt and Pst, 2 biological agents that cause wheat rust disease. For each pathogen, we validated 3 primer sets that target the second largest subunits of the RNA polymerase II (rpb2) and β-tubulin 1 (tub1) genes. The specificities of the primers were verified using naturally infected plant materials with visual symptoms of disease. All primer sets amplified a single DNA fragment of the expected length. The primer sets LidPr15/16, LidPr1/2, and LidPs13/14 were able to detect small amounts of pure fungal DNA with sensitivities of 0.1, 1, and 10 pg/μL, respectively. A sufficient detection limit (1 pg/μL to 5 ng/μL) was observed for all assays when the sensitivity test was performed with host plant DNA. The study also evaluated the simultaneous detection of both rust pathogens, and the multiplex PCR assay generated amplicons of 240 and 144 bp in length for Pts (LidPs9/10) and Pt (LidPr1/2), respectively.

A Review of Conventional PCR Assays for the Detection of Selected Phytopathogens of Wheat

Infection of phyllosphere (stems, leaves, husks, and grains) by pathogenic fungi reduces the wheat yield and grain quality. Detection of the main wheat pathogenic fungi provides information about species composition and allows effective and targeted plant treatment. Since conventional procedures for the detection of these organisms are unreliable and time consuming, diagnostic DNA-based methods are required. Nucleic acid amplification technologies are independent of the morphological and biochemical characteristics of fungi. Microorganisms do not need to be cultured. Therefore, a number of PCR-based methodologies have been developed for the identification of key pathogenic fungi, such as <i>Fusarium</i> spp., <i>Puccinia</i> spp., <i>Zymoseptoria tritici</i>, <i>Parastagonospora nodorum</i>,<i> Blumeria graminis </i>f. sp.<i> tritici</i>, and<i> Pyrenophora tritici-repentis</i>. This article reviews frequently used DNA regions for fungus identification and discusses already known PCR assays for detection of the aforementioned wheat pathogens. We demonstrate that PCR-based wheat pathogen identification assays require further research. In particular, the number of diagnostic tests for <i>Fusarium graminearum</i>, <i>Puccinia</i> spp., and <i>P. tritici-repentis</i> are insufficient.

Identification of a Novel Alternaria alternata Strain Able to Hyperparasitize Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust

The obligate bitrophic fungus Puccinia striiformis f. sp. tritici (Pst) causes stripe (yellow) rust on wheat worldwide. Here, we report a novel fungal strain able to hyperparasitize Pst. The strain was isolated from gray-colored rust pustules, and was identified as Alternaria alternata (Fr.: Fr.) keissler based on a combination of morphological characteristics and multi-locus (ITS, GAPDH, and RPB2) phylogeny. Upon artificial inoculation, the hyperparasite reduced the production and viability of urediniospores, and produced a typical gray-colored rust pustule symptom. Scanning electron microscopy demonstrated that the strain could efficiently penetrate and colonize Pst urediniospores. This study first demonstrates that A. alternata could parasitize Pst and indicates its potential application in the biological control of wheat stripe rust disease.

Development of SCAR Markers and an SYBR Green Assay to Detect Puccinia striiformis f. sp. tritici in Infected Wheat Leaves

Stripe rust, caused by the pathogenic fungus Puccinia striiformis f. sp. tritici, is an important disease of wheat worldwide. A rapid and reliable detection of the pathogen in latent infected wheat leaves is useful for accurate and early forecast of outbreaks and timely application of fungicides for managing the disease. Using the previously reported primer pair Bt2a/Bt2b, a 362-bp amplicon was obtained from P. striiformis f. sp. tritici and a 486-bp amplicon was obtained from both P. triticina (the leaf rust pathogen) and P. graminis f. sp. tritici (the stem rust pathogen). Based on the sequence of the 362-bp fragment, two pairs of sequence characterized amplified region (SCAR) primers were designed. PSTF117/PSTR363 produced a 274-bp amplicon and TF114/TR323 produced a 180-bp amplicon from P. striiformis f. sp. tritici, whereas they did not produce any amplicon from P. triticina, P. graminis f. sp. tritici, or any other wheat-infecting fungi. The detection limit of PSTF117/PSTR363 was 1 pg/µl and TF114/TR323 was 100 fg/µl. Both SCAR markers could be detected in wheat leaves 9 h post inoculation. An SYBR Green RT-PCR method was also developed to detect P. striiformis f. sp. tritici in infected leaves with the detection limit of 1.0 fg DNA from asymptomatic leaf samples of 6 h after inoculation. These methods should be useful for rapid diagnosis and accurate detection of P. striiformis f. sp. tritici in infected wheat leaves for timely control of the disease.

An immunofluorescence assay for the detection of wheat rust species using monoclonal antibody against urediniospores of Puccinia triticina

AIMS

Wheat (Triticum aestivum) is one of the most important crop species, but yields are often drastically reduced by rust epidemics. In this report, we describe a rapid and sensitive immunofluorescence method for the detection of urediniospores of the fungi Puccinia striiformis f. sp. tritici, Puccinia triticina and Puccinia graminis f. sp. tritici, which are causal agents of wheat rust.

METHODS AND RESULTS

The method uses monoclonal antibody LPT-2 against the urediniospores of P. triticina and PE-cy3 goat anti-mouse. Urediniospores of P. triticina or those of two species that are difficult to distinguish from P. triticina, P. striiformis f. sp. tritici or P. graminis f. sp. tritici were immobilized on a glass slide, and the sample was then treated with LPT-2. Thereafter, a second antibody, goat anti-mouse conjugated PE-cy3, was added, and the slide was observed in a fluoroscope. The fluorescent signal was strong with P. triticina urediniospores, weak with P. striiformis f. sp. tritici urediniospores and weak-to-intermediate with P. graminis f. sp. tritici urediniospores. The detection limit of this method was 2 ng ml(-1) of the monoclonal antibody LPT-2.

CONCLUSIONS

In this article, we describe the production and diagnostic application of a novel mouse monoclonal antibody specific to urediniospores of P. triticina.

SIGNIFICANCE AND IMPACT OF THE STUDY

After further technical development, this method may become a tool for on-site identification of P. triticina urediniospores and will therefore help in the selection and timing of fungicide applications for control of wheat rust outbreaks.