A Rapid PCR-Based Method for the Detection of Magnaporthe oryzae from Infected Perennial Ryegrass

Rapid and Visual Detection of Pyricularia oryzae Using Coupled Recombinase Polymerase Amplification-Lateral Flow Dipstick Assay

Rice blast, caused by Pyricularia oryzae, is one of the most destructive fungal diseases in rice, severely impacting rice production worldwide every year. Rapid, accurate, and visual detection of P. oryzae is essential for more effective prevention and control. In this study, we developed a recombinase polymerase amplification-lateral flow dipstick (RPA-LFD) assay to detect P. oryzae. Species-specific RPA primer pairs and probe were designed based on the target gene MGG_15975. The optimized reaction temperature and time were set at 37°C and 25 min, respectively. Specificity analysis showed that the assay could specifically detect P. oryzae isolates from rice, whereas other fungal species or Pyricularia species from grasses were not detected. Additionally, this assay demonstrated high sensitivity, capable of detecting as low as 10-2 ng/μl of P. oryzae genomic DNA, which was found to be 100 times more sensitive than conventional PCR. Furthermore, using this assay, P. oryzae was effectively detected in diseased leaves in rice fields and could also be identified at an early stage of infection before obvious lesions appeared in artificially inoculated rice seedlings. Therefore, the RPA-LFD assay developed in our study for the detection of P. oryzae is rapid, highly sensitive, and efficient, which has the potential application for early diagnosis of P. oryzae infection in rice fields.

The Geographic Distribution and Natural Variation of the Rice Blast Fungus Avirulence Gene AVR-Pita1 in Southern China

The avirulence (AVR) genes of the filamentous ascomycete fungus Magnaporthe oryzae (M. oryzae) are known to mutate rapidly under a higher selection pressure, allowing the pathogen to evade recognition by rice resistance (R) genes. Understanding the geographic distribution and natural variation of AVR genes is critical for the rational utilization and prolonging of the effectiveness of R genes. In this study, a total of 1060 M. oryzae strains collected from 19 rice blast nurseries in 13 provinces across southern China were subjected to presence/absence variation (PAV), genetic variation, and virulence analyses of the AVR-Pita1 gene. PCR amplification results indicated that AVR-Pita1 was present in only 57.45% of the blast strains, with significant geographic variation in distribution frequency. Specifically, the highest frequency (100%) was observed in strains from Chengmai, Hainan, while the lowest (1.79%) was observed in strains from Baoshan, Yunnan. A sequencing analysis identified 29 haplotypes of AVR-Pita1, characterized by insertions, deletions, and base substitutions. A phylogenetic analysis indicated that haplotypes of AVR-Pita1 identified in this study were clustered into one clade. A further amino acid sequence analysis of these haplotypes led to the identification of 25 protein variants. Notably, four haplotypes of AVR-Pita1 exhibited pathogenicity toward its corresponding rice R gene, PtrA. Additionally, we performed allele profiling of Ptr in a collection of elite parental lines that are widely used in rice breeding in southern China and found that the functional Ptr alleles (PtrA, PtrB, and PtrC) accounted for over 70%.

Comparison of plant microbiota in diseased and healthy rice reveals methylobacteria as health signatures with biocontrol capabilities

Introduction

Rice (Oryza sativa) is a staple food worldwide, but its production is under constant pressure from both abiotic and biotic stresses, resulting in high use of agrochemicals. The plant microbiome harbours microorganisms that can benefit plant health and provide alternatives to the use of agrochemicals. The composition of plant microbiomes depends on many factors (soil composition, age, and health) and is considered a primary driver of future plant health. To identify plant microbiomes that protect against disease, we hypothesised that asymptomatic rice plants in fields under high pathogen pressure (i.e., healthy islands of plants among predominantly diseased plants) might harbour a microbiota that protects them from disease.

Material and Methods

We sampled healthy and leaf-diseased plants in rice fields with high disease incidence in Cambodia and profiled their microbiota at leaf, root, and rhizosphere levels using 16S V3V4 and 18S V4 amplicon barcoding sequencing.

Results

Comparison of amplicon sequence variants (ASV) of the microbiota of healthy and diseased samples revealed both disease and healthy signatures (significant enrichment or depletion at ASV/species/genus level) in both fields. The genera Methylobacterium and Methylorubrum were identified health taxa signatures with several species significantly enriched in healthy leaf samples (Methylobacterium indicum, Methylobacterium komagatae, Methylobacterium aerolatum, and Methylorubrum rhodinum). A cultivation approach on rice samples led to the isolation of bacterial strains of these two genera, which were further tested as bioinoculants on rice leaves under controlled conditions, showing for some of them a significant reduction (up to 77%) in symptoms induced by Xanthomonas oryzae pv. oryzae infection.

Discussion

We validated the hypothesis that healthy plants in fields under high disease occurrence can host specific microbiota with biocontrol capacities. This strategy could help identify new microbes with biocontrol potential for sustainable rice production.

A Rapid and Simple Method for DNA Preparation of Magnaporthe oryzae from Single Rice Blast Lesions for PCR-Based Molecular Analysis

Rice blast is one of the most destructive diseases of rice worldwide, and the causative agent is the filamentous ascomycete Magnaporthe oryzae. With the successful cloning of more and more avirulence genes from M. oryzae, the direct extraction of M. oryzae genomic DNA from infected rice tissue would be useful alternative for rapid monitoring of changes of avirulence genes without isolation and cultivation of the pathogen. In this study, a fast, low-cost and reliable method for DNA preparation of M. oryzae from a small piece of infected single rice leaf or neck lesion was established. This single step method only required 10 min for DNA preparation and conventional chemical reagents commonly found in the laboratory. The AvrPik and AvrPi9 genes were successfully amplified with the prepared DNA. The expected DNA fragments from 570 bp to 1,139 bp could be amplified even three months after DNA preparation. This method was also suitable for DNA preparation from M. oryzae strains stored on the filter paper. All together these results indicate that the DNA preparation method established in this study is reliable, and could meet the basic needs for polymerase chain reaction-based analysis of M. oryzae.

First Report of Gray Leaf Spot Caused by Pyricularia oryzae on Common Millet in Italy

Common millet (Panicum miliaceum L.) is a niche crop cultivated in Italy for its high nutritional and gluten-free characteristics. These aspects combined with its sustainability and adaptability to paddy soils make it relevant in crop rotation with rice in some organic farms in Northwestern Italy. In September 2021, in a farm producing organic rice located in Rovasenda (VC), Italy (GPS: 45°54'82"N, 8°.31'96"E), plants of millet (var. San Marino), sown on July 1st and almost at physiological maturity, were observed with gray leaf spot symptoms with an incidence of 50% in a 12.5 ha field cultivated in a yearly rotation with rice. Oval shape lesions (between 1 and 5 cm long and 0.5 to1 cm wide) with a light gray colored centers and dark reddish-brown edges were observed on the length of the leaf blade. Gray colonies producing conidia morphologically like Pyricularia developed from 140 symptomatic leaf fragments with a 2% frequency. Monosporic cultures were obtained from five colonies and were grown on Potato Dextrose Agar for morphological and molecular identification. The colonies showed gray, fluffy mycelium, with a smooth margin, with a radius of 28 to 30 mm after 10 days at 28°C. The isolates produced hyaline, pyriform, and 2-septate conidia 17.9 to 33.5 µm (average 25.7 µm) long and 8.3 to 11.7 µm (average 10. µm) wide (n=50) on PDA. Conidiophores were solitary, erect, straight, or curved, septate, and measured 80.2 to 221.3 µm (average 150.7 µm) long and 3.6 to 5.8 µm (average 4.7 µm) wide (n=50). The molecular identification of one single-conidia isolate was confirmed by PCR and sequence comparison of the region of the transposon Pot2 (Harmon et al., 2003). BLASTn searches of GenBank using transposon Pot2 (ON843711) representative isolate 21-03-C, revealed 99.79% identity to P. oryzae (Syn. Magnaporthe oryzae) isolate MD1 (MK608664). Pathogenicity tests were carried out by suspending conidia from a 14-days old culture on PDA in sterile water at a concentration of 1×105 CFU/ml. Twenty seeds of P. miliaceum were sown in pots filled with a steamed mix of white peat and perlite, 80:20 v/v, and maintained at 28°C under a 12 hours day/night light cycle. Diseased leaves of 10 plants were inoculated by aspersion of 10 ml of the conidial suspension of isolate 21-03-C 2 weeks after the sowing (Harmon et al.; 2003). Plants were incubated in a near moisture-saturated environment in plastic bags at 28°C for 72h, after which symptoms were visually assessed. Ten control plants, inoculated with 10 ml of sterile distilled water remained healthy. P. oryzae was reisolated from leaves showing oblong, whitish lesions, surrounded by light brown margins and identified by resequencing of transposon Pot2. P. oryzae has been already reported on millet in South Korea as causal agent of blast (Klaubauf et al.; 2014). To our knowledge, this is the first report of P. oryzae as a pathogen of millet in Italy and in Europe. Further studies should be conducted to characterize these millet isolates by assessing their virulence on Oryza sativa and the implications in the adoption of P. miliaceum in rotation with rice, to prevent possible carry over of the pathogen on the main crop.

Rapid Detection of the Recently Identified Turfgrass Pathogen Magnaporthiopsis meyeri-festucae Using Recombinase Polymerase Amplification

Magnaporthiopsis meyeri-festucae is a recently identified root-infecting pathogen of fine fescue (Festuca spp.) turfgrasses. Although it is phylogenetically similar to other root-infecting turfgrass pathogens such as M. poae, management of M. meyeri-festucae is distinct and highlights the need for fast and accurate identification. The objective of this study was to develop a rapid detection method for M. meyeri-festucae using recombinase polymerase amplification (RPA) to assist turfgrass managers in identifying the disease in the field and facilitate further epidemiological research on the pathogen. Three isolates of M. meyeri-festucae and eight isolates from four related Magnaporthiopsis species were used to test the specificity of the RPA assay targeting M. meyeri-festucae. Rapid visualization of the RPA assay results using a mixture of purified amplicon and SYBR-Safe fluorescence emitting asymmetrical cyanine dye showed that the assay was effective at detecting M. meyeri-festucae on turfgrass roots with no observed incidence of false positives or false negatives. The assay also differentiated between M. meyeri-festucae and other Magnaporthiopsis species, although overall sensitivity was lower compared with a PCR-based method. The RPA assay successfully detected M. meyeri-festucae following inoculation onto and grinding of turfgrass roots, indicating possible use as a rapid field diagnostic tool for turfgrass managers. The fast and accurate RPA M. meyeri-festucae detection method presented here will be used for additional field and laboratory applications that will help improve the management of this emerging pathogen.

Foliar Diseases and the Associated Fungi in Rice Cultivated in Kenya

We conducted a survey to assess the occurrence and severity of rice blast and brown spot diseases on popular cultivars grown in the Busia, Kirinyaga, and Kisumu counties of Kenya in 2019. Working with agricultural extension workers within rice production areas, we interviewed farmers (n = 89) regarding their preferred cultivars and their awareness of blast disease, as this was the major focus of our research. We scored the symptoms of blast and brown spot and assessed the lodging, plant height, and maturity of the crops (days after planting). Furthermore, we collected leaf and neck tissues for the assessment of the prevailing fungal populations. We used specific DNA primers to screen for the prevalence of the causal pathogens of blast, Magnaporthe oryzae, and brown spot, Cochliobolus miyabeanus, on asymptomatic and symptomatic leaf samples. We also conducted fungal isolations and PCR-sequencing to identify the fungal species in these tissues. Busia and Kisumu had a higher diversity of cultivars compared to Kirinyaga. The aromatic Pishori (NIBAM 11) was preferred and widely grown for commercial purposes in Kirinyaga, where 86% of Kenyan rice is produced. NIBAM108 (IR2793-80-1) and BW196 (NIBAM 109) were moderately resistant to blast, while NIBAM110 (ITA310) and Vietnam were susceptible. All the cultivars were susceptible to brown spot except for KEH10005 (Arize Tej Gold), a commercial hybrid cultivar. We also identified diverse pathogenic and non-pathogenic fungi, with a high incidence of Nigrospora oryzae, in the rice fields of Kirinyaga. There was a marginal correlation between disease severity/incidence and the occurrence of causal pathogens. This study provides evidence of the need to strengthen pathogen surveillance through retraining agricultural extension agents and to breed for blast and brown spot resistance in popular rice cultivars in Kenya.

Loop-Mediated Isothermal Amplification for Detection of Plant Pathogens in Wheat (Triticum aestivum)

Wheat plants can be infected by a variety of pathogen species, with some of them causing similar symptoms. For example, Zymoseptoria tritici and Parastagonospora nodorum often occur together and form the Septoria leaf blotch complex. Accurate detection of wheat pathogens is essential in applying the most appropriate disease management strategy. Loop-mediated isothermal amplification (LAMP) is a recent molecular technique that was rapidly adopted for detection of plant pathogens and can be implemented easily for detection in field conditions. The specificity, sensitivity, and facility to conduct the reaction at a constant temperature are the main advantages of LAMP over immunological and alternative nucleic acid-based methods. In plant pathogen detection studies, LAMP was able to differentiate related fungal species and non-target strains of virulent species with lower detection limits than those obtained with PCR. In this review, we explain the amplification process and elements of the LAMP reaction, and the variety of techniques for visualization of the amplified products, along with their advantages and disadvantages compared with alternative isothermal approaches. Then, a compilation of analyses that show the application of LAMP for detection of fungal pathogens and viruses in wheat is presented. We also describe the modifications included in real-time and multiplex LAMP that reduce common errors from post-amplification detection in traditional LAMP assays and allow discrimination of targets in multi-sample analyses. Finally, we discuss the utility of LAMP for detection of pathogens in wheat, its limitations, and current challenges of this technique. We provide prospects for application of real-time LAMP and multiplex LAMP in the field, using portable devices that measure fluorescence and turbidity, or facilitate colorimetric detection. New technologies for detection of plant pathogen are discussed that can be integrated with LAMP to obtain elevated analytical sensitivity of detection.

Turfgrass Disease Diagnosis: Past, Present, and Future

Turfgrass is a multibillion-dollar industry severely affected by plant pathogens including fungi, bacteria, viruses, and nematodes. Many of the diseases in turfgrass have similar signs and symptoms, making it difficult to diagnose the specific problem pathogen. Incorrect diagnosis leads to the delay of treatment and excessive use of chemicals. To effectively control these diseases, it is important to have rapid and accurate detection systems in the early stages of infection that harbor relatively low pathogen populations. There are many methods for diagnosing pathogens on turfgrass. Traditional methods include symptoms, morphology, and microscopy identification. These have been followed by nucleic acid detection and onsite detection techniques. Many of these methods allow for rapid diagnosis, some even within the field without much expertise. There are several methods that have great potential, such as high-throughput sequencing and remote sensing. Utilization of these techniques for disease diagnosis allows for faster and accurate disease diagnosis and a reduction in damage and cost of control. Understanding of each of these techniques can allow researchers to select which method is best suited for their pathogen of interest. The objective of this article is to provide an overview of the turfgrass diagnostics efforts used and highlight prospects for disease detection.

Cautionary Notes on Use of the MoT3 Diagnostic Assay for Magnaporthe oryzae Wheat and Rice Blast Isolates

The blast fungus Magnaporthe oryzae is comprised of lineages that exhibit varying degrees of specificity on about 50 grass hosts, including rice, wheat, and barley. Reliable diagnostic tools are essential given that the pathogen has a propensity to jump to new hosts and spread to new geographic regions. Of particular concern is wheat blast, which has suddenly appeared in Bangladesh in 2016 before spreading to neighboring India. In these Asian countries, wheat blast strains are now co-occurring with the destructive rice blast pathogen raising the possibility of genetic exchange between these destructive pathogens. We assessed the recently described MoT3 diagnostic assay and found that it did not distinguish between wheat and rice blast isolates from Bangladesh. The assay is based on primers matching the WB12 sequence corresponding to a fragment of the M. oryzae MGG_02337 gene annotated as a short chain dehydrogenase. These primers could not reliably distinguish between wheat and rice blast isolates from Bangladesh based on DNA amplification experiments performed in separate laboratories in Bangladesh and in the United Kingdom. Specifically, all eight rice blast isolates tested in this study produced the WB12 amplicon. In addition, comparative genomics of the WB12 nucleotide sequence revealed a complex underlying genetic structure with related sequences across M. oryzae strains and in both rice and wheat blast isolates. We, therefore, caution against the indiscriminate use of this assay to identify wheat blast and encourage further development of the assay to ensure its value in diagnosis.

Specific Detection of the Wheat Blast Pathogen (Magnaporthe oryzae Triticum) by Loop-Mediated Isothermal Amplification

Wheat blast, caused by the Magnaporthe oryzae Triticum pathotype, is an economically important fungal disease of wheat. Wheat blast symptoms are similar to Fusarium head scab and can cause confusion in the field. Currently, no in-field diagnostic exists for M. oryzae Triticum. Loop-mediated isothermal amplification (LAMP) primers were designed to target the PoT2 and MoT3 loci, previously shown to be specific for M. oryzae and M. oryzae Triticum, respectively. Specificity was determined using 158 M. oryzae strains collected from infected wheat and other grasses and representing geographic and temporal variation. Negative controls included 50 Fusarium spp. isolates. Sensitivity was assessed using 10-fold serial dilutions of M. oryzae Triticum gDNA. PoT2- and MoT3-based assays showed high specificity for M. oryzae and M. oryzae Triticum, respectively, and sensitivity to approximately 5 pg of DNA per reaction. PoT2 and MoT3 assays were tested on M. oryzae Triticum-infected wheat seed and spikes and identified M. oryzae and M. oryzae Triticum, respectively, using a field DNA extraction kit and the portable Genie II system. The mitochondrial NADH-dehydrogenase (nad5) gene, an internal control for plant DNA, was multiplexed with PoT2 and MoT3 and showed results comparable with individual assays. These results show applicability for M. oryzae Triticum field surveillance, as well as identifying nonwheat species that may serve as a reservoir or source of inoculum for nearby wheat fields.

Elevated temperature increases in planta expression levels of virulence related genes in Magnaporthe oryzae and compromises resistance in Oryza sativa cv. Nipponbare

Temperature changes have the potential to alter the incidence and severity of plant disease epidemics and pressures, as well as to reshape the co-evolutionary relationships between plants and pathogens. However, the molecular basis of temperature modulation of pathogenicity of plant pathogens is still unclear. Here, we studied the effect of temperature on biomass of Magnaporthe oryzae in planta using qPCR. Additionally, the transcriptomes of M. oryzae and rice were analysed using RNA-seq. Rice seedlings were exposed to 35°C and 28°C for 7 days before pathogen inoculation. Inoculated plants were kept in the dark at 28°C for 24h and later re-exposed to 35°C and 28°C for an additional 24h before sample collection. Plants grown and predisposed to 35°C prior to inoculation exhibited accelerated tissue necrosis compared with plants grown and inoculated at 28°C. In accordance with the disease severity observed on infected leaves, in planta fungal biomass was significantly higher at 35°C than 28°C. Moreover, M. oryzae exhibited increased expression levels of putative fungal effector genes in plants exposed to 35°C compared with plants exposed to 28°C. Collectively, this study revealed that temperature elevation could favour M. oryzae infection by compromising plant resistance and accelerating plant tissue colonisation with the pathogen.

Early Detection of Airborne Inoculum of Magnaporthe oryzae in Turfgrass Fields Using a Quantitative LAMP Assay

Gray leaf spot (GLS) is a destructive disease of perennial ryegrass caused by a host specific pathotype of the ascomycete Magnaporthe oryzae. Early diagnosis is crucial for effective disease management and the implementation of Integrated Pest Management practices. However, a rapid protocol for the detection of low levels of airborne inoculum is still missing. We developed a pathogen-specific quantitative loop-mediated isothermal amplification (qLAMP) assay coupled with a spore trap system for rapid detection and quantification of airborne inoculum of the M. oryzae perennial ryegrass pathotype, and tested its suitability for implementation in GLS-infected turfgrass fields. In summer 2015, two perennial ryegrass plots were artificially inoculated with the pathogen, with four continuously running custom impaction spore traps placed in each plot. Sampling units were replaced daily and tested with the developed qLAMP assay, while plots were monitored for symptom development. Results confirmed that the qLAMP assay-trap system was able to detect as few as 10 conidia up to 12 days before symptoms developed in the field. LAMP technology is particularly appropriate for field implementation by nontechnical users, and has the potential to be a powerful decision support tool to guide timing of fungicide applications for GLS management.

Genomics-Based Marker Discovery and Diagnostic Assay Development for Wheat Blast

Wheat blast has emerged as a major threat to wheat production in South America. Although originally restricted to Brazil, the disease has since been observed in the neighboring countries of Argentina, Bolivia, and Paraguay and recently the pathogen, Magnaporthe oryzae Triticum pathotype, was isolated from infected wheat in Bangladesh. There is growing concern that the pathogen may continue to spread to other parts of the world, including the United States, where several M. oryzae pathotypes are endemic. M. oryzae pathotypes are morphologically indistinguishable and, therefore, must be characterized genotypically. Symptoms of wheat blast include bleaching of the head, which closely resembles the symptoms of Fusarium head blight, further complicating efforts to monitor for the presence of the pathogen in the field. We used a genomics-based approach to identify molecular markers unique to the Triticum pathotype of M. oryzae. One of these markers, MoT3, was selected for the development of a polymerase chain reaction (PCR)-based diagnostic assay that was evaluated for specificity using DNA from 284 M. oryzae isolates collected from a diverse array of host species. Conventional PCR primers were designed to amplify a 361-bp product, and the protocol consistently amplified from as little as 0.1 ng of purified DNA. The specificity of the MoT3-based assay was also evaluated using Fusarium spp. DNA, from which no amplicons were detected.

Quick and Accurate Detection and Quantification of Magnaporthe oryzae in Rice Using Real-Time Quantitative Polymerase Chain Reaction

Rice blast, caused by Magnaporthe oryzae, is one of the most severe fungal diseases in rice worldwide. In this study, we developed methods to quickly and accurately detect and quantify M. oryzae in the pure cultures of the fungus, rice plants, and rice seed by using SYBR Green I of the real-time quantitative polymerase chain reaction (qPCR). Results of absolute qPCR show that Magnaporthe oryzae can be detected at as low as 6.9 × 10^-5 ng of genomic DNA. Results also show that all 10 varieties of rice seed examined in this study contain this fungus, indicating that M. oryzae is generally widespread in rice seed. We report the quantification of DNA of M. oryzae in rice leaves collected in the field, instead of in the lab, using relative qPCR by using rice actin gene as a housekeeping gene. Our results show great practical significance because we would know the potential fungal infection even before planting.

Quantification of rice blast disease progressions through Taqman real-time PCR

Rice blast caused by Magnaporthe oryzae is a major disease in the paddy field and also a representative model system in the investigation of plant-microbe interactions. This study was undertaken to provide the quantitative evaluation method that specifically determines the amount of M. oryzae proliferation in planta. Real-time PCR was used as the detection strategy in combination with the primer pair and Taqman probe specific to MHP1, a unigene encoding HYDROPHOBIN that is indispensable for normal virulence expression. Based on the crossing point values from the PCR reactions containing a series of increasing concentration of cloned amplicon or fungal genomic DNA, correlation among the template's copy number or its amount and amplification pattern was calculated. Reliability of this equation was further confirmed using the DNA samples from the rice leaves infected with compatible or incompatible strains of M. oryzae. The primer pair used in the Taqman real-time PCR reaction can recognize the existence of fungal DNA as low as 1 pg. In sum, our quantitative evaluation system is applicable and reliable in the blast diagnosis and also in the estimation of objective blast disease progression.

A Comparison of Standard and High-Fidelity PCR: Evaluating Quantification and Detection of Pathogen DNA in the Presence of Orchid Host Tissue

The polymerase chain reaction (PCR) has been used with increasing frequency for detecting and identifying plant pathogens. Although PCR is sensitive, research has shown that amplification of target microbial DNA from within another organism, such as an arthropod or plant, can be inhibited by the presence of host DNA. In this study, the sensitivity of standard and high-fidelity PCR, which incorporates a second DNA polymerase with proofreading ability, to detect and amplify DNA from the fungal pathogen Pseudocercospora odontoglossi while in the presence of Cattleya orchid DNA, was compared. Different dilutions of plasmids containing internal transcribed spacer (ITS)1, 5.8S, and ITS2 rDNA from P. odontoglossi were spiked with Cattleya orchid plant DNA. The high-fidelity PCR could detect and amplify as few as 207 plasmids containing the fungal DNA, whereas the standard PCR required over 200 million copies. The high-fidelity PCR was more efficient than conventional PCR in detecting Sclerotium rolfsii and a Dickeya sp. from freshly inoculated orchid plants, demonstrating its increased sensitivity in early detection of fungal and bacterial pathogens that are difficult to discriminate early in disease development.

A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue

A high-throughput method of isolating and cloning geminivirus genomes from dried plant material, by combining an Extract-n-Amp-based DNA isolation technique with rolling circle amplification (RCA) of viral DNA, is presented. Using this method an attempt was made to isolate and clone full geminivirus genomes/genome components from 102 plant samples, including dried leaves stored at room temperature for between 6 months and 10 years, with an average hands-on-time to RCA-ready DNA of 15 min per 20 samples. While storage of dried leaves for up to 6 months did not appreciably decrease cloning success rates relative to those achieved with fresh samples, efficiency of the method decreased with increasing storage time. However, it was still possible to clone virus genomes from 47% of 10-year-old samples. To illustrate the utility of this simple method for high-throughput geminivirus diversity studies, six Maize streak virus genomes, an Abutilon mosaic virus DNA-B component and the DNA-A component of a previously unidentified New Word begomovirus species were fully sequenced. Genomic clones of the 69 other viruses were verified as such by end sequencing. This method should be extremely useful for the study of any circular DNA plant viruses with genome component lengths smaller than the maximum size amplifiable by RCA.

Detection and Quantification of Rhizoctonia solani AG-1 IA, the Rice Sheath Blight Pathogen, in Rice Using Real-Time PCR

Rhizoctonia solani Kühn is the causal organism of sheath blight, a major rice disease worldwide that severely impairs yield and quality. It is difficult to identify the pathogen in the early phase of the infection and to accurately quantify the fungal development based on visual inspection. Therefore, a rapid and reliable method is advantageous for the detection and quantification of the pathogen causing this important rice disease. In this study, a real-time, quantitative polymerase chain reaction (QPCR) assay was developed to detect and quantify R. solani AG-1 IA DNA from infected rice plants. A specific primer pair was designed based on the internal transcribed spacer region of the fungal ribosomal DNA. The specific detection of R. solani DNA was successful with quantities as low as 1 pg. The QPCR assay could be used for detecting the rice sheath blight pathogen, quantifying fungal aggressiveness, and evaluating the resistance level of rice cultivars.

Quantitative and qualitative influence of inoculation methods on in planta growth of rice blast fungus

ABSTRACT Molecular analyses of early disease events require infected plant tissue in which the pathogen is present in high quantities and interacts with the plant in a way found in the field. In this study, a quantitative polymerase chain reaction (Q-PCR) assay was developed to determine an "infection ratio" of fungal to plant cells in infected tissues. This assay was used to evaluate four inoculation methods (spray, mist, dip, and sheath) as well as use of whole plants or excised parts. Fluorescence stereomicroscopy was used to follow individual lesions developing from appressoria to macroscopic symptoms. Disease progression and outcomes were documented from 24 to 96 h postinoculation (hpi), as well as effectiveness of Pi-ta-mediated resistance. Even at 96 hpi, fungus proliferated well ahead of visible plant damage, especially in veins. Developing lesions sometimes were surrounded by greener areas in detached leaves. Spray inoculation was not sufficient for detecting fungal gene expression in planta before 96 h. Alternatively, a leaf sheath assay produced infected tissues containing 10 to 30% fungal DNA by 34 h. Used together, Q-PCR quantification and fluorescence stereomicroscopy will facilitate studies of early plant invasion because infection density and fungal growth stages are directly observed, not assumed from incubation time.

A PCR-Based Method for the Detection of Ophiosphaerella agrostis in Creeping Bentgrass

Dead spot is a relatively new disease of creeping bentgrass and hybrid bermudagrass that is incited by Ophiosphaerella agrostis. Initial symptoms are difficult to diagnose and clinicians generally rely on the presence of pseudothecia within infected tissue or isolation of O. agrostis on an artificial medium. The main goal of this study was to develop a polymerase chain reaction-based technique capable of quickly identifying O. agrostis within infected creeping bentgrass tissues. Oligonucleotide primers specific for O. agrostis were developed based on the internal transcribed spacer (ITS) rDNA regions (ITS1 and ITS2) of three previously sequenced isolates of O. agrostis. The 22-bp primers amplified a 445- or 446-bp region of 80 O. agrostis isolates collected from creeping bentgrass and bermudagrass in 11 states. Primers did not amplify DNA from other common turfgrass pathogens, including three closely related species of Ophiosphaerella. Selective amplification of O. agrostis was successful from field-infected creeping bent-grass samples and primers did not amplify the DNA of noninfected, field-grown creeping bent-grass or hybrid bermudagrass plants. Amplification of purified O. agrostis DNA was successful at quantities between 50 ng and 5 pg. The entire process, including DNA isolation, amplification, and amplicon visualization, may be completed within 4 h. These results indicate the specificity of these primers for assisting in the accurate and timely identification of O. agrostis and the diagnosis of dead spot in both bentgrass and bermudagrass hosts.