Conventional and real-time PCR for the identification of Fusarium fujikuroi and Fusarium proliferatum from diseased rice tissues and seeds

Fusarium fujikuroi is a species of the Gibberella fujikuroi species complex (GFSC) and the causal agent of bakanae disease on rice. Even if F. fujikuroi is the most abundant Fusarium species found on rice, other species can also be isolated from rice, such as F. proliferatum. Multiple alignment of translation elongation factor (TEF) gene sequences of different Fusarium spp., showed a deletion of six nucleotides in F. fujikuroi sequence and a two nucleotide polymorphism in the same region of F. proliferatum sequence. These elements of variability were used to develop a conventional and Real-Time PCR assay for diagnosis. The species specific primer pairs (Fuji1F/TEF1R and Proli1F/TEF1R) gave a product of 179 and 188?bp for F. fujikuroi and F. proliferatum respectively. Primer specificity was confirmed by analyzing the DNA of the most representative species of the GFSC and 298 strains of Fusarium spp. isolated from rice plants and seeds in Italy. The specific primers were also successfully used to detect fungal presence directly from infected rice tissues and seeds, providing a rapid tool for the early detection of pathogen contamination.     

Infection processes of Ustilaginoidea virens during artificial inoculation of rice panicles

Ustilaginoidea virens is a ubiquitous plant pathogen that causes rice false smut disease, one of the most destructive diseases of rice (Oryza sativa L.) production. However, data concerning the effect of inoculation on disease development and the infection process of this pathogen are not comprehensive. In this study, the developmental processes of U. virens in rice panicles were characterized using an enhanced green fluorescent protein (EGFP) labelled strain. A mixture of hyphae and conidia of U. virens was used to inoculate rice panicles by leaf sheath injection during the booting stage of rice plants grown in a greenhouse. The panicles were assessed to determine the relationship between artificial inoculation and disease occurrence. Increasing volumes of inocula (0.2, 0.5, 1, and 2 ml of a mixture of hyphae-fragment and 2?×?10⁶ conidia/ml suspension) caused more severe infections, and small differences were also observed for the different inoculation sites at the base, apex and mid-point of rice panicles. The optimum inoculation condition was 1–2 ml inoculum injected into the mid-point of rice panicles. Spikelet samples were collected as the disease progressed and observed by confocal laser scanning microscopy and scanning electron microscopy. The images collected showed that the primary site of U. virens colonization was at the base of the filaments with the inner spikelets becoming infected by hyphae at 24 h post inoculation (hpi). The accumulation of hyphae reached its highest level at 168 hpi, before the rice heading stage, as the infection extended upward from basal filaments to the anther apex, and then enclosed all the floral organs to produce a velvety smut ball.     

辽宁省稻曲病菌遗传多样性和致病力分析

为有效防治辽宁省稻曲病菌Ustilaginoidea virens,利用重复序列PCR(repetitive elementbased PCR,rep-PCR)分子指纹技术,对2017年自辽宁省8个市8个主产稻区采集的51株稻曲病菌菌株进行遗传多样性和致病力分析。结果显示,在3对引物中,以BOX1/BOX2和ERIC1/ERIC2为引物扩增的DNA指纹图谱的遗传多样性值分别为0.764、0.707,均大于0.7,故选择这2种引物扩增的DNA指纹图谱进行遗传多样性分析;当DNA指纹相似系数为0.78时,以BOX1/BOX2为引物和以ERIC1/ERIC2为引物扩增的DNA指纹图谱分别将供试菌株划分为12个和10个遗传类群;供试菌株致病力可划分为弱致病型、中等致病型和强致病型3个致病型,所占比例分别为33.33%、58.82%和7.85%,强致病型菌株仅在沈阳市、鞍山市和大连市出现;所有优势类群均包含3种致病型菌株。表明辽宁省稻曲病菌遗传结构复杂,不同地理来源的稻曲病菌菌株致病力存在一定差异,相同致病型的稻曲病菌菌株分属于不同的遗传类群,同一遗传类群中包含不同的致病型菌株。     

The role of <Emphasis Type="Italic">Ustilaginoidea virens</Emphasis> sclerotia in increasing incidence of rice false smut disease in the subtropical zone in China

Rice false smut is heavily and increasingly occurring in subtropical zones in China in the past decades. The pathogen of the disease, Ustilaginoidea virens, can produce both chlamydospores and sclerotia, and the sclerotia seem to form frequently in temperate or high-altitude regions in China. Which of these structures play a dominant role in the pathogen’s life cycle in subtropical zones remains unclear. Here we found that Ustilaginoidea virens could produce a great number of sclerotia in subtropical zones and the maximal number of sclerotia could reach to 2.25 million per hectare. In the year with relatively low autumn temperatures, the disease severity and sclerotia numbers of U. virens increased significantly. Although there was a few sclerotia in subtropical zones capable of overwintering successfully, one individual sclerotium could produce large numbers of ascospores. In the rice-growing paddy field, the ascospores could be trapped in both temperate and subtropical zones in May–September, when rice was at the booting stage, the critical infection period of rice false smut. This suggested that the sclerotia of rice false smut in subtropical zone played an important role in the life cycle of Ustilaginoidea virens and acted as the primary inoculum. Experiments in the laboratory showed that mature sclerotia of rice false smut remained dormant for about 2–5 months, and that light was essential for fruiting body differentiation. As with ergot, the fruiting bodies of Ustilaginoidea virens secreted sticky droplets on the stromata that prevented the ascospores from dispersing into the air, implying that the transfer of ascospores of Ustilaginoidea virens to rice plants in paddy field needed an intermediary vector.     

Use of ITS nuclear sequences from Phelipanche aegyptiaca as a direct tool to detect single seeds of broomrape species in the soil

Broomrape (Phelipanche and Orobanche spp.) are obligate holoparasites that attack roots of almost all economically-important crops in semiarid regions of the world. Broomrape seeds are extremely small (dust-like seeds), averaging 200 to 300?μm in size and because of the miniscule seed size it is difficult to detect and confirm via conventional methods. In this study our aim was to develop a PCR-based assay specific for broomrape soil-borne seeds and sensitive enough to detect a single or few broomrape seeds in a soil sample. For this purpose, we used complementary polymerase chain reaction (PCR) primers based upon unique sequences in the internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA of Phelipanche aegyptiaca. Genomic DNA was extracted from soil samples artificially infested with broomrape seeds or tissue of Phelipanche aegyptiaca Pers., Orobanche cumana Wallr. and Phelipanche crenata Forsk. and subjected to PCR analysis. Using ITS-350 primers, a specific PCR product (350?bp) was amplified and detected in all samples containing broomrape species, but was not detected in soil sample free of broomrape seeds or tissues. Additionally, the PCR-based assay was sensitive enough to detect even a single broomrape seed in the soil. As expected the universal internal control primers amplified a PCR product (555?bp) of genomic DNA extracted from soil samples with or without broomrape tissues or seeds. This diagnostic method is simple, reliable and rapid and could help for assessment of broomrape seed contamination in a crop field.     

Frequency distribution of sensitivity of Ustilaginoidea virens to four EBI fungicides, prochloraz, difenoconazole, propiconazole and tebuconazole, and their efficacy in controlling rice false smut in Anhui Province of China

False smut, caused by Ustilaginoidea virens, is an important emerging disease of rice (Oryza sativa L.) in China. Up to now, as most varieties with high yielding and good quality are susceptible or even highly susceptible to false smut in most rice-growing ecological regions, especially in Anhui Province, chemical control with fungicides would be an important measure for the control of this disease. The ergosterol biosynthesis inhibitor (EBI) fungicides, such as prochloraz, difenoconazole, propiconazole and tebuconazole, are extensively used in China for the control of rice diseases, such as rice sheath blight and rice blast. In this study, a total of 102 U. virens isolates (from Anhui Province of China) were tested for their sensitivity to these four EBI fungicides during the stage of mycelial growth. The EC₅₀ ranges of values for prochloraz, difenoconazole, propiconazole and tebuconazole inhibiting mycelial growth of the 102 U. virens isolates were 0.04–0.75, 0.04–1.08, 0.04–0.38 and 0.03–0.57 μg?ml^?1, with the average EC₅₀ values of 0.32?±?0.08, 0.45?±?0.08, 0.19?±?0.03 and 0.21?±?0.06 μg?ml^?1, respectively. These values suggested that the tested U. virens isolates were very sensitive to these four EBI fungicides. Results of field trials showed that two sprays of three of the fungicides exhibited greater control efficacy than a single spray for the control of rice false smut. Two sprays of each was better than a single spray for the control of rice sheath blight. Two sprays of 50% propiconazole EC at 300 g a.i. ha^?1 gave the best control of rice false smut at both two sites during the two consecutive years, 2010 and 2011, with the control efficacy ranging from 71.5 to 74.3%. Sensitivity of the field U. virens isolates to EBI fungicides should be monitored. Mixtures, as well as alternation with other fungicides with different modes of action, should be tested.     

稻曲病菌离体培养体系的构建与优化

稻曲病是水稻穗期的一种重要病害,严重影响稻米的产量和品质。稻曲病菌Ustilaginoidea virens 在离体培养条件下生长缓慢,严重制约了杀菌剂室内生测试验的观察和高效筛选。本研究以稻曲病菌培养基为研究对象,通过筛选、组合和优化固体培养体系的氮源、碳源、凝固剂以及阳离子浓度,以期构建适合稻曲病菌生长的室内培养体系。结果发现:在5种常见的商品化培养基中,稻曲病菌的生长速率仅为0.7~2.3 mm/d;而在18种配制培养基中,有77%的培养基对稻曲病菌表现出不同程度的生长促进效应,其中蛋白胨蔗糖结冷胶 (PSGG) 培养基的促进效果最显著 (P < 0.05),生长速率达3.4 mm/d,且其对不同地理分布的稻曲病菌菌株均有生长促进效应。此外,在以结冷胶作为凝固剂的培养基中添加质量分数为0.02%的硫酸镁 (Mg2+),可有效提高培养基的凝固程度,且对菌丝体的生长速率无影响。在适合稻曲病菌生长的PSGG培养基中,蛋白胨和蔗糖是合适的氮源和碳源组合,结冷胶是合适的凝固剂。此研究结果可提高室内培养稻曲病菌的生长速率,为进一步理解稻曲病菌在离体条件下的生长机制及提高室内杀菌剂生测试验的效率提供了重要参考。     

Quantification of the rice false smut pathogen <Emphasis Type="Italic">Ustilaginoidea virens</Emphasis> from soil in Japan using real-time PCR

Ustilaginoidea virens is the causal agent of false smut disease of rice. In this study, we developed a real-time polymerase chain reaction (PCR) assay to clarify the relationship between false smut occurrence on rice and quantification of U. virens from soil in Japan. The method here described is sensitive, detecting less than 50 fg of pathogen DNA, and specific to the nuclear ribosomal DNA for U. virens when tested across 27 rice-pathogenic fungi and bacteria, 26 other fungi and bacteria and four plant species. As few as eight chlamydospores of U. virens per gram soil were detected when added to sterilized Gley and Ando soils. The real-time PCR assay for the soil samples was at least 100-fold more sensitive than the conventional and nested-PCR assays tested. By quantification of U. virens with real-time PCR using DNA extracted from naturally contaminated Gley soils and visual assessment of the disease in agricultural fields, a linear correlation between cycle threshold (C_T) values and the number of false smut balls was revealed. Therefore, this specific quantitative assay could be a useful tool for optimization of disease control strategies, and for studying the ecology of U. virens.     

四川省籼稻区水稻稻曲病菌遗传多样性分析

应用ERIC-PCR指纹技术,对采自四川省6个籼稻自然生态区的60个稻曲病菌菌株进行了DNA分子水平上的遗传多样性研究,并进行UPGMA聚类分析和相似性分析.结果表明,所采用的ERIC引物在不同供试菌株中分别扩增出5～20条不等的带谱;在0.75相似水平上,供试菌株被划分为11个遗传型群,其中L1、L4、L5为优势群,并存在次要小型群和特异性型群;来自同一地区的稻曲病菌菌株具有较高的遗传相似性,而不同地区的稻曲病菌则表现出程度不同的变异,且寄主品种与稻曲病菌遗传差异之间的相关性较小.     

Colonization of the vegetative stage of rice plants by the false smut fungus Villosiclava virens,as revealed by a combination of species‐specific detection methods

Rice false smut disease caused by the ascomycete fungus Villosiclava virens (Clavicipitaceae) reduces rice yield worldwide. It invades rice panicles and forms dark‐green false smut balls composed of thick‐walled conidia. Although the infection process during the booting stage is well studied, its infection route before this is unclear. It was hypothesized that the thick‐walled conidia in soil penetrate rice roots, and the fungus latently colonizes roots and tiller buds at the vegetative stage. This hypothesis was tested using species‐specific detection methods. First, real‐time PCR with species‐specific primers and probe was used to estimate thick‐walled conidial number in the paddy field soil. Secondly, nested PCR with species‐specific primers showed that fungal DNA was detected in roots and shoot apices of rice plants in the vegetative stage. Thirdly, colourimetric in situ hybridization with a species‐specific oligonucleotide probe targeting 18S rRNA suggested that sparse mycelia or tightly condensed mycelia were present on the external surface of tiller buds enveloped by juvenile leaf sheaths at the vegetative stage. Thin hyphae were found around leaf axils at the surface of elongated stems at the heading stage, and the fungal hyphae grew in the rice root tissues. In addition, it was demonstrated that eGFP‐tagged transformants of the fungus invaded rice roots and colonized the surface of roots and leaf sheaths under artificial conditions.     

Isolation and characterization of <Emphasis Type="Italic">Ustilaginoidea virens</Emphasis> and survey of false smut disease of rice in India

The intensity of rice false smut disease in selected states of northwest and south India was studied. In northern Indian states as a whole, disease incidence (percentage of false smut-infected tillers) varied from 2% to 75%. In the state of Haryana, maximum infection was recorded on hybrids like PA 6444 and PA 6129 while in Punjab state, 10–20% disease incidence was recorded in popular inbred rice varieties like PR 114, PA 116 and PAU 201. In the southern state of Tamil Nadu, the disease incidence varied from 5% to 85%. A heavy incidence of the disease was noticed in variety BPT 5204 and due to this, the air above the infected field gave a black smoky appearance from a distance as a result of release of spore mass in the atmosphere. In severe cases the number of infected grains reached even more than 100 per panicle. The pathogen Ustilaginoidea virens was isolated in potato dextrose agar medium and was characterized by both pathogenicity test and molecular analysis. Under glasshouse conditions, when a conidial suspension of the pathogen was injected during boot leaf stage of the rice variety TN1, typical smut balls were observed. The identity of the pathogen was further confirmed through polymerase chain reaction (PCR) analysis using U. virens-specific internal transcribed spacer (ITS) primers. The primer pair US 1-5/US3-3 and US2-5/US4-3 amplified 380 bp and 232 bp product, respectively, which are typical for the U. virens fungus.     

Control efficacy against rice sheath blight of Platycladus orientalis extract and its antifungal active compounds

The control efficacy of Platycladus orientalis extract against Rhizoctonia sonali Kühn, the causal agent of rice sheath blight, was evaluated by pot experiments under greenhouse conditions, and the antifungal compounds were isolated and identified through antifungal bioassay-guided fractionation using R. sonali as a tested fungus. The results indicate that the extracts from P. orientalis exhibited a significant reduction in the severity of rice sheath blight. The petroleum ether fraction partitioned from the ethanolic crude extract, showing the highest antifungal activity, was further separated, and two diterpenoid compounds with antifungal property, totarol and sclareol, were isolated and identified from the active subfractions. Totarol and sclareol possessed antifungal activity against most of the tested fungal pathogens of cereal crops such as R. solani, R. cerealis and Fusarium graminearum, indicating a similar broad antifungal spectrum. These findings suggest that the P. orientalis extract and its derived active compounds may be promising candidate agents for controlling plant fungal diseases like rice sheath blight.     

A refined inoculation method to evaluate false smut resistance in rice

False smut, caused by Ustilaginoidea virens, is a serious disease of rice worldwide. To evaluate false smut resistance in rice, we developed a method combining the cultivation of the main culm of rice plants in the greenhouse and rapid preparation of a conidial suspension to inject into the leaf sheath. The method was used to evaluate false smut resistance in 18 varieties/lines of rice. For comparison, field trials were also carried out in 2007 and 2008. The results indicated that the greenhouse method was more reproducible than field trials: commercial varieties tested were resistant; almost all the forage varieties were highly susceptible; and blast-resistant varieties/lines were mostly resistant to false smut. Thus, this inoculation method will be useful for determining the level of false smut resistance in rice and for breeding resistant varieties.     

Development of a loop-mediated isothermal amplification assay for sensitive and specific detection of <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> f. sp. <Emphasis Type="Italic">cucumerinum</Emphasis> Owen

Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum Owen (FOC), is a destructive disease affecting cucumber production worldwide. Developing an accurate and reliable method for detection of FOC is important for disease prediction and control. In this study, a loop-mediated isothermal amplification (LAMP) assay was developed and validated for specific and sensitive detection of FOC. Four LAMP primers were designed based on the sequence of the FOC-specific random amplified polymorphic DNA (RAPD) marker OPZ-12₈₆₅. LAMP reactions were performed at different temperatures and for different durations, and the optimal temperature and duration were 63 °C for 60 min, respectively. Hence, a LAMP assay for detection of FOC was established. The specificity of the LAMP method was evaluated against 119 isolates of FOC and other pathogens, and only FOC isolates yielded positive results. In sensitivity tests, the lowest concentration of genomic DNA required for the LAMP assay was 10 fg in a 25 μL reaction. The LAMP assay was successfully applied to detect FOC in cucumber tissues and soil from infested fields, and the positive ratios of LAMP, PCR, and traditional tissue isolation for detecting FOC from diseased cucumber root samples were100%, 86.6 and 83.3%, respectively. Therefore, the LAMP assay developed herein should serve as a simple, cost-effective, rapid, highly specific, and sensitive tool for the visual detection of FOC and contribute to improved disease management.     

Management of bakanae and bacterial seedling blight diseases in nurseries by irradiating rice seeds with atmospheric plasma

The control of seedborne rice seedling diseases in the seed beds is important to avoid epidemics in rice nurseries and paddies, which may result in severe yield loss. Recently, irradiation with plasma containing electrons, creating positive or negative ions and neutral species, has been shown to have an antimicrobial effect, probably via generation of reactive oxygen species. This study examines whether two seedborne rice seedling diseases, bakanae disease caused by the fungal pathogen Fusarium fujikuroi, and bacterial seedling blight caused by Burkholderia plantarii, are suppressed by irradiation of infected rice seeds with atmospheric plasma. Seed germination and seedling growth were not inhibited in plasma‐treated healthy seeds. When F. fujikuroi‐infected rice seeds were irradiated with plasma after being immersed in sterile distilled water, bakanae disease severity index and the percentage of plants with symptoms were reduced to 18.1% and 7.8% of non‐irradiated control, respectively, depending on the duration of plasma irradiation. The bacterial seedling blight disease index was also reduced by plasma irradiation in vacuum‐inoculated seeds to 38.6% of the non‐irradiated control, and in infected seeds harvested from spray‐inoculated heads of rice plants to 40.1% of the control. Therefore, plasma irradiation seems to be effective in controlling two independent seedborne rice seedling diseases.     

Species-specific DNA markers for identification of two root-knot nematodes of coffee: Meloidogyne arabicida and M. izalcoensis

Seven root-knot nematodes (RKN), including Meloidogyne exigua, M. incognita, M. paranaensis, M. enterolobii, M. arabicida, M. izalcoensis and M. arenaria are major pathogens of coffee crop in the Americas. Species-specific primers for their identification have been developed for five of them and constitute a fast and reliable method of identification. Here we report a PCR-based assay for specific detection of M. arabicida and M. izalcoensis. Random Amplified Polymorphic DNA fragments specific for these two species were converted into sequence characterized amplified region (SCAR) markers. PCR amplification using the SCAR primers produced a specific fragment of 300 bp and 670 bp for M. arabicida and M. izalcoensis, respectively, which were absent in other coffee-associated Meloidogyne spp. tested. SCAR primers also allowed successful amplification of DNA from single second-stage juveniles (J2), males and females. In addition, these primers were able to unambiguously detect the target species in nematode suspensions extracted from soil and roots samples, in different isolates of the same species or when used in multiplex PCR reactions containing mixtures of species. These results demonstrated the effectiveness of these SCAR markers and their multiplex use with those previously developed for M. exigua, M. incognita, M. paranaensis, M. enterolobii and M. arenaria constitute an essential detection tool. This diagnostic kit will contribute for specific J2 identification of the major RKN infecting coffee from field samples in the Americas.     

籼型杂交水稻对稻曲病的田间抗性差异

为了解不同水稻品种在田间的抗性差异及其与农艺性状的相互关系,在相同的土壤环境和栽培条件下,利用稻曲病菌诱发接种鉴定,对56个籼型杂交水稻进行田间抗性差异比较,初步探讨了抽穗期和农艺性状与品种田间抗性的关系.结果表明,不同水稻品种对稻曲病田间抗性存在显著差异,病穗率为0.43%～33.04%,病情指数为0.05～16.14;不同抽穗期的品种稻曲病发病率不同,同一抽穗期的品种对稻曲病的抗性亦表现出明显差异;水稻株高与品种抗性之间呈正相关,相关系数为026(P<0.05);水稻分蘖率、有效穗数、剑叶性状等与品种的田间抗性有一定相关性,但差异不显著(P>0.05);水稻株叶形态和叶色与品种田间抗性没有直接相关性.     

Development of a loop-mediated isothermal amplification assay for rapid and sensitive detection of Fusarium oxysporum f. sp. cubense race 4

Fusarium wilt (Panama disease), caused by the fungus Fusarium oxysporum f. sp. cubense race 4 (Foc race 4), is one of the most destructive diseases affecting banana (Musa). Early and accurate detection of Foc race 4 is essential to protect the banana industry. We developed a novel and highly specific loop-mediated isothermal amplification (LAMP) assay for the detection of Foc race 4 based on a SCAR marker sequence. The detection limit for this assay was 10 fg per 25 μl reaction in pure culture and DNA amplification was completed within 60 min. The assays detected 69 different isolates of Foc race 4 from geographically distinct counties in China, and no cross-reaction was observed with other fungal pathogens. When 26 infected and eight healthy looking but infested banana samples naturally from different fields were examined, the detection rate of LAMP was 100 %. The LAMP assay developed in this study was simple, fast, sensitive, and specific, and can be used in the field to detect Foc race 4 in infected banana plant tissue in resource-poor settings.     

Fusarium commune associated with wilt and root rot disease in rice

Wilt and root rot disease in plants has been caused mainly by Fusarium species. Previous studies reported that members of the Fusarium oxysporum species complex (FOSC) were usually associated with this disease, but there has been no report of it being caused in rice by specific Fusarium species. However, in this study, Fusarium commune was identified and characterized as a causal agent of wilt and root rot disease of rice. Four Fusarium isolates (BD005R, BD014R, BD019R, and BD020R) were obtained from different parts (root, stem, and seeds) of diseased rice plants. In morphological studies, these isolates produced key characteristics of F. commune, such as long and slender monophialides, polyphialides, and abundant chlamydospores. In molecular studies, the isolates were identified as F. commune based on sequences of the translation elongation factor 1-α (TEF1) gene that had 99.7%–100% sequence identity with the reference strain F. commune NRRL 28058. The phylogenetic tree showed that all four isolates belonged to the F. commune clade. A mating type test determined that three isolates carried MAT1-2. Their teleomorph stage was still unknown. Pathogenicity assays showed that all the isolates produced wilt and root rot symptoms and the isolate BD019R was observed as the most virulent among the isolates. To our knowledge, this is the first report of F. commune causing wilt and root rot disease on rice.