Simple and rapid detection of rice false smut pathogen Ustilaginoidea virens in rice seeds

A method for simple and rapid detection of Ustilaginoidea virens in rice seeds was developed based on specific polymerase chain reaction (PCR). To design the specific primers for detection of U. virens, the comparison was made on 5.8S rDNA intra- and inter-specific variations in nucleotide sequences of U. virens and other pathogens: Fusarium verticillioides, Sclerotinia sclerotiorum, Tilletia barclayana, Fusarium graminearum and Magnaporthe oryzae. A 346-bp fragment could be amplified by using the specific primers uvr-F and uvr-R in U. virens, but not in other test fungi, indicating that the designed primers were specific for the detection of U. virens. U. virens was detected in nine of the 24 tested rice samples, indicating that 37.5% of the rice samples were contaminated with the false smut pathogen. The development of the simple and rapid detection technique using specific primers will be applicable for direct identification of U. virens in rice seeds to screen large numbers of samples.     

Genetic diversity and population structure analysis of isolates of the rice false smut pathogen Ustilaginoidea virens in India

Genetic diversity assessment and population structure analysis are essential for characterization of pathogens and their isolates. Markers are essential tools for exploring genetic variation among the isolates. False smut of rice caused by Ustilaginoidea virens, formerly Villosiclava virens, is a major emerging disease of rice in India. A high level of variability is observed at the field level, but no information is available from India on genetic diversity and population structure. This is the first report of genetic diversity and population structure of U. virens from India that included 63 isolates distributed across the vast geographical area of eastern and north-eastern India (18.9 to 26.7°N and 82.6 to 94.2°E). Seventeen RAPDs and 14 SSRs were identified as polymorphic and a total of 140 alleles were detected across the populations. The average number of alleles per locus for each primer was 4.5. All the isolates were grouped into two major clusters, with partial geographical segregation that was supported by principal coordinate analysis. Mantel test suggested genetic distance within the isolates increased with increasing geographical distance. Analysis of molecular variation showed more genetic variation within populations and less among populations. This outcome will help in understanding genetic diversity of U. virens from eastern and north-eastern India and in planning effective management strategies.     

来源于同一穗不同稻曲球的稻曲病菌的致病性及遗传多样性

 本研究从源于6穗稻曲病穗的48个稻曲球中分离获得稻曲病菌（Ustilaginoidea virens）48株,从3个稻曲球的不同部位分离获得稻曲病菌23株。用注射接种法将菌株分别接种到水稻品种两优培九（感病品种）、淮稻5号（中抗品种）和武育粳3号（抗病品种）上,结果显示分离的菌株致病力分化较大,而菌株在水稻品种上的致病力强弱与已知水稻品种对稻曲病菌的感、抗性趋势基本一致。相同孢子量接种水稻,不同分离菌株之间仍有致病力分化,生长速率测定也发现菌株之间可能存在差异。利用REP PCR (repetitive extragenic palindromic sequence PCR)技术进行菌株遗传多样性分析表明,同穗不同稻曲球分离的菌株中,1号穗分离的4个菌株聚在同一簇群,其余5穗的菌株分别聚在3～5个簇群;同一稻曲球不同部位分离的菌株中,一个稻曲球分离的8个病菌聚在同一簇群,而其余2个稻曲球分离的病菌则分别聚在2～3个簇群。由此推测同一稻穗上不同稻曲球可能是由来源不同的稻曲病菌侵染所形成;而一个稻曲球可以由同一稻曲病菌引起,也存在多个侵染源共同侵染的可能。     

Detection of quantitative resistance loci associated with resistance to rice false smut (Ustilaginoidea virens) using introgression lines

False smut, caused by Ustilaginoidea virens, is a rice disease of increasing importance worldwide, with no source of high‐level resistance in the existing rice germplasm. To facilitate breeding varieties with good levels of field resistance to false smut, quantitative resistance loci (QRL) were identified using 213 introgression lines (ILs) from a cross between Teqing (recipient) and Lemont (donor) evaluated using natural infection at two hotspots of false smut in northeast China. Ten QRL affecting percentages of diseased hills, diseased panicles and diseased spikelets were detected and mapped to rice chromosomes 2, 3, 4, 6, 8, 10, 11 and 12. The Lemont alleles at all QRL increased false smut resistance. Four QRL (qFSR‐6‐7, qFSR‐10‐5, qFSR‐10‐2 and qFSR‐11‐2) had relatively larger and consistent effects across the two testing sites. Promising resistant ILs were identified, most of which had multiple QRL, suggesting that pyramiding multiple QRL by marker‐assisted selection would be an effective strategy for improving rice resistance to false smut. The identified QRL and their linked DNA markers will facilitate this breeding effort in the future.     

Epiphytic colonization of Ustilaginoidea virens on biotic and abiotic surfaces implies the widespread presence of primary inoculum for rice false smut disease

Ustilaginoidea virens (Uv), the causative agent of rice false smut disease, infects developing rice spikelets at the booting stage, and transforms individual grains of the panicle into smut balls. Epidemics of the disease occur when the rice booting and heading stages coincide with rainy days. Using a green fluorescent protein (GFP)‐labelled Uv isolate that can form false smut balls on rice panicles, it was found that under high humidity and free water conditions the Uv isolate could colonize leaves of plants belonging to various families including the Poaceae (Oryza sativa, Echinochloa crusgalli, Digitaria sanguinalis and Leptochloa chinensis), the Brassicaceae (Arabidopsis thaliana) and the Solanaceae (Nicotiana benthamiana) without symptoms. Over several days, some conidia could germinate on the leaves of these plants and in water on the surface of Parafilm and cellophane, form hyphae and differentiate conidiophores to generate a large number of secondary conidia, while other conidia were able to directly produce secondary conidia. Conversely, in the absence of water some conidia could either bud to form new conidia or were converted into chlamydospores. These data indicate that Uv is one of a few fungal pathogens reported to have epiphytic characteristics. The rapid generation of a large number of spores on biotic and abiotic surfaces greatly increases the inoculum that can infect rice spikelets, resulting in the occurrence of rice false smut disease epidemics. These findings are important in the development of disease control strategies.     

Effect of calcined lime (CaO) on chlamydospores of the rice false smut pathogen,Villosiclava virens,and their root attachment and infection

Rice false smut caused by Villosiclava virens is a devastating disease. The smut balls contain chlamydospores, which fall onto paddy soils to become the primary inoculum. After transplanting, the chlamydospores subsequently germinate and infect rice roots. The application of a CaO-containing fertilizer to paddy soils can inhibit the development of rice false smut disease; however, the underlying mechanism is unknown. In this study, we evaluated the suppression of chlamydospore behaviour due to CaO. Specifically, we clarified the effects of the following on chlamydospore morphology and germination: (a) pH, (b) calcium (Ca) concentration, (c) Ca concentration (pH adjusted to 6.5), and (d) CaO-added soil solution. Germination was suppressed at pH 4 and 10, in contrast with the normal germination at pH 6, 7, and 8. Treatments with more than 10 mg/L Ca melted the outer layer of chlamydospores and suppressed germination regardless of whether the pH was adjusted to 6.5. A saturated CaO solution induced bursting of chlamydospores. Suppressed germination and a melted outer chlamydospore layer were also observed, even though the soil buffering effect initially prevented the CaO-mediated pH increase. Furthermore, the chlamydospores within 15 mm from the CaO small lump exhibited suppressed germination in soil. In addition, there was no effect of CaO treatment on chlamydospore attachment to rice roots and hyphal invasion of rice roots in in vitro inoculation tests. These results suggest that Ca concentration is an important factor for inhibiting the occurrence of rice false smut disease.     

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.     

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.     

Genetic analysis of the population structure of the rice false smut fungus,Villosiclava virens,in China using microsatellite markers mined from a genome assembly

Studies on population genetics of Villosiclava virens are limited because of the lack of polymorphic markers. Based on a draft genome sequence of isolate HWD‐2 produced in this study, 20 of 403 potential simple sequence repeats (SSR) loci showed polymorphisms in preliminary screening using eight diverse V. virens isolates. Among polymorphic loci, most of them with tetra‐ to hexanucleotide unit motifs showed higher levels of polymorphism than loci with smaller motifs. After testing with 20 polymorphic SSR markers, the 87 isolates of V. virens from eight populations in China showed a high level of genetic diversity, with each as a unique haplotype. This differs from some previous findings showing little to no genetic variation based on random amplified polymorphic DNA and amplified fragment length polymorphism analyses. Among eight populations from major rice production areas of China, the population from Guangxi province in south China showed the highest levels of polymorphism, which led to the speculation that it might be closer to the centre of origin of this pathogen. The northern, central and eastern populations (Jilin, Liaoning, Hubei, Hunan, Jiangxi and Zhejiang), when considered together as a group, showed significant molecular variation compared to the southern populations (Fujian and Guangxi) (Φ_PT = 0·043, P = 0·037). A significant relationship (Mantel test, P = 0·027) but with low correlation (R² = 0·23) was also found between geographic distance and genetic distance. The 20 polymorphic SSR primer pairs designed in this study provide a tool for further research on the population diversity of this emerging fungal pathogen of rice.     

水稻品种生育期、田块和播种期对稻曲病发生严重度的影响

利用早熟组和晚熟组各8个水稻品种采用随机区组设计连续进行两年田间试验,分析生育期与稻曲病严重度的关系,同时采用晚熟组5个品种分析田间厚垣孢子数量、播期与稻曲病发生严重度的关系。结果表明,水稻生育期、田间菌量与稻曲病田间发生的严重度呈显著正相关。早熟组各水稻品种的发病率均显著低于晚熟组各水稻品种,2005年晚熟组和早熟组品种的病穴率、病穗率和病粒率分别为76.3%、26.6%、4.6%和5.4%、0.8%、0.02%,2006年分别为75.7%、29.8%、4.7%和16.8%、3.3%、0.08%。此外,在上一年田间遗落菌量多的田块中各水稻品种稻曲病的发生程度显著高于菌量小的田块。晚熟组水稻品种的发病严重度与播种期无明显的相关性。据此认为,以种植晚熟水稻品种为主的北方稻区,种植早熟品种或进行轮作是防治该病的有效方法。     

Intercellular invasion of rice roots at the seedling stage by the rice false smut pathogen, <Emphasis Type="Italic">Villosiclava virens</Emphasis>

False smut is a serious disease affecting rice production worldwide. Initial infection of rice seedlings by Villosiclava virens was clarified using axenically cultured chlamydospores to inoculate rice roots. Chlamydospores were found on rice roots at 1 day post inoculation (dpi), and were germinating at 1–4 dpi. At 4 dpi, the infection germ tube had invaded the intercellular space between epidermal rice root cells. Between 5 and 11 dpi, branching and fusion-like structures were observed that may contribute to the establishment of the hyphal network on the root surface.     

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.     

采用AFLP技术分析稻曲病菌的遗传多样性Ⅰ:同一块稻田中稻曲病菌的遗传结构

 采用AFLP (Amplified fragment length polymorphism)技术分析了来自北京昌平同一块稻田中不同水稻品种和育种中间材料上稻曲病菌(Ustilaginoidea virens)的遗传多样性。从256对EcoRⅠ和MseⅠ引物中选择30对扩增40个菌株。结果表明,同一块稻田中稻曲病菌菌株间的相似性系数达0.72以上,来自同一小区的多数菌株能聚成亚类;发现从同一水稻品种分离的菌株没有特异性的AFLP谱带。初步推断稻曲病菌与水稻品种不存在明显的专化性互作。     

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.     

安徽省稻曲病气象等级预报方法研究—以池州为例

为进一步明确安徽省稻曲病发生关键期, 探索稻曲病气象等级预报方法, 以满足对该病害气象等级预报的服务需求?本文以安徽省池州市为例, 利用1995年-2018年一季稻稻曲病观测数据和同期气象资料, 通过相关分析确定稻曲病发生关键期?根据稻曲病大发生对适温高湿环境的需求及不同降水等级和温度对稻曲病发生程度的影响不同, 以稻曲病发生关键期降水日数为基础, 引入雨量系数和温度系数, 形成稻曲病发生综合气象条件指数, 通过最优曲线回归分析, 建立稻曲病预报模型?结果表明, 7月下旬至8月中旬是池州市一季稻稻曲病发生关键期; 综合气象条件指数与稻曲病病穗率相关性明显高于降水日数与病穗率相关性; 预报模型回代检验准确率为81.0%, 2016年-2018年模型预测结果均与实际情况相吻合, 由于样本中轻发生和大发生年份较少, 对轻发生和大发生预报的准确性需在样本丰富条件下进一步验证?模型在业务应用中, 可结合CFSv2模式逐日降水和气温预报产品, 提前10~30 d开展稻曲病气象等级预报, 对做好稻曲病的防治工作具有重要参考价值?     

Identification of genes expressed by Phakopsora pachyrhizi,the pathogen causing soybean rust,at a late stage of infection of susceptible soybean leaves

Soybean is one of the top five agricultural products in the United States and is highly susceptible to Phakopsora pachyrhizi, an exotic obligate biotrophic fungus. The little amount of genomic information about P. pachyrhizi limits understanding of the soybean–soybean rust pathogen interaction and the possibility of engineering resistance to this pathogen in soybean. Illumina mRNA‐Seq analysis revealed P. pachyrhizi genes expressed during a biotrophic interaction between P. pachyrhizi and soybean during fungal sporulation 10 days after inoculation. Approximately 2·4 million DNA sequences representing portions of potential P. pachyrhizi genes were assembled into 32 940 contigs that were used to search against expressed sequence tag (EST), protein and conserved domain databases. About 7500 contigs represent newly discovered P. pachyrhizi sequences. Of these, 527 shared similarity to genes encoding fungal proteins involved in different metabolic pathways such as galactose and glycogen metabolism, glycolysis, the citrate cycle, fatty acid metabolism, amino acid metabolism, proteolysis, protein synthesis, cell cycle division and mitosis, and cell wall biogenesis. Almost 7000 potential P. pachyrhizi genes are still of unknown function. Such information may be useful in the development of new methods of broadening resistance of soybean to P. pachyrhizi, including the silencing of important P. pachyrhizi genes, and also to understand the molecular basis of soybean–P. pachyrhizi interactions.