松材线虫PCR快速检测方法研究

松材线虫是许多国家的检疫性有害生物 ,其形态与拟松材线虫非常相似。为克服传统的形态学鉴定的不足 ,本研究依据松材线虫rDNA基因部分序列 ,通过单个碱基的故意错配 ,设计了一对特异性引物 ,运用PCR方法 ,最终实现了对单条松材线虫的快速检测。该检测方法具有很好的实用性和稳定性     

向日葵黑茎病菌TaqMan-MGB探针实时荧光快速检测方法

 向日葵黑茎病菌是我国进境检疫性有害生物名录中的一种检疫性真菌。根据向日葵黑茎病菌及其近似种的ITS序列差异,设计并合成特异性引物和探针,建立了向日葵黑茎病菌的实时荧光PCR检测方法。特异性试验结果表明,该检测方法能特异性检测向日葵黑茎病菌;灵敏度试验结果表明,最低检测限量为20 μL反应体系中总DNA含量0.1 pg;实时荧光PCR优化反应条件为引物终浓度0.6 μmol·L^-1,探针终浓度0.3 μmol·L^-1。实际样品检测结果表明,该方法可用于疑似携带向日葵黑茎病菌样品的检测与初筛。此方法快速、灵敏,整个反应过程约1 h,检测过程完全闭管,无需PCR后续处理,为早期快速检测向日葵黑茎病菌提供了重要参考。     

应用TaqMan-MGB探针进行松材线虫的实时荧光定量检测技术研究

 松材线虫是国际公认的最重要的检疫性有害生物之一,也是我国2类检疫危险性有害生物,我国口岸多次从货物的木质包装中截获该线虫。由于松材线虫与拟松材线虫在形态上极其相似,难以区分,幼虫更无法用于鉴定。传统的形态学鉴定、生化以及其他分子技术等方法存在费时、准确度不高、灵敏度低等缺点,不易形成标准。我们设计筛选一对引物以及一条MGB探针,对松材线虫进行实时荧光PCR检测。建立了一条从1 pg到10⁴pg标准曲线,相关系数r=0.965。该检测方法省时、准确、快速、无污染。     

Detection of the pine wood nematode using a real-time PCR assay to target the DNA topoisomerase I gene

A species-specific real-time PCR assay targeting the DNA topoisomerase I gene has been developed to detect Bursaphelenchus xylophilus. The specificity of the assay was confirmed by the lack of amplification of genomic DNA from other Bursaphelenchus or Seinura species. The sensitivity test showed that the limit of the reaction was 0.01 ng of genomic DNA or one individual nematode, as small as an egg. The validity of the real-time PCR assay was evaluated by analyzing mixed nematode samples extracted from diseased pine trees in which B. xylophilus was associated with several closely related species, B. mucronatus, B. hofmanni, Aphelenchoides macronucleatus, S. lii and S. wuae. These results demonstrate the potential of the assay to provide rapid, specific and sensitive molecular identification of B. xylophilus for use in pest risk assessment and quarantine regulations.     

利用TaqMan探针实时荧光PCR方法检测香石竹细菌性萎蔫病菌

 根据香石竹细菌性萎蔫病菌基因组16S-23S rRNA保守序列,设计并合成了一对特异性引物和一条具有稳定点突变特异性探针,建立了对香石竹细菌性萎蔫病菌的TaqMan实时荧光PCR检测方法。除香石竹细菌性萎蔫病菌外,还对其他7种病原细菌菌株进行了荧光PCR检测。结果表明,只有香石竹细菌性萎蔫病菌产生荧光,其他病原细菌均没有荧光产生。与常规PCR相比,实时荧光PCR检测特异性强,灵敏度高,能检测到浓度为0.4 pg/μL的DNA,且能直接用于苗木等样品的检测,适合病害的快速诊断和口岸检验检疫应用。      

A nested PCR assay targeting the DNA topoisomerase I gene to detect the pine wood nematode, <Emphasis Type="Italic">Bursaphelenchus xylophilus</Emphasis>

The pine wood nematode (PWN), Bursaphelenchus xylophilus, is a disastrous pathogen of the pine forests in East Asia and Europe. Plant quarantine is one of the most important ways to prevent its infection in current situation. A nested polymerase chain reaction (PCR) assay targeting the topoisomerse I gene has been developed to detect PWN in this study. To assess the specificity of the assay, 44 morphologically characterized nematode isolates including B. xylophilus, B. mucronatus, B. hofmanni, Seinura wuae, S. lii and Aphelenchoides macronucleatus were tested. Positive reactions characterized by amplification product of 509 bp were shown from all isolates of PWN. The nested PCR assay can detect 50 femtogram (fg) of template DNA or one individual nematode, as small as an egg. The validity was evaluated by analyzing the nematode samples extracted from the nematode-infested wood in the field. These results show that the assay is a specific, sensitive method for detection of PWN with the potential in relation to the pest risk assessment and quarantine regulations.     

木质包装中松材线虫的实时荧光PCR检测

松材线虫是进境木质包装中的重要检疫对象之一。本研究以进境木质包装中截获的12种伞滑刃属线虫,包括4种不同来源的松材线虫、3种不同来源的拟松材线虫、豆伞滑刃线虫、大尖尾伞滑刃线虫、阿苏里伞滑刃线虫、伯氏伞滑刃线虫及拟小刺伞滑刃线虫为材料,进行实时荧光PCR检测。结果显示,仅松材线虫可观察到明显的荧光强度变化,而其他线虫的荧光强度没有变化。通过研磨样品的方法,提取单条松材线虫的DNA,进行实时荧光PCR试验,检测成功率为100%,且不论是雄虫、雌虫或幼虫均能检测出来。该研究对于我国口岸进境木质包装中松材线虫的检测具有一定的实际意义。     

基于TaqMan MGB探针的葡萄茎枯病菌实时荧光PCR检测方法

 葡萄茎枯病菌是我国进境植物检疫性有害生物。带菌植物材料是病害传播的重要载体,准确、灵敏、快速的检测方法是严格执行口岸检疫措施及研究病害防控措施的有力工具。根据葡萄茎枯病菌及其近似种的细胞骨架蛋白(Actin)基因序列差异,设计并合成1对引物和1条特异性TaqMan-MGB探针,建立了葡萄茎枯病菌的实时荧光PCR检测方法。通过对反应体系的优化,确定了葡萄茎枯病菌的实时荧光PCR最佳反应条件:引物终浓度为0.6 μmol·L^-1,探针终浓度为0.6 μmol·L^-1。灵敏度试验结果显示,最低检测限为总DNA含量20 pg(20 μL反应体系)。此方法快速灵敏,整个反应1 h即可完成,检测过程完全闭管,无需PCR产物后续处理,为快速检测葡萄茎枯病菌提供了重要参考。该方法用于口岸疑似菌株检测,可成功检测出葡萄茎枯病菌。本研究建立的基于TaqMan MGB探针的荧光定量PCR检测方法为葡萄茎枯病菌的早期快速检测监测提供了有力工具。     

基于TaqMan MGB探针的葡萄茎枯病菌实时荧光PCR检测方法

 葡萄茎枯病菌是我国进境植物检疫性有害生物。带菌植物材料是病害传播的重要载体,准确、灵敏、快速的检测方法是严格执行口岸检疫措施及研究病害防控措施的有力工具。根据葡萄茎枯病菌及其近似种的细胞骨架蛋白(Actin)基因序列差异,设计并合成1对引物和1条特异性TaqMan-MGB探针,建立了葡萄茎枯病菌的实时荧光PCR检测方法。通过对反应体系的优化,确定了葡萄茎枯病菌的实时荧光PCR最佳反应条件:引物终浓度为0.6 μmol·L^-1,探针终浓度为0.6 μmol·L^-1。灵敏度试验结果显示,最低检测限为总DNA含量20 pg(20 μL反应体系)。此方法快速灵敏,整个反应1 h即可完成,检测过程完全闭管,无需PCR产物后续处理,为快速检测葡萄茎枯病菌提供了重要参考。该方法用于口岸疑似菌株检测,可成功检测出葡萄茎枯病菌。本研究建立的基于TaqMan MGB探针的荧光定量PCR检测方法为葡萄茎枯病菌的早期快速检测监测提供了有力工具。     

Duplex PCR 快速检测松材线虫

利用duplex PCR技术对松材线虫(Bursaphelenchus xylophilus)与拟松材线虫(B. mucronatus)的rDNA部分核苷酸序列扩增.根据松材线虫与拟松材线虫的ITS1序列区别,设计出特异性引物,检测松材线虫的存在;在5.8S,28S保守序列区设计通用引物,检测伞滑刃线虫的存在.     

松材线虫rDNA的测序和PCR-SSCP分析

 本文为克服形态鉴定的不足,用分子生物学的方法鉴别松材线虫。线虫核糖体DNA(r DNA)的内部转录间隔区(ITS1)区(约308bp)的测序结果显示:松材线虫种内区别很小,不超过1bp;拟松材线虫种内区别较大,最大达7bp;这2种线虫的种间区别为32~39bp。根据以上测序结果,本文结合单条线虫DNA的提取技术,对14个松材线虫和拟松材线虫样本进行了单链构象多态性(PCR-SSCP)分析,结果表明PCR-SSCP分析技术可明确区分这2种线虫,该技术可为单条松材线虫的鉴定提供一套灵敏而可靠的方法。     

Using the TxtAB operon to quantify pathogenic Streptomyces in potato tubers and soil

The phytotoxin thaxtomin, produced by plant pathogenic Streptomyces species, is the only known pathogenicity determinant for common scab diseases of potato and other root and tuber crops. Genes encoding thaxtomin synthetase (txtAB) are found on a pathogenicity island characteristic of genetically diverse plant pathogenic Streptomyces species. In this study, an SYBR Green quantitative real-time polymerase chain reaction (PCR) assay using primers designed to anneal to the txtAB operon of Streptomyces was developed to quantify pathogenic bacterial populations in potatoes and soil. The real-time PCR assay was specific for pathogenic Streptomyces strains. The detection limit of the assay was 10 fg of the target DNA, or one genome equivalent. Cycle threshold (Ct) values were linearly correlated with the concentration of the target DNA (correlation coefficient R(2) = 0.99) and were not affected by the presence of plant DNA extracts, indicating the usefulness of the assay for quantitative analyses of the pathogenic bacteria in plant tissues. The amount of pathogenic Streptomyces DNA in total DNA extracts from 1 g asymptomatic and symptomatic tubers was quantified using the assay and ranged from 10(1) to 10(6) pg. A standard curve was established to quantify pathogenic Streptomyces in soil. Using the standard curve, numbers of pathogenic Streptomyces colony forming units were extrapolated to range from 10(3) to 10(6) per gram of soil from potato fields where common scab was found. This real-time PCR assay using primers designed from the txtAB operon allows rapid, accurate, and cost effective quantification of pathogenic Streptomyces strains in potato tubers and in soil.     

3种根萤叶甲实时荧光PCR检测技术研究

根萤叶甲属(Diabrotica)被我国列为进境植物检疫性有害生物,该属中的玉米根萤叶甲(D.virgifera virgifera)、十一星根萤叶甲(D.undecimpunctata)、巴氏根萤叶甲(D.barberi)是北美的主要农业害虫。为了建立一种快速的分子鉴定方法以鉴定这3种根萤叶甲,本研究从田间采集的成虫样品中获得其部分mtDNA COI序列,与Gen Bank中的相关序列进行比对,设计筛选出3种根萤叶甲的特异性引物和TaqMan探针,并进行实时荧光PCR特异性和灵敏度检测。特异性检测结果表明,用目标种根萤叶甲DNA和其特异性探针和引物进行实时荧光PCR反应时,在30个循环反应内(Ct值30)有近S型扩增曲线出现,同时其他种均无荧光信号增长。此外,灵敏度结果显示,玉米根萤叶甲和巴氏根萤叶甲可检测的最小DNA模板浓度,即实时荧光PCR反应的灵敏度为0.1 ng/μL,十一星根萤叶甲为0.01 ng/μL。     

Real-time PCR detection systems for Flavescence dorée and Bois noir phytoplasmas in grapevine: comparison with conventional PCR detection and application in diagnostics

A new real-time PCR detection system was developed for grapevine yellows (GY) using TaqMan minor groove binder probes and including two amplicons for group-specific detection of Flavescence dorée (FD) and Bois noir (BN) phytoplasmas, plus a universal phytoplasma amplicon. FD and BN amplicons were designed to amplify species-specific genomic DNA fragments and the universal amplicon to amplify the 16S ribosomal DNA region. Efficiency of PCR amplification, limit of detection, range of linearity and dynamic range were assessed for all three amplicons. The specificity of detection systems was tested on several other isolates of phytoplasmas and bacteria and on healthy field grapevine and insect samples. No cross-reactivity with other phytoplasma strains, plant or insect DNA was detected. The assay was compared with conventional PCR on more than 150 field grapevine, insect and field bindweed samples. Real-time PCR showed higher sensitivity as phytoplasmas were detected in several PCR-negative and in all PCR-positive samples. A data-mining analysis of results from both detection approaches also favoured real-time PCR over conventional PCR diagnostics. The developed procedure for detection of phytoplasmas in grapevine also included amplification of plant DNA co-extracted with phytoplasmic DNA, providing additional quality control for the DNA extraction and PCR amplification for each sample. The newly developed assay is a reliable, specific and sensitive method easily applicable to high-throughput diagnosis of GY.     

单管实时荧光RT PCR方法同时检测大豆种子中的菜豆荚斑驳病毒和烟草环斑病毒

 本研究建立了大豆种子中菜豆荚斑驳病毒（BPMV）和烟草环斑病毒（TRSV）单管双重实时荧光PCR检测方法。将含有相同浓度的分别带有BPMV和TRSV CP基因的质粒溶液作为阳性对照,以受两种病毒侵染的大豆种子作为待测样品进行实时荧光PCR检测,结果表明能从同一管中同时检测出这两种病毒而不发生交叉反应。尽管在阳性对照中,二者的检测限相当,均可达到35 pg/mL,但在实际应用中,两种病毒由于在大豆种子中的浓度不一致而存在一定的差别。该方法快速、灵敏、简便,同时特异性更强,在出入境检验检疫中具有广泛的应用前景。     

Use of real-time PCR to examine the relationship between disease severity in pea and <Emphasis Type="Italic">Aphanomyces euteiches</Emphasis> DNA content in roots

Aphanomyces euteiches causes severe root rot of peas. Resistance is limited in commercial pea cultivars. Real-time fluorescent PCR assay specific for A. euteiches was used to study the relationship between disease severity and pathogen DNA content in infected peas. Five pea genotypes ranging in levels of resistance were inoculated with five isolates of A. euteiches. Plants were visually rated for disease development and the amount of pathogen DNA in roots was determined using the PCR assay. The susceptible genotypes Genie, DSP and Bolero tended to have significantly more disease and more pathogen DNA than the resistant genotypes 90-2079 and PI 180693. PI 180693 consistently had less disease, while 90-2079 had the lowest amount of pathogen DNA. The Spearman correlation between pathogen DNA quantity and disease development was positive and significant (P < 0.05) for three isolates, but was not significant for two other isolates. This suggests that the real-time PCR assay may have limited application as a selection tool for resistance in pea to A. euteiches. Its utility as a selection tool would be dependent on the correlation between disease development and pathogen DNA content for a given pathogen isolate. The accuracy and specificity of the real-time PCR assay suggests considerable application for the assay in the study of mechanisms of disease resistance and the study of microbial population dynamics in plants.     

Detection and Quantification of Spongospora subterranea in Soil, Water and Plant Tissue Samples Using Real-Time PCR

A sensitive real-time polymerase chain reaction (PCR) assay was developed for the quantification of Spongospora subterranea, the cause of powdery scab and root galling in potato, and the vector of Potato mop top virus. A specific primer pair and a fluorogenic TaqMan® probe were designed to perform a quantitative assay for the detection of S. subterranea in soil, water and plant tissue samples. The assay was tested using DNA from cystosori, zoospores, plasmodia and zoosporangia of the pathogen. DNA was extracted directly from cystosori suspended in water and from clay soil with varying levels of added cystosori. DNA obtained from zoospores released into nutrient solution by cystosori in the presence of tomato bait plants was also tested, as was DNA from plasmodia and zoosporangia in infected tomato roots. In many cases, detection was successful even at low inoculum levels. This specific quantitative assay could therefore be a useful tool for studying the biology of S. subterranea, and for the optimisation of disease avoidance and control measures.     

Guidance on sampling to detect pine wood nematode Bursaphelenchus xylophilus in trees, wood and insects

The pine wood nematode Bursaphelenchus xylophilus is the causal agent of pine wilt disease. It is a quarantine pest for most countries in the world. Surveys for the occurrence of the nematode may be necessary in the framework of internationally agreed phytosanitary standards, in order to delimit infested areas or to demonstrate the absence of B .  xylophilus and thus to identify pest free areas. Import inspections of wood and wood products also need sound monitoring systems. It is obvious that the quality of survey/monitoring, as well as the results of diagnosis, are strongly dependent on the sampling procedure. Although, in the literature, numerous results of surveys and monitoring are documented, sampling procedures vary and there is no scientific or statistically based sampling system published for B. xylophilus . The current paper relates background information concerning the biology of the nematode, its vector beetles and the development of pine wilt disease and the influence of these factors on sampling procedures, and attempts to define a more systematic methodology.     

Real-Time Fluorescent Polymerase Chain Reaction Detection of Phytophthora ramorum and Phytophthora pseudosyringae Using Mitochondrial Gene Regions

ABSTRACT A real-time fluorescent polymerase chain reaction (PCR) detection method for the sudden oak death pathogen Phytophthora ramorum was developed based on mitochondrial DNA sequence with an ABI Prism 7700 (TaqMan) Sequence Detection System. Primers and probes were also developed for detecting P. pseudosyringae, a newly described species that causes symptoms similar to P. ramorum on certain hosts. The species-specific primer-probe systems were combined in a multiplex assay with a plant primer-probe system to allow plant DNA present in extracted samples to serve as a positive control in each reaction. The lower limit of detection of P. ramorum DNA was 1 fg of genomic DNA, lower than for many other described PCR procedures for detecting Phytophthora species. The assay was also used in a three-way multiplex format to simultaneously detect P. ramorum, P. pseudosyringae, and plant DNA in a single tube. P. ramorum was detected down to a 10(-5) dilution of extracted tissue of artificially infected rhododendron 'Cunningham's White', and the amount of pathogen DNA present in the infected tissue was estimated using a standard curve. The multiplex assay was also used to detect P. ramorum in infected California field samples from several hosts determined to contain the pathogen by other methods. The real-time PCR assay we describe is highly sensitive and specific, and has several advantages over conventional PCR assays used for P. ramorum detection to confirm positive P. ramorum finds in nurseries and elsewhere.     

Comparison of PCR assays for detection and quantification of Phomopsis sclerotioides in plant and soil

We developed a real-time PCR assay using a TaqMan probe (TM-qPCR) for specific detection and quantification of Phomopsis sclerotioides, causal agent of black root rot of cucurbit crops. The design of the primer sets and hybridization probe was based on the internal transcribed spacer region of the ribosomal DNA. The TM-qPCR assay was compared with a conventional, standard PCR (sPCR) assay and on a quantitative real-time PCR (SG-qPCR) assay based on SYBR Green I. The TM-qPCR assay had a detection limit of ca. 0.4 fg of P. sclerotioides DNA, which was approximately 100 times more sensitive than the sPCR assay and almost equivalent to the SG-qPCR assay. The TM-qPCR and SG-qPCR assays both were able to detect various quantities of P. sclerotioides DNA from diseased plants and infested soils, including DNA levels that were not detectable by the sPCR assay. However, the TM-qPCR was advantageous for samples containing PCR-inhibiting substances because its multiplex real-time PCR function allows the adjustment of cycle threshold values with an internal control. Based on the high specificity and sensitivity required for analyzing DNA in natural samples, the newly developed TM-qPCR assay was the most reliable tool for rapidly detecting and quantifying P. sclerotioides in plant and soil samples.