4种葡萄卷叶伴随病毒多重RT-PCR检测

 葡萄受卷叶伴随病毒侵染后,树势减弱,抗逆性变差,果穗着色不良,成熟期推迟,含糖量降低。目前已报道11种葡萄卷叶伴随病毒(Grapevine leafroll-associated virus,GLRaV)。为提高检测效率,降低检测费用,本文在研究单个卷叶伴随病毒RT-PCR检测技术基础上,对4种葡萄卷叶伴随病毒的多重RT-PCR模板浓度、引物浓度和退火温度进行优化,建立了同时检测葡萄卷叶伴随病毒-1(GLRaV-1)、葡萄卷叶伴随病毒-3(GLRaV-3)、葡萄卷叶伴随病毒-4(GLRaV-4)和葡萄卷叶伴随病毒-5(GLRaV-5)的多重RT-PCR技术体系。模板浓度、引物浓度、Taq DNA聚合酶浓度、退火温度和循环次数对多重RT-PCR检测结果均有较大影响,而在一定范围内改变延伸时间和dNTP浓度对检测结果影响较小。对4种葡萄卷叶伴随病毒的PCR产物进行克隆和测序,扩增基因片段与GenBank中登录的基因序列同源性为95%~99%。所建立的多重RT-PCR技术检测田间样品效果良好。     

基于DPO引物的SYBR Green I实时荧光RT-PCR检测葡萄卷叶伴随病毒3号

葡萄卷叶病是葡萄上一种重要的病毒病,在国内分布较为普遍,引起该病的葡萄卷叶伴随病毒(Grapevine leafroll-associated virus,GLRaV)是由多种病毒单独或复合侵染造成.已报道的GLRaVs至少有5种,其中GLRaV-3是葡萄卷叶病毒属Ampleovirus典型成员(Ling et a1.,2004).目前,检测GL-RaV-3的方法主要有指示植物法、酶联免疫吸附法、分子生物学检测法等,而这几种技术均存在不足.SYBR Green Ⅰ实时荧光RT-PCR技术关键要避免引物之间、引物与其它模板之间的非特异性互作干扰.由于DPO引物自身以及引物之间很少形成二级结构且对退火温度不敏感等特点(Chun et al.,2007),因此,本研究结合SYBR Green和DPO引物的各自优点,建立一种特异性强、灵敏度高的GL-RaV-3检测方法,以期为葡萄卷叶病毒的快速检测及预防提供技术支持.     

马铃薯4种病毒多重PCR检测体系的建立

我国马铃薯病毒主要有马铃薯Y病毒(PVY)、马铃薯X病毒(PVX)、马铃薯S病毒(PVS)、马铃薯卷叶病毒(PLRV),常发生复合侵染。根据GenBank中4种马铃薯病毒的外壳蛋白(coat protein,CP)基因全长设计引物,通过RT-PCR扩增得到4种病毒CP基因全长片段,测序结果显示序列同源性96%以上;针对4种病毒CP基因的保守序列分别设计引物,在一个PCR体系中同步对4种病毒进行扩增,得到421、202、516、330bp的特异性条带,优化建立了能同步检测PVY、PVX、PVS和PLRV的多重RT-PCR检测体系。检测结果证明优化后的多重RT-PCR体系能在田间样品中快速、高效地检测出4种病毒。     

应用特异引物和简并引物检测百合斑驳病毒

应用特异引物和简并引物对百合斑驳病毒(LMoV)进行RT-PCR检测.结果表明,特异引物和简并引物均能从LMoV感病百合组织中扩增出与预期大小一致的目标片段,而健康组织无此扩增产物,简并引物还能从感染TBV的郁金香病叶中扩增出目标片段.将感染LMoV组织总RNA以10倍梯度稀释成不同浓度检测,特异引物检测的灵敏度为10-4,简并引物的灵敏度为10-3.对特异引物的PCR产物进行克隆和测序,序列分析表明与LMoV不同分离物的序列同源性为90%～99%,说明采用本研究确定的方法检测百合斑驳病毒结果准确可靠.     

双重RT-PCR同步检测马铃薯A病毒和马铃薯卷叶病毒

根据马铃薯A病毒全基因序列和马铃薯卷叶病毒衣壳蛋白区序列分别设计PVA和PLRV的特异性引物,应用双重RT-PCR同步检测马铃薯A病毒和马铃薯卷叶病毒,分别得到300bp和222bp大小的扩增片段.试验从反转录、PCR等方面对双重RT-PCR同步检测2种病毒进行了探索和优化.结果表明反转录反应中dNTPs浓度、2种病毒下游引物浓度比例以及PCR反应中Mg2+浓度对双重RT-PCR同时检测PVA和PLRV有较大的影响.     

番茄斑萎病毒属6种病毒的多重RT-PCR检测

根据番茄斑萎病毒属(Tospovirus)中6种病毒S RNA上的N基因序列设计特异性引物,建立可同时检测这6种Tospovirus病毒的多重PCR体系。多重PCR扩增结果显示,番茄环纹斑点病毒(776 bp)、甜瓜黄斑病毒(505 bp)、鸢尾黄斑病毒(296 bp)、凤仙花坏死斑病毒(221 bp)、番茄斑萎病毒(175 bp)和番茄褪绿斑病毒(110 bp)均出现清晰的目标条带,各病毒的特异性引物不会对其他病毒产生非特异性扩增。本研究建立的6种Tospovirus病毒的多重PCR检测方法,有助于提高目标病毒的检测效率。     

三种甘薯病毒多重RT-PCR检测技术的建立

本文根据GenBank中甘薯G病毒(SPVG)、甘薯卷叶病毒(SPLCV)和甘薯羽状斑驳病毒(SPFMV)外壳蛋白(CP)基因序列设计特异引物,对多重RT-PCR退火温度、延伸温度、模板浓度、引物浓度进行改良优化,建立能同时检测3种甘薯病毒的多重RT-PCR方法。该方法能同时扩增出SPVG、SPLCV和SPFMV特异片段,其大小分别是800、276和570bp。测序结果表明,扩增出的3种病毒序列与相应参考序列相似性达到98%以上。灵敏度分析结果表明,多重RT-PCR方法能够检测cDNA的量为0.1ng。应用建立的多重RT-PCR检测方法对田间样品进行检测,结果显示该方法可以特异、快速、灵敏地同时检测3种甘薯病毒。这些研究结果可为甘薯病毒检测提供参考。     

一种豇豆重花叶病毒RT-PCR检测方法的研究

对一种豇豆重花叶病毒(Cowpeas evere mosaic virus,CPSMV)反转录PCR分子检测方法进行了研究。利用从美国菌种保藏中心和德国微生物毒株保藏中心引进的CPSMV标准毒株,设计了一对特异性简并引物(CPSMVf/CPSMVr),建立了CPSMVRT-PCR检测方法。该方法具有良好的扩增反应及特异性,灵敏度可达1pg的总病叶组织RNA量。CPSMV双抗夹心酶联免疫法(DAS-ELISA)灵敏度为10μg叶组织。该方法适用于豇豆等豆类蔬菜种子及种苗中对豇豆重花叶病毒的快速检测。     

侵染唐菖蒲和百合3种病毒的多重RT-PCR检测方法

本文针对侵染百合和唐菖蒲的南芥菜花叶病毒、百合无症病毒和菜豆黄花叶病毒,建立了同时检测3种病毒的多重RT-PCR检测方法.该方法根据上述3种病毒保守的衣壳蛋白基因序列,设计特异性引物,优化了反应条件.通过对9种不同寄主和6种病毒的检测,验证该检测方法具有很高的特异性、稳定性,其灵敏度为植物总RNA稀释101～102倍.特别是,该方法缩短了检测周期,适合于植物病毒快速检测工作的需要.     

五种烟草病毒TMV、CMV、TEV、PVY及TVBMV的多重RT-PCR同步检测

 我国烟草病毒主要有烟草花叶病毒(TMV)、黄瓜花叶病毒(CMV)、烟草蚀纹病毒(TEV)、马铃薯Y病毒(PVY)和烟草脉带花叶病毒(TVBMV),通常发生复合侵染。本研究对我国5种烟草病毒的外壳蛋白基因部分序列设计引物,通过优化引物和模板浓度,摸索扩增参数,在一个体系中成功对5种病毒复合侵染的烟草材料进行多重RT-PCR扩增,得到237、273、347、456和547 bp共5条特异性条带,建立了能同时检测TMV、CMV、TEV、PVY和TVBMV的多重RT-PCR检测体系。对田间样品检测结果证明,多重RT-PCR体系能够同时检测5种病毒,并且灵敏度高。     

No evidence of transmission of grapevine leafroll-associated viruses by phylloxera (<Emphasis Type="Italic">Daktulosphaira vitifoliae</Emphasis>)

Grapevine leafroll disease is associated with several species of phloem-limited grapevine leafroll-associated viruses (GLRaV), some of which are transmitted by mealybugs and scale insects. The grape phylloxera, Daktulosphaira vitifoliae (Fitch) Biotype A (Hemiptera: Phylloxeridae), is a common vineyard pest that feeds on the phloem of vine roots. There is concern that these insects may transmit one or more GLRaV species, particularly GLRaV-2, a species in the genus Closterovirus. A field survey was performed in vineyards with a high incidence of grapevine leafroll disease and D. vitifoliae was assessed for acquisition of GLRaV. In greenhouse experiments, the ability of D. vitifoliae to transmit GLRaV from infected root sections or vines to co-planted virus-free recipient vines was tested. There were no GLRaV-positive D. vitifoliae in the field survey, nor did D. vitifoliae transmit GLRaV-1, ?2, ?3, or -4LV in greenhouse transmission experiments. Some insects tested positive for GLRaV after feeding on infected source vines in the greenhouse, however there was no evidence of virus transmission to healthy plants. These findings, in combination with the sedentary behaviour of the soil biotype of D. vitifoliae, make it unlikely that D. vitifoliae is a vector of any GLRaV.     

Detection of four calla potyviruses by multiplex RT-PCR using nad5 mRNA as an internal control

Dasheen mosaic virus (DsMV), Turnip mosaic virus (TuMV), Konjac mosaic virus (KoMV) and Zantedeschia mild mosaic virus (ZaMMV) are important potyviruses previously identified in calla lily plants in Taiwan. In order to save time and cost of virus detection, a multiplex RT-PCR assay was developed for these calla potyviruses. Specific primers for each virus were designed based on the sequences of 3′ terminal region of respective viruses. To prevent false negative results, a primer pair specific to plant mitochondrial nad5 mRNA was used to produce a 185-bp fragment as an internal control of RT-PCR. The specificities of primers were confirmed by means of simplex and multiplex PCR assays. Optimal primer concentration ratio was identified by multiplex PCR assay. Total RNAs purified from virus-infected plants were used directly or mixed in different combinations, and then tested by multiplex RT-PCR. The result indicated that the expected RT-PCR products could be specifically amplified and identified on the basis of their molecular sizes. The detection sensitivity of multiplex RT-PCR was 25–625 times higher than that of indirect-ELISA (I-ELISA) depending on the virus. When applied to field surveys, multiplex RT-PCR could detect more single as well as mixed infection samples than I-ELISA. Accordingly, our multiplex RT-PCR assay provides a simple, rapid and reliable method for multiple potyvirus detection in calla lily.     

A Multiplex Real-Time Polymerase Chain Reaction (TaqMan) Assay for the Simultaneous Detection of Meloidogyne chitwoodi and M. fallax

ABSTRACT This study describes a multiplex real-time polymerase chain reaction (PCR) approach for the simultaneous detection of Meloidogyne chitwoodi and M. fallax in a single assay. The approach uses three fluorogenic minor groove binding (MGB) TaqMan probes: one FAM-labeled to detect M. chitwoodi, one VIC-labeled to detect M. fallax, and one NED-labeled to detect the internal amplification control (IAC) to monitor false negative results. One common primer set is used for the amplification of part of the internal transcribed spacer (ITS) region of M. chitwoodi and M. fallax and one primer set for the amplification of the IAC. The test enabled detection of M. chitwoodi and/or M. fallax in DNA samples extracted from batches of juveniles, from single juveniles, and from infected plant material. Compared with current assays to detect M. chitwoodi and M. fallax, the multiplex real-time PCR offers the following advantages: it is faster because the test can simultaneously detect both quarantine species without the need for post-PCR processing; and it is at least 10 times more sensitive than a comparable regular PCR also targeting the ITS sequence. Inclusion of the IAC facilitates the interpretation of the FAM and VIC cycle threshold (Ct) values and can prevent the scoring of false negative results when FAM, VIC, and NED Ct values are high. The test allows precise quantification when only one of the two species is present in the sample. However, experiments with mixtures of genomic DNA of M. chitwoodi and M. fallax revealed that the ability of the multiplex real-time PCR assay to detect small quantities of DNA of one species is reduced when large quantities of DNA of the other species are present.     

Development of a specific molecular tool for the detection of epidemiologically active mulberry causing-disease strains of Ralstonia solanacearum phylotype I (historically race 5-biovar 5) in China

Ralstonia solanacearum causes bacterial wilt disease in many plant species, including mulberry. Here, we used a suppression subtractive hybridization (SSH) approach to identify specific DNA fragments in R. solanacearum race 5-biovar 5. The genome of the R. solanacearum M7 strain was subtracted from that of the GMI1000 strain, resulting in the identification of 85 subtracted fragments. The primer set MG67-F/R for identification of Ralstonia solanacearum race 5-biovar 5 strains was designed on the basis of the clone MG67 sequence. Furthermore, a multiplex PCR was developed by using the primer set MG67-F/MG67R in combination with the species-specific primer pair 759/760. A 156 bp r5-bv5-specific fragment, together with a 282 bp species-specific fragment, was amplified from all tested R. solanacearum r5-bv5 strains. The sensitivity of the multiplex PCR made it possible to detect concentrations as low as 10² CFU ml^?1 of pure culture. Moreover, the r5-bv5-specific multiplex PCR was successfully applied to detect Ralstonia solanacearum race 5-biovar 5 strains in diseased mulberry samples. Therefore, the multiplex PCR assay can be used as a reliable diagnostic technique to enable researchers to rapidly identify isolates of R. solanacearum race 5-biovar 5.     

Detection of <Emphasis Type="Italic">Agrobacterium vitis</Emphasis> by PCR using novel <Emphasis Type="Italic">virD2</Emphasis> gene-specific primers that discriminate two subgroups

Tumour tissue samples were collected from vines grown in various regions of Italy and other parts of Europe and extracted for detection of Agrobacterium vitis. Fifty strains were isolated on agar plates and screened by PCR with consensus primers from the virD2 gene. They were confirmed as A. vitis with a species-specific monoclonal antibody. The isolates were further analyzed by PCR for their opine synthase genes and ordered into octopine, nopaline and vitopine strains. Primers designed on the octopine synthase gene did not detect octopine strains of Agrobacterium tumefaciens. For quantitative PCR, virD2 fragments were sequenced: two classes of virD2 genes were found and two primer sets designed, which detected octopine and nopaline strains or only vitopine strains. For simultaneous identification of all opine-type strains, multiplex real-time PCR with either primer pair and SYBR Green was performed: the combined sets of primers gave signals with DNA from any A. vitis strain. Specificity of the new primers for real-time PCR was evaluated using several unidentified bacterial isolates from grapevines and other plant species. An elevated level of non-specific background was observed when the combined primer sets were used in multiplex PCR assays. The real-time PCR protocol was also used to detect A. vitis cells directly from grapevine tumours; avoiding direct isolation procedures a sensitivity in the range of one to ten cells per assay was found. Inhibition of the PCR reaction by plant material was overcome by treating tumour extracts with a DNA purification kit as a step for the isolation of nucleic acids.     

多重PCR检测转基因菜籽粕中的转基因成分

以油菜内源基因PEP、抗除草剂基因(BAR、PAT)、筛选基因NPTII、常见启动子(CaMV35S、FMV35S)和终止子NOS为检测对象,通过研究不同引物终浓度的配比以及退火温度对转基因菜籽粕多重PCR检测的影响,建立了菜籽粕转基因成分7重PCR检测体系。结果表明,本研究所建立的检测体系能有效检测出菜籽粕以及其他作物(大豆、玉米、大米、棉花籽)中的转基因成分,检测过程简便、准确,值得推广应用。     

PCR-based Assays to Assess Wheat Varietal Resistance to Blotch (Septoria Tritici and Stagonospora Nodorum) and Rust (Puccinia Striiformis and Puccinia Recondita) Diseases

A multiplex Polymerase Chain Reaction (PCR) assay was developed to detect and quantify four fungal foliar pathogens in wheat. For Septoria tritici (leaf blotch) and Stagonospora nodorum (leaf and glume blotch), the -tubulin gene was used as the target region. Diagnostic targets for Puccinia striiformis (stripe or yellow rust) and P. recondita (brown rust) were obtained from PCR products amplified with -tubulin primer sequences. Final primer sets were designed and selected after being tested against several fungi, and against DNA of infected and healthy wheat leaves. For detection of the four pathogens, PCR products of different sizes were amplified simultaneously, whereas no products were generated from wheat DNA or other non-target fungi tested. The presence of each of the diseases was wheat tissue- and cultivar specific. Using real-time PCR measurements with the fluorescent dye SYBR Green I, PCR-amplified products could be quantified individually, by reference to a standard curve generated by adding known amounts of target DNA. Infection levels for each of the diseases were measured in the flag leaf of 19 cultivars at Growth Stage (GS) 60–64 in both 1998 and 1999. The infection levels for the cultivars were ranked, and showed, with a few exceptions, a good correlation with the NIAB Recommended List for winter wheat, which is based on visual assessment of symptoms. With PCR, the presence of the different pathogens was accurately diagnosed and quantification of pre-symptomatic infection levels was possible. Although sampling and DNA detection methods need further optimisation, the results show that multiplex PCR and quantitative real-time PCR assays can be used in resistance screening to measure the interaction between different pathogens and their hosts at different growth stages, and in specific tissues. This should enable an earlier identification of specific resistance mechanisms in both early-stage breeding material and field trials.     

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.