山东省沙地葡萄茎痘相关病毒的检测

为明确沙地葡萄茎痘相关病毒(GRSPaV)在山东省发生的情况,2006-2007年在葡萄主栽区和葡萄品种资源圃进行了田间调查、样品采集和病原检测。应用GRSPaV外壳蛋白基因表达获得的多克隆抗体,经间接酶联免疫吸附试验(PTA-ELISA)和斑点酶联免疫吸附试验(Dot-ELISA)检测,在2a采集的298个样品中,125个样品为阳性反应,阳性率41.95%。125个阳性样品涉及43个品种,品种被侵染率74.14%。研究对检测的样品用RT-PCR法验证,有3对引物均扩增出了预期片段,分别为解旋酶基因340bp片段、外壳蛋白(CP)基因842bp片段和RNA聚合酶(RdRp)基因499bp片段。     

利用内标为基础的RT-PCR技术检测葡萄茎痘伴随病毒

 选取经RT-PCR检测确认带葡萄茎痘伴随病毒的‘全球红’葡萄品种。以葡萄叶片、韧皮部作为试材, 采用SDS法提取高质量总RNA作为模板, 以GRSPaV的特异互补引物引导, 反转录合成cDNA,通过PCR扩增, 获得830 bp的预期目的片段。以线粒体nad5基因为内标, 建立了GRSPaV与nad5共扩增体系, 将扩增的GRSPaV特异性片段及nad5目的片段分别克隆测序, 与NCB I中所提交的核酸序列进行比对, GRSPaV与序列号AF057136的同源性达96%; nad5与序列号D37958的同源性达96.67%。     

山东省葡萄几种主要病毒病调查及检测研究

对采自山东省不同葡萄园类别的葡萄样品,采用PTA-ELISA法和Dot-ELISA法对葡萄茎痘相关病毒(GRSPaV)进行了检测,采用DAS-ELISA法对葡萄卷叶病的3个毒原(GL-RaV-1-、2-、3)进行了检测。GRSPaV检测结果表明:检测的61个品种518个样品,阳性样品率33.6%,阳性品种率73.8%,其中资源圃样品阳性率32.7%,生产园样品阳性率34.0%。对检测到阳性样品辅以RT-PCR法验证,2对引物均扩增出了预期片段,分别为解旋酶基因340 bp片段、CP基因842 bp片段。GLRaV-1-、2-、3的检测结果表明:鲜食品种3种病原的阳性样品率分别为33.7%、7.1%、62.2%,酿酒品种阳性样品率分别为35.1%、16.2%、54.1%,综合3种病毒的阳性样品率为76.3%,品种感染率87.7%。通过该类研究对推动国内葡萄无毒化生产有重要意义。     

沙地葡萄茎痘伴随病毒双重巢式RT-PCR检测方法的建立与应用

根据GenBank数据库中的沙地葡萄茎痘伴随病毒（grapevine rupestris stem pitting-associated virus,GRSPaV）全基因组序列设计了2组巢式RT-PCR检测引物repF1/R1→repF2/R2和cp F1/R1→cpF2/R2，扩增片段分别为902 bp和438 bp。通过对第1轮PCR扩增中引物组合repF1/R1-cpF1/R1、dNTPs、Taq DNA聚合酶和c DNA用量的优化，以及第2轮PCR扩增中引物组合repF2/R2-cpF2/R2、dNTPs和Taq DNA聚合酶用量的优化，建立了GRSPaV双重巢式RT-PCR检测方法。采用该方法对109份葡萄样品进行检测，结果显示，2对普通PCR引物RSP 52/53和RSP 9F/9R的合计检出率为65.1%,2组单一巢式PCR引物repF1/R1→repF2/R2和cp F1/R1→cpF2/R2的检出率总和为93.6%，而双重巢式PCR引物组合repF1/R1-cpF1/R1→repF2/R2-cpF2/R2的检出率也达到93.6%。该技术在保证检测效率的基础上降低了检测...     

葡萄4 种病毒多重RT-PCR 检测体系的建立

 以复合感染4种病毒的‘红地球’（Red Globe）葡萄样品为试材,对影响多重PCR的dNTPS浓度、Taq酶浓度、引物浓度、退火温度及模板量进行了调整和优化,建立了能同时检测葡萄卷叶伴随病毒3（Grapevine leafroll-associated virus-3,GLRaV-3）、沙地葡萄茎痘相关病毒（Grapevine rupestris stem pitting associated virus,GRSPaV）、葡萄病毒B（Grapevine virus B,GVB）和葡萄病毒A（Grapevine virus A,GVA）的多重RT-PCR方法。灵敏度测验结果显示,多重RT-PCR与单一RT-PCR检测灵敏度基本一致。多重RT-PCR获得的特异性片段大小分别为905、546、460和196 bp,经过克隆、测序及序列比对,表明其序列与已报道的病毒序列具有较高的同源性。对7个已知带病毒的葡萄样品进行检测验证的结果表明,所建立的多重RT-PCR技术可用于大量田间样品中这些病毒的检测。     

香蕉两种主要病毒多重PCR检测方法的建立

 根据香蕉束顶病(Banana bunchy top virus, BBTV) 和香蕉花叶心腐病(Cucumber mosaic virus,CMV) 的复制酶基因、外壳蛋白基因序列分别设计特异性引物对, 在BBTV单一PCR和CMV RT-PCR优化体系的基础上, 建立了可同时检测BBTV、CMV的多重PCR检测方法。此方法可以特异地从感染BBTV和CMV的样品中扩增出2条带, BBTV (748 bp) 和CMV (557 bp) 。扩增产物序列测定结果表明, BBTV扩增产物与GenBank中其他分离物的核苷酸序列同源性为91% ～99% , CMV扩增产物与GenBank中其他分离物的核苷酸序列同源性为93%～98%。     

葡萄茎痘病毒病的RT-PCR检测

根据症状随机选取石河子大学校园内的多年生全球红、无核白等葡萄为试材,采用SDS法提取高质量总RNA作为模板,以GRSPaV的特异互补引物引导,反转录合成cDNA,通过PCR扩增,获得830bp的预期目的片段。将此目的片段纯化回收,克隆测序分析。与NCBI中的此病相关序列同源性达到96%。     

应用RT-PCR和斑点杂交法检测新疆梨树上的苹果锈果类病毒

利用自行设计的方法分离提取总RNA,通过一对特异引物,分别扩增出不同梨树品种上苹果锈果类病毒的特异片段,通过对库尔勒香梨品种上获得的特异片段回收、克隆和测序。结果表明,该片段长250bp,与已发表的AF421195同源性为99%,在此基础上利用克隆的ASSVd质粒,通过RT-PCR合成了生物素标记的cDNA探针,利用该探针对梨样品进行了斑点杂交检测,取得了很好的检测效果。进一步证明该反应体系能很好地用于梨树苹果锈果类病毒的RT-PCR检测。     

果树R基因同源序列克隆的初步研究

用2对根据已知植物抗病基因(R基因)编码的蛋白质的NBS保守区而设计的特异简并引物,对荔枝、龙眼、芦柑、柚子及银杏的基因组DNA进行体外扩增.其中一对引物(P1/P2)在荔枝、龙眼、芦柑和柚子中获得的扩增产物均表现为一条大小约500bp的明亮谱带,而银杏扩增产物的亮带则在约750bp处,且弥散在400 ～ 1000bp之间.另一对引物在荔枝、龙眼、芦柑和柚子中没有特异扩增带,而在银杏中获得了一条400 ～ 600bp的较亮的宽带.将荔枝、龙眼、芦柑和柚子的500bp特异扩增带以及银杏的400 ～ 600bp条带回收克隆,并分别筛选几类阳性克隆进行测序.共获得15个片段的序列.经比较发现,来自荔枝、龙眼、芦柑和柚子的12个片段均属于NBS-LRR类抗病基因同源序列(RGA),与已知R基因相应区段的氨基酸序列的一致性为15.5% ～ 47.1%;而3个来自银杏的片段均不是RGA,其中1个与反转录酶有较高的同源性,另2个在GeneBank中没有找到同源序列.该结果显示,应用同源扩增技术克隆果树RGA是可行的,但银杏作为古老的裸子植物,其抗病基因的结构与现代物种可能有很大差异.     

西瓜NBS类同源序列的克隆与分析(摘要)

R基因产物是植物抵抗病原物侵害的重要组成部分,在目前已经发现的植物抗病基因中,NBSLRR类占了绝大多数,在植物抗病基因中占有重要地位。NBS结构域是NBS-LRR基因编码蛋白中最保守的部分,含有8个保守基序,包括P-loop(又称Kinase-1a)、Kinase-2a、Kinase-3a和GLPL疏水结构域等。对西瓜NBS的克隆和分析将有助于筛选西瓜抗病基因及各种抗病基因的分子标记,而且通过对西瓜NBS的结构、表达和调控的研究,将有助于深入阐释西瓜的抗病机制。以根结线虫抗病西瓜材料‘红籽瓜’和感病西瓜材料‘ZDPI0006’为试材,根据西瓜NBS保守区设计简并引物及特异引物50对,根据葫芦科抗病基因序列在西瓜基因组数据库搜索同源序列,并以此设计特异引物1对,分别提取西瓜叶片g DNA和RNA并反转录成c DNA,采用PCR扩增西瓜抗病基因同源序列,琼脂糖电泳检测回收目标条带,克隆测序后结果提交到Gene Bank进行序列比对,提交至Pfam在线分析蛋白质功能,利用Clustalx与其他物种的抗病基因进行同源性分析,利用dnasp等软件进行序列多态性分析。结果表明,49对引物中共有43对引物在抗、感材料中成功扩增到目的片段,其中有4对引物在抗感材料中扩增出差异片段,简并引物W856在抗、感材料间扩增到一条约750bp的差异片段,测序结果提交至NCBI比对显示其与预测的黄瓜抗TMV的N端类似蛋白存在88%的同源性,根据葫芦科抗病基因在西瓜基因组数据库搜索同源序列设计的特异引物W6580在抗、感材料间扩增出大小一致的约800bp的片段,测序结果提交至NCBI比对,结果显示其与预测的黄瓜抗线虫类似蛋白存在90%的同源性,dnasp软件分析显示抗、感材料之间存在4个单核苷酸多态性位点。     

DNA sequencing reveals false positives during the detection of aster yellows phytoplasmas in leafhoppers

During the summer of 2001 and 2002, 850 and 865 carrot plants and 926 and 2584 leafhoppers associated with aster yellow (AY)-type disease were collected from five fields in Manitoba, Canada. DNA was extracted from 999 individual leafhoppers and 381 leaf tissues from both apparently healthy and AY-like infected carrot plants. All DNA samples were examined by PCR for the presence of phytoplasmas using three universal primer pairs P1/P6, P1/P7 and R16F2n/R2 derived from phytoplasma rDNA sequences. DNA amplification with these three primer pairs generated the expected amplification products of 1.7, 1.5 and 1.2 kb, respectively. Diluted PCR products obtained using universal primer pair P1/P6 were nested with R16F2n/R16R2n. The latter set of primers amplified DNA samples from 92 carrot plants and 83 leafhopper samples. In order to assess the diversity among insect and plant phytoplasmas, nested PCR products from all 92 carrot and 83 leafhopper samples were subjected to RFLP analysis using restriction endonucleases KpnI, MseI, and HhaI. This RFLP analysis showed similar patterns among carrot and leafhopper samples. Phytoplasmas detected in most samples belonged to the subgroup 16Sr-IA. To understand why the R16F2n/R16R2n of primers did not amplify the PCR product obtained from the first PCR in the remaining samples, four PCR products of P1/P6 from two plants (representing 16Sr-IA and 16Sr-IB) and two leafhopper samples that did not amplify with nested PCR, were used for DNA sequencing. ¹ The BLAST analysis of the obtained sequences showed that the PCR amplicons from the two carrot samples precisely matched with the GenBank sequences of known phytoplasmas. Alignments of these two sequences have shown very slight variations (transition/transversion ratio mean of 0.539) that would correspond to the minor differences at the 16S level between the 16Sr-IA and 16Sr-IB phytoplasma subgroups. The sequences of PCR products obtained from the two insect samples had similarity (>98%) with the sequences of phytoplasma in carrot except that their length differed from the carrot samples by 6 bp. They actually matched bacterial sequences from the GenBank, indicating that a single PCR using P1/P6 was not enough to detect phytoplasma in leafhoppers.     

Discovery and characterization of SNPs in Vitis vinifera and genetic assessment of some grapevine cultivars

Single nucleotide polymorphisms (SNPs) are among the current generation of molecular markers. SNPs occur at high frequencies in both plant and animal genomes and can provide broader genome coverage and reliable estimates of genetic relevance. In this study, 144 sequences, amplified by 9 pairs of primers from 16 cultivars of Vitis vinifera, were cloned. The sequence alignment of the 9 group sequences derived from 16 sample cultivars yielded 154 SNPs in a combined length of 3443 bp genomic sequences. SNPs were discovered with an average frequency of one SNP per 23 bp. The distribution of the SNPs comprised of 70% transitions, 20% transversions, 8% InDels and 2% others. A phylogenetic tree constructed from these data showed that all the 16 cultivars were separated well and grouped differently in the entire dendrogram derived from the SNP data, therefore confirming that single nucleotide polymorphisms could be an efficient and powerful method for grapevine cultivar identification and genetic diversity analysis in grapevine.     

杏鲍菇枯萎病菌PCR检测方法的建立与初步应用

以杏鲍菇枯萎病菌侧耳泛菌(Pantoea pleuroti)为试材,采用PCR引物设计的方法,通过分析P.pleuroti基因组的测序结果,设计合成并筛选出可检测P.pleuroti的引物,并研究其检测效果,以期建立P.pleuroti的高效PCR检测体系,并为科学防控杏鲍菇枯萎病提供分子基础。结果表明:K3143F/R和K37F/R 2对引物特异性强,仅P.pleuroti基因组DNA作为模板时,PCR扩增产物分别呈现1条660 bp和1条666 bp的特异性条带,15株Pantoea属细菌和3株食用菌常见病原菌的基因组DNA及阴性对照作为模板扩增产物均无条带;基于这2对引物建立的检测体系均不受杏鲍菇组织液的干扰,灵敏度高,可检测出最低3.6 pg·μL^-1的P.pleuroti基因组DNA;应用这2种体系对接种P.pleuroti 48 h后的杏鲍菇样品进行了检测,最低可检测出子实体内100 cfu的杏鲍菇枯萎病菌;此外,整体上,引物K3143F/R比K37F/R的检测效率更高。     

槜李等15个李品种S基因型鉴定及其多态性分析

利用李属S-RNase基因特异性引物,对15个供试李品种进行PCR扩增,共获得30个目的条带。对这些目的条带进行测序鉴定出15个李品种的S基因型。通过与NCBI中利用BLASTn与GenBank+EMBL+DDBJ+PDB等数据库中的序列比对,结果表明,其中9个为新S-RNases基因,对9个新S-RNases核苷酸序列进行分析发现,位于高变区内的内含子大小为141～1758bp,其同源性为33.9%(S-18～S-19)～81.6%(S-20～S-21),表现出丰富的长度和序列多态性;编码区的核苷酸序列比对结果,其同源性为73.3%(S-16～S-19)～91.7%(S-17～S-22);其推导氨基酸序列相似性为67.3%(S-16～S-19)～89.1%(S-17～S-22);包含李属S-RNase一级结构所共有的C2、C3保守区和高变区(RHV)。系统进化分析表明,9个新S-RNases与李属其它树种S-RNases聚类在一起,归属为李亚科(Prunoideae)。     

Elimination of a new ampelovirus (GLRaV-Pr) and Grapevine rupestris stem pitting associated virus (GRSPaV) from two Vitis vinifera cultivars combining in vitro thermotherapy with shoot tip culture

A new virus species designated as Grapevine leafroll associated virus-Pr (GLRaV-Pr), which is classified in a distinct phylogenetic group of the genus Ampelovirus (Closteroviridae), was recently characterized from Greek grapevine cultivars. Elimination studies of GLRaV-Pr were carried out in two grapevine cultivars, ‘Mantilaria’ and ‘Prevezaniko’, co-infected with Grapevine rupestris stem pitting associated virus (GRSPaV, Flexiviridae). Both viruses were detected by nested RT-PCR assays. Virus elimination was achieved by combining in vitro thermotherapy with meristem (≤0.2 mm) or shoot tip culture (≤0.5 cm). The survival and regeneration rate of meristems was very low. On the other hand, high survival rates were observed in the cultured shoot tips accompanied with high elimination rates for both viruses. Data obtained in this study indicate that virus elimination depends on the genotype of grapevine. The results confirmed that sanitation is easier for species of the Closteroviridae family than for GRSPaV, whereas it seems that eradication of GLRaV-Pr and GRSPaV is feasible even with larger plant tissue parts if combined with an appropriate thermotherapy profile in vitro.