4种常见根结线虫基因组DNA的RAPD分析

 用120个随机引物对4种常见根结线虫10个小种和类型进行了全基因组随机扩增DNA多态性(RAPD)分析,筛选出的11个适宜引物共扩增出91条RAPD谱带,86条是多态性谱带,占总谱带的94.5%;OPL12、OPK01对4种根结线虫种及其小种扩增的谱型有明显的特异性。聚类分析显示在种间水平上4种根结线虫中花生根结线虫和爪哇根结线虫亲缘关系最近,遗传距离为0.532,北方根结线虫与另外3种根结线虫的亲缘关系最远,平均遗传距离为0.786;种下水平上同种根结线虫的不同小种和类型间存在不同程度的遗传差异,南方根结线虫4个生理小种间,花生根结线虫2个生理小种间亲缘关系较近,爪哇根结线虫2个酯酶谱带类型间,北方根结线虫2个细胞生物学小种间遗传差异较大。在RAPD技术的基础上探索根结线虫分类鉴定的分子方法有着良好的前景。     

南方、爪哇和花生根结线虫的快速灵敏的PCR鉴定方法

 为了研制南方、爪哇和花生根结线虫快速灵敏的检测和鉴定方法,分别分离了4个南方根结线虫和3个爪哇根结线虫特异性的随机扩增多态性DNA (RAPD)片段。在这些RAPD标记DNA序列的基础上,设计了多对SCAR PCR引物,并用源于国内外的南方、爪哇、花生、北方和象耳豆根结线虫群体验证其扩增特异性和灵敏度。最终确定了3对高效扩增的SCAR引物,它们组合使用可以可靠灵敏地鉴定南方、爪哇和花生根结线虫。3对引物的扩增灵敏度达1/3条的二龄幼虫、雄虫或雌虫,这表明本研究研制的PCR鉴定法可用于生产实践中土样和根样中3种根结线虫快速灵敏的鉴定。     

A Molecular Marker Correlated with Selected Virulence Against the Tomato Resistance Gene Mi in Meloidogyne incognita, M. javanica, and M. arenaria

ABSTRACT Root-knot nematodes of the genus Meloidogyne are economically important pathogens of a wide range of crops. The tomato resistance gene Mi typically confers resistance to the three major species, M. incognita, M. javanica, and M. arenaria. However, virulent populations completely overcoming the Mi resistance still occur. In an attempt to develop molecular markers for virulence against Mi and gain insights into the genetic relationships among virulent populations of different species and origins, random amplified polymorphic DNA (RAPD) analyses of laboratory-selected virulent, field virulent, and avirulent populations of M. incognita, M. javanica, and M. arenaria were carried out. A RAPD marker, specific for selected virulent populations, was identified, and subsequently, converted to a sequence characterized amplified region (SCAR). Sequence characterization of the SCAR locus showed that alleles from laboratory- and field-selected virulent populations were highly similar to each other and clearly different from alleles from natural virulent and avirulent populations. This result suggests that the genetic mechanism for virulence against Mi may be similar among selected virulent populations of the three Meloidogyne spp., but different between selected and natural virulent populations. Based on the nucleotide polymorphisms at the SCAR locus, codominant and dominant polymerase chain reaction-based markers were developed enabling rapid diagnosis of selected virulent genotypes in M. incognita, M. javanica, and M. arenaria.     

Identification of Meloidogyne chitwoodi, M. fallax and M. hapla Based on SCAR-PCR: A Powerful Way of Enabling Reliable Identification of Populations or Individuals that Share Common Traits

This study describes the development of species-specific pairs of PCR primers for the root-knot nematodes Meloidogyne chitwoodi, M. fallax and M. hapla that amplify species-specific RAPD fragments. After sequencing the fragments, longer primers were designed to complement the terminal sequences of the polymorphic DNA fragments. The resulting pairs of primers were used to generate the sequence-characterized amplified regions (SCARs). Using the developed pairs of SCAR primers, SCAR fragments of M. chitwoodi, M. fallax or M. hapla were easily amplified from DNA extracts from juveniles, egg masses, females of the particular nematode species investigated, either present alone, in a mixture with other nematode species or in infested plant material. A specially designed multiplex assay using three pairs of SCAR primers enabled the identification of multiple species in a mixture in a single PCR step. Single juveniles were easily identified by applying this multiplex assay followed by a subsequent multiplex PCR using three pairs of nested primers. The SCAR-PCR-based assays described have potential to be optimized for routine practical diagnostic tests. The usefulness of converting RAPD markers into SCAR markers is discussed.     

Meloidogyne virulence locus molecular marker for characterization of selected mi-virulent populations of Meloidogyne spp. is correlated with several genera of betaproteobacteria

Resistance to root-knot nematodes in tomato is conferred by the Mi resistance gene to the three most important species of Meloidogyne: M. arenaria, M. incognita, and M. javanica. Nevertheless, the Mi gene is unable to inhibit the reproduction of selected and naturally Mi-virulent populations of root-knot nematodes. As pathogenicity assays are time consuming, molecular markers were developed for the easy identification of Mi-virulent populations of Meloidogyne. The sequence characterized amplified region-Meloidogyne virulence locus (MVC) molecular marker is reported to differentiate Mi-avirulent and naturally Mi-virulent from selected Mi-virulent populations. This marker was used to compare acquired virulence in populations of M. javanica from Spain. The original populations used to develop the MVC marker were included as control for reference. Results showed that this marker did not amplify genomic DNA extracted from single juveniles or females of any of the populations tested either from Spain or Japan. In silico analyses performed with the recently published complete genome of M. incognita, indicated that the MVC marker is not correlated to a MVC or to any eukaryotic organism but to several betaproteobacteria genus from the family Comamonadaceae.     

Identification of plant-parasitic nematodes by PCR amplification of DNA fragments1

A study concerning the detection and characterization of a DNA fragment from plant-parasitic nematodes to be used as a molecular marker for the identification of different nematodes is described. A fragment of DNA, which is known to consist of a variable region flanked by two conserved regions, has been studied by using PCR amplification. A portion of about 600 nucleotides at the 5’end of the larger rRNA gene has been amplified in different nematodes, using heterologous primers which hybridize with the conserved regions. The results obtained clearly indicate that the same primers can be used for the amplification of this segment in nematodes of different species and of different genera: Meloidogyne artiellia, M. incognita, Xiphinema index, X. diversicaudatum and Globodera pallida. The amplified regions have been partially sequenced. The nucleotide sequences have been analysed by comparison with the published sequence of Caenorhabditis elegans.     

Genetic diversity of the root‐knot nematode Meloidogyne enterolobii and development of a SCAR marker for this guava‐damaging species

The objectives of this work were to evaluate the genetic variability of Meloidogyne enterolobii by molecular markers, and develop species‐specific molecular markers for application in detection. Sixteen M. enterolobii isolates from different geographical regions (Brazil and other countries) and hosts were used in this study. The identification and purification of the populations were carried out based on isoenzyme phenotype. The DNA amplification of the intergenic region (IGS) of the rDNA and of the region between the cytochrome oxidase subunit II (COII) and 16S rRNA genes (mtDNA) produced specific fragments of the expected size for this nematode, i.e. 780 and 705 bp, respectively. Intraspecific variability among the isolates was evaluated with three different neutral molecular markers: AFLP, ISSR and RAPD. The results showed a low level of diversity among the isolates tested, indicating that M. enterolobii is a genetically homogeneous root‐knot nematode species. The RAPD method allowed the identification of a species‐specific RAPD fragment for M. enterolobii. This fragment was cloned and sequenced, and from the sequence obtained, a set of primers was designed and tested. The amplification of a 520‐bp‐long fragment occurred only for the 16 isolates of M. enterolobii and not for the 10 other Meloidogyne species tested. In addition, positive detection was achieved in a single individual female, egg‐mass and second stage juvenile of this nematode. This SCAR species‐specific marker for M. enterolobii represents a new molecular tool to be used in the detection of this nematode from field samples and as a routine diagnostic test for quarantine devices .     

Assessment of PCR-based tools for the specific identification of some temperate Meloidogyne species including M. chitwoodi,M. fallax and M. minor

Several conventional PCR tests have been developed for the identification of the European quarantine root-knot nematodes Meloidogyne chitwoodi and M. fallax but data are lacking for the evaluation of their performance in terms of sensitivity, repeatability, reproducibility and specificity against a large range of populations. This study evaluated the performance criteria of three conventional PCR tests recommended by the consensus diagnostic protocol for Meloidogyne chitwoodi and Meloidogyne fallax published by the European and Mediterranean Plant Protection Organization (EPPO): a species-specific PCR (IGS target), a SCAR PCR, and a rDNA ITS PCR-RFLP. Evaluation was carried out with DNA extracts from juveniles, males and females according to EPPO recommendations for test validation. A minimum of 34 populations of target and non target nematode species were tested to check the specificity of these three PCR assays. The three PCR tests were ranked according to their specificity (with regard to cross reaction with other nematodes species or genus) and their sensitivity (detection of a single juvenile or mixed with other species). The species-specific PCR proved to be more sensitive but less specific than the SCAR PCR. The PCR-RFLP enables the identification of several Meloidogyne species but profile analysis can be difficult when several species are present in the mixture. Specific PCR products and RFLP profiles were also observed for M. arenaria and M. enterolobii, and described for M. minor and M. artiellia.     

RAPD Characterization of Single Females of the Root-knot Nematodes, Meloidogyne Spp.

Random amplified polymorphic DNA fingerprinting was performed on single females of root-knot nematodes, Meloidogyne spp., using a new procedure for DNA isolation. One-fourth of the total DNA amount isolated from a single female proved to be sufficient as a template in a polymerase chain reaction. Electrophoretic patterns of the amplified fragments were reproducible between replicates from a single female or sister females from the same progeny, and identical to those obtained with genomic DNA purified from a large number of nematodes. Moreover, a comparative analysis over three successive generations showed stability of the amplification patterns, thus demonstrating the utility of this procedure for epidemiological and ecological studies on root-knot nematodes.     

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.     

Genetic diversity of the root‐knot nematode Meloidogyne ethiopica and development of a species‐specific SCAR marker for its diagnosis

Meloidogyne ethiopica is an important nematode pathogen causing serious economic damage to grapevine in Chile. In Brazil, M. ethiopica has been detected with low frequency in kiwifruit and other crops. The objectives of this study were to evaluate the intraspecific genetic variability of M. ethiopica isolates from Brazil and Chile using AFLP and RAPD markers and to develop a species‐specific SCAR‐PCR assay for its diagnosis. Fourteen isolates were obtained from different geographic regions or host plants. Three isolates of an undescribed Meloidogyne species and one isolate of M. ethiopica from Kenya were included in the analysis. The results showed a low level of diversity among the M. ethiopica isolates, regardless of their geographical distribution or host plant origin. The three isolates of Meloidogyne sp. showed a high homogeneity and clustered separately from M. ethiopica (100% bootstrap). RAPD screenings of M. ethiopica allowed the identification of a differential DNA fragment that was converted into a SCAR marker. Using genomic DNA from pooled nematodes as a template, PCR amplification with primers designed from this species‐specific SCAR produced a fragment of 350 bp in all 14 isolates of M. ethiopica tested, in contrast with other species tested. This primer pair also allowed successful amplification of DNA from single nematodes, either juveniles or females and when used in multiplex PCR reactions containing mixtures of other root‐knot nematode species, thus showing the sensitivity of the assay. Therefore, the method developed here has potential for application in routine diagnostic procedures.     

我国南方地区主要根结线虫DNA变异的RAPD分析

 本试验用5组随机引物对来自我国南方地区的30个根结线虫种群进行RAPD分析,并从中筛选出多态性较好的引物12个。共扩增出179条DNA多态带,各供试种群间存在着丰富的遗传多态性。扩增结果表现出种间差异大于种内差异的共同趋势,这表明上述12个引物能够较客观地反映种群间亲缘关系的远近。北方根结线虫与另外3种线虫(南方根结线虫、爪哇根结线虫、花生根结线虫)的亲缘关系最远;在3种主要根结线虫中,爪哇根结线虫与南方根结线虫的亲缘关系相对较近。基于种群间的相似系数分析和应用UPGMA法构建的聚类树状图,显示出不同的根结线虫在较低的相似性系数范围聚类,而绝大多数种内的不同种群均以较高的相似性系数聚在一起,这与形态分类基本一致,反映了形态学分类的分子遗传本质,同时也表明了应用RAPD技术进行根结线虫亲缘关系分析和种类鉴定具有合理性和可行性。本文还对RAPD方法对南方根结线虫小种鉴定的可能性进行了初步探讨。     

采用环介导等温扩增法(LAMP)快速检测苹果根结线虫

为高效、简便、快速地对我国进境植物检疫性有害生物名录中的非中国种—苹果根结线虫Meloidogyne mali进行检疫,通过比较Gen Bank中根结线虫相关序列,以苹果根结线虫28S r DNA非保守区域序列设计环介导等温扩增(loop-mediated isothermal amplification,LAMP)的特异性引物,并优化反应条件,建立一种可快速检测苹果根结线虫的LAMP检测体系。结果显示:d NTPs浓度为0.4 mmol/L、Mg~(2+)浓度为5.0 mmol/L、不添加甜菜碱、反应时间为60 min时,LAMP检测体系扩增效率最高;用琼脂糖凝胶电泳、SYBR Green I染色和LFD试纸均能检测到苹果根结线虫的扩增产物。所建立的LAMP检测体系能够从10种供试植物线虫种群中特异性地检测出苹果根结线虫,灵敏度为1/20 000条线虫DNA,比常规PCR灵敏度高10倍。表明所建立的苹果根结线虫LAMP快速检测体系可用于我国口岸进境植物中苹果根结线虫检疫。     

Identification of <Emphasis Type="Italic">Pratylenchus thornei</Emphasis>, the cereal and legume root-lesion nematode,based on SCAR-PCR and satellite DNA

Two different molecular tools for the diagnosis of the cereal and legume root-lesion nematode Pratylenchus thornei were developed. A randomly amplified DNA (RAPD) fragment specific to P. thornei was identified. After sequencing the fragment, longer primers were designed that complement the terminal sequences of the RAPD fragment, and this pair of specific primers was used to amplify the sequence-characterized amplified region (SCAR). Using the developed pair of SCAR primers, the SCAR fragment specific to P. thornei was easily amplified with DNA extracts obtained from different life stages of the nematode. The described SCAR-PCR-based assay has the potential to be optimized for routine practical diagnostic tests. In addition, the use of a species-specific satellite DNA sequence to distinguish P. thornei from other Pratylenchus spp. is discussed.     

Protection of olive planting stocks against parasitism of root-knot nematodes by arbuscular mycorrhizal fungi

The effects were investigated, under controlled conditions, of single and joint inoculation of olive planting stocks cvs Arbequina and Picual with the arbuscular mycorrhizal fungi (AMF) Glomus intraradices , Glomus mosseae or Glomus viscosum , and the root-knot nematodes Meloidogyne incognita and Meloidogyne javanica , on plant performance and nematode infection. Establishment of the fungal symbiosis significantly increased growth of olive plants by 88·9% within a range of 11·9–214·0%, irrespective of olive cultivar, plant age and infection by M. incognita or M. javanica . In plants free from AMF, infection by Meloidogyne spp. significantly reduced the plant main stem diameter by 22·8–38·6%, irrespective of cultivar and plant age. Establishment of AMF in olive plants significantly reduced severity of root galling by 6·3–36·8% as well as reproduction of both Meloidogyne spp. by 11·8–35·7%, indicating a protective effect against parasitism by root-knot nematodes. Infection by the nematodes influenced root colonization by AMF, but the net effect depended on the AMF isolate–olive cultivar combination. It is concluded that prior inoculation of olive plants with AMF may contribute to improving the health status and vigour of cvs Arbequina and Picual planting stocks during nursery propagation.     

The use of species-specific DNA probes for the identification of Mycosphaerella fijiensis and M. musicola, the causal agents of Sigatoka disease of banana

The polymerase chain reaction (PCR)-based technique of random amplification of polymorphic DNA (RAPD) was used to differentiate DNA from species of the genus Mycosphaerella. DNA from two pathogens which cause Sigatoka leafspot diseases of banana, M. fijiensis and M. musicola , and two other Mycosphaerella species which are commonly found on banana, M. musae and M. minima , gave distinct RAPD banding patterns with all PCR primers tested. PCR, using primer RC07, amplified a 1250bp RAPD fragment from all isolates of M. fijiensis obtained from 11 geographical origins. This fragment was absent from the other species of Mycosphaerella. In Southern blots of genomic DNA, this band hybridized exclusively to DNA from M. fijiensis , and the pattern of hybridization suggested that it was binding to repeated DNA. A RAPD band amplified with primer PM06 obtained from M. musicola was also found to be species-specific. Southern analysis suggested that the fragment hybridized to a single-copy sequence in the M. musicola genome. Total genomic DNA from M. musicola was found to be a species-specific hybridization probe. Dot-blots confirmed the specificity of these probes, and could be used to identify isolates of Mycosphaerella which cause Sigatoka disease of banana in south-east Asia.     

Distribution analyses of Meloidogyne spp. and Pratylenchus coffeae sensu lato in coffee plots in Costa Rica and Guatemala

The distribution of the plant-parasitic nematodes Pratylenchus coffeae sensu lato and Meloidogyne spp. were studied in two plots, one in Guatemala ( P. coffeae and M. paranaensis ) and the other in Costa Rica ( P. coffeae and M. exigua ). The quantity of nematodes per g fresh weight root were counted for each coffee tree sampled. The distributions were aggregated, and generally fitted well to negative binomial distributions. Population aggregation was greater when a smaller number of nematodes were involved, suggesting that initial colonization develops in foci. Analyses of the relationships between population levels of the species suggested that there was competition between Pratylenchus coffeae and Meloidogyne spp. This competition was expressed differently depending on the relative population density of the different species.     

Early brown rot infections in sweet cherry fruit are detected by monilinia-specific DNA primers

ABSTRACT Visible and nonvisible quiescent infections of immature and mature fruit are an integral component of the disease cycle of brown rot of sweet cherry in California. Detection of these infections is critical for developing efficient and efficacious fungicide management programs. The previously published DNA amplification primers mfs3 and NS5 for the identification of Monilinia fructicola were very specific in amplifying DNA of M. fructicola only and not M. laxa. This primer set, however, only detected DNA from some of the California isolates of M. fructicola. This genetic diversity was supported by random amplified polymorphic DNA (RAPD) analysis. Using eight 10-mer primers, seven M. fructicola isolates from California were all identified as genetically distinct. Using the same primers, only one polymorphism was detected among seven isolates of M. laxa. The multiple genotypes identified within the small population sample of M. fructicola, but not of M. laxa, using RAPD analysis could be indicative of genetic recombination within M. fructicola but not within M. laxa. To detect early brown rot infections in fruit, two primer sets that were developed from DNA sequences of either ribosomal DNA (MF5/ITS4/ITS3) or a RAPD fragment (X-09intF3/X-09R) specifically amplified DNA from isolates of M. fructicola and Monilinia species, respectively. No amplification products were present when using DNA from Botrytis cinerea or from other fungi commonly found on sweet cherry fruit. Primers X-09intF3 and X-09R were more sensitive and reliable for detecting small amounts of target DNA either extracted from conidia or from laboratory-inoculated cherry fruit with early brown rot infections that showed no visual symptoms or with visible quiescent infections. Furthermore, these primers also were effective for detecting visible quiescent infections in cherry fruit that were collected in the field.     

Molecular Detection of Phytophthora ramorum, the Causal Agent of Sudden Oak Death in California, and Two Additional Species Commonly Recovered from Diseased Plant Material

ABSTRACT Sudden oak death is a disease currently devastating forest ecosystems in several coastal areas of California. The pathogen causing this is Phy-tophthora ramorum, although species such as P. nemorosa and P. pseudo-syringae often are recovered from symptomatic plants as well. A molecular marker system was developed based on mitochondrial sequences of the cox I and II genes for detection of Phytophthora spp. in general, and P. ramorum, P. nemorosa, and P. pseudosyringae in particular. The first-round multiplex amplification contained two primer pairs, one for amplification of plant sequences to serve as an internal control to ensure that extracted DNA was of sufficient quality to allow for polymerase chain reaction (PCR) amplification and the other specific for amplification of sequences from Phytophthora spp. The plant primers amplified the desired amplicon size in the 29 plant species tested and did not interfere with amplification by the Phytophthora genus-specific primer pair. Using DNA from purified cultures, the Phytophthora genus-specific primer pair amplified a fragment diagnostic for the genus from all 45 Phytophthora spp. evaluated, although the efficiency of amplification was lower for P. lateralis and P. sojae than for the other species. The genus-specific primer pair did not amplify sequences from the 30 Pythium spp. tested or from 29 plant species, although occasional faint bands were observed for several additional plant species. With the exception of one plant species, the resulting amplicons were smaller than the Phytophthora genus-specific amplicon. The products of the first-round amplification were diluted and amplified with primer pairs nested within the genus-specific amplicon that were specific for either P. ramorum, P. nemorosa, or P. pseudo-syringae. These species-specific primers amplified the target sequence from all isolates of the pathogens under evaluation; for P. ramorum, this included 24 isolates from California, Germany, and the Netherlands. Using purified pathogen DNA, the limit of detection for P. ramorum using this marker system was approximately 2.0 fg of total DNA. However, when this DNA was spiked with DNA from healthy plant tissue extracted with a commercial miniprep procedure, the sensitivity of detection was reduced by 100- to 1,000-fold, depending on the plant species. This marker system was validated with DNA extracted from naturally infected plant samples collected from the field by comparing the sequence of the Phytophthora genus-specific amplicon, morphological identification of cultures recovered from the same lesions and, for P. ramorum, amplification with a previously published rDNA internal transcribed spacer species-specific primer pair. Results were compared and validated with three different brands of thermal cyclers in two different laboratories to provide information about how the described PCR assay performs under different laboratory conditions. The specificity of the Phytophthora genus-specific primers suggests that they will have utility for pathogen detection in other Phytophthora pathosystems.     

海南省蔬菜根结线虫发生种类与分布

2014年-2018年, 对海南省蔬菜根结线虫病害进行了田间随机采样调查和病原种类分子鉴定?结果显示, 蔬菜根结线虫病在海南18市县均有发生, 且大部分旱田连作地块病株率达到80%以上?进一步对采集的295份根结线虫样本种类进行了分子鉴定, 共鉴定出象耳豆根结线虫?南方根结线虫和爪哇根结线虫3种病原种?其中, 象耳豆根结线虫单一检出率达到62.37%, 南方根结线虫单一检出率为23.39%, 爪哇根结线虫的检出率仅为5.76%, 象耳豆根结线虫和南方根结线虫复合侵染检出率为8.47%?除五指山市样本以外, 海南其余17市县样本均检测到象耳豆根结线虫侵染为害?本研究显示象耳豆根结线虫为海南省蔬菜上的优势病原根结线虫种类, 该结果对指导品种布局?制定根结线虫病害的防治策略具有重要意义?