Development of a multiplex AmpliDet RNA for the simultaneous detection of Potato leafroll virus and Potato virus Y in potato tubers

Klerks, M.M.; Leone, G.; Verbeek, Matthew; Heuvel, J.F.J.M. van den; Schoen, C.D.

doi:10.1016/s0166-0934(01)00258-0

Cited by 44 publications

(15 citation statements)

References 18 publications

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“…Several classical and real-time PCR protocols are available for the routine molecular detection of many bacterial (Louws and Couples 2001), viral (Mumford et al 1996, Klerks et al 2001, fungal , Li and Hartman 2003, Destefano et al 2004) and nematode pathogens (Amiri et al 2002, Hü bschen et al 2004. However, there are few, if any, similar tests available for soil-dwelling insects and none for grape phylloxera.…”

Section: Discussionmentioning

confidence: 99%

Developing and Testing a Diagnostic Probe for Grape Phylloxera Applicable to Soil Samples

Herbert

Powell

McKay

et al. 2008

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Grape phylloxera, Daktulosphaira vitifoliae (Fitch) (Hemiptera Phylloxeridae) is a damaging pest of grapevines (Vitis spp.) around the world, and the management of this pest requires early detection of infestations. Here, we describe the development and validation of a sensitive DNA test for grape phylloxera that can be applied to soil. Species-specific primers were developed for grape phylloxera in the internal transcribed space region 2, and their specificity was confirmed after thorough screening by using a wide range of vineyard organisms and aphid genera. Preliminary testing of the detection limits of the grape phylloxera-specific primers was conducted using field-sourced soil types spiked with a known number of grape phylloxera. The assay was converted to a real-time polymerase chain reaction format (TaqMan MGB). This assay, in combination with DNA extraction from soil, can detect phylloxera crawlers added to soil. The assay was evaluated in the field at a recently detected grape phylloxera infestation site from the Yarra Valley in Victoria, Australia. The DNA assay proved to be substantially more sensitive than a standard ground survey for detecting grape phylloxera presence on vine roots in the infested vineyard. Moreover, unlike the ground survey, the assay provided quantitative information on grape phylloxera infestations, because grape phylloxera DNA concentrations in samples from vines closely matched the numbers of grape phylloxera crawlers collected with emergence traps placed at the base of vines. Unlike other detection techniques, the method can be applied at any time of the year, and it can be potentially modified to provide specific information on the virulence levels of the particular grape phylloxera genotypes responsible for any new infestations.

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Section: Discussionmentioning

confidence: 99%

Developing and Testing a Diagnostic Probe for Grape Phylloxera Applicable to Soil Samples

Herbert

Powell

McKay

et al. 2008

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“…This method, however, is expensive, time-consuming and generally cannot be carried out on dormant tubers [9]. Some alternative approaches were gradually developed including nucleic acid sequence-based amplification [10], reverse transcription polymerase chain reaction (RT-PCR) [11], Northern blotting [12], Multiplex AmpliDet RNA [13], realtime RT-PCR [3,14], and immunocapture reverse transcription polymerase chain reaction (IC-RT-PCR) [15], all of which were unfortunately time-consuming and require expensive or carcinogenic materials to visualize DNA amplification [16]. Meanwhile, extraction of RNA is another exhausting task, accomplished commonly under various protocols, all of which are typically accompanied by some drawbacks.…”

Section: Introductionmentioning

confidence: 99%

Assessment of Performance Ability of Three Diagnostic Methods for Detection of Potato Leafroll Virus (PLRV) Using Different Visualizing Systems

Almasi

Moradi

Nasiri

et al. 2012

Appl Biochem Biotechnol

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To diminish the time required for some diagnostic assays including reverse transcription PCR (RT-PCR), reverse transcription loop-mediated isothermal amplification (RT-LAMP; due to mainly RNA extraction step) and also DAS-ELISA into a minimum level, an innovative immunocapture RT-LAMP (IC-RT-LAMP) and immunocapture reverse transcription (IC/RT-PCR) protocol on the basis of Potato Leafroll virus (PLRV) genome were used and optimized. In this regard, all six IC-RT-LAMP primers (i.e. F3, B3, FIP, BIP, LF and LB) together with IC/RT-PCR primers were designed on the basis of the highly conserved sequence (ORF3) of coat protein gene (GenBank accession number: U73777) of PLRV genome. Even though DAS-ELISA, IC/RT-PCR and IC-RT-LAMP assays could successfully detect positive infected plant samples, considering the time, safety, sensitivity, cost and simplicity, the last one was overall superior. Meanwhile, among five different visual dyes to accurately detect IC-RT-LAMP products, both hydroxynaphthol blue and GeneFinder™ could produce long stable colour change and brightness in a close tube-based approach to prevent cross-contamination risk, concluded eventually as the best ones. Altogether, as IC-RT-LAMP is sensitive, cost-effective, fairly user friendly and also can generate more accurate results than previous diagnostic procedures, we accordingly propose this colorimetric assay as a highly reliable alternative viral recognition system regarding PLRV recognition and probably other viral-based diseases.

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“…In the 1990s this work mainly focused on molecular methods; during this time, a range of different potato virus assays was designed including assays based on conventional PCR (Spiegel and Martin 1993;Mumford et al 1994), the ligase chain reaction (O'Donnell et al 1996), NASBA (Klerks et al 2001;Leone et al 1997), and real-time PCR (Schoen et al 1996;Boonham et al 2000). While these and other reports demonstrated that such methods could be used for the sensitive detection of potato viruses direct from tubers, it was also clear that much more work was required to turn this early progress into a useable, routine diagnostic service.…”

Section: Direct Tuber Testingmentioning

confidence: 99%

Exploiting generic platform technologies for the detection and identification of plant pathogens

Boonham¹,

Glover²,

Tomlinson³

et al. 2008

Eur J Plant Pathol

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The detection and identification of plant pathogens currently relies upon a very diverse range of techniques and skills, from traditional culturing and taxonomic skills to modern molecular-based methods. The wide range of methods employed reflects the great diversity of plant pathogens and the hosts they infect. The well-documented decline in taxonomic expertise, along with the need to develop ever more rapid and sensitive diagnostic methods has provided an impetus to develop technologies that are both generic and able to complement traditional skills and techniques. Realtime polymerase chain reaction (PCR) is emerging as one such generic platform technology and one that is well suited to high-throughput detection of a limited number of known target pathogens. Real-time PCR is now exploited as a front line diagnostic screening tool in human health, animal health, homeland security, biosecurity as well as plant health. Progress with developing generic techniques for plant pathogen identification, particularly of unknown samples, has been less rapid. Diagnostic microarrays and direct nucleic acid sequencing (de novo sequencing) both have potential as generic methods for the identification of unknown plant pathogens but are unlikely to be suitable as high-throughput detection techniques. This paper will review the application of generic technologies in the routine laboratory as well as highlighting some new techniques and the trend towards multidisciplinary studies.

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Development of a multiplex AmpliDet RNA for the simultaneous detection of Potato leafroll virus and Potato virus Y in potato tubers

Cited by 44 publications

References 18 publications

Developing and Testing a Diagnostic Probe for Grape Phylloxera Applicable to Soil Samples

Developing and Testing a Diagnostic Probe for Grape Phylloxera Applicable to Soil Samples

Assessment of Performance Ability of Three Diagnostic Methods for Detection of Potato Leafroll Virus (PLRV) Using Different Visualizing Systems

Exploiting generic platform technologies for the detection and identification of plant pathogens

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