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

Abstract

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.

DNA barcoding for biosecurity: case studies from the UK plant protection program

“…The advent of any new diagnostic protocol is typically the start of a lengthy process of evolution, before those techniques that are truly widely applicable, robust, and practical make their way into diagnostic laboratories. Whilst sequencing is not a new concept, the neat conceptual framework of DNA barcoding make it an attractive proposition for diagnostic laboratories, which often need generic methodologies to use alongside species-specific tests (Boonham et al 2008) and morphological identification.…”

A One-Step, Real-Time Reverse Transcription Loopmediated Isothermal Amplification Assay to Detect Potato Virus Y

“…However, our attempts to detect PVY directly in diluted sap have failed so far, mainly due to the high fluorescence of sap components (Zacharzewska B., Chołuj J. and Treder K., unpublished). At the moment, the only true point-of-care method of virus detection is the lateral flow assay (LFA), a test based on immunochromatography (Danks and Barker 2000;Boonham et al 2008;De Boer and Lopez, 2012). The LFA test is very simple, requires no training or laboratory equipment to perform, operates directly on diluted plant sap, and produces results in several minutes, with sensitivity equal to that of DAS-ELISA (compare Fig.…”

Fast and reliable molecular methods to detect fungal pathogens in woody plants

“…Lateral flow devices (LFDs) are a simple paper-based dipstick assay to detect the presence or absence of a target analyte in a liquid sample without the need for specialized laboratory equipment. This method has become widespread over the last few years allowing rapid in-field detection of plant pathogens (Boonham et al 2008;Tomlinson et al 2010). The LFD method is simple to use and is able to detect and identify the causal agents of disease in few minutes.…”