With Next Generation Sequencing, you can find out within 25 hours whether or not plant material is infected with pathogens. As this techniqu captures both the usual and unknown suspects, it is a true breakthrough in genetic plant diagnostics.
'Inspection services for agricultural products usually analyse suspicious lots with PCR diagnosis', says Peter Bonants of Wageningen University & Research. 'This technique detects pathogens like fungi, viruses and bacteria by multiplying specific parts of their DNA. The disadvantage of this is that your search is highly selective: you base your assessment of which pathogen is likely to be present on certain symptoms, and then you adapt the analysis accordingly. Next Generation Sequencing (NGS) eliminates the need to make that determination in advance, as all of the possible pathogens can be directly identified.'
Billions of building blocks per sample
Unlike the old sequencing techniques, NGS maps billions of genetic sequences for an entire plant sample. As Bonants describes, 'You scan billions of nucleotides, the building blocks of DNA, and the order of these nucleotides determines to which type they belong. This reveals the plant's own sequences and allows us to see which divergent sequences are present in the sample. We conduct our analysis using advanced software that we have 'fed' with our genetic information on plants and pathogens, which enable us to quickly issue a reliable and definitive answer. Depending on the quality of the DNA sample, that answer can even be provided within 25 hours.'
This speed is a major advantage in a sector where time is money. For instance, if a quarantine organism is discovered in a shipment, the lot of potatoes, oranges or other products is detained. This leads to a significant loss of value. The same principle applies to cultivation: the longer it takes to acquire results that are certain, the longer you have to wait to combat a disease. Bonants notes, 'All parties in the chain — the producers, importers and exporters — benefit from rapid diagnostics because it can give them considerable cost savings.'
Tracking & Tracing
The NGS technology is also suitable for tracking and tracing. Bonants explains, 'We know, for example, that many bacteria and viruses are transmitted via plant material like seeds. Because this material is transported on such a large scale, however, it is sometimes difficult to trace the origin of an infection. By ascertaining the sequence of a pathogen with NGS, we figure out information such as "this occurs naturally in New Zealand." This allows you to promptly take targeted measures in the country of origin.'
As part of the PPS project 'Developing Diagnostics for Quarantine and Quality Diseases in Plants various inspection services are gaining experience with Next Generation Sequencing under the guidance of Wageningen University and Research. Bonants notes the keen interest in the technology. 'The European Plant Protection Organisation (EPPO) has even asked us to collaborate with them on further developing NGS for diagnostics. I expect that it will be the go-to standard for diagnostics within a few years. We're currently working on a device that allows you to analyse data in the field using your mobile phone, after which you can download a diagnosis directly from the cloud. These kinds of technologies are developed within at least five years.'