In order to guarantee the quality of plant material for export and to protect crops from pests and diseases, early detection and diagnosis of quarantine organisms in plant (starting) material and also in growth substrates is necessary. Innovations in the field of detection and diagnosis are essential to support the prominent position that the Netherlands currently occupies in the world of plant products and raw material.
In recent years several innovative research in diagnostics using Next Generation Sequencing (NGS) has been performed. These technologies have a huge potential and could be used for much broader diagnostics. For this it is important that there is good coordination between the various parties and standardization of procedures and analysis methods. Cooperation as embodied in this PPP with key inspection services and research institution Wageningen Plant Research could play an important international role.
In order to deploy NGS for diagnostics further fundamental research is needed. Use of these new methods will, in combination with more traditional techniques, be more practical and should be used in conjunction with the entire chain (sampling, extraction, molecular methods and analysis). Which methods are most effective, and where in the chain? In addition, it is shown that NGS will give new insights in detection and diagnosis, for example in the field of phylogeny versus pathogenicity / function. The use of genomic information compared to the present use of a single gene or a few genes (so-called barcodes) for the diagnostics. This is called PanGenomics. The added value is to look instead of one piece of the puzzle, we look now at all the pieces of the puzzle simultaneously. This creates an overall picture, which allows to control things better or validate it more efficiently.
In search for the causal agent of faba bean gall disease in herbarium samples.
Next Generation Sequence Technology reveals bacteria and virusesProphyta Annual 2017 (2017). - ISSN 1388-381X - p. 42 - 43.
Next Generation Sequence Technology to evaluate the presence of plant pathogens in tomato seeds: What’s in a Pipeline?
Sequence analysis of 43-year old samples of Plantago lanceolata show that Plantain virus X is synonymous with Actinidia virus X and is widely distributedPlant Pathology 70 (2021)2. - ISSN 0032-0862 - p. 249 - 258.
What’s in a pipeline: Understanding the basics of NGS.