Evaluation and optimization of a high-throughput sequencing based strategy to detect viruses and bacteria in view of certification and in vitro therapy to create virus free mother plants (VIRVRIJUIT)

The aim of this research project is to produce virus-free starting materials (seeds, cuttings, planting material, tissues...) of commercial crops and to provide the sector with a useful technology to achieve this goal. We focus on crop-specific procedures, based on high-throughput sequencing (HTS), which we evaluate and further optimize for use in both certification (tree nursery and fruit trees), the in vitro sector, and for obtaining virus-free mother plants. The different target groups will thus receive a tailor-made HTS strategy for their need for detection of viruses and also (specific) bacteria. The implementation of HTS technology on a broader scale is expected to result in greater speed, performance, accuracy and lower costs, and will certainly have a considerable (beneficial) economic impact on the professional actors involved.

For each crop group (subsector) we develop or improve an optimal extraction method and validate a simple, fast and affordable HTS strategy, including an efficient data analysis. We also determine the phytosanitary risk of the detected known and unknown viruses. We then test and validate in vitro techniques for virus eradication and make a general cost-benefit analysis. We help the end-user companies involved with the practical integration into their existing analysis procedures. We enter into consultation with the policy authorities in order to arrive at an improved, recognized and workable certification strategy. In addition, we examine to what extent the obtained data are useful for the detection of specific bacteria and other pathogenic organisms. The project results will be widely disseminated and communicated to the sector.

The implementation of HTS technology can significantly reduce costs in virus detection in plants, according to the researchers. Previous studies indicate a decrease in certification cost of roughly 80% (Al Rwahnih, UC Davis USA, 2017). As a result, we expect a positive impact on the competitive position of Belgian breeding companies. Participating companies are in a race with foreign competition. Whoever can supply their customers with planting material with a guaranteed virus-free status wins the market. Absolute virus-free status is increasingly becoming a must for propagation material and their end products. For example, the testing requirements in the international plant trade are changing (tightening) under the new Plant Health Law implemented in 2019 and the split into Q-organisms and RNQP-organisms. The researchers plan very broad dissemination and communication of their project results to the stakeholder groups involved.