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European Journal of Plant Pathology

, Volume 152, Issue 4, pp 909–919 | Cite as

The impact of high throughput sequencing on plant health diagnostics

  • Ian P. AdamsEmail author
  • Adrian Fox
  • Neil Boonham
  • Sébastien Massart
  • Kris De Jonghe
SI: Plant Pathology for Innovative Agroecology

Abstract

High throughput sequencing informed diagnostics is revolutionising plant pathology. The application of this technology is most advanced in plant virology, where it is already becoming a front-line diagnostic tool and it is envisaged that for other types of pathogen and pests this will be the case in the near future. However, there are implications to deploying this technology due to a number of technical and scientific challenges. Firstly, interpretation of data and the assessment of plant health risk against a limited baseline of existing knowledge of the presence of pathogens in a given geographic region. Secondly, evidence of causality and the separation of pathogenic from commensal organisms in the sequence data, thirdly, the tension between the generation of a rapid sequence result with the necessary but laborious epidemiological characterisation in support of plant health risk assessment. Finally, the validation and accreditation of methods based on this rapidly evolving technology. These in turn present challenges for plant health policy and regulation. This review discusses the development of this technology, its application in plant health diagnostics, and explores the implications of applying this technology in the plant health setting.

Keywords

High throughput sequencing NGS Diagnostics Validation Accreditation 

Notes

Acknowledgements

The data presented on viruses in Kenyan farms was produced in collaboration with Francesca Stomeo, funded by the Swedish International Development Cooperation Agency (SIDA) through an award to the BecA-ILRI Hub. This publication is partially based upon work and exchanges carried out in the frame of COST Action FA1407 (DIVAS), supported by COST (European Cooperation in Science and Technology).This work has received support from the UK government Department for Environment, Food and Rural Affairs funded "future proofing plant health" project (PH0469).

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Copyright information

© Koninklijke Nederlandse Planteziektenkundige Vereniging 2018

Authors and Affiliations

  • Ian P. Adams
    • 1
    Email author
  • Adrian Fox
    • 1
  • Neil Boonham
    • 2
  • Sébastien Massart
    • 3
  • Kris De Jonghe
    • 4
  1. 1.Fera Science LtdYorkUK
  2. 2.IAFRI, Newcastle UniversityTyne and WearUK
  3. 3.Laboratory of Integrated and Urban Phytopathology, TERRA, Gembloux AgroBio TechUniversité de LiègeGemblouxBelgium
  4. 4.Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO)MerelbekeBelgium

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