Using precision diagnostic technologies to tailor tree disease management strategies

For major foliar and trunk pathogens of apple (Venturia inaequalis [scab], Podosphaera leutricha [powdery mildew] and Neonectria ditissima [European apple canker]) there is a wealth of evidence, both for the host relating to major gene resistances, and for the pathogen about population-level variation and structure that is associated with host development. However, this information is currently not applied in the field to inform deployment. Rapid single molecule sequencing of DNA and RNA is now possible using Oxford Nanopore Technology (ONT). The aim of this project is to develop this technology for the rapid in-field monitoring of pathogen populations, in order to inform management strategies. The PhD project fully meets the BBSRC objectives of better countering of diseases of crops and greater resilience of crops to abiotic stresses.
NIAB EMR are early access members of the ONT MinION and VolTRAX programmes and have been working for over 14 months on applications for these technologies in the horticultural industry. Currently it is being applied to bacterial and fungal genomes, resulting in complete assembled genomes for many major horticultural pathogens. Bioinformatics pipelines are now well established and significant investment in hardware has been made to ensure that planned future developments in the technology do not impede progress.