MARPLE: Mobile and Real-Time Plant Disease Diagnostics for Enhancing Wheat Rust Surveillance

Plant pathogens are a serious constraint to crop production worldwide, being responsible for considerable economic loss annually. Rapid detection of disease incidences can be critical for enacting timely control measures and thereby limiting the severity of costly disease outbreaks. With recent technological advances in genome and gene sequencing technologies and parallel reductions in cost, DNA-based plant disease diagnostics methods are now becoming embedded in surveillance systems for many critical crop disease threats. In this chapter, we consider one such diagnostic technique, termed Mobile And Real-time PLant disEase (MARPLE) diagnostics. The MARPLE diagnostics platform is a point-of-care (POC) platform that utilizes amplicon re-sequencing on the portable MinION sequencer to type individual strains of the wheat yellow rust (Puccinia striiformis f. sp. tritici; Pst) or wheat stem rust (Puccinia graminis f. sp. tritici; Pgt) pathogens. The system is designed to amplify genes highly variable between strains of the Pst or Pgt pathogens, and following amplicon re-sequencing, the sequences of these genes can be used for phylogenetic analysis, comparing "new" samples to a set of reference isolates from around the world. The MARPLE diagnostics method is also very simple, with very little training required and equipment needed, making the method highly suited for use in resource-poor environments. The following chapter contains everything you need to know to set up and execute MARPLE diagnostics.