MARPLE Diagnostics

Mobile And Real-time PLant disEase (MARPLE) diagnostics is a portable, genomics-based, strain-level disease diagnostics methodology developed at the JIC in partnership with the International Maize and Wheat Improvement Center (CIMMYT). This system focuses on the wheat rust pathogens, providing real-time, point-of-care identification of specific strains within just 2 days of field sampling, a process that previously took many, many months. MARPLE diagnostics can also be conducted directly on location, with all components needed to execute the methodology contained within a single hardcase.

The wheat rusts are major fungal diseases of wheat that spread long-distance via spore dispersal on wind currents. MARPLE diagnostics targets two of the major wheat rusts – yellow and stem rust – that collectively lead to losses of over 11 million tonnes of wheat across the globe each year. To protect wheat crops from attack, farmers employ good agronomic practices, alongside planting resistant varieties and (where available) applying appropriate fungicides. However, new fungal strains frequently emerge that can overcome the resistance introduced into these crops, leading to large-scale disease outbreaks. Therefore, the key to protecting farmers’ crops against rust damage is to quickly identify new strains as they emerge to better inform disease management strategies and action control measures before outbreaks spread.

How it works

This highly innovative approach is based on amplicon re-sequencing where a small number of genes in the pathogen genome are targeted for sequence analysis. These genes have been identified at JIC as being highly variable in sequence between different rust strains. Focusing on these variable gene subsets reduces the amount of data needed for each sample to accurately type strains and makes it highly suited for use with the hand-held MinION nanopore sequencer, built by Oxford Nanopore Technologies. Once data is generated, a custom, fully automated pipeline is run to type strains through comparative analysis with a collection of global strains of the wheat rust pathogens.

Funding

MARPLE diagnostics is currently supported by the Bill & Melinda Gates Foundation and the Foreign, Commonwealth and Development Office (DEWAS project INV-048345), the UK Biotechnology and Biological Sciences Research Council (BBSRC) Innovator of the Year Award. It has also received support from the Feed the Future Innovation Lab for Current and Emerging Threats to Crops funded by the United States Agency for International Development (USAID) and the CGIAR Big Data Platform Inspire Challenge.

Research publications

Radhakrishnan, G.V., Cook, N.M., Bueno-Sancho, V. et al. (2019), MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens. BMC Biol 17, 65. Read article.

Saunders D.G.O. Hodson, D.P. (2019) Answering the call for real-time plant disease diagnostics in resource-poor regions. BMC Biol. Read article

Find out more

More details about the system and details of all the resources needed to implement MARPLE diagnostics for wheat yellow and stem rust are provided on the project website.