Wheat rust fungi have threatened crop production almost since the dawn of agriculture. There are many different strains of rust, all with unique characteristics that cannot be told apart without lengthy in-lab tests. The best defence is to grow varieties resistant to infection and now scientists have developed MARPLE, a hand-held DNA sequencing device, that can define the precise strain of the wheat rust fungus in a farmer’s field within just 48 hours of collecting samples.
Knowing which wheat rust strains are in the local area can feed into advising which wheat varieties are safest to grow. This new mobile surveillance technique will give researchers vital time needed to spot and control emerging epidemics.
Trial in Ethiopia
The best way to stay ahead of the rusts is to quickly identify and track the disease in the field, the new approach is described in a paper; ‘MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens‘ published in BMC Biology. It shows how a research partnership reduced the speed of diagnostics from many months in high-end labs, to just 2 days from the side of an Ethiopian field.
Dr Dave Hodson, a rust pathologist at CIMMYT in Ethiopia and co-author comments: ‘Knowing which strain you have, is critical information that can be incorporated into early warning systems and results in more effective control of disease outbreaks in farmer’s fields” said
Rapid diagnosis
The new MARPLE (Mobile And Real-time PLant disEase) diagnostic platform the researchers created, targets parts of the rust genetic code that can be sequenced on the portable MinION sequencing platform from Oxford Nanopore.
First author Dr Guru Radhakrishnan from the John Innes Centre explains: “This helps us tell strains apart and quickly recognise those we’ve seen before or spot new ones that could be a new threat.”
“What started as a proof of concept is now already being used in the field,’ said Dr Saunders, “this development will enable increased surveillance of crop disease pressure and more targeted control.”
For their work on creating the MARPLE platform, the team were awarded Innovator of the Year award for international impact from the Biotechnology and Biological Sciences Research Council in May this year. Following this award and through the support of the CGIAR Inspire challenge and the Delivering Genetic Gain in Wheat Project, a further four field stations across Ethiopia will be setup to use the MARPLE mobile lab.
“This is real national and international work that ultimately helps the resource-poor farmers” said Dr Badada Girima, Rust Pathologist, Delivering Genetic Gain in Wheat program.
Read more on the John Innes Centre website.