2017 Winner & Scale Up Runner 2018Real-time diagnostics for devastating wheat rust
The Inspire Challenge is an initiative to challenge partners, universities, and others to use CGIAR data to create innovative pilot projects that will scale. We look for novel approaches that democratize data-driven insights to inform local, national, regional, and global policies and applications in agriculture and food security in real time; helping people–especially smallholder farmers and producers–to lead happier and healthier lives.
This proposal was selected as a 2017 winner, with the team receiving 100,000 USD to put their ideas into practice. The team came runners up for the Scale Up award the following year, receiving an additional USD 125,000 for their outstanding ability to demonstrate the project’s proven viability and potential for impact.
Real-time diagnostics for devastating wheat rust in Ethiopia (MARPLE Diagnostics)
Wheat yellow rust, caused by Puccinia striiformis f. sp. tritici (PST), is currently considered the most damaging wheat disease globally, with yield losses sometimes higher than 60%. Furthermore, in the last decade new PST races have emerged that are adapted to warmer temperatures, have expanded virulence profiles, and are more aggressive than previously characterized races leading to wide scale epidemics. Understanding the rapidly shifting nature of pathogen populations and dispersal in near real-time is critical to implement effective early warning and control.
This requires new, innovative, data-driven, diagnostic tools.
Considerable progress has been made in establishing global monitoring systems and surveillance networks for wheat rusts (https://rusttracker.cimmyt.org/), but pathogen diagnostics still rely on lengthy and costly controlled bioassays undertaken at a very limited number of specialized laboratories.
Advances in sequencing technologies and bioinformatics pipelines have permitted the development of new in-field pathogenomics methods which have been tested and validated for PST by JIC and partners in the UK (Genome Biology 2015 16:23). If these new pathogen diagnostic methods, plus open access software and data management tools, could be made quicker, cheaper and readily deployed in developing countries it would revolutionize pathogen surveillance and reduce the risk for smallholder farmers.
This project aims to develop and mainstream an affordable, mobile in-field pathogenomics platform called MARPLE (Mobile And Real-time PLant disEase) diagnostics to revolutionize crop pathogen surveillance and diagnostics in real time. It will rely on the MinION mobile genome sequencer platform and assess its deployment in situ in Ethiopia.
Step by step
The project was one of five winners of the Inspire Challenge 2017 and was awarded US$100K at the inaugural annual convention of the CGIAR Platform Big Data in Agriculture, during 19-22 of September.
The team first collected representative Ethiopian PST samples that would be later sequenced using a new mobile MinION sequencer (Oxford Nanopore) coupled with current field pathogenomics methodology to give rapid diagnostics. This would the first application of this new technology to a major crop disease.
Training of EIAR scientist at JIC, DNA extraction and creation of sequencing libraries
Dr Diane Saunders and Abel Mitiku
One Ethiopian scientist was extensively trained at the JIC (UK) for 5 months, whilst others received training directly from JIC scientists in Ethiopia. The team evaluated samples collected in Ethiopia, validated the use of the MARPLE platform, and trained scientists in how to analyze the resulting data in country.
Confirming the accuracy of sequencing on MinION
PST field samples from Ethiopia were assigned to genetic groups using the MinION mobile platform and cross checked against known control samples that have previously been subjected to Illumina sequencing at JIC to confirm the accuracy of MinION technology.
A set of highly variable genes, which discriminated the main genetic groups of yellow rust, were identified from an extensive collection of genomic data from global yellow rust isolates by JIC scientists. Targeted amplicon resequencing of this differential gene panel (approx. 200 genes) using MinION nanopore sequencing and a custom built bioinformatics pipeline then provided an accurate diagnostic.
This scientific methodology, which allows the accurate diagnosis of complex fungal pathogens like PST with large genomes, is a completely new approach.
Piloting MARPLE in Ethiopia
The new and innovative pathogen diagnostics system, which is called MARPLE for Mobile And Real-time PLant disEase diagnostics, was successfully tested in Ethiopia. In the pilot phase, accurate diagnosis of yellow rust strains from field samples to genetic group was obtained within 3 days of sample collection. This represents a truly significant advance in crop pathogen diagnostics. The pilot demonstrated the first ever accurate identification of individual yellow rust strains whilst crops were at an early growth stage and disease was just starting to emerge in the field. Using conventional diagnostics this has never been possible.
Informing disease management decisions in Ethiopia
The data generated by the pilot has already been incorporated into national early wheat rust warning systems, illustrating that the MARPLE diagnostic platform is fully functional and able to generate essential data to inform disease management decisions.
The pilot field testing has rapidly confirmed (in 3 days) that the PstS11 race of yellow rust is currently present. This new information can help prioritize and target control activities since wheat varieties known to be susceptible can now easily been identified. Successful pilot testing and deployment of the MARPLE diagnostics system in Ethiopia opens the door for technology scaling to help protect wheat crops in East Africa.
The project was a runner up in the Inspire Challenge Scale Up 2018 and was awarded US$125K at the second annual convention of the CGIAR Platform for Big Data in Agriculture, during 3-5 of October.
Mainstreaming MARPLE in Ethiopia
This new system is the first operational system in the world using nanopore sequence technology for rapid diagnostics and surveillance of complex fungal pathogens. Furthermore, MARPLE is entirely mobile, deployable in a field-based setting and tailored for use in developing countries. The entire “lab” and analytics fits in a suitcase and runs effectively even in the absence of stable electricity. In addition, the bioinformatics pipeline runs totally offline.
The objective now is to optimize and mainstream the MARPLE diagnostics technique within the wheat research system in Ethiopia. In 2019, the initial focus will be on MARPLE optimization and strengthening a central MARPLE hub. This will lay the foundation to create 3 additional future MARPLE hubs distributed at key, and strategically located, wheat research stations in the country. This model will ensure that rapid diagnostic capacity for yellow rust is distributed throughout the main wheat growing regions of Ethiopia and will permit sentinel monitoring of yellow rust races appearing on crops on an annual basis.
Expanding to other pathogens
Having established the distributed MARPLE platform and operating capacity it would then be possible to potentially expand the rapid monitoring system to other important pathogens once nanopore sequencing diagnostic methods are developed through future research. In this way Ethiopia would be the lead nation in Africa in having a robust, rapid monitoring system for important transboundary diseases. Ethiopia is the highest priority African country for such a system as it is the gateway for wind dispersed pests and pathogens between Africa and the Middle East/Asia.