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Dave Hodson highlights “major breakthroughs” in rust disease response at the 2020 Borlaug Global Rust Initiative Technical Workshop

By Madeline Dahm

Dave Hodson, principal scientist at the International Maize and Wheat Improvement Center (CIMMYT), examined over a decade of progress from global partners in the battle to detect and respond to global wheat rust diseases at a keynote address at the Borlaug Global Rust Initiative (BGRI) Technical Workshop in early October.

International training participants learning to evaluate stem rust symptoms on wheat. Photo: Petr Kosina/CIMMYT.

Rust response in the 2000s: sounding the alarm

When the first signs of Ug99 – a deadly strain of wheat stem rust – were noticed in Uganda in 1998, farmers and researchers did not understand the full threat of this disease, or where it would travel next. After Nobel Prize-winning breeder Norman Borlaug sounded the alarm to world leaders, the BGRI was formed and stakeholders from around the world came together to discuss this quickly growing problem. They realized that first, they must develop effective monitoring and surveillance systems to track the pathogen.

Starting in 2008, the initial vision for the global rust monitoring system was developed and the first steps taken to build the global rust surveillance community. Expanding surveillance networks requires a strong database, increased capacity development and well-established national focal points. With standardized surveillance protocols, training and GPS units distributed to over 29 countries, data began to flow more efficiently into the system. This, combined with a preliminary study of the influence of wind and rainfall patterns, improved scientists’ ability to predict areas of higher risk. Furthermore, the group knew that it would be key to integrate race analysis data, expand access to information and eventually expand the system to include other rusts as well.

“Fast forward to today, and we’re now looking at one of the world’s largest international crop disease monitoring systems. We have over 39,000 geo-referenced survey records from >40 countries in the database now, and 9500+ rust isolate records,” said Hodson.

Implementation  of the Durable Rust Resistance in Wheat (DRRW) and Delivering Genetic Gain in Wheat (DGGW) projects – predecessors to Accelerating Genetic Gains in Maize and Wheat for Improved Livelihoods (AGG)  – and other key projects advanced this surveillance system, providing early warnings of potential rust epidemics to scientists and farmers.

An important part of this success comes from the Global Rust Reference Center in Denmark, where scientists have put together a state-of-the-art data management system, known as the “Wheat Rust Toolbox,”; providing a flexible centralized database,  rapid data input from mobile devices, data export and a suite of database-driven display tools. The system is flexible enough to handle multiple crops and multiple diseases, including all three wheat rusts.  

A united front

Another critical element to this surveillance system is a global network of rust pathotyping labs around the world. 

“We currently have good surveillance coverage across the world, especially the developing country wheat-growing areas,” says Hodson. “Coupling sampling from that survey network to these labs have enabled us to track the pathogen.”

This is particularly important in the face of a rapidly mutating pathogen. Not only are new variants of Ug99 appearing and spreading, but also other important new races of stem rust are being detected and spreading in places as far-flung as Sicily, Sweden, Siberia, Ecuador, Ethiopia and Georgia. In many regions, we are seeing a re-emergence of stem rust as a disease of concern.

“We now know there are 14 races of Ug99 confirmed across 13 countries. We have seen increased virulence of the pathogen, it  is mutating and migrating, and [has] spread over large distances.”

Furthermore, yellow rust has emerged as a disease of major global importance. The spread of yellow rust and appearance of highly virulent new races seems to be increasing over time. Several regions are now experiencing large-scale outbreaks as a result of the incursion of new races. For example, in South America, causing one of the largest outbreaks in 30 years.

Major breakthroughs in prediction and surveillance

Despite the increased spread and virulence of wheat rusts, the global community of partners has made serious advances in prediction, tracking and treatment of pathogens.

The University of Cambridge and the UK Met Office have developed advanced spore dispersal and epidemiological models for wheat rusts, resulting in a major leap forward in terms of understanding rust movements and providing a foundation for operational, in-season early warning systems. Operational, early warning is already a reality in Ethiopia and similar systems are now being tested in South Asia.

“These models are actually able to predict many of the movements we are now seeing globally,” says Hodson.

“In Ethiopia, information is going out to partners in weekly advisories, as well as targeted SMS alerts using the 8028 farmer hotline developed by the Ethiopian Agricultural Transformation Agency (ATA), with over 4 million subscribers. It makes it possible to get ahead of the disease in key areas–a major breakthrough,” he said, noting plans underway to expand the system to more countries.

In addition, innovative diagnostics such as  the award-winning MARPLE rapid, field-based diagnostic tool developed with the John Innes Centre and Ethiopian Institute of Agricultural Research (EIAR), are transforming the time it takes to detect potentially damaging new races. Resulting in more opportunities for early warning and timely, effective control responses.

The future of wheat research and disease management 

“Clearly, we’re going to need more multidisciplinary approaches to combat these increasing threats from transboundary diseases,” he says, though very optimistic for the future of wheat rust disease forecasting, early warning systems and diagnostics.

Thanks to a “truly fantastic” global community of partners and donors, the global scientific community has built one of the world’s largest crop disease monitoring systems to track and combat aggressive, rapidly spreading wheat rust diseases. Its continued success will depend on embracing state of the art technology – from molecular diagnostics to artificial intelligence – and developing a plan for long-term sustainability.


Scientists develop an early warning system that delivers wheat rust predictions directly to farmer’s phones

New research describes a revolutionary new early warning system that can predict and mitigate wheat rust diseases in Ethiopia.

One of the researchers behind the study, Yoseph Alemayehu, carries out a field survey in Ethiopia by mobile phone. (Photo Dave Hodson/CIMMYT)

Using field and mobile phone surveillance data together with forecasts for spore dispersal and environmental suitability for disease, an international team of scientists has developed an early warning system which can predict wheat rust diseases in Ethiopia. The cross-disciplinary project draws on expertise from biology, meteorology, agronomy, computer science and telecommunications.

Reported last week in Environmental Research Letters, the new early warning system, which is the first of its kind to be implemented in a developing country, will allow policy makers and farmers all over Ethiopia to gauge the current rust situation and forecast wheat rust up to a week later.

The system was developed by the University of Cambridge, the UK Met Office, the Ethiopian Institute of Agricultural Research (EIAR), the Ethiopian Agricultural Transformation Agency (ATA) and the International Maize and Wheat Improvement Center (CIMMYT).

Ethiopia is the largest wheat producer in sub-Saharan Africa but the country still spends in excess of $600 million annually on wheat imports. More can clearly be grown at home and the Ethiopian government has targeted to achieve wheat self-sufficiency by 2023. However increasing yields has its challenges.

One major challenge to wheat production are wheat rusts. The fungal diseases can be dispersed by wind over long distances, quickly causing devastating epidemics which can dramatically reduce wheat yields. Just one outbreak in 2010 affected 30% of Ethiopia’s wheat growing area and reduced production by 15-20%.

The pathogens that cause rust diseases are continually evolving and changing over time, making them difficult to control. “New strains of wheat rust are appearing all the time – a bit like the flu virus,” explained Dave Hodson, principal scientist CIMMYT and co-author of the research study.

In the absence of resistant varieties, one solution to wheat rust is to apply fungicide, however the Ethiopian government has limited supplies. The early warning system will help to prioritize areas at highest risk of the disease, so that the allocation of fungicides can be optimized.

The early warning system works by taking near real-time information from wheat rust surveys carried out by EIAR, regional research centers and CIMMYT using a smartphone app called Open Data Kit (ODK). This is complemented by crowd sourced phone surveys using ATA’s 8028 Farmers’ Hotline. 

The University of Cambridge and the UK Met office then provide automated 7 day advanced forecast models for wheat rust spore dispersal and environmental suitability based on disease presence.

Example of weekly stripe rust spore deposition based on dispersal forecasts. Darker colors represent higher predicted number of spores deposited. (Graphic: University of Cambridge/UK Met Office)

Interestingly, the dispersal model was originally developed by the UK Met Office for volcanic eruptions and nuclear accidents to predict where particles would be dispersed in the air. The University of Cambridge and the UK Met Office then adapted the model to predict where wheat rust spores would be dispersed and to provide a 7-day forecast.

 “It’s world-class science from the UK being applied to real world problems,” said Hodson.

All of this information is fed into an early warning unit that receives updates automatically on a daily basis. An advisory report is sent out every week to development agents and the national authorities and the information also gets passed on to researchers and farmers.

“If there’s a high risk of wheat rust developing, farmers will get a targeted alert by SMS sent by ATA. This gives the farmer about three weeks to take action,” explained Hodson. The ATA Farmers’ Hotline now has over four million farmers and extension agents registered, enabling rapid information dissemination throughout Ethiopia.

“Rust diseases are a grave threat to wheat production in Ethiopia. The timely information from this new system will help us protect farmers’ yields, and reach our goal of wheat self-sufficiency,” said EIAR Director Mandefro Nigussie.

Example of weekly stripe rust environmental suitability forecast. Yellow to Brown show the areas predicted to be most suitable for stripe rust infection. (Graphic: University of Cambridge/UK Met Office)

The system puts Ethiopia at the forefront of early warning systems for wheat rust.

“Nowhere else in the world really has this type of system. It’s fantastic that Ethiopia is leading the way on this,” said Hodson.

At the same time, CIMMYT and partners have been racing to develop wheat rust resistant varieties to allow farmers to avoid the diseases altogether. Recent estimates, based on DNA fingerprinting, indicate that these rust resistant varieties have been widely adopted throughout Ethiopia, and that varietal replacement is occurring frequently. 

The near real-time diagnostics tool MARPLE (Mobile And Real-time PLant disEase diagnostics) is also making huge leaps in wheat rust detection. Strains of yellow rust can be identified in just 48 hours using this suitcase sized kit – a process that normally takes months. The researchers recommended that this new technology be used in conjunction with the Early Warning System, to allow more accurate assessments and predictions of disease spread in Ethiopia.

Read the full article:

https://doi.org/10.1088/1748-9326/ab4034

Read the press release on CIMMYT.org. 

This study was made possible through the support provided by the BBSRC GCRF Foundation Awards for Global Agriculture and Food Systems Research, which brings top class UK science to developing countries, the Delivering Genetic Gains in Wheat (DGGW) Project managed by Cornell University and funded by the Bill & Melinda Gates Foundation and the UK Department for International Development (DFID). The Government of Ethiopia also provided direct support into the early warning system.