A new case study by the Biotechnology and Biological Sciences Research Council shines a spotlight on the MARPLE (Mobile and Real-time PLant disEase) Diagnostics kit, a revolutionary technology that can identify fungus strains in just two days.
MARPLE, which was developed by the John Innes Centre in collaboration with the International Maize and Wheat Improvement Center (CIMMYT) and the Ethiopian Institute of Agricultural Research (EIAR), is currently being rolled out across five major research hubs in Ethiopia. As sub-Saharan Africa’s largest wheat producer, Ethiopia is considered “a gateway for new rust pathogen strains entering from Asia”.
CIMMYT Senior Scientist Dave Hodson is a guest on Plantopia, a podcast produced by Cornell University that explains how protecting plant health can ensure a sustainable future. On the “Arms Race Part 1: Ug99” episode, Hodson discusses the striking parallels between wheat rusts and global pandemics in humans, pointing out that in both cases, we’re just one step ahead of the pathogen.
This story by Matthew O’ Leary was originally published on the CIMMYT website.
An early warning system set to deliver wheat disease predictions directly to farmers’ phones is being piloted in Bangladesh and Nepal by interdisciplinary researchers.
Experts in crop disease, meteorology and computer science are crunching data from multiple countries to formulate models that anticipate the spread of the wheat rust and blast diseases in order to warn farmers of likely outbreaks, providing time for pre-emptive measures, said Dave Hodson, a principal scientist with the International Maize and Wheat Improvement Center (CIMMYT) coordinating the pilot project.
Around 50,000 smallholder farmers are expected to receive improved disease warnings and appropriate management advisories through the one-year proof-of-concept project, as part of the UK Aid-funded Asia Regional Resilience to a Changing Climate (ARRCC) program.
Early action is critical to prevent crop diseases becoming endemic. The speed at which wind-dispersed fungal wheat diseases are spreading through Asia poses a constant threat to sustainable wheat production of the 130 million tons produced in the region each year.
“Wheat rust and blast are caused by fungal pathogens, and like many fungi, they spread from plant to plant — and field to field — in tiny particles called spores,” said Hodson. “Disease strain mutations can overcome resistant varieties, leaving farmers few choices but to rely on expensive and environmentally-damaging fungicides to prevent crop loss.”
“The early warning system combines climate data and epidemiology models to predict how spores will spread through the air and identifies environmental conditions where healthy crops are at risk of infection. This allows for more targeted and optimal use of fungicides.”
The system was first developed in Ethiopia. It uses weather information from the Met Office, the UK’s national meteorological service, along with field and mobile phone surveillance data and disease spread modeling from the University of Cambridge, to construct and deploy a near real-time early warning system.
Initial efforts focused on adapting the wheat stripe and stem rust model from Ethiopia to Bangladesh and Nepal have been successful, with field surveillance data appearing to align with the weather-driven disease early warnings, but further analysis is ongoing, said Hodson.
“In the current wheat season we are in the process of comparing our disease forecasting models with on-the-ground survey results in both countries,” the wheat expert said.
“Next season, after getting validation from national partners, we will pilot getting our predictions to farmers through text-based messaging systems.”
CIMMYT’s strong partnerships with governmental extension systems and farmer associations across South Asia are being utilized to develop efficient pathways to get disease predictions to farmers, said Tim Krupnik, a CIMMYT Senior Scientist based in Bangladesh.
“Partnerships are essential. Working with our colleagues, we can validate and test the deployment of model-derived advisories in real-world extension settings,” Krupnik said. “The forecasting and early warning systems are designed to reduce unnecessary fungicide use, advising it only in the case where outbreaks are expected.”
Local partners are also key for data collection to support and develop future epidemiological modelling, the development of advisory graphics and the dissemination of information, he explained.
Strong scientific partnership champions diversity to achieve common goals
The meteorological-driven wheat disease warning system is an example of effective international scientific partnership contributing to the UN Sustainable Development Goals, said Sarah Millington, a scientific manager at Atmospheric Dispersion and Air Quality Group with the Met Office.
“Diverse expertise from the Met Office, the University of Cambridge and CIMMYT shows how combined fundamental research in epidemiology and meteorology modelling with field-based disease observation can produce a system that boosts smallholder farmers’ resilience to major agricultural challenges,” she said.
The atmospheric dispersion modeling was originally developed in response to the Chernobyl disaster and since then has evolved to be able to model the dispersion and deposition of a range of particles and gases, including biological particles such as wheat rust spores.
“The framework together with the underpinning technologies are transferable to forecast fungal disease in other regions and can be readily adapted for other wind-dispersed pests and disease of major agricultural crops,” said Christopher Gilligan, head of the Epidemiology and Modelling Group at the University of Cambridge.
Fungal wheat diseases are an increasing threat to farmer livelihoods in Asia
While there has been a history of wheat rust disease epidemics in South Asia, new emerging strains and changes to climate pose an increased threat to farmers’ livelihoods. The pathogens that cause rust diseases are continually evolving and changing over time, making them difficult to control.
Stripe rust threatens farmers in Afghanistan, India, Nepal and Pakistan, typically in two out of five seasons, with an estimated 43 million hectares of wheat vulnerable. When weather conditions are conducive and susceptible cultivars are grown, farmers can experience losses exceeding 70%.
Populations of stem rust are building at alarming rates and previously unseen scales in neighboring regions. Stem rust spores can spread across regions on the wind; this also amplifies the threat of incursion into South Asia and the ARRCC program’s target countries, underscoring the very real risk that the disease could reemerge within the subcontinent.
The devastating wheat blast disease, originating in the Americas, suddenly appeared in Bangladesh in 2016, causing wheat crop losses as high as 30% on a large area, and continues to threaten South Asia’s vast wheat lands.
In both cases, quick international responses through CIMMYT, the CGIAR research program on Wheat (WHEAT) and the Borlaug Global Rust Initiative have been able to monitor and characterize the diseases and, especially, to develop and deploy resistant wheat varieties.
The UK aid-funded ARRCC program is led by the Met Office and the World Bank and aims to strengthen weather forecasting systems across Asia. The program is delivering new technologies and innovative approaches to help vulnerable communities use weather warnings and forecasts to better prepare for climate-related shocks.
The early warning system uses data gathered from the online Rust Tracker tool, with additional fieldwork support from the Cereal Systems Initiative for South Asia (CSISA), funded by USAID and the Bill & Melinda Gates Foundation, both coordinated by CIMMYT.
This article was originally posted on the Alliance for Accelerated Crop Improvement in Africa (ACACIA) website.
A network of Ethiopian researchers across the country are championing a new mobile lab to provide near real-time, strain-level diagnostics during wheat rust outbreaks.
Since winning the international impact category of the BBSRC innovator of the year award the MARPLE (Mobile And Real-time PLant disEase) diagnostic platform is now being established in research hubs across the wheat growing areas of Ethiopia. This marks the next step for the platform after its first trial in country just over a year ago. The UK-Ethiopian partnership hopes to have these platforms fully operational in time for the next growing season in 2020.
“Wheat yellow rust continues to cause huge losses for Ethiopian farmers,” says Diane Saunders whose lab led the creation of MARPLE diagnostics, “finally we have a proven mobile pipeline that gives us information on precisely which strain is present in a farmer’s field in near real-time. This provides the time needed to plan informed defensive responses. Our goal is now to put this technology in the hands of the researcher hubs on the ground.”
New research describes a revolutionary new early warning system that can predict and mitigate wheat rust diseases in Ethiopia.
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.
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
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.
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.
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,”
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 () 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.
part of a global network to combat the Ug99 race of
wheat stem rust, the International Maize and Wheat Improvement Center (CIMMYT),
in collaboration with Cornell University and the Kenya Agricultural and
Livestock Research Organization (KALRO), established a stem rust phenotyping platform
in Njoro, Kenya in 2008.
the aegis of the Durable Rust Resistance in Wheat (DRRW) project and with
support from the Bill & Melinda Gates Foundation, the platform evaluates the resistance of germplasm against Ug99 from
25 to 30 countries around the world.
Mandeep Randhawa — a wheat breeder and geneticist — joined CIMMYT’s Global Wheat Program in 2015 and took responsibility as manager of the Njoro wheat stem rust phenotyping platform in 2017.
In the following Q&A — based on an interview with Chris Knight of
Cornell University’s Borlaug Global Rust Initiative — Mandeep talks about his
role and his thoughts on global wheat production and the fight against Ug99.
Q: Could you describe the
significance of the work that goes on here to global wheat production and
global food security with respect to wheat?
A: CIMMYT has a global mandate to serve developing countries in terms of developing new wheat and maize varieties. Under the CIMMYT-Kenya shuttle breeding program, seed of about 2000 segregated populations are imported and evaluated against stem rust races for two seasons in Njoro, and spikes from resistant plants of each cross are selected, harvested and threshed together. Then, seed from each cross is shipped back to Obregon [the Campo Experimental Norman E. Borlaug in Obregon, Mexico].
In Obregon, CIMMYT selects for resistance against leaf rust and stem rust diseases using the local rust races. Plants are selected in Obregon and about 90,000 to 100,000 plants harvested. After grain selection, 40,000 to 50,000 small plots are grown in other testing sites in Mexico where another round of selections are made. About 10,000 lines undergo first year yield trials in Obregon, and are tested for stem rust resistance here in Kenya for two seasons.
combining data from the various test sites with the stem rust score from Kenya,
the top performing lines (about 10%) undergo second year yield tests in
high-yielding lines are distributed internationally to our national partners,
and are available to the public for use in breeding program for release as
believe that it is helpful to develop new varieties with higher yield to
Q: Twenty years have now passed
since Ug99 was first identified. One way to frame the story is how high the
stakes were at the time. If we didn’t have this screening platform, if we hadn’t
come together around trying to fight Ug99, what would have happened to global
a good question. We have done so much for the last 10 years using this
platform. We are developing high-yielding lines that are rust resistant, which
are benefiting not only the world’s wheat community, but will eventually
benefit the farmer and help raise global wheat production. If we had not acted
at the right time, we would not be able to know the effect of these emerging races
and how they’re evolving and affecting the world of our wheat. If we didn’t
have proper surveillance on rusts, we wouldn’t be able to know what types of stem
rust races are evolving.
If we did
not have this platform, we would see wheat varieties simply killed by stem rust
and we wouldn’t have enough resources to tackle it today.
are at a place where several Ug99-resistant genes have been identified – they
are very useful in the breeding programs.
are two types of resistance. One is race specific resistance and another is
race non-specific resistance. If you deploy race specific resistance, there is
always the fear that these genes will be rendered ineffective because of the
evolution of new races. It has been seen in East Africa with the wheat
varieties Robin and Digelu that were rendered susceptible with the emergence of
virulent strains of wheat stem rust pathogen. To avoid sudden breakdown of
resistance, we at CIMMYT are working to identify, characterize and combine race
non-specific type of rust resistance sources. Race non-specific resistance is
considered more durable. At least four to five genes need to be combined in one
cultivar to have a stronger immunity or resistance.
Q: Let’s talk a little bit about
the future. We’ve made a lot of progress, we’ve developed this platform, we
brought a community of more than 25 countries together to work on this problem.
What do we need to do in the next 20 years?
rust was considered a disease prevalent in warmer environments, but now we can
see that races have also evolved in Europe, which means that stem rust is
adapting to cooler climates. In the near future, or in the next 20 years, I
think we have to continue testing wheat germplasm at this platform to develop
high-yielding rust resistant varieties that can be released in different
countries, which will be helpful to the global wheat community. And globally
speaking, it will be helpful to increase our wheat production.
Q: That’s really exciting.
Thinking about the number of wheat lines that are screened here, how many wheat
lines are screened here every year, and how many countries do we serve?
the platform initially formed, my predecessors struggled a lot. It was very
hard to plant wheat here. Now we have progressed in the last ten years to reach
a level that we can test about 25,000 lines in one season. We have two seasons
here in Kenya: one is the off-season starting from January to April/May, and
then the main season starts from June and goes to the end of October. During
these two seasons, about 50,000 lines per year can be tested at this platform. About
25 to 30 countries are benefitting by testing their germplasm here.
not only need to cultivate the wheat, we need to cultivate the next generation
of scientists. So can you talk about the trainings that are run here on a
regular basis? People from all over the world come here to learn about rust
pathology and wheat breeding, right?
the last 10 years, we have been implementing capacity building where young
scientists are coming to attend a stem rust training course every year, in
September and October. Every year we train about 20 to 30 young scientists from
national programs in East Africa, South Asia, the Middle East and South
America. Every year Dr. Bob McIntosh — he’s a living legend, an encyclopedia
of rust resistance – comes over to Njoro to give field demonstrations, teach new
technologies, how we can work together, how you can evaluate rust in the field
and in the greenhouse. And in addition, a team of scientists from CIMMYT,
ICARDA and Cornell University have been coming to provide lectures on genetics
and breeding for rust resistance and rust surveys every year for the last 10
years. We have trained more than 200 scientists.
you have a final word of motivation for all of the collaborators around the
world who are supporting and helping together to achieve these goals?
We have seen in the last two decades of work here that rust never
sleeps, as Dr. Norman Borlaug said. It continues to evolve, and the different
races keep on moving around and tend to survive on wheat without any resistance.
Not only in east Africa: you can see the stem rust is already in Europe – in Sicily,
in Germany and the UK. And there is a risk to South Asia as well, as the wind
is blowing toward the bread wheat producing area there. If stem rust reaches
there, it can cause a huge loss to global wheat production.
So, I request that countries’ national agriculture research systems contact us: me or Ruth Wanyera, the wheat rust pathologist in KALRO if they want to test or evaluate their material at this platform. We are more than happy to evaluate the germplasm from any country.