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funder_partner: John Innes Centre (JIC)

Using the MARPLE kit to diagnose wheat rust in Ethiopia

MARPLE (Mobile and Real-time PLant disEase) Diagnostics is a revolutionary mobile lab developed by a team from the John Innes Centre (JIC), the International Maize and Wheat Improvement Center (CIMMYT) and the Ethiopian Institute of Agricultural Research (EIAR). It uses nanopore sequence technology to rapidly diagnose and monitor wheat rust in farmers’ fields.

Designed to be used without constant electricity and in varying temperatures, the suitcase-sized lab allows researchers to identify wheat rust to strain level in just 48 hours — something that used to take months using other tools.

The MARPLE team was recognized as Innovator of the Year for international impact in 2019 by the UK Biotechnology and Biological Sciences Research Council (BBSRC).

A new video from the John Innes Centre shows how the MARPLE Diagnostics kit will allow Ethiopia to quickly identify wheat rust strains, instead of sending samples to labs abroad.

Research, innovation, partnerships, impact

On May 15, 2019, as part of the CGIAR System Council meeting held at the ILRI campus in Addis Ababa, Ethiopia, around 200 Ethiopian and international research and development stakeholders convened for the CGIAR Agriculture Research for Development Knowledge Share Fair. This exhibition offered a rare opportunity to bring the country’s major development investors together to learn and exchange about how CGIAR investments in Ethiopia help farmers and food systems be more productive, sustainable, climate resilient, nutritious, and inclusive.

Under the title One CGIAR — greater than the sum of its parts — the event offered the opportunity to highlight close partnerships between CGIAR centers, the Ethiopian government and key partners including private companies, civil society organizations and funding partners. The fair was organized around the five global challenges from CGIAR’s business plan: planetary boundaries, sustaining food availability, promoting equality of opportunity, securing public health, and creating jobs and growth. CGIAR and its partners exhibited collaborative work documenting the successes and lessons in working through an integrated approach.

There were 36 displays in total, 5 of which were presented by CIMMYT team members. Below are the five posters presented.

How can the data revolution help deliver better agronomy to African smallholder farmers?

This sustainability display showed scalable approaches and tools to generate site-specific agronomic advice, developed through the Taking Maize Agronomy to Scale in Africa (TAMASA) project in Nigeria, Tanzania and Ethiopia.

Maize and wheat: Strategic crops to fill Ethiopia’s food basket

This poster describes how CGIAR works with Ethiopia’s research & development sector to support national food security priorities.

Addressing gender norms in Ethiopia’s wheat sector

Research shows that restrictive gender norms prevent women’s ability to innovate and become productive. This significantly impacts Ethiopia’s economy (over 1% GDP) and family welfare and food security.

Quality Protein Maize (QPM) for better nutrition in Ethiopia

With the financial support of the government of Canada, CIMMYT together with national partners tested and validated Quality Protein Maize as an alternative to protein intake among poor consumers.

Appropriate small-scale mechanization

The introduction of small-scale mechanization into the Ethiopian agriculture sector has the potential to create thousands of jobs in machinery service provision along the farming value chain.

About the CGIAR System Council

The CGIAR System Council is the strategic decision-making body of the CGIAR System that keeps under review the strategy, mission, impact and continued relevancy of the System as a whole. The Council meets face-to-face not less than twice per year and conducts business electronically between sessions. Additional meetings can be held if necessary.

Related outputs from the Share Fair 2019

MARPLE team recognized for international impact

MARPLE team members Dave Hodson and Diane Saunders (second and third from left) stand for a photograph after receiving the International Impact award. With them is Malcolm Skingle, director of Academic Liaison at GlaxoSmithKline (first from left) and Melanie Welham, executive chair of BBSRC. (Photo: BBSRC)
MARPLE team members Dave Hodson and Diane Saunders (second and third from left) stand for a photograph after receiving the International Impact award. With them is Malcolm Skingle, director of Academic Liaison at GlaxoSmithKline (first from left) and Melanie Welham, executive chair of BBSRC. (Photo: BBSRC)

The research team behind the MARPLE (Mobile And Real-time PLant disEase) diagnostic kit won the International Impact category of the Innovator of the Year 2019 Awards, sponsored by the United Kingdom’s Biotechnology and Biological Sciences Research Council (BBSRC).

The team — Diane Saunders of the John Innes Centre (JIC), Dave Hodson of the International Maize and Wheat Improvement Center (CIMMYT) and Tadessa Daba of the Ethiopian Institute for Agricultural Research (EIAR) — was presented with the award at an event at the London Science Museum on May 15, 2019. In the audience were leading figures from the worlds of investment, industry, government, charity and academia, including the U.K.’s Minister of State for Universities, Science, Research and Innovation, Chris Skidmore.

The BBSRC Innovator of the Year awards, now in their 11th year, recognize and support individuals or teams who have taken discoveries in bioscience and translated them to deliver impact. Reflecting the breadth of research that BBSRC supports, they are awarded in four categories of impact: commercial, societal, international and early career. Daba, Hodson and Saunders were among a select group of 12 finalists competing for the four prestigious awards. In addition to international recognition, they received £10,000 (about $13,000).

“I am delighted that this work has been recognized,” Hodson said. “Wheat rusts are a global threat to agriculture and to the livelihoods of farmers in developing countries such as Ethiopia. MARPLE diagnostics puts state-of-the-art, rapid diagnostic results in the hands of those best placed to respond: researchers on the ground, local government and farmers.”

On-the-ground diagnostics

The MARPLE diagnostic kit is the first operational system in the world using nanopore sequence technology for rapid diagnostics and surveillance of complex fungal pathogens in the field.

In its initial work in Ethiopia, the suitcase-sized field test kit has positioned the country — one of the region’s top wheat producers — as a world leader in pathogen diagnostics and forecasting. Generating results within 48 hours of field sampling, the kit represents a revolution in plant disease diagnostics. Its use will have far-reaching implications for how plant health threats are identified and tracked into the future.

MARPLE is designed to run at a field site without constant electricity and with the varying temperatures of the field.

“This means we can truly take the lab to the field,” explained Saunders. “Perhaps more importantly though, it means that smaller, less-resourced labs can drive their own research without having to rely on a handful of large, well-resourced labs and sophisticated expertise in different countries.”

In a recent interview with JIC, EIAR Director Tadessa Daba said, “we want to see this project being used on the ground, to show farmers and the nation this technology works.”

The MARPLE team uses the diagnostic kit in Ethiopia. (Photo: JIC)
The MARPLE team uses the diagnostic kit in Ethiopia. (Photo: JIC)

Development of the MARPLE diagnostic kit was funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the CGIAR Platform for Big Data in Agriculture’s Inspire Challenge. Continued support is also provided by the BBSRC’s Excellence with Impact Award to the John Innes Centre and the Delivering Genetic Gain in Wheat project, led by Cornell University and funded by the UK’s Department for International Development (DFID) and the Bill & Melinda Gates Foundation.

More information on the award can be found on the JIC website, the BBSRC website and the website of the CGIAR Research Program on Wheat.

CIMMYT trains early career scientists on wheat rust diagnosis and management

NJORO, Kenya (CIMMYT) — The International Maize and Wheat Improvement Center (CIMMYT), in collaboration with Kenya Agricultural & Livestock Research Organization (KALRO) and Cornell University, recently trained 29 scientists from 13 countries on wheat rust disease diagnosis and management techniques, as well as innovative wheat breeding practices. The training, part of the Delivering Genetic Gains in Wheat (DGGW) project, took place on October 1-9, 2018, at the KALRO research station in Njoro, Kenya, where CIMMYT’s wheat breeding and rust screening facility is located.

More than 200 scientists have increased their capacity at these annual trainings since CIMMYT started organizing them ten years ago. The trainings focus particularly on studying resistance to black (stem) rust, yellow (stripe) rust and brown (leaf) rust. Future wheat champions in national agricultural research systems (NARS) get new skills on innovative and cost-effective wheat breeding. These trainings are also a chance for CIMMYT’s Global Wheat Program to establish new partnerships and to collaborate on emerging challenges related to wheat breeding in different farming regions.

“The focus of this year’s event was to train the scientists on how to identify and record notes for stem rust occurrences and how to evaluate wheat material in the field, to better understand how wheat rust pathogens keep evolving,” said Mandeep Randhawa, wheat breeder and wheat rust pathologist at CIMMYT.

Robert McIntosh from University of Sydney's Plant Breeding Institute demonstrates stem rust inoculation using a syringe. (Photo: KALRO)
Robert McIntosh from University of Sydney’s Plant Breeding Institute demonstrates stem rust inoculation using a syringe. (Photo: KALRO)
Scientists Ruth Wanyera (center) and Mandeep Randhawa (right) demonstrate stem inoculation devices. (Photo: KALRO)
Scientists Ruth Wanyera (center) and Mandeep Randhawa (right) demonstrate stem inoculation devices. (Photo: KALRO)
CIMMYT scientist Mandeep Randhawa indicates exact wheat plant stage for stem rust inoculation during the wheat stem rust training. (Photo: KALRO)
CIMMYT scientist Mandeep Randhawa indicates exact wheat plant stage for stem rust inoculation during the wheat stem rust training. (Photo: KALRO)
CIMMYT scientist Mandeep Randhawa explains trainees early booting stage for stem rust inoculation. (Photo: KALRO)
CIMMYT scientist Mandeep Randhawa explains trainees early booting stage for stem rust inoculation. (Photo: KALRO)
Participants of the wheat stem rust training pose for a group photograph. (Photo: KALRO)
Participants of the wheat stem rust training pose for a group photograph. (Photo: KALRO)
Participants of CIMMYT's annual wheat improvement training in Njoro, Kenya, attend a class session. (Photo: KALRO)
Participants of CIMMYT’s annual wheat improvement training in Njoro, Kenya, attend a class session. (Photo: KALRO)

Despite its importance for global food security and nutrition, wheat remains susceptible to endemic and highly destructive rust diseases which can lead to 60-100 percent yield losses. Developing and distributing rust resistant wheat varieties is regarded as the most cost-effective and eco-friendly control measure, especially in developing countries, where the majority are resource-poor smallholder farmers with no access to fungicides to control the disease.

As a global leader in wheat and maize breeding systems, CIMMYT has sustained efforts to develop high-yielding, disease-resistant and stress-tolerant varieties. In partnership with KALRO, CIMMYT identified and released over 15 commercial wheat varieties since the establishment of the stem rust screening facility in Njoro in 2008. Despite the appearance of new devastating strains of stem rust over the period, most of these released wheat varieties are high-yielding with stem rust resistance, according to Randhawa.

“Adequate management practices, including timely planting and application of right fungicides, have kept some of the high-yielding varieties such as Kenya Korongo and Eagle10 in production,” Randhawa explained.

Several high-yielding rust resistant wheat lines are in pipeline for national evaluation to release as wheat varieties in Kenya, he said.

The development of a portable, real-time diagnostics tool for wheat yellow rust, namely the Mobile and Real-time Plant DisEase Diagnostics (MARPLE) was another breakthrough in identifying and combating wheat rust. This mobile plant health diagnosis tool helps identify rust strains in three days instead of months. This is a game changer for the wheat sector, as rust control measures could be deployed before new rust becomes a large-scale epidemic. Led by senior scientist David Hodson, MARPLE is the result of the collaboration between CIMMYT, the Ethiopian Institute of Agricultural Research (EIAR) and the John Innes Centre. There are plans to scale up this innovation in Ethiopia, where it is expected to provide five million wheat farmers a lifeline to control wheat yellow rust.

At the training, participants such as Zafar Ziyaev from Uzbekistan, were glad to gain deeper understanding on how to use modern tools for rust surveillance and the control measures. Others acknowledged the importance of sensitizing and supporting farmers to grow rust-resistant wheat varieties.

Emeritus Professor Robert McIntosh, one of the trainers from the Plant Breeding Institute at the University of Sydney, acknowledged the need for wheat scientists to remain vigilant on rust outbreaks globally and the evolving nature of the pathogens.

“As rust pathogens spread from country to country and region to region, such trainings allow national scientists to learn about the need for constant awareness, the basic principles of epidemiology and genetics that provide the basis of breeding for durable resistance, and what the Njoro rust testing platform can offer to the NARS,” McIntosh said.

Suitcase-sized lab speeds up wheat rust diagnosis

A farm landscape in Ethiopia. (Photo: Apollo Habtamu/ILRI)
A farm landscape in Ethiopia. (Photo: Apollo Habtamu/ILRI)

Despite her unassuming nature, the literary character Miss Marple solves murder mysteries with her keen sense of perception and attention to detail. But there’s another sleuth that goes by the same name. MARPLE (Mobile And Real-time PLant disEase) is a portable testing lab which could help speed-up the identification of devastating wheat rust diseases in Africa.

Rust diseases are one of the greatest threats to wheat production around the world. Over the last decade, more aggressive variants that are adapted to warmer temperatures have emerged. By quickly being able to identify the strain of rust disease, researchers and farmers can figure out the best course of action before it is too late.

The Saunders lab of the John Innes Centre created MARPLE. In collaboration with the Ethiopian Institute of Agricultural Research (EIAR) and the International Maize and Wheat Improvement Center (CIMMYT), researchers are testing the mobile diagnostic kit in Holeta, central Ethiopia.

“These new pathogen diagnostic technologies … offer the potential to revolutionize the speed at which new wheat rust strains can be identified,” says Dave Hodson, a CIMMYT rust pathologist in Ethiopia. “This is critical information that can be incorporated into early warning systems and result in more effective control of disease outbreaks in farmers’ fields.”

Hodson and his colleagues will be presenting their research at the CGIAR Big Data in Agriculture Convention in Nairobi, on October 3-5, 2018.

Read more about the field testing of the MARPLE diagnostic kit on the ACACIA website.

Deadly strain of wheat stem rust disease surfaces in Europe

Wheat stem rust was reported by the Greeks and Romans, and the latter sacrificed to the gods to avoid disease outbreaks on their wheat crops. Photo: CIMMYT/Petr Kosina
Wheat stem rust was reported by the Greeks and Romans, and the latter sacrificed to the gods to avoid disease outbreaks on their wheat crops.
Photo: CIMMYT/Petr Kosina

As reported today in Communications Biology, an international team of researchers led by the John Innes Centre, U.K., found that 80 percent of U.K. wheat varieties are susceptible to the deadly stem rust strain. The group also confirmed for the first time in many decades that the stem rust fungus was growing on barberry bush, the pathogen’s alternate host, in the UK.

“This signals the rising threat of stem rust disease for wheat and barley production in Europe,” said Dave Hodson, senior scientist at the International Maize and Wheat Improvement Center (CIMMYT) and co-author on the study.

A scourge of wheat since biblical times, stem rust caused major losses to North American wheat crops in the early 20th century. Stem rust disease was controlled for decades through the use of resistant wheat varieties bred in the 1950s by scientist Norman Borlaug and his colleagues. Widespread adoption of those varieties sparked the Green Revolution of the 1960s and 70s.

In 1999 a new, highly-virulent strain of the stem rust fungus emerged in eastern Africa. Spores of that strain and variants have spread rapidly and are threatening or overcoming the genetic resistance of many currently sown wheat varieties. Scientists worldwide joined forces in the early 2000s to develop new, resistant varieties and to monitor and control outbreaks of stem rust and yellow rust, as part of collaborations such as the Borlaug Global Rust Initiative led by Cornell University.

Barberry is a shrub found throughout the temperate and subtropical regions. Photo: CIMMYT archives
Barberry is a shrub found throughout the temperate and subtropical regions. Photo: John Innes Centre

The Communications Biology study shows that 2013 U.K. stem rust strain is related to TKTTF, a fungal race first detected in Turkey that spread across the Middle East and recently into Europe. It was the dominant race in the 2013 stem rust outbreak in Germany and infected 10,000 hectares of wheat in Ethiopia’s breadbasket the same year.

Because disease organisms mutate quickly to overcome crop resistance controlled by single genes, researchers are rushing to identify new resistance genes and to incorporate multiple genes into high-yielding varieties, according to Ravi Singh, CIMMYT wheat scientist who participated in the reported study.

“The greatest hope for achieving durable resistance to rust diseases is to make wheat’s resistance genetically complex, combining several genes and resistance mechanisms,” Singh explained.

Barberry, which serves as a spawning ground for the stem rust fungus, was largely eradicated from the U.K. and U.S. last century, greatly reducing the spread and genetic diversification of rust disease races. Now barberry is being grown again in the U.K. over the last decade, according to Diane G.O. Saunders, John Innes Centre scientist and co-author of the study.

“The late Nobel laureate Norman Borlaug said that the greatest ally of the pathogen is our short memory,” Saunders stated. “We recommend continued, intensive resistance breeding. We would also welcome work with conservationists of endangered, barberry-dependent insect species to ensure that planting of common barberry occurs away from arable land, thus safeguarding European cereals from a large-scale re-emergence of wheat stem rust.”

Click here to read the John Innes Centre media release about the Communications Biology report and view the report.