Posts Tagged ‘John Innes Centre’

MARPLE team awarded for international impact

Research team behind a revolutionary field test for wheat disease wins prestigious BBSRC prize

International Impact winners Diane Saunders and Dave Hodson with Malcolm Skingle, director of Academic Liaison, GlaxoSmithKline 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 annual Innovator of the Year Awards sponsored by the UK 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 of Agricultural Research (EIAR) — was presented with the award at a high-profile event at the London Science Museum on 15 May 2019 before an audience of leading figures from the worlds of investment, industry, government, charity and academia, including Chris Skidmore MP, Minister of State for Universities, Science, Research and Innovation.

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.

Diane Saunders of John Innes Centre and Dave Hodson of CIMMYT pose with the MARPLE diagnostics kit. Credit: JIC

As finalists in the international impact category, Saunders, Hodson and Daba were among a select group of 12 finalists competing for the prestigious Innovator of the Year 2019 award. In addition to international recognition, they received a £10,000 award.

“I am delighted that this work has been recognized,” said Hodson. “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.”

MARPLE diagnostics 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, among 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 with far-reaching implications for how plant health threats are identified and tracked into the future.

The MARPLE mobile lab in Ethiopia. Credit: JIC

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.”



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 Inspire Challenge. Continued support is also provided by the BBSRC Excellence with Impact Award to the John Innes Centre and the Delivering Genetic Gain in Wheat project led by Cornell University International Programs that is funded by the UK Department for International Development (DFID) and the Bill & Melinda Gates Foundation.

More information on the JIC-CIMMYT-EIAR team’s BBSRC recognition can be found on the JIC website, the BBSRC website and the website of the CGIAR Research Program on Wheat.

Q&A with Dave Hodson on MARPLE and Big Data

CIMMYT’s Dave Hodson taking wheat rust samples with Ethiopian farmers. Photo credit: John Innes Centre

The MARPLE (Mobile And Real-time PLant disease) project – a project to test and pilot a revolutionary mobile lab in Ethiopia, led by the John Innes Centre, the International Maize and Wheat Improvement Center (CIMMYT) and the Ethiopian Institute of Agricultural Research (EIAR)—won the CGIAR Platform for Big Data in Agriculture Inspire Challenge Scale Up award in 2018.

The Inspire Challenge encourages CGIAR partners, universities and others to use big data approaches through innovative pilot projects to advance agricultural research and development. To be named a winner, projects must have real potential for developmental impact, have mobilized underused or misused data, and demonstrate meaningful partnerships with CGIAR and other sector members. Ultimately, the Inspire Challenge looks for novel approaches to inform policies and applications in agriculture and food security.

We sat down with CIMMYT Principal Scientist and rust pathologist Dave Hodson to ask him about the project and its relationship with Big Data for Agriculture.

What is the significance of Big Data to your work?
Advances in sequencing technology, and the use of innovative big data approaches on sequence data from thousands of yellow rust isolates, opened the door for Diane Saunders and colleagues at the John Innes Centre in the UK to develop revolutionary, near-real time, mobile pathogen diagnostic techniques using portable palm-sized gene sequencers. The final result being the first operational system in the world using nanopore sequence technology for rapid diagnostics and surveillance of complex fungal pathogens in situ.

How do you see the role of the CGIAR Platform for Big Data in Agriculture in your work?
Support from the CGIAR Big Data Platform was critical to establish the partnership between John Innes, the Ethiopian Institute of Agricultural Research (EIAR) and CIMMYT and enable piloting and testing of the new MARPLE diagnostic platform in Ethiopia. The choice of Ethiopia to be the first country for initial testing was based on several key factors. Firstly, a strong national partner in EIAR; secondly, the critical importance of wheat and wheat rust diseases in the country. Ethiopia is the largest wheat producer in sub-Saharan Africa, but it is also considered the gateway for new wheat rust strains entering into Africa from Asia. All these factors made Ethiopia the highest priority country to take the lead in testing this revolutionary new and rapid pathogen diagnostics platform.

How did it impact this MARPLE project?
The pilot and subsequent scale-up project from the CGIAR Big Data Platform has enabled in-country capacity to be developed, and cutting edge technology for rapid pathogen diagnostics to be deployed in the front-line in the battle against devastating wheat rust diseases. The scientific innovation in developing the MARPLE platform, coupled to the suitability of the technology for developing country partners has now attracted support and interest from other donors. Matching funds were recently obtained for the scale -up phase of MARPLE from the Delivering Genetic Gain in Wheat project (implemented by Cornell University and funded by the Bill and Melinda Gates Foundation and the UK Department for International Development). This scale-up phase of the project will see a set of distributed MARPLE hubs established and embedded within the Ethiopian wheat research system – resulting in a sentinel system for the rapid detection of new yellow rust races that is unparalleled anywhere in the world. The scientific breakthrough in developing rapid diagnostics for complex fungal pathogens using nanopore sequencing will permit the development of similar systems for other important fungal diseases in the future.

The MARPLE project 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.

Mutating diseases drive wheat variety turnover in Ethiopia, new study shows

Yellow spores of the fungus Puccinia striiformis f.sp. tritici, which causes stripe rust disease in wheat. Photo: CIMMYT/Mike Listman.

By Mike Listman

Rapidly emerging and evolving races of wheat stem rust and stripe rust disease—the crop’s deadliest scourges worldwide—drove large-scale seed replacement by Ethiopia’s farmers during 2009-14, as the genetic resistance of widely-grown wheat varieties no longer proved effective against the novel pathogen strains, according to a new study by the International Maize and Wheat Improvement Center (CIMMYT).

Based on two surveys conducted by CIMMYT and the Ethiopian Institute of Agricultural Research (EIAR) and involving more than 2,000 Ethiopian wheat farmers, the study shows that farmers need access to a range of genetically diverse wheat varieties whose resistance is based on multiple genes.

After a severe outbreak in 2010-11 of a previously unseen stripe rust strain, 40 percent of the affected farm households quickly replaced popular but susceptible wheat varieties, according to Moti Jaleta, agricultural economist at CIMMYT and co-author of the publication.

“That epidemic hit about 600,000 hectares of wheat—30 percent of Ethiopia’s wheat lands—and farmers said it cut their yields in half,” Jaleta said. “In general, the rapid appearance and mutation of wheat rust races in Ethiopia has convinced farmers about the need to adopt newer, resistant varieties.”

The fourth most widely grown cereal after tef, maize, and sorghum, wheat in Ethiopia is produced largely by smallholder farmers under rainfed conditions. Wheat production and area under cultivation have increased significantly in the last decade and Ethiopia is among Africa’s top three wheat producers, but the country still imports on average 1.4 million tons of wheat per year to meet domestic demand.

National and international organizations such as EIAR, CIMMYT, and the International Centre for Agricultural Research in the Dry Areas (ICARDA) are working intensely to identify and incorporate new sources of disease resistance into improved wheat varieties and to support the multiplication of more seed to meet farmer demand.

New wheat varieties have provided bigger harvests and incomes for Ethiopia farmers in the last decade, but swiftly mutating and spreading disease strains are endangering wheat’s future, according to Dave Hodson, CIMMYT expert in geographic information and decision support systems, co-author of the new study.

Ethiopian wheat farmers like Abebe Abora, of Doyogena, have benefitted from adopting high-yielding wheat varieties but face threats from fast mutating races of wheat rust disease pathogens. Photo: CIMMYT/Apollo Habtamu.

Ethiopian wheat farmers like Abebe Abora, of Doyogena, have benefitted from adopting high-yielding wheat varieties but face threats from fast mutating races of wheat rust disease pathogens. Photo: CIMMYT/Apollo Habtamu.

“In addition to stripe rust, highly-virulent new races of stem rust are ruining wheat harvests in eastern Africa,” he explained. “These include the deadly Ug99 race group, which has spread beyond the region, and, more recently, the stem rust race TKTTF.”

As an example, he mentioned the case of the wheat variety Digalu, which is resistant to stripe rust and was quickly adopted by farmers after the 2010-11 epidemic. But Digalu has recently shown susceptibility to TKTTF stem rust and must now be replaced.

“In rust-prone Ethiopia, the risks of over-reliance on a widely-sown variety that is protected by a single, major resistance gene—Digalu, for example—are clearly apparent,” he added. “CIMMYT and partners are working hard to replace it with a new variety whose resistance is genetically more complex and durable.”

Hodson said as well that continuous monitoring of the rust populations in Ethiopia and the surrounding region is essential to detect and respond to emerging threats, as well as to ensure that the key pathogen races are used to screen for resistance in wheat breeding programs.

Hodson and partners at the John Innes Centre, UK, and EIAR are leading development of a handheld tool that allows rapid identification of disease strains in the field, instead of having to send them to a laboratory and lose precious time awaiting the results.

CIMMYT and partners are also applying molecular tools to study wheat varietal use in Ethiopia. “There are indications that yields reported by farmers were much lower than official statistics, and farmer recollections of varietal names and other information are not always exact,” Hodson explained. “We are analyzing results now of a follow-up study that uses DNA fingerprinting to better document varietal use and turnover.”

The authors would like to acknowledge the Standing Panel for Impact Assessment (SPIA) for financing, the Diffusion and Impacts of Improved Varieties in Africa (DIIVA) project that supported the first survey in 2011, and Cornell Universitythe Bill & Melinda Gates Foundation, and United Kingdom’s Department for International Development (DFID) through the Durable Rust Resistance in Wheat (DRRW, now called Delivering Genetic Gain in Wheat) project for support for the second survey in 2014.

Deadly strain of wheat stem rust disease surfaces in Europe

Scientists have shown that the first appearance of wheat stem rust disease in the U.K. in nearly 60 years, which occurred in 2013, was caused by the same virulent fungal strain responsible for recent wheat stem rust outbreaks in Ethiopia, Denmark, Germany, and Sweden.

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.