Tag: technology

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 recognized for international impact

Written by Marcia MacNeil on May 17, 2019. Posted in News.

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 11^th 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)

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.

Mainassara Zaman-Allah conducts a demonstration of the use of unmanned aerial vehicles (UAV) at the Chiredzi research station in Zimbabwe.

Digital imaging tools make maize breeding much more efficient

Written by Shiela Chikulo on March 11, 2019. Posted in News.

To keep up with growing maize demand, breeders aim at optimizing annual yield gain under various stress conditions, like drought or low fertility soils. To that end, they identify the genetic merit of each individual plant, so they can select the best ones for breeding.

To improve that process, researchers at the International Maize and Wheat Improvement Center (CIMMYT) are looking at cost-effective ways to assess a larger number of maize plants and to collect more accurate data related to key plant characteristics. Plant phenotyping looks at the interaction between the genetic make-up of a plant with the environment, which produces certain characteristics or traits. In maize, for example, this may manifest in different leaf angles or ear heights.

Recent innovations in digital imagery and sensors save money and time in the collection of data related to phenotyping. These technologies, known as high-throughput phenotyping platforms, replace lengthy paper-based visual observations of crop trials.

Authors of a recent review study on high-throughput phenotyping tools observe that obtaining accurate and inexpensive estimates of genetic value of individuals is central to breeding. Mainassara Zaman-Allah, an abiotic stress phenotyping specialist at CIMMYT in Zimbabwe and one of the co-authors, emphasizes the importance of improving existing tools and developing new ones. “Plant breeding is a continuously evolving field where new tools and methods are used to develop new varieties more precisely and rapidly, sometimes at reduced financial resources than before,” he said. “All this happens to improve efficiency in breeding, in order to address the need for faster genetic gain and reduction of the cost of breeding.”

“Under the Stress Tolerant Maize for Africa (STMA) project, we are working on implementing the use of drone-based sensing, among other breeding innovations, to reduce time and cost of phenotyping, so that the development of new varieties costs less,’’ said Zaman-Allah. “The use of drones cuts time and cost of data collection by 25 to 75 percent compared to conventional methods, because it enables to collect data on several traits simultaneously — for example canopy senescence and plant count,” he explained.

Another great innovation developed under this CIMMYT project is what Zaman-Allah calls the ear analyzer. This low-cost digital imaging app allows to collect maize ear and kernel trait data 90 percent faster. This implies higher productivity and rigor, as more time is dedicated to data analysis rather than time spent on data collection. Using digital image processing, the ear analyzer gives simultaneous data of more than eight traits, including ear size and number, kernel number, size and weight.

*Measuring maize attributes such as ear size, kernel number and kernel weight is becoming faster and simpler through digital imaging technologies.*

Some national agricultural research systems and NGOs have adopted this digital imagery tool to better assess maize yields in farmers’ fields. For instance, CIMMYT and GOAL have used this tool to assess the extent of fall armyworm impact on maize crops yield in eastern Zimbabwe.

Scientists are exploring the use of different sensors for phenotyping, such as Red, Green and Blue (RGB) digital imaging or Light Detection and Ranging (LIDAR) devices. Infrared thermal and spectral cameras could lead to further progress towards faster maize breeding.

Such sensors can help collect numerous proxy data relating to important plant physiological traits or the plant environment, like plant height and architecture, soil moisture and root characteristics. This data can be used to assess the maize crop yield potential and stress tolerance.

Such breeding innovations are also making maize research more responsive to climate change and emerging pests and diseases.

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

Suitcase-sized lab speeds up wheat rust diagnosis

Written by on September 10, 2018. Posted in News.

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.