Posts Tagged ‘big data’

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.


Launching the AgriFoodTrust platform

This story by Matthew O’Leary was originally published on the CIMMYT website.

A new testing and learning platform for digital trust and transparency technologies — such as blockchain — in agri-food systems was launched at the Strike Two Summit in late February. 

AgriFoodTrust debuted at the summit which brought together key agri-food system players to discuss how blockchain and related technologies can contribute to food safety, quality and sustainability, said Gideon Kruseman, an economist with the International Maize and Wheat Improvement Center (CIMMYT), who co-founded the platform. 

“Blockchain is often associated with the digital security that led to cryptocurrencies. However, growing research is providing evidence on its unique potential to bring greater efficiency, transparency and traceability to the exchange of value and information in the agriculture sector,” said Kruseman. 

“Many of the wicked problems and seemingly insuperable challenges facing dynamic, complex agri-food system value chains, especially in low and middle-income countries, boil down to a lack of trust, transparency and reliable governance structures,” said the researcher who also leads the Socio-Economic Data Community of Practice of the CGIAR Platform for Big Data in Agriculture.  

Future Food panelist speak at the Strike Two Summit in Amsterdam, the Netherlands. (Photo: The New Fork)

A blockchain is a ledger that is almost impossible to forge. It can be described as a data structure that holds transactional records and ensures security, transparency and decentralization. Technology may be at the foundation of the solutions, but technology is the easy part; solving the softer side has proven to be a seemingly insuperable challenge over the past decades, Kruseman explained. 

Digital trust and transparency technologies can be used to improve governance structures and limit corruption in agri-food systems in low and middle income countries, said Marieke de Ruyter de Wildt, co-founder of AgriFoodTrust. 

“This new generation of decentralized technologies is, in essence, improving governance structures. People often think it is about technology, but it’s not. It is about people and how we organize things.”  

“These technologies are neutral, immutable and censorship resistant. You can mimic this if you think about rules without a ruler. Just imagine what opportunities arise when a system is incorruptible,” said de Ruyter de Wildt.  

It is hoped, accessible via QR codes, for example, that the technology can be used to tackle challenges, such as preventing the sale of counterfeit seeds to smallholder farmers, ensuring the nutritional value of biofortified crop varieties and promoting the uptake of sustainable agricultural principles whilst improving the implementation and monitoring of international agreements related to agriculture. 

“This is where the platform comes in as a knowledge base. The AgriFoodTrust platform sees researchers from CGIAR Centers and academia, such as Wageningen University, experiment with these technologies on top of other solutions, business models and partnerships to determine what works, how, when and for whom, in order to share that information,” Kruseman added. 

Findings on the new platform will be used to build capacity on all aspects of the technologies and their application to ensure this technology is inclusive and usable. 

Along with Kruseman, AgriFoodTrust co-founders include digital agriculture experts de Ruyter de Wildt, the Founder and CEO of The New Fork, and Chris Addison, Senior Coordinator of Data for Agriculture at CTA. Seed funding for the platform has been raised through CTA, the CGIAR Platform for Big Data in Agriculture and the CGIAR Programs on MAIZE and WHEAT. 

“AgriFoodTrust sets out to accelerate understanding about these technologies and fundamentally make food systems more integer and resilient,” explained de Ruyter de Wildt. 

By 2050, farmers will need to grow enough diverse and nutritious food to feed 10 billion people on less land using less resources while faced with the challenges of a changing climate. This has led researchers to push for agricultural technologies that engender more inclusive, sustainable food systems. It is hoped that increased trust and transparency technologies can help overcome counterproductive incentives, poor governance structures, prevailing institutional arrangements and market failures. 

For more information, subscribe to the Socio-Economic Data Community of Practice newsletter.

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.

Past, present and future of crop modelling for food security

This new publication summary was originally posted on the CIMMYT blog

Resource-poor farmers worldwide stand to gain from developments in the field of crop modelling. Photo: H. De Groote/CIMMYT.

“Crop modelling has the potential to significantly contribute to global food and nutrition security,” claim the authors of a recently published paper on the role of modelling in international crop research. “Millions of farmers, and the societies that depend on their production, are relying on us to step up to the plate.”

Among other uses, crop modelling allows for foresight analysis of agricultural systems under global change scenarios and the prediction of potential consequences of food system shocks. New technologies and conceptual breakthroughs have also allowed modelling to contribute to a better understanding of crop performance and yield gaps, improved predictions of pest outbreaks, more efficient irrigation systems and the optimization of planting dates.

While renewed interest in the topic has led in recent years to the development of collaborative initiatives such as the Agricultural Model Intercomparison and Improvement Project (AgMIP) and the CGIAR Platform for Big Data in Agriculture, further investment is needed in order to improve the collection of open access, easy-to-use data available for crop modelling purposes. Strong impact on a global scale will require a wide range of stakeholders – from academia to the private sector – to contribute to the development of large, multi-location datasets.

In “Role of Modelling in International Crop Research: Overview and Some Case Studies,” CGIAR researchers, including CIMMYT wheat physiologist Matthew Reynolds,  outline the history and basic principles of crop modelling, and describe major theoretical advances and their practical applications by international crop research centers. They also highlight the importance of agri-food systems, which they view as key to meeting global development challenges. “The renewed focus on the systems-level has created significant opportunities for modelers to participant in enhancing the impact of science on developments. However, a coherent approach based on principles of transparency, cooperation and innovation is essential to achieving this.”

The authors call for closer interdisciplinary collaboration to better serve the crop research and development communities through the provision of model-based recommendations which could range from government-level policy development to direct crop management support for resource-poor farmers.

Read the full article in Agronomy 2018, Volume 8 (12).