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Tag: data sharing

Building global capacity to combat wheat blast

Researchers and experts from 15 countries convened in Zambia, between 4-15 March 2024, for an international training on wheat blast disease screening, surveillance, and management.

Wheat blast, caused by pathogen Magnaporthe oryzae pathotype triticum, is threatening global wheat production especially in warmer and humid regions. The disease was first observed in Parana state of Brazil in 1985 and subsequently spread to Bolivia, Paraguay, and Argentina. Outside of South America, wheat blast incidences were recorded for the first time in Bangladesh in 2016 and in Zambian wheat fields in 2018.

To mitigate the impact of this potential plant pandemic, the Zambia Agriculture Research Institute (ZARI), in collaboration with CIMMYT and other partners, organized a comprehensive training for building research capacity and raising awareness within the local and international community, especially in at-risk countries.

“This collaborative effort, supported by various international partners and funders, underscores the importance of global cooperation in addressing agricultural challenges such as wheat blast. The objective of the training was to empower researchers with knowledge and tools for enhanced wheat production resilience in regions vulnerable to this destructive disease,” said Pawan Kumar Singh, principal scientist and project leader at CIMMYT. Singh collaborated with Batiseba Tembo, wheat breeder at ZARI-Zambia, to coordinate and lead the training program.

Thirty-eight wheat scientists, researchers, professors, policymakers, and extension agents from countries including Bangladesh, Brazil, Ethiopia, India, Kenya, Mexico, Nepal, South Africa, Sweden, Tanzania, United Kingdom, Uruguay, Zambia, and Zimbabwe convened at the Mt. Makulu Central Research Station in Chilanga, Zambia.

“Wheat blast is a devastating disease that requires concerted efforts to effectively manage it and halt further spread. The disease is new to Africa, so developing capacity amongst country partners before the disease spreads more widely is critical,” said Tembo.

Participants at the International Training on Wheat Blast Screening and Surveillance. (Photo: CIMMYT)

Highlights from the training: discussions, lab exercises, and field visits

During the training, participants engaged in lectures, laboratory exercises, and field visits. There were insightful discussions on key topics including the fundamentals of wheat blast epidemiology, disease identification, molecular detection of the wheat blast pathogen, isolation and preservation techniques for the pathogen, disease scoring methods, disease management strategies, and field surveillance and monitoring.

The course also provided practical experience in disease evaluation at the Precision Phenotyping Platform (PPP) screening nursery located in Chilanga research station. This involved characterization of a diverse range of wheat germplasm with the aim of releasing resistant varieties in countries vulnerable to wheat blast. Additionally, participants undertook field visits to farmers’ fields, conducting surveillance of wheat blast-infected areas. They collected samples and recorded survey data using electronic open data kit (ODK) capture tools.

Participants listen to a lecture by B.N. Verma, director of Zambia Seed Co., on the history of wheat production in Zambia. (Photo: CIMMYT)

“The killer disease needs to be understood and managed utilizing multi-faceted approaches to limit the expansion and damages it can cause to global wheat production. The Bangladesh Wheat and Maize Research Institute (BWMRI) is willing to share all the strategies it deployed to mitigate the effect of wheat blast,” said Golam Faruq, BWMRI’s director general.

Participants visited seed farms to gain practical insights into seed production processes and quality assurance measures. These visits provided first-hand knowledge of seed selection, breeding techniques, and management practices crucial for developing resistant wheat varieties. Participants also visited research sites and laboratories to observe advanced research methodologies and technologies related to wheat blast management. These visits exposed them to cutting-edge techniques in disease diagnosis, molecular analysis, and germplasm screening, enhancing their understanding of effective disease surveillance and control strategies.

Field visit. (Photo: CIMMYT)

“The training and knowledge sharing event was a significant first step in developing understanding and capacity to deal with wheat blast for partners from several African countries. It was wonderful to see the efforts made to ensure gender diversity among participants,” said Professor Diane Saunders from the John Innes Centre, UK.

CIMMYT and BWMRI host international training program on surveillance and management strategies for wheat blast

The devastating disease wheat blast is a threat to crop production in many South Asian countries. In Bangladesh, it was first identified in seven southern and southwestern districts in 2016, and later spread to 27 others causing significant damage. The International Maize and Wheat Improvement Center (CIMMYT) is working with the Bangladesh Wheat and Maize Research Institute (BWMRI) and other national partners to conduct research and extension activities to mitigate the ongoing threat.

From March 1-10, 2023, a group of 46 wheat researchers, government extension agents, and policy makers from ten countries — Bangladesh, Brazil, China, Ethiopia, India, Japan, Mexico, Nepal, Sweden, and Zambia — gathered in Jashore, Bangladesh to learn about and exchange experiences regarding various wheat diseases, particularly wheat blast. Following the COVID-19 pandemic, this was the first in-person international wheat blast training held in Bangladesh. It focused on the practical application of key and tricky elements of disease surveillance and management strategies, such as resistance breeding and integrated disease management.

Training participants get hands-on practice using a field microscope, Bangladesh. (Photo: Ridoy/CIMMYT)

“This is an excellent training program,” said Shaikh Mohammad Bokhtiar, executive chairman of the Bangladesh Agriculture Research Council (BARC), during the opening session.  “Participants will learn how to reduce the severity of the blast disease, develop and expand blast resistant varieties to farmers, increase production, and reduce imports.”

This sentiment was echoed by Golam Faruq, director general of BWMRI. “This program helps in the identification of blast-resistant lines from across the globe,” he said. “From this training, participants will learn to manage the devastating blast disease in their own countries and include these learnings into their national programs.”

Hands-on training

The training was divided into three sections: lectures by national and international scientists; laboratory and field experiment visits; and trips to farmers’ fields. Through the lecture series, participants learned about a variety of topics including disease identification, molecular detection, host-pathogen interaction, epidemiology and integrated disease management.

Hands-on activities were linked to working on the Precision Phenotyping Platform (PPP), which involves the characterization of more than 4,000 wheat germplasm and releasing several resistant varieties in countries vulnerable to wheat blast. Participants practiced taking heading notes, identifying field disease symptoms, tagging, and scoring disease. They conducted disease surveillance in farmers’ fields in Meherpur and Faridpur districts — both of which are extremely prone to wheat blast — observing the disease, collecting samples and GPS coordinates, and completing surveillance forms.

Muhammad Rezaul Kabir, senior wheat breeder at BWMRI, explains the Precision Phenotyping Platform, Bangladesh. (Photo: Md. Harun-Or-Rashid/CIMMYT)

Participants learned how to use cutting-edge technology to recognize blast lesions in leaves using field microscopes. They went to a pre-installed spore trapping system in a farmer’s field to learn about the equipment and steps for collecting spore samples, observing them under a compound microscope, and counting spores. They also visited the certified seed production fields of Shawdesh Seed, a local company which has played an important role in promoting wheat blast resistant varieties BARI Gom 33 and BWMRI Gom 3 regionally, and Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU) in Gazipur to see current wheat blast research in action.

Blast-resistance in Bangladesh

“I am so happy to see the excellent infrastructure and work ethics of staff that has made possible good science and impactful research come out of the PPP,” said Aakash Chawade, associate professor in Plant Breeding at the Swedish University of Agricultural Sciences. “Rapid development of blast-resistant varieties and their dissemination will help Bangladesh mitigate the effects of wheat blast, not only inside the country but by supporting neighboring ones as well.”

Training participants scout and score disease in a blast-infected wheat field, Bangladesh. (Photo: Md. Harun-Or-Rashid/CIMMYT)

“Besides the biotic and abiotic challenges faced in wheat production, climate change and the Russia-Ukraine crisis are further creating limitations to wheat production and marketing,” said Pawan Kumar Singh, head of Wheat Pathology at CIMMYT and lead organizer of the training. “Due to the development of blast-resistant wheat varieties and its commercial production under integrated disease management practices, the domestic production of wheat in Bangladesh has increased and there is increased interest from farmers in wheat.”

Dave Hodson, a principal scientist at CIMMYT and one of the training’s resource speakers, added: “This is a remarkable success that researchers developed two blast resistant varieties in Bangladesh urgently. It was only achievable because of the correct measures taken by the researchers and support of Government policies.”

However, there are still some barriers to widespread adoption of these varieties. As such, in parallel to other activities, a team from Bangladesh Agricultural University (BAU) joined the field trip to meet local farmers and conduct research into the socio-economic factors influencing the adoption and scaling of relevant wheat varieties.

The Australian High Commission, ACIAR and BARC delegates recognizes the BWMRI-CIMMYT collaborative wheat blast research platform in Bangladesh

Delegates with other officials in front of the seminar room. (Photo: Biswajit/BWMRI)

Representatives from Australian Centre for International Agricultural Research (ACIAR) and Bangladesh Agricultural Research Council (BARC) paid a visit to Bangladesh to see the valuable work of the Precision Phenotyping Platform (PPP).

PPP was established in response to the devastating wheat blast disease, which was first reported in the country in 2016.

Technical and financial support from the International Maize and Wheat Improvement Center (CIMMYT), the Australian Commission for International Agricultural Research and the Australian Centre for International Agricultural Research, along with other funders, has contributed to the effort to combat the disease.

This is achieved by generating precise data for wheat blast resistance in germplasm in Bangladesh, as well as other wheat growing countries. This PPP has been used to screen elite lines and genetic resources from various countries.

On February 16 and 17, 2023, two groups of national and international delegations visited the BWMRI-CIMMYT collaborative research platform PPP at the BWMRI regional station in Jashore, Bangladesh.

The first group was made up of representatives from both the Australian Commission for International Agricultural Research and the Australian Centre for International Agricultural Research. This included seven commissioners under the direction of Fiona Simson, along with ACIAR senior officials from Australia and India.

The other group was from BARC, which was led by Executive Chairman Shaikh Mohammad Bokhtiar, along with Golam Faruq, Director General of BWMRI, and Andrew Sharpe, Bangabandhu Research Chair, Global Institute of Food Security (GIFS), University of Saskatchewan in Canada.

Both delegations were welcomed by Muhammad Rezaul Kabir, the Senior Wheat Breeder at BWMRI. Kabir gave a brief presentation about the platform and other wheat blast collaborative research programs in the seminar room.

The delegations then went to the PPP field, where BWMRI researchers Kabir and Robiul Islam, as well as CIMMYT researcher Md. Harun-Or-Rashid, explained further information about the BWMRI-CIMMYT collaborative research. Both commissioners and delegates appreciated seeing the work being conducted in person by the national and international collaborations of BWMRI and CIMMYT on wheat blast research.

Visitors observing blast disease symptoms in wheat leaves. (Photo: Muhammad Rezaul Kabir/BWMRI)

“It is important, innovative work, that is affecting not only Bangladesh but many countries around the world that are now starting to be concerned about the impacts of wheat blast,” commissioner Simson said. “This study is very important for Australia and we are pleased to be contributing to it.”

Lindsay Falvey, another commissioner, added, “This is a wonderful experiment, using high-level science and technologies to combat wheat blast in Bangladesh. The experiment is well-planned. Overall, it is an excellent platform.”

ACIAR delegate Eric Huttner added to the praise for the project. “The platform is performing extremely well for the purpose of evaluating lines, resistance to the disease and that’s very useful for Bangladesh and rest of the world,” he said. “This is a gift that Bangladesh is giving to the neighboring countries to protect wheat.”

The delegates pledged to share their expert advice with the Minister of Foreign Affairs in Bangladesh in order to increase investments and improve facilities for agricultural research programs in the country.

Golam Faruq, Director General of BWMRI discussing the PPP with Shaikh Mohammad Bokhtiar, Executive Chairman of BARC (Photo: Md. Harun-Or-Rashid/CIMMYT)

“This is an excellent work,” Executive Chairman of BARC, Bokhtiar said. “We can get more information from screening activities by using bioinformatics tools and training people through the BARC-GIFS program.”

Pawan Kumar Singh, Head of Wheat Pathology at CIMMYT-Mexico and Project Leader, coordinated the visits virtually and expressed his thanks to the delegations for their visit to the platform. This PPP, within a short span of few years, has been highly impactful, characterizing more than 15,000 entries and releasing several resistant varieties in countries vulnerable to wheat blast.

Can you help shape the future of plant disease detection?

Artificial Intelligence (AI) and Machine Learning (ML) are increasingly being applied across a diverse range of disciplines. Many aspects of our lives and work are now benefiting from these technologies. Disease recognition, for both human and plant health, is no exception. Ever more powerful AI/ML techniques are now opening up exciting opportunities to improve surveillance, monitoring and early warning for disease threats.

Scientists from Penn State University/PlantVillage, working with CGIAR centers, FAO and national country partners, are at the forefront of AI/ML technology development applied to crop pest and disease recognition. Development of the “PlantVillage Nuru” mobile app has provided an accurate and simple automated disease diagnostic tool that can be used by non-experts, including farmers. A recent paper published in Frontiers of Plant Science demonstrated that Nuru could diagnose symptoms of cassava diseases at higher accuracy than agricultural extension agents or farmers.

“The value of tools like PlantVillage Nuru is that we can greatly increase the coverage and speed of surveillance,” says CIMMYT scientist and disease surveillance expert Dave Hodson. “Trained pathologists can only visit a limited number of fields at fixed times in the season. With tools like Nuru, extension agents and farmers can all contribute to field surveys. This can result in much faster detection of disease outbreaks, better early warning and improved chances of control”.

New advances in AI/ML technology are now promising even greater improvements in these already powerful tools. CIMMYT scientists have had a long-standing partnership with the PlantVillage group, working to try and develop improved diagnostics for important wheat diseases such as rusts and blast. Considerable progress in developing automated diagnostics for wheat diseases has already been made, but the introduction of advanced image segmentation and tiling techniques promises to be a major leap forward.

“Advances in computer science are constantly happening and this can benefit the mission of CGIAR and PlantVillage,” explains David Hughes, Dorothy Foehr Huck and J. Lloyd Huck Chair in Global Food Security at Penn State and founder of PlantVillage.

“Image segmentation and tiling techniques are a great example. They used to require intensive computing requirements. Now due to advances in computer science these powerful techniques are becoming more accessible and can be applied to plant disease problems like wheat rusts.”

By using these image segmentation and tiling techniques the developers at PlantVillage are now seeing a major improvement in the ability to automatically and accurately detect wheat rusts from in situ photos. “We could not identify rusts with the older approaches but this segmentation and tiling tool is a game changer. The computer goes pixel by pixel across the images which is well suited to diseases like rusts that can be spread across the leaf or stem of the plant. The computer now has a much more powerful search algorithm.”

The team led by Pete McCloskey, lead A.I. engineer at Plant Village, actually used a multi-step process. First they removed the background to help the machine focus in on the leaf. They then digitally chopped the leaf into segments giving the AI a further helping hand so it can focus in and find the rust. Then the whole leaf is stitched together and the rust is highlighted to help humans working in the PlantVillage cloud system.

Fig: Examples of manual, hand labelled images (top rows) compared to AI generated images using segmentation and tiling (bottom rows) for stem rust (upper image panel) and stripe rust (lower image panel).

This exciting new development in rapid, accurate field detection of wheat rusts now needs validation and improvement. As with all AI/ML applications, numbers of images included in the models really improve the quality of the final predictions. “The success of any machine learning model is rooted in the quality and quantity of the data it is trained on,” notes McCloskey. “Therefore, it is critical to source vast and diverse amounts of high-quality images from around the world in order to develop a global wheat rust recognition system.” In this aspect we hope that the CIMMYT global wheat community can help drive the development of these exciting new tools forward.

CIMMYT and PlantVillage are hoping to expand the current wheat rust image dataset and as a result produce an even more valuable, public good, disease detection tool. Given the extensive field work undertaken in wheat fields around the world by CIMMYT staff and partners, we hope that you can help us. Any photos of wheat rusts (stem, stripe and leaf rust) in the field would be valuable.

We would like to have images with one infected leaf or stem per image, it should be vertical in the image so you can see the whole leaf or stem segment. The leaf or stem needs to be in focus and should be roughly centered in the image. It helps to hold the tip of the leaf away from the stem, so it is outstretched and flat. Ideally for training data, the leaf should have only one type of rust and no other disease symptoms. It is okay to have other leaves/stems/soil/sky in the background. It is also okay to have hands and other body parts in the image.

Below are some example images. Any images can be uploaded here.

Sample images show a variety of wheat rusts (stem, stripe and leaf rust) in the field. (Photos: CIMMYT)

For more information contact Dave Hodson, CIMMYT (d.hodson@cgiar.org) or Pete McCloskey, PlantVillage (petermccloskey1@gmail.com). 

Digital groundwater monitoring

A farmer in Nepal operates a water pump for drip irrigation. (Photo: Sharad Maharjan/IMWI)
A farmer in Nepal operates a water pump for drip irrigation. (Photo: Sharad Maharjan/IWMI)

Taken together, digital monitoring and readily available data on the status of groundwater resources provide a critical foundation for sustainable irrigation development. While much is known about surface water resources and hydrological and meteorological linkages between the Terai, Mid-Hills and Himalaya regions of the country, Nepal currently lacks a comprehensive system for groundwater resource monitoring.

To respond to this crucial information gap, the International Maize and Wheat Improvement Center (CIMMYT) and International Water Management Institute (IWMI) are partnering with the Government of Nepal’s Groundwater Resources Development Board to conduct a pilot which will develop and test a potential groundwater monitoring system with the goal of identifying an approach which can be gradually scaled out after project completion.

To this end, the project team organized an Inception and Consultation Workshop, which took place virtually on October 14, 2020. This was the first in a series under the Cereal Systems Initiative for South Asia (CSISA) Nepal COVID-19 and Resilience project, funded by the United States Agency for International Development (USAID) Nepal, which supports farmers and rural economies in their response to COVID-19 and addresses, among others, various issues and ways forward for sustainable irrigation development.

The session aimed to introduce the digital groundwater monitoring pilot to local stakeholders, identify monitoring objectives and information needs, facilitate multi-stakeholder and inter-ministerial dialogue, and generate feedback and endorsement of the project plan. Participants were from a wide range of backgrounds and disciplines, and included members of local and national authorities, research centers and universities.

Participants meet virtually at the multi-stakeholder dialogue for Nepal’s Digital Groundwater Monitoring pilot (Photo: Tim Krupnik/CIMMYT)
Participants meet virtually at the multi-stakeholder dialogue for Nepal’s Digital Groundwater Monitoring pilot (Photo: Tim Krupnik/CIMMYT)

Madhukar Rajbhandari, director general of the Government of Nepal’s Department of Water Resources and Irrigation, opened the event and during his address highlighted the importance of groundwater irrigation for Nepal’s farming systems and livelihoods. He also captured the challenges which the country faces when developing groundwater irrigation, from polluted water resources through urbanization to lack of market access and the high maintenance costs of irrigation infrastructure. Rajbhandari noted that “agricultural and irrigation projects lack coordination” and expressed his hope that “through this pilot, the way is paved for a collaborative approach to develop practical groundwater solutions for farmers.”

The session introduced participants to the project and its background, leading breakout sessions for two groups: the first containing local, state and national government representatives; the second comprising farmers, researchers and members of industry. Each group was asked to identify the groundwater monitoring objectives and information needs that they would have as different types of users, and to provide feedback and recommendations to improve the project work plan.

The feedback showed that while government representatives are largely interested in developing a better understanding of the groundwater development potential, researchers and farmers are more concerned with possible discharge and water quality. Monitoring frequency was also identified as useful for daily to monthly timescales.

The group discussion revealed participants’ keen interest in consolidating and monitoring groundwater information, which highlights the importance of stakeholder engagement when developing pilots such as these, to ensure that when scaling is achieved, it caters to specific needs. Participants also expressed a strong interest in bringing the results of the project within the ambit of national policy, which would achieve the streamlining of data collection protocols for standardized, publicly accessible, data collection mechanisms.

“It is very encouraging to see such active participation and engagement from all the participants throughout the workshop,” noted Timothy Krupnik, project leader and a senior scientist at CIMMYT. “We look forward to maintaining this momentum, to support Nepal’s efforts in strengthening its capacity for sustainable irrigation.”

Creating impact through wider data sharing

Farmer speaks on mobile phone in field.
Farmer speaks on his mobile phone in Bihar, India. (Photo: M. DeFreese/CIMMYT)

The Bihar Convergence Platform for agriculture, a synergistic partnership to innovate and initiate targeted interventions that help farmers to have informed choices with proven scientific recommendations, has been consistently working to accelerate interventions and improve the lives and capacity of small and marginal farmers since its establishment in October 2019.

The Cereal Systems Initiative for South Asia (CSISA), in association with CABI and the Open Data Institute, hosted a six-day virtual interactive training in September for platform members on the theme “creating impact through wider data sharing.” The training aimed at strengthening technical expertise of the participants, creating an enabling environment to unlock the benefits of data sharing and developing space for participants to discuss, brainstorm and co-design initiatives to be implemented together by the platform in coming days.

The training ended with a common understanding about the challenges and constraints in agriculture because data is in silos. Furthermore, participants agreed on the need to look at the existing data with a broader lens to accelerate the pace of development in agriculture in the state. Participants expressed that sharing the data under set norms with standardized licensing could act as a catalyst to increase the benefits for smallholder farmers.

To constructively deal with the challenges in agriculture together, the platform members stressed the need to start analyzing existing data from a wider perspective and data sharing as the key for designing fact-based interventions for larger good and impact.

Platform members interact during virtual training.
Platform members interact during virtual training. (Photo: Sugandha Munshi/CIMMYT)

The platform is chaired by the Vice Chancellor of Bihar Agriculture University, with key members from Bihar Rural Livelihood Promotion Society known as Jeevika, Bihar Agriculture University, Dr Rajendra Prasad Central Agriculture University, Agriculture Technology Application Resource Institute, ICAR-RCER, and the CSISA project, along with private groups like IFFCO, Bayer, and ITC.

Out of the many activities jointly implemented by the platform, the Data Ecosystem is the key arena where the platform works together in strengthening the impact of data and incorporating them in accelerating quality interventions for farmers.

This story was first published on the CSISA website.