funder_partner: Global Rust Reference Center

Successful surveillance results in early first detection of Ug99 in South Asia

Written by Julian Bañuelos-Uribe on April 3, 2024. Posted in News.

Successful global wheat disease surveillance and monitoring has resulted in early detection of wheat stem rust Ug99 in Nepal. A combination of vigilant field surveys and sampling by Nepal’s National Plant Pathology Research Centre (NPPRC) and National Wheat Research Program (NWRP), supported by rigorous and accurate disease diagnostics at the Global Rust Reference Center (GRRC), Denmark, resulted in confirmed detection of the Ug99 strain named TTKTT. The long running and sustained surveillance efforts undertaken by NPPRC and NWRP, including off-season surveys, proved vital in the detection of Ug99 in Nepal. Confirmed results were obtained from two field samples collected in early November 2023 from off-season summer wheat crops in Dolakha district, Nepal. Repeated experiments and high quality pathotyping and genotyping at GRRC confirmed the results.

“The combination of molecular genotyping of incoming samples, without prior recovery in our laboratory and independent diagnostic assays of recovered stem rust isolates, confirmed the presence of Ug99 and a highly virulent race variant termed TTKTT,” says professor Mogens Hovmøller, leader of the GRRC at Aarhus University in Denmark.

Suraj Baidya (NPPRC) and Roshan Basnet (National Wheat Research Program) undertake field surveys at Dandunghe, Dolakha, Nepal. (Photo: CIMMYT)

Ug99 was first detected in East Africa in 1998/99, and its unique virulence sparked fears that a large proportion of wheat cultivars globally would be at risk from this potentially devastating disease. The international wheat community came together through the Borlaug Global Rust Initiative (BGRI) to address the threats posed by Ug99. The BGRI partners have successfully monitored the evolution and spread of Ug99 and bred hundreds of resistant wheat varieties that are now being grown at scale in priority wheat growing regions. Migration of Ug99 from Africa to other regions, including South Asia, was always seen as likely due to the transboundary nature of the disease and long-distance dispersal of rust spores by wind.

Detection of a Ug99 race in Nepal is not therefore a surprise, but it highlights the effectiveness of the wheat rust surveillance and monitoring systems that have been developed. The disease was present at extremely low levels in the fields in Nepal, and early detection is one of the main factors in preventing disease spread. Other factors also contribute to reduced risk. The wheat on which the Ug99 race TTKTT was detected were fodder crops and cut soon after the surveys were completed, which prevented further buildup of disease. In addition, no wheat is grown in the main season in these areas, with farmers shifting to cultivation of potato (a non-host crop for stem rust).

According to Suraj Baidya, senior scientist and chief of NPPRC, “Extensive follow up surveys in the Dolakha detection area by NPPRC in the 2023/24 main season resulted in no wheat being observed and no detection of stem rust.” Similarly, extensive surveys by NPPRC throughout other wheat growing areas of Nepal in the 2023/24 main season have resulted in no reports of stem rust in the country. To date, extensive surveys in other countries in South Asia (Pakistan, Bangladesh, Bhutan) have not detected stem rust in 2023/24.

Although the current risk of stem rust outbreaks is considered to be low, detection of the Ug99 race TTKTT in Nepal is a clear reminder of the threat posed to wheat production in South Asia by the incursion of virulent stem rust races or other plant diseases of concern. “The spread and risk from transboundary diseases like stem rust is increasing,” says Dave Hodson, leader of the Wheat Disease Early Warning Advisory Systems (DEWAS) project at CIMMYT. “Sustained and increased surveillance efforts are needed across the region and expanded to include other important emerging diseases.” Successful deployment of Ug99 resistant cultivars through the BGRI partners, including CIMMYT, ICARDA and NARS, has decreased vulnerability, but it is important to note that the race TTKTT is a recently evolved variant of Ug99 with additional virulence compared to the original strains. As a result, not all cultivars in South Asia may have effective resistance today. Screening of germplasm and major cultivars from South Asia against TTKTT at the Kenya Agriculture and Livestock Research Organization (KALRO)/CIMMYT international stem rust screening nursery in Kenya is extremely important to get an accurate picture of current vulnerability.

The details of the diagnostic confirmation of Ug99 in Nepal are available at the GRRC website (see GRRC lab report)

Work on wheat disease surveillance and monitoring, plus breeding of resistant varieties is being supported by the DEWAS and AGG projects funded by BMGF and FCDO, UK.

Key partners –

National Plant Pathology Research Centre (NPPRC), Nepal. Contact: Suraj Baidya (suraj_baidya222@yahoo.co.in)

National Wheat Research Program (NWRP), Nepal. Contact: Roshan Basnet

Global Rust Reference Center (GRRC), Aarhus University, Denmark. Contact: Mogens Hovmøller (mogens.hovmoller@agro.au.dk)

Cornell University. Contact: Maricelis Acevedo (ma934@cornell.edu)

CIMMYT. Contact: David Hodson (d.hodson@cgiar.org)

Wheat pathogen surveillance system set to expand through new investment

Written by Julian Bañuelos-Uribe on October 18, 2023. Posted in Press releases.

One of the world’s largest crop pathogen surveillance systems is set to expand its analytic and knowledge systems capacity to protect wheat productivity in food vulnerable areas of East Africa and South Asia.

Researchers announced the Wheat Disease Early Warning Advisory System (Wheat DEWAS), funded through a $7.3 million grant from the Bill & Melinda Gates Foundation and the United Kingdom’s Foreign, Commonwealth & Development Office, to enhance crop resilience to wheat diseases.

The project is led by David Hodson, principal scientist at CIMMYT, and Maricelis Acevedo, research professor of global development and plant pathology at Cornell University’s College of Agriculture and Life Sciences. This initiative brings together research expertise from 23 research and academic organizations from sub-Saharan Africa, South Asia, Europe, the United States and Mexico.

Wheat DEWAS aims to be an open and scalable system capable of tracking important pathogen strains. The system builds on existing capabilities developed by the research team to provide near-real-time model-based risk forecasts and resulting in accurate, timely and actionable advice to farmers. As plant pathogens continue to evolve and threaten global food production, the system strengthens the capacity of countries to respond in a proactive manner to transboundary wheat diseases.

The system focuses on the two major fungal pathogens of wheat known as rust and blast diseases. Rust diseases, named for a rust-like appearance on infected plants, are hyper-variable and can significantly reduce crop yields when they attack. The fungus releases trillions of spores that can ride wind currents across national borders and continents and spread devastating epidemics quickly over vast areas.

Wheat blast, caused by the fungus Magnaporte oryzae Tritici, is an increasing threat to wheat production, following detection in both Bangladesh and Zambia. The fungus spreads over short distances and through the planting of infected seeds. Grains of infected plants shrivel within a week of first symptoms, providing little time for farmers to take preventative actions. Most wheat grown in the world has limited resistance to wheat blast.

“New wheat pathogen variants are constantly evolving and are spreading rapidly on a global scale,” said Hodson, principal investigator for Wheat DEWAS. “Complete crop losses in some of the most food vulnerable areas of the world are possible under favorable epidemiological conditions. Vigilance coupled with pathogen-informed breeding strategies are essential to prevent wheat disease epidemics. Improved monitoring, early warning and advisory approaches are an important component for safeguarding food supplies.”

Previous long-term investments in rust pathogen surveillance, modelling, and diagnostics built one of the largest operational global surveillance and monitoring system for any crop disease. The research permitted the development of functioning prototypes of advanced early warning advisory systems (EWAS) in East Africa and South Asia. Wheat DEWAS seeks to improve on that foundation to build a scalable, integrated, and sustainable solution that can provide improved advanced timely warning of vulnerability to emerging and migrating wheat diseases.

“The impact of these diseases is greatest on small-scale producers, negatively affecting livelihoods, income, and food security,” Acevedo said. “Ultimately, with this project we aim to maximize opportunities for smallholder farmers to benefit from hyper-local analytic and knowledge systems to protect wheat productivity.”

The system has already proven successful, contributing to prevention of a potential rust outbreak in Ethiopia in 2021. At that time, the early warning and global monitoring detected a new yellow rust strain with high epidemic potential. Risk mapping and real-time early forecasting identified the risk and allowed a timely and effective response by farmers and officials. That growing season ended up being a production record-breaker for Ethiopian wheat farmers.

While wheat is the major focus of the system, pathogens with similar biology and dispersal modes exist for all major crops. Discoveries made in the wheat system could provide essential infrastructure, methods for data collection and analysis to aid interventions that will be relevant to other crops.

Wheat Disease Early Warning Advisory System (DEWAS)

Written by Sarah McLaughlin on March 10, 2023. Posted in Uncategorized.

The Wheat Disease Early Warning Advisory System (Wheat DEWAS) project is bringing new analytic and knowledge systems capacity to one of the world’s largest and most advanced crop pathogen surveillance systems. With Wheat DEWAS, researchers are building an open and scalable system capable of preventing disease outbreaks from novel pathogen strains that threaten wheat productivity in food vulnerable areas of East Africa and South Asia.

The system builds from capabilities developed previously by multi-institutional research teams funded through long-term investments in rust pathogen surveillance, modelling, and diagnostics. Once fully operationalized, the project aims to provide near-real-time, model-based risk forecasts for governments. The result: accurate, timely and actionable advice for farmers to respond proactively to migrating wheat diseases.

The Challenge

Farmers growing wheat face pathogen pressures from a range of sources. Two of the most damaging are the fungal diseases known as rust and blast. Rust is a chronic issue for farmers in all parts of the world. A study in 2015 estimated that the three rust diseases — stem, stripe and leaf — destroyed more than 15 million tons of wheat at a cost of nearly $3 billion worldwide. Wheat blast is an increasing threat to wheat production and has been detected in both Bangladesh and Zambia. Each of these diseases can destroy entire harvests without warning, wiping out critical income and food security for resource-poor farmers in vulnerable areas.

The Response

Weather forecasts and early-warning alerts are modern technologies that people rely on for actionable information in the case of severe weather. Now imagine a system that lets farmers know in advance when dangerous conditions will threaten their crop in the field. Wheat DEWAS aims to do just that through a scalable, integrated, and sustainable global surveillance and monitoring system for wheat.

Wheat DEWAS brings together research expertise from 23 research and academic organizations from sub-Saharan Africa, South Asia, Europe, the United States and Mexico.

Together, the researchers are focused on six interlinked work packages:

Work package	Lead	Objectives
Data Management	Aarhus University; Global Rust Reference Center	Maintain, strengthen and expand the functionality of the existing Wheat Rust Toolbox data management system Create new modules within the Toolbox to include wheat blast and relevant wheat host information Consolidate and integrate datasets from all the participating wheat rust diagnostic labs Develop an API for the two-way exchange of data between the Toolbox and the Delphi data stack Develop an API for direct access to quality-controlled surveillance data as inputs for forecast models Ensure fair access to data
Epidemiological Models	Cambridge University	Maintain operational deployment and extend geographical range Productionalize code for long-term sustainability Multiple input sources (expert, crowd, media) Continue model validation Ensure flexibility for management scenario testing Extend framework for wheat blast
Surveillance (host + pathogen)	CIMMYT	Undertake near-real-time, standardized surveys and sampling in the target regions Expand the coverage and frequency of field surveillance Implement fully electronic field surveillance that permits near real-time data gathering Target surveillance and diagnostic sampling to validate model predictions Map vulnerability of the host landscape
Diagnostics	John Innes Centre	Strengthen existing diagnostic network in target regions & track changes & movement Develop & integrate new diagnostic methodology for wheat rusts & blast Align national diagnostic results to provide a regional & global context Enhance national capacity for wheat rust & blast diagnostics
Information Dissemination and Visualization Tools	PlantVillage; Penn State	Create a suite of information layers and visualization products that are automatically derived from the quality-controlled data management system and delivered to end users in a timely manner Deliver near real time for national partners to develop reliable and actionable advisory and alert information to extension workers, farmers and policy makers
National Partner Capacity Building	Cornell University	Strengthening National partner capacity on pathogen surveillance, diagnostics, modeling, data management, early warning assessment, and open science publishing

Wheat DEWAS partners

Academic organizations: Aarhus University / Global Rust Reference Center; Bangabandhu Sheikh Mujibur Rahman Agricultural University; Cornell University / School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology Section; Hazara University; Penn State University / PlantVillage; University of Cambridge; University of Minnesota

Research organizations: Bangladesh Wheat and Maize Research Institute (BWMRI); CIMMYT; Department of Agricultural Extension (DAE), Bangladesh; Ethiopian Agricultural Transformation Institute (ATI); Ethiopian Institute of Agricultural Research (EIAR); ICARDA; John Innes Centre (JIC); Kenya Agricultural and Livestock Research Organization (KALRO); National Plant Protection Centre (NPPC), Bhutan; Nepal Agricultural Research Council (NARC); Pakistan Agricultural Research Council (PARC); UK Met Office; Tanzania Agricultural Research Institute (TARI); The Sainsbury Laboratory (TSL) / GetGenome; U.S. Department of Agriculture, Agricultural Research Service; Zambia Agricultural Research Institute (ZARI)