Posts Tagged ‘monitoring’

Constantly vigilant: Q&A with rust disease scientist Sridhar Bhavani

Sridhar Bhavani at a UG99 wheat stem rust screening event in Njoro, Kenya. Photo: University of Minnesota, David Hansen

International Maize and Wheat Improvement Center (CIMMYT) Senior Scientist and Head of Rust Pathology and Molecular Genetics Sridhar Bhavani has been fighting the spread of deadly wheat rusts for over 15 years.  He recently presented “A Decade of Stem Rust Phenotyping Network: Opportunities, Challenges and Way Forward” at the Borlaug Global Rust Initiative Technical Workshop in October.

We picked his brain about the growing danger of rust diseases, the newest weapons fighting them, and how researchers both within and outside the CGIAR system can best help wheat smallholder farmers in this seemingly never-ending battle.


Q: It seems like the rust races keep mutating, growing, and spreading and crop breeders and scientists are constantly in a position of reacting. Is this happening faster than in the past or does it just seem that way? Is this a factor of climate change, less diverse modern varieties, something else? Will we ever get ahead of the curve?

A: That’s right. Such events can in part be attributed to climate change. In the case of yellow rust races, we have seen the evolution of new aggressive races that are adapted to warmer temperatures in the last two decades, an unusual acclimatization for this disease. These races initiate early infection and with faster disease progression,  produce large amounts of spores and rapidly evolve to overcome resistant genes. The northern Himalayan region has been identified as a diversity hotspot for these aggressive races, resulting in significant yield losses and global migration of these races.

Interestingly, stem rust races of the Ug99 group have also adapted to cooler environments at altitudes over 3000 meters, which have been identified in the foothills of Mt. Kenya. Recent reports of stem rust variants of the “Digelu” race group, which has resurfaced in the United Kingdom and Europe, is a grave concern considering that the disease was practically under control for over 30 years.

Such diverse, fast-evolving, migrating populations pose a great challenge for breeding programs to continuously scout and deploy new resistant genes. For example, in Mexico, a new race with virulence has evolved every other year over the course of 12 years.

The lack of diversity of resistance genes (genetic uniformity) or combinations of multiple genes in varieties occupying vast production areas (mega varieties) compounds the issue of climate change. This can result in significant yield losses when resistant genes break down.

Different approaches have been used to enhance resistance durability, enabling breeders to stay ahead of the curve:

  • Pyramiding: Combining 2-3 resistance genes in a single variety makes it difficult for pathogens to overcome multiple genes at once.
  • Deploying complex race- non-specific pleotropic adult plant resistance (APR) genes: These genes, such as Sr2, Lr34, Lr46, Lr67 and Lr68, condition partial resistance against multiple diseases (leaf rust, stem rust, yellow rust, powdery mildew, etc.) and are present in CIMMYT germplasm. Combinations of three to four APR genes can enhance resistance to near-immune levels. Though cumbersome, it has been quite effective to keep rust under control over the last two decades.
  • Transgenic cassette approach: It is now possible to transform wheat lines with a cassette of up to eight multiple-cloned resistance genes. This approach stacks multiple resistance genes in the same cultivar and can enhance durability for longer periods. However, current regulatory framework in developed and developing nations doesn’t allow cultivation of transgenic wheat.
Stem rust. Photo: David Hansen, University of Minnesota

Q: What do you think are the areas where the global crop science/agricultural policy community can do better to help smallholder farmers?

A: The community should focus on developing long-term sustainable solutions:

  • Focus on genetic solutions for resource-poor smallholder farmers who lack access to fungicides
  • Eliminate older, susceptible varieties from wheat production areas.
  • Improve rapid dissemination of tools and technologies through on-farm trials and demonstrations, efficient seed systems, strong national extension networks and communities of practice.
  • Enhance national-level emergency preparedness for crop disease. A country’s response time and ability to contain the infected area and mitigate the damage through both immediate and long-term solutions makes a huge difference.
  • Promote policies that fast-track release, multiplication and testing time of improved resistant varieties, which historically takes six to eight years from the time the line is developed.  

Sridhar inspects rust-infected wheat crops. Photo: David Hansen, University of Minnesota

Q: Where do you see your field of research 20 years from now?  Where do you see the global rust situation 20 years from now? What are you concerned about or optimistic about?

A: I am optimistic that recent advances in sequencing-annotated wheat reference genomes and detailed analyses of gene content among sub-genomes will accelerate our understanding of bread wheat genetics. Wheat breeders can now use this information to identify agronomic traits, like grain quality, yield, abiotic stress tolerance and disease resistance.

Furthermore, the global rust monitoring and surveillance network has helped to understand pathogenic diversity in different geographies and possible migration patterns; and develop early forecasts and warning measures in risk-prone areas. These tools enable breeders to stay ahead of the race, and pre-emptive breeding helps them prepare for incursion of new races.

One of my bigger concerns is the “yield is king” mindset in developed countries. High-yielding but rust-susceptible varieties are being promoted with the view that the yield benefit will compensate for the cost of fungicides in disease years. Since this notion is also being promoted in developing countries, a major epidemic–coupled with fungicide supply shortages–can lead to disasters that will seriously impact smallholder farmers.


Q: Do you see the coming reform of CGIAR as having an impact on rust screening and resistance research?  Do you have a message for funders and/or those who are setting the One CGIAR research agenda?

A: Disease and pest resistance for crops, livestock, fisheries and forestry should be high on the agenda. We have witnessed significant impact of pest and pathogen resurgence in the last decade, beyond rust races. The variability and constant evolution of pests puts extreme pressure on breeders and researchers to be constantly vigilant against the emergence of new races, biotypes or strains.

Several threats have been effectively mitigated through global collaboration for surveillance and breeding. This facilitates screening and selection at hot spot sites and accelerates varietal release and adoption. Information-sharing partnerships to detect changes in virulence patterns would greatly reduce the need for fungicide and promote greater stability and sustainability of yield across agricultural environments.

A multidisciplinary approach involving pathologists, breeders, geneticists, physiologists, agronomists, simulation specialists and upstream bioinformaticians at different stages of research and development will be necessary to develop improved cultivars with stable and durable resistance to pests and diseases.

View Sridhar Bhavani’s full BGRI Workshop Presentation, “A Decade of Stem Rust Phenotyping Network: Opportunities, Challenges and Way Forward”


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.


New infographic highlights an early warning system for wheat blast in Bangladesh

Wheat blast is a devastating fungal disease threatening agricultural productivity and food security in the Americas and South Asia. First identified in Brazil in 1984, it spread to Bangladesh in 2016, prompting the government to request scientists for an early warning system.

A new infographic, developed by researchers at the Cereal Systems Initiative for Asia (CSISA) explains how wheat blast is spread and how an early warning system can help extension agents and farmers get ahead of the disease.