Posts Tagged ‘Yellow rust’

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 genetic analysis advances the global quest for yellow rust resistant wheat

A wheat leaf infected with yellow rust, also known as stripe rust. Photo: Thomas Lumpkin/CIMMYT

Yellow rust, also known as stripe rust, is a tenacious and widespread fungal disease that threatens wheat all over the world. The fungal pathogen that causes the rust — Puccinia striiformis — is prevalent in more than 60 countries, and an estimated 88% of the world’s wheat production is considered vulnerable, with up to 100% losses. 

A number of factors – including favorable weather conditions, the adaptation of existing races and emergence of new ones, and a changing climate – have caused a recent uptick in severe outbreaks. Farmers can use fungicides and farming management practices to battle the fungus, but sowing resistant seeds is widely considered as the most cost-effective, environmentally-safe and sustainable way to beat it.

A new analysis by wheat scientists at the International Maize and Wheat Improvement Center (CIMMYT) published in Scientific Reports provides valuable insights and a deep resource of genetic information to increase the speed and accuracy of efforts to breed yellow rust resistant wheat.

To understand the shared genetic basis of yellow rust resistance over time and in three geographic regions, CIMMYT scientists performed a large genome-wide association study leveraging a dataset of 43,706 observations on 23,346 wheat lines evaluated between 2013 and 2019 at sites in India, Kenya and Mexico.

Photo: Flickr/ Wheat Genetics Lab

They found more than 100 repeatable –that is, statistically significant in multiple datasets — genome-wide markers associated with yellow rust that aligned to the reference genome of wheat.

 “These findings represent a significant advancement in our knowledge about the genetics of yellow rust resistance in bread wheat and provide exciting opportunities for designing future genomics-based breeding strategies for tackling yellow rust,” said CIMMYT wheat scientist Philomin Juliana, the lead author of the paper.

CIMMYT wheat scientists have been breeding for yellow rust resistance since the early 1970s. Breeding for resistance is a painstaking process involving crossing parents with slow rusting genes, selecting early-generation plants which exhibit resistance in Toluca, Mexico, and then subjecting the advanced generations to intense screening in sites like Karnal (in collaboration with the Indian Institute of Wheat and Barley Research) and Ludhiana (in collaboration with the Borlaug Institute for South Asia) in India; Njoro in Kenya; and Celaya (in collaboration with the Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias), El Batan and Toluca in Mexico. Identifying genes related to resistance can increase the efficiency of this selection process, giving breeders a head start by allowing them to begin the crossing process with varieties that are more likely to have resistance genes.

In the study, the wheat scientists also conducted “allelic fingerprinting” on the largest panel of wheat breeding lines to date — 52,067 lines, genomically characterizing them for yellow rust resistance.  The resulting data creates opportunities using molecular markers to identify varieties with desired combinations of resistance genes.

“This information advances our knowledge on the genetics of yellow rust resistance in thousands of wheat lines, and has important implications for the future design of resistant crosses and varieties,” Juliana said.

Overall, the markers and fingerprints identified in this study are a valuable resource not only for CIMMYT breeders but also for the global wheat breeding community in its efforts to accelerate yellow rust resistance breeding.

This work was made possible by the generous support of the Delivering Genetic Gain in Wheat (DGGW) project funded by the Bill & Melinda Gates Foundation and the UK  Department for International Development (DFID) and managed by Cornell University; the U.S. Agency for International Development’s Feed the Future Initiative; and the genotyping support of Dr. Jesse Poland from the innovation lab at Kansas State University.

Read the full article here:
https://doi.org/10.1038/s41598-020-67874-x

Juliana, P., Singh, R.P., Huerta-Espino, J. et al. 2020. “Genome-wide mapping and allelic fingerprinting provide insights into the genetics of resistance to wheat stripe rust in India, Kenya and Mexico.” Nature Scientific Reports.

Mutating diseases drive wheat variety turnover in Ethiopia, new study shows

Yellow spores of the fungus Puccinia striiformis f.sp. tritici, which causes stripe rust disease in wheat. Photo: CIMMYT/Mike Listman.

By Mike Listman

Rapidly emerging and evolving races of wheat stem rust and stripe rust disease—the crop’s deadliest scourges worldwide—drove large-scale seed replacement by Ethiopia’s farmers during 2009-14, as the genetic resistance of widely-grown wheat varieties no longer proved effective against the novel pathogen strains, according to a new study by the International Maize and Wheat Improvement Center (CIMMYT).

Based on two surveys conducted by CIMMYT and the Ethiopian Institute of Agricultural Research (EIAR) and involving more than 2,000 Ethiopian wheat farmers, the study shows that farmers need access to a range of genetically diverse wheat varieties whose resistance is based on multiple genes.

After a severe outbreak in 2010-11 of a previously unseen stripe rust strain, 40 percent of the affected farm households quickly replaced popular but susceptible wheat varieties, according to Moti Jaleta, agricultural economist at CIMMYT and co-author of the publication.

“That epidemic hit about 600,000 hectares of wheat—30 percent of Ethiopia’s wheat lands—and farmers said it cut their yields in half,” Jaleta said. “In general, the rapid appearance and mutation of wheat rust races in Ethiopia has convinced farmers about the need to adopt newer, resistant varieties.”

The fourth most widely grown cereal after tef, maize, and sorghum, wheat in Ethiopia is produced largely by smallholder farmers under rainfed conditions. Wheat production and area under cultivation have increased significantly in the last decade and Ethiopia is among Africa’s top three wheat producers, but the country still imports on average 1.4 million tons of wheat per year to meet domestic demand.

National and international organizations such as EIAR, CIMMYT, and the International Centre for Agricultural Research in the Dry Areas (ICARDA) are working intensely to identify and incorporate new sources of disease resistance into improved wheat varieties and to support the multiplication of more seed to meet farmer demand.

New wheat varieties have provided bigger harvests and incomes for Ethiopia farmers in the last decade, but swiftly mutating and spreading disease strains are endangering wheat’s future, according to Dave Hodson, CIMMYT expert in geographic information and decision support systems, co-author of the new study.

Ethiopian wheat farmers like Abebe Abora, of Doyogena, have benefitted from adopting high-yielding wheat varieties but face threats from fast mutating races of wheat rust disease pathogens. Photo: CIMMYT/Apollo Habtamu.

Ethiopian wheat farmers like Abebe Abora, of Doyogena, have benefitted from adopting high-yielding wheat varieties but face threats from fast mutating races of wheat rust disease pathogens. Photo: CIMMYT/Apollo Habtamu.

“In addition to stripe rust, highly-virulent new races of stem rust are ruining wheat harvests in eastern Africa,” he explained. “These include the deadly Ug99 race group, which has spread beyond the region, and, more recently, the stem rust race TKTTF.”

As an example, he mentioned the case of the wheat variety Digalu, which is resistant to stripe rust and was quickly adopted by farmers after the 2010-11 epidemic. But Digalu has recently shown susceptibility to TKTTF stem rust and must now be replaced.

“In rust-prone Ethiopia, the risks of over-reliance on a widely-sown variety that is protected by a single, major resistance gene—Digalu, for example—are clearly apparent,” he added. “CIMMYT and partners are working hard to replace it with a new variety whose resistance is genetically more complex and durable.”

Hodson said as well that continuous monitoring of the rust populations in Ethiopia and the surrounding region is essential to detect and respond to emerging threats, as well as to ensure that the key pathogen races are used to screen for resistance in wheat breeding programs.

Hodson and partners at the John Innes Centre, UK, and EIAR are leading development of a handheld tool that allows rapid identification of disease strains in the field, instead of having to send them to a laboratory and lose precious time awaiting the results.

CIMMYT and partners are also applying molecular tools to study wheat varietal use in Ethiopia. “There are indications that yields reported by farmers were much lower than official statistics, and farmer recollections of varietal names and other information are not always exact,” Hodson explained. “We are analyzing results now of a follow-up study that uses DNA fingerprinting to better document varietal use and turnover.”

The authors would like to acknowledge the Standing Panel for Impact Assessment (SPIA) for financing, the Diffusion and Impacts of Improved Varieties in Africa (DIIVA) project that supported the first survey in 2011, and Cornell Universitythe Bill & Melinda Gates Foundation, and United Kingdom’s Department for International Development (DFID) through the Durable Rust Resistance in Wheat (DRRW, now called Delivering Genetic Gain in Wheat) project for support for the second survey in 2014.