Stem Rust Tools and charts

A series of display tool have been created by the Global Rust Reference Center, Aarhus University. These tools permit analysis and display of information relating to the historical and current distribution and importance of stem rust, leaf rust and yellow rust – mainly in Africa/Central and West Asia. Tools on this page focus on Stem Rust. Click on the images to access the tools. The tools are are also available on

2018 Preliminary stem rust race analysis report available from Turkey-ICARDA Regional Cereal Rust Research Center (RCRRC) Cereal Rust Biosafety Laboratory Izmir, Turkey

The Turkey-ICARDA Cereal Rust Biosafety Laboratory (CRBL) become operational after the official inauguration of Regional Cereal Rust Research center (RCRRC) on May 30, 2018. Following the inauguration, the CRBL has received official import permits from Food and Control Directorate of Turkey for importing cereal rust pathogens from outside Turkey and to conduct race analysis of Puccinia striiformis, P. graminis, and P. triticina at CRBL. The Turkey-ICARDA RCRRC is now fully operational and the first report on stem rust samples is now available (Turkey-ICARDA RCRRC 2018 Preliminary Stem Rust Race Analysis Report).

This report presents the race analysis data of wheat stem rust (Puccinia graminis) samples collected during the 2018 rust survey from Azerbaijan, Ethiopia, Iran, Iraq, Kenya, Lebanon, and Turkey which were submitted to the Cereal Rust Biosafety Laboratory (CRBL) at Turkey-ICARDA Regional Cereal Rust Research Center (RCRRC) in Izmir, Turkey. From a total of 129 samples received, results are presented 52 isolates. A total of 4 stem rust races were detected – TKKTF, TKTTF, TTKTT and TTTTF, with races TKKTF and TKTTF showing wide geographical distribution across countries (Fig.1).

Figure 1.  Total number of P. graminis races from Azerbaijan, Ethiopia, Iran, Iraq, and Lebanon, RCRRC, 2018

GRRC annual report on wheat yellow rust 2017 released

Unusual and severe epidemics of yellow rust were observed on several continents in 2017. In a number of cases, epidemic sites at different continents were inter-related by prevalence of genetically identical yellow rust genotypes and races.

Key highlights

  • South America: Three distinct genotypes were detected in severe yellow rust epidemics in Argentina in 2017. These genotypes have been associated with recent rust epidemics in Europe/northern Africa.
  • Central Asia/East Africa: Region specific genotypes were prevalent in Central Asia. One of these (PstS11) was also detected in East Africa in 2016, prevalent in severe yellow rust epidemics in Ethiopia. The spread of PstS11 was confirmed by the presence of identical races in Central Asia and Africa.
  • Europe: Warrior(-) was the most prevalent race in Europe (lineage PstS10). Original Warrior (PstS7) and Kranich (PstS8) races were less prevalent, but spreading to new areas.
  • North Africa/South Europe: A distinct race of lineage PstS14, first detected in 2016, became widespread and caused severe yellow rust epidemics in Morocco 2017. Another distinct race of PstS13, first detected in 2015, caused epidemics on both bread wheat and durum wheat in Italy.
  • SSR genotyping was successfully implemented as part of the Pst race surveys, expanding testing capacity significantly, and providing results for both recovered and non-recovered samples.
  • Summary of SSR genotyping and race phenotyping results from GRRC (2008-2017), is available online (http://www., including a new page with documentation of relationship between races and genetic lineages.

Increased capacity

The number of incoming samples of rust infected plant material has increased in recent years. At the same time, the testing capacity has increased by the implementation of rapid and robust SSR (DNA) genotyping procedures, which does not require prior recovery and multiplication of alive spore samples.

It has been possible to establish a unique relationship between SSR genotyping and race typing results from huge datasets based on extensive yellow rust sampling across many years and multiple locations at six continents. In a number of cases of recent emerged genetic lineages, only a single race was present within a single lineage. In other cases, several races were present within individual lineages, reflecting the rapid evolution of virulence in the yellow rust fungus.

The naming system and relationships between genetic lineages and race phenotypes are documented here

New facilities in the Wheat Rust Toolbox

The Wheat Rust Toolbox is a data management system holding all data, tools and services from GRRC. The toolbox also generates the maps and charts with results of the SSR genotype and race phenotype test. These maps can be embedded into relevant web portals and information systems e.g. and RustTracker – to be integrated with additional information and visualised in different contexts.

New maps and charts have been developed to descriminate the results based on SSR genotyping and race phenotyping. All samples reveived by GRRC are now genotyped using 19 SSR markers. Based on the results from this analysis only a subset of isolates are race phenotyped. Therefore, some results for a single isolate appears on both race phenotype maps and charts and the maps for genetic lineages.

A similar discrimination of results from SSR or SNP genotyping based on D-samples (dead) and race phenotyping from live samples is under development for stem rust data. Until this new system for SR is agreed upon and data have been organised accordingly, we have unhided maps and charts for SR at the GRRC web site.

GRRC annual report on wheat yellow rust 2017

This post by Jens Grønbech Hansen on 21st Feb 2017 originally appeared on the Global Rust Reference Center website 

New Ug99 video documentary released “Out of Uganda: An Aggressive Crop Killer That Threatens Global Food”

Out of Uganda: An Aggressive Crop Killer That Threatens Global Food

Fungal disease in wheat crops has been a serious but controllable problem, but a newer strain of what’s called “stem rust” has scientists worried.

January 8, 2018 by Kerstin Hoppenhaus & Sibylle Grunze

The video below is the first part in a six-part series examining the scourge of Ug99, a type of fungus that causes disease in wheat crops — one that scientists worry could threaten global food supplies. Visit our series archive for all published episodes.

There was a time when one of the most dangerous crop diseases a wheat farmer could encounter in the field was stem rust. It is caused by a fungus, and its spores look like flecks of rust on metal — first red, later black in color. The fungus spreads along stems and leaves of cereal plants, consuming nutrients and causing the grains to shrivel.

Crops affected by stem rust are often entirely destroyed, and until the 1950s, the fungus was able to wreak havoc on agriculture across the globe — including in the United States. Researchers eventually managed to identify strong resistance genes against the fungus, and successfully bred those genes into new plant varieties beginning in the 1960s, leaving the fungus all but forgotten.

A generation later, however a new strain of wheat stem rust appeared — this time in Uganda in 1998. This new strain, which scientists called Ug99 (Ug for the country where it was first discovered, 99 for the year when it was officially named), was immune to most of the known resistance genes — and it remains a threat today. It is more aggressive than most known stem rusts, and it evolves far more quickly. Indeed, where there was only one strain in 1999, there are now at least 13 new pathotypes of Ug99, and they are spreading fast.

“Why Ug99 is important, first of all is, because it has virulence for may resistance genes,” says Julio Huerta, a wheat breeder and plant pathologist with the International Maize and Wheat Improvement Center. “Second, it’s very aggressive. Extremely aggressive.”

“This is not a race that sleeps,” Huerta added. “That’s why we say rust never sleeps.”

Winds can carry the spores across borders, and scientists have now found Ug99 and its descendants throughout Eastern Africa, from South Africa to Egypt. Reports have also surfaced from Yemen and Iran, and the fungus probably won’t stop there.

Scientists worry that Ug99 will eventually spread further east and reach the wheat and barley breadbasket regions of India and China, and the consequences of this, they say, could be catastrophic — not only for local populations and economies, but for the world.

Coming on Thursday, Part 2: A Precious Crop Under Threat

Kerstin Hoppenhaus and Sibylle Grunze are the founders of Hoppenhaus & Grunze Media, a Berlin-based film production studio specializing in documentary coverage of science.

This article was originally published on Undark. Read the original article.

New, ground-breaking stem rust research highlighted in the journal Science

New, ground-breaking stem rust research is highlighted in the prestigious journal Science published on Dec 22 2017. A perspective entitled “The Quest for Durable Resistance” by Matthew J. Moscou and Peter van Esse provides context and outlines the significance of two research papers that independently identify two Avr effectors from the fungal pathogen Puccinia graminis f.sp. tritici, the causal agent of wheat stem rust. These research papers are considered a milestone in terms of improving our understanding the biology of rust pathogens.

In the first research paper entitled Variation in the AvrSr35 gene determines Sr35 resistance against wheat stem rust race Ug99”, Andres Salcedo and colleagues identify a fungal gene named AvrSr35 that is required for Sr35 avirulence. The effector protein encoded by this gene binds to the Sr35 resistance protein and as a result activates the plant’s immune response. In the second paper entitled Loss of AvrSr50 by somatic exchange in stem rust leads to virulence for Sr50 resistance in wheat”, Jiapeng Chen and colleagues identify the gene AvrSr50 that is required for Sr50 avirulence. Similarly this effector protein interacts directly with the Sr50 protein, triggering Sr50-dependant defense responses. In the case of both identified Avr effectors, removal or inactivation renders the plant susceptible to fungal attack.

The results reported in these two papers represent a significant step forward in terms of getting a much better understanding of how plants interact with the rust pathogen.

Related news stories can be found at:

EurekaAlert!: Breakthrough pulls science ahead in race against devastating wheat disease.

BBC News: Milestone reached in fighting deadly wheat disease

Stem rust attacks in Sweden heralds the return of a previously vanquished foe

stem rust. Almunge, Sweden 2017. (Credit: Anna Berlin, SLU)

Scientists at the Swedish University of Agricultural Sciences (SLU) are reporting that stem rust has returned to Sweden. In a recently released press release, lead researcher Anna Berlin from the Department of Forest Mycology and Plant Pathology outlines an unusually intense stem rust attack in wheat fields in Almunge, Uppland in the summer of 2017. The last major stem rust outbreak reported from Sweden was in 1951, so this latest outbreak and the initial indications that it is a sexual population emerging from barberry is a major cause for concern.

Full details of the report from the Swedish University of Agricultural Sciences (SLU) can be found at:

Detection of stem rust race RRTTF in Ecuador. A potentially important new race for the Americas

Stem Rust Ecuador, 29 Feb 2016 (Photo: Charlie Barnes)

A team of scientists from Ecuador, Canada and the USA recently published on the detection of race RRTTF based on samples collected in Ecuador in February 2016. The study led by Dr Charlie Barnes from the Instituto Nacional de Investigaciones Agropecuarias (INIA), Quito, Ecuador has just been published in Plant Disease. Race RRTTF is distinctive by its combined virulence to genes Sr38 and Sr13 and poses a significant threat to wheat production in North and South America as a large proportion of current commercial cultivars are known to be susceptible. The origin of Pgt race RRTTF in Ecuador is unknown, but it is similar to previous isolates of RRTTF from Asia (Pakistan), eastern Africa (Ethiopia), and the Middle East (Yemen). It is unknown whether race RRTTF is a recent long-distance exotic introduction into Ecuador, or a de novo variant of an existing South America lineage that was introduced earlier. Further study is needed to determine how widespread this race is in Ecuador and its potential to migrate to large-scale wheat production areas in South and North America.

Assessing the Stem Rust Situation in Western Siberia – Aug 2017

By: Dave Hodson, Mogens Hovmøller, Alexey Morgunov, Elena Salina and Vladimir Shamanin

3 September 2017

During the period 14-18th Aug 2017 a field trip was made to the Omsk, Novosibirsk and Altai Krai regions of Western Siberia, Russian Federation by CIMMYT and the Global Rust Reference Center (GRRC), Aarhus University. Organised by Dr. Alexey Morgunov (CIMMYT-Turkey), the visit aimed to get more information on the recent reports of large scale stem rust outbreaks covering millions of hectares in the region (Shamanin et al., 2016). It provided the opportunity to meet with the leading wheat scientists in the region and visit key wheat research institutes to gain a better understanding of the current stem rust situation. With approximately 7 million ha of short season high latitude spring wheat grown in Western Siberia, along with smaller – but increasing areas of winter wheat and some durum wheat, the region is an extremely important wheat production area.

Photo 1. Susceptible stem rust reactions on late maturing variety.

In the Omsk region, most field plots and commercial fields were 1-2 weeks prior to harvest time (90-100 day growing season) whereas wheat crops were close to maturity or mature in the Novosibirsk and Altai regions (80-90 day growing season). 2017 proved to be a non-epidemic year for stem rust, but even so the disease was universally present at every site visited. Bread wheat, durum wheat and barley were all affected, especially late maturing materials. Several grass species were also affected and barberry, including B. vulgaris, was relatively common in urban areas. Some resistant materials were present, but several susceptible or highly susceptible lines or varieties were observed in the trials visited (Photo 1). Stem rust was not considered economically important until 2015 when a local epidemic occurred in the Omsk region of Russia and neighboring areas of Kazakhstan and affected more than 1 million ha. Stem rust occurred again in 2016 though the spread, severity and losses were less (Shamanin et al., 2016). The weather in 2015 and 2016 was conducive for stem rust – not too hot and dry in June (which is often the case) followed by moist and warm weather in July.

Omsk Region

The trip started in Omsk with visits to the research trials of the Omsk Agrarian State University (Photo 2) and the Siberian Research Institute of Agriculture. This region was of special interest, as in 2015 wheat production in this area was affected by a major stem rust epidemic on an estimated 1 million ha. The biggest outbreak in this region in recent history. In 2015, stem rust appeared early with symptoms visible in the field at the end of July (heading). Typically in the past  stem rust would not appear until mid August, too late to build up and cause any damage.

Photo 2. Prof . Vladimir Shaminin (Omsk Agrarian State University) inspecting wheat plots at Omsk Agrarian State University with Dr Alexey Morgunov (CIMMYT) and Prof. Mogens Hovmøller (GRRC, Aarhus University)

The 2017 season proved to be a more typical year with hot and dry conditions and absence of June rains. As a result stem rust had only appeared after the first week of August, too late to cause any damage in commercial fields. Trials in commercial production areas approximately 120 km south-east of Omsk were affected by drought stress and only trace levels of stem rust were present. Trial sites close to Omsk city had significantly higher incidence and severity of stem rust. Some late planted or late maturing susceptible materials were showing reactions up to 40-50S. Stem rust was observed on bread wheat, durum wheat and barley. Grasses, notably bromus sp were also observed to be infected with stem rust. Leaf rust was prevalent throughout the trial sites visited. Trace amounts of yellow rust were detected at one site – an extremely unusual occurrence for this region and so far not reported according to our local hosts. Barberry, including B. vulgaris, was present in urban areas – commonly planted as hedges. But apparently it was rare or absent in natural forested areas. Previous sampling of stem rust in the Omsk area in 2016 has revealed high race diversity for stem rust (14 races from 14 samples – see GRRC report). Samples of stem rust from the 2017 season will be analysed by the GRRC in Denmark.

Novosibirsk Region

In research trials of the Institute of Cytology and Genetics, Novosibirsk, stem rust was universally present, but incidence and severity was lower than in Omsk. In this region, it was considered that stem rust was appearing too late to cause any economic damage and no large scale epidemics were reported. A randomly surveyed commercial field on the way to Barnaul, revealed low levels of stem rust on late tillers (and also grass sp.) but the crop was close to maturity and uneffected by stem rust.

Altai Krai Region

Research trials of the Altai Research Institute of Agriculture, Barnaul were visited (Photo 3). As at previous locations, stem rust was universally present throughout the trials. But as with other locations, in 2017 it appeared late and was not a problem in commercial production fields. Late planted durum materials on station were heavily affected by stem rust.

Photo 3. Inspecting field plots at the Altai Research Institute of Agriculture, Barnaul

In 2016, the situation reported was entirely different in this region. Rains in June (and July) combined with warm temperatures had resulted in stem rust appearing in mid July. An estimated 2 million ha were considered to have been severely affected, resulting in an estimated 30% total production loss in the region. Increasing areas planted to winter wheat were also considered another potential factor that may be influencing the stem rust cycle in the region, giving the pathogen an opportunity to move from maturing spring wheat to emerging winter wheat at the end of the season. Control efforts in 2016 were compounded by the unusual rainfall, making it difficult to undertake spraying operations. An example was cited of two adjacent fields both growing the same variety; one field was able to be sprayed with a resultant yield of 3 t/ha, the other was unsprayed resulting in a yield of 1.7 t/ha.


The visit highlighted the importance of wheat in this region and the strength of the research programs, but also the vulnerability of grown varieties to stem rust. Significant changes appear to have occurred in recent years, making stem rust an emerging disease of economic concern. Further research is urgently needed, both to understand the pathogen dynamics and also to increase the proportion of resistant varieties. The scale of the reported epidemics if weather conditions are suitable, coupled with the apparent high race diversity may have serious implications for neighboring regions and beyond.


Sincere thanks are given to all the wheat scientists at all the institutes visited for the time they dedicated to show their research activities and for the wonderful hospitality that was offered throughout the trip.


Shamanin, V., Salina, E., Wanyera, R. et al. Euphytica (2016) 212: 287.

GRRC report: Samples of stem rust infected wheat from Russia, 2016 season. 01/2017

CAUTION: February 2, 2017: Risk of wheat stem rust in Mediterranean Basin in the forthcoming 2017 crop season following outbreaks on Sicily in 2016

Results of extensive lab tests of samples of stem rust have shown that the 2016 stem rust epidemics in Sicily were caused by a new, highly virulent variant of race TTTTF. The samples were collected during serious and unusual outbreaks of wheat stem rust on both durum wheat and bread wheat in Sicily during April – June 2016.

Picture Showing Stem rust on durum wheat, Sicily

Heavily infected fields of commercial durum wheat, Sicily May 2016 (Photo credit: Dr Biagio Randazzo)

The epidemics were estimated to cover several thousands of hectares resulting in high inoculum load that could pose a threat to surrounding wheat areas in the forthcoming 2017 crop season, if environmental conditions prove suitable. Growers in at risk areas should be aware of the possible risk (on both durum and bread wheat), monitor crops for the early appearance of stem rust and undertake timely control if necessary.

Sicily 2016 Outbreak

Unusual, early stem rust infections (at heading stage) were first detected by Dr Biagio Randazzo on April 19th 2016 in experimental plots at Ciminna, Palermo province. High and unusual levels of yellow rust were observed as well. It is unknown if rust was extensively present in surrounding areas prior to this first detection. Low levels of stem rust were observed at Ciminna at the end of the previous season (June 2015) and a mild winter may have contributed to the early infections in 2016. The majority of wheat breeding lines being tested at Ciminna showed high susceptibility to both rust diseases.

Samples of rust infected leaves and stems were sent to the Global Rust Reference Centre (GRRC), Aarhus University, Denmark for race analysis. In the GRRC report: Samples of stem rust infected wheat from Italy, a single race of stem rust was reported among the 16 samples investigated – race TTTTF using the North American nomenclature – but additional virulence on resistance gene Sr13 and others were also identified. This is one of the few races known to be virulent to the combination of resistance genes Sr9e and Sr13, both being common sources of resistance in many durum wheat varieties. Although it should be noted that Sr13 virulence has been previously reported from Turkey. Race TTTTF has complex virulence, but is not related to the Ug99 race group and it is avirulent on genes Sr31, Sr24 and Sr25. Similar races have been detected in nearby regions and appear to be spreading rapidly, isolates from these regions are currently being investigated and compared with isolates from the Sicily epidemic. Yellow rust samples from Sicily revealed three races including a new one with a wide virulence spectrum (see – New races caused epidemics of yellow rust in Europe, East Africa and Central Asia in 2016). Rust samples were also sent to the John Innes Centre, UK for genotyping, and analysis is still on-going. Results on maps and charts are available from the GRRC, Aarhus University and RustTracker, CIMMYT. Continue reading

November 4, 2016: Surveys in Kenya Showed High Prevalence of Stem Rust

Kenya Survey 2016

stem rust Incidence, 2016 Survey, Kenya.

In 2016  surveys were carried out in all the four key wheat growing regions: South Rift (June, July), Mount Kenya region (July), and North Rift (September) and Central Rift (part of August and September). A total of 304 farms were sampled. Stem rust was detected in 235(78.3%), yellow rust in twenty-eight (9.3%) and leaf rust in fourteen (4.7%) of the farms. The disease severity was ranging from trace to 90S; trace to 60S and trace to 50S for stem rust, yellow rust and leaf rust respectively. Stem and yellow rusts were detected in all the wheat growing regions while leaf was detected in South, North and Central Rift. Stem rust infection ranged from TR to 90S with maximum infection in Central Rift( 88.3%), Mt. Kenya region (80.3%); South Rift(76.5%) and North Rift (72.4%). Yellow rust infection ranged TR to 60S with maximum infection in Central Rift (16.7%); North Rift(13.3 %) and minimum infection in South Rift( 4.9%),) and Mt. Kenya region ( 1.7%). Leaf rust infection ranged from trace to 50S with maximum infection in North Rift (10.2%) minimum infection in Central Rift (3.3 %) and South Rift (1.2%). Continue reading

Sept 15th, 2016: Surveys in Azerbaijan and Iraq indicate increasing presence of stem rust


2016 stem rust Severity from surveys in Azerbaijan and Iraq

Rust surveys undertaken in Azerbaijan by Konul Aslanova and colleagues from the Azerbaijan Agricultural Research Institute of Crop Husbandry in May/June 2015. Of the 11 widely dispersed sites surveyed, stem rust was observed at 6 sites (55%). High or moderate severity of stem rust was observed at all these sites, with both bread and durum wheat infected. Stem rust incidence and severity was highest in the Jalilabad area in the south-east Caspian Sea region of Azerbaijan, close to the Iranian border. Samples are currently undergoing race analysis and the current race(s) are unknown. In previous years the Digalu race (TKTTF) has been reported from Azerbaijan.

Rust surveys undertaken by Dr Emad Al-Maaroof and colleagues from Suleimaniyah University, Iraq in April/May 2016 covered 89 fields in Central and North-east Iraq. In the North-East – the Suleimanyah, Kirkuk, Erbil region – stem rust was detected in 40 fields, with high or moderate severity at most sites. The durum variety Adana-99 was most severely affected. Samples are currently undergoing race analysis and the current race(s) are unknown. In previous years the Digalu race (TKTTF) has been reported from Iraq.

These surveys combined indicate the potential increasing presence of stem rust in the region.