Stem Rust

Wheat stem rust (Puccinia graminis f. sp. tritici) is historically the most damaging disease of wheat. Under suitable conditions, yield losses of 70% or more are possible. In 1999, a new virulent race of stem rust was identified from wheat fields in Uganda – popularly known as Ug99 after the year and country of discovery. The unique virulence associated with Ug99, or variants, has rendered a large proportion of global wheat cultivars susceptible.

Regularly updated situation reports on cereal rusts are given based on information provided by a global network of rust workers. It is important to note that not all reports of stem rust relate to Ug99 or variants – other local races are also included.

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:

https://www.slu.se/en/ew-news/2017/11/stem-rust-attacks-in-sweden-heralds-the-return-of-a-previously-vanquished-foe/

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

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.

Study identifies likely scenarios for global spread of devastating crop disease

New research reveals for the first time the most likely months and routes for the spread of new strains of airborne ‘wheat stem rust’ that may endanger global food security by ravaging wheat production across Africa, the Middle East, Asia and the wider world.

Stem rust (or black rust), named for the blackening pustules that infect plant stems, caused devastating crop epidemics and for centuries before being tamed largely by use of resistance genes.

Since the turn of the century, however, aggressive new strains have emerged – such as ‘Ug99’, first detected in Uganda in 1999 – that infect widely grown varieties of wheat. These diseases threaten to disperse trillions of pathogenic fungal spores on winds across countries and continents.

The fear is that these airborne and highly virulent strains could spread from known sites to some of the world’s most important ‘breadbasket’ regions, such as the Punjab in South Asia, where these strains have not yet been detected.

Now, a team of scientists of the University of Cambridge, the UK Met Office and CIMMYT (International Maize and Wheat Improvement Centre) have adapted modelling systems previously used to forecast, ash dispersal from erupting volcanoes and radiation from nuclear accidents (NAME), to predict when and how Ug99 and other such strains are most likely to spread.

The research, published today in the journal Nature Plants, quantifies for the first time the circumstances – routes, timings and outbreak sizes – under which dangerous strains of stem rust pose a threat from long-distance dispersal out of East Africa to the large wheat-producing areas in India and Pakistan.

The results highlight the role of Yemen as a potential ‘stepping stone’ for the transmission of the disease between continents.  The key scenario for disease spread is from Yemen directly to Pakistan or India.  In case of a large outbreak in Eastern Yemen results indicate a 30% chance for transmission to occur.

Another important scenario for wheat rust to spread is from Yemen through Middle Eastern countries, in particular Iran, to Central and South Asia. If Iran were to suffer a moderate outbreak of Ug99 – on more than 1000 hectares – then spores would likely spread to Afghanistan, and from there potentially further to the northern plains of Pakistan and India. However, transmission along this route is restricted to a relatively short time-window in March and April, before wheat is typically harvested in South Asia.

“New races of wheat rust are threatening wheat worldwide, and we need to know which areas are at risk,” said senior author Prof Chris Gilligan, from Cambridge’s Department of Plant Sciences.

 “From our work, we now believe that if we start to see Ug99 or other new wheat rust strains take hold in Yemen in early Spring then action must be taken immediately to mitigate the risk of further spread.”

 

Network map of the atmospheric transmission of spores causing wheat stem rust.

(A) Long-distance dispersal network of spores between all major wheat producing countries in Southern/East Africa, the Middle East and Central/South Asia. Nodes represent countries; communities of the same colour indicate regions with high airborne connectivity; the size of nodes indicates node-strength; pie charts show the fraction of out-strength to total node strength (indicating donor and receptor countries).

(B) Spore transmission frequencies along principal migration routes in the Rift Valley zone for the scenario of large outbreaks.

However, the modelling work also offers some encouraging news: the airborne transmission of the disease from East African countries directly to South Asia is highly unlikely, with transmission events possible only on less than one day a year.

The scientific team used field disease surveys from the International Maize and Wheat Improvement Centre (CIMMYT) and weather data from the UK Met Office as key input for the modelling framework.

This research has allowed us to obtain the first quantitative estimates of long-term airborne spore transmission frequencies for different outbreak scenarios. We compiled risk assessments for pathogen dispersal from key disease locations to important wheat-producing countries. These assessments can effectively inform surveillance and control strategies,” said Cambridge’s Marcel Meyer, the study’s first author.

The team say their work, including 3-D spore dispersal animations and a catalogue of spore dispersal trends (indicating likely directions, frequencies, pathogen loads), provides new ways to raise awareness, communicate risks, and inform agricultural stakeholders.

Their modelling framework can be applied as a tool to analyse risks in case new disease strains should be uncovered in other geographic areas. This has already recently helped in estimating dispersal risks from detection sites of related wheat rust diseases in Europe and Siberia. In ongoing work the team is developing an Early Warning System forecasting disease risk in Ethiopia, East Africa’s largest wheat producing country.

The combined expertise from plant sciences and atmospheric dispersion sciences has delivered ground breaking tools that highlight the risks, and support the management of the devastating potential of these diseases,” said Dr Matthew Hort, co-author from the UK’s Met Office.

Source: University of Cambridge

Author contacts:

Chris Gilligan, University of Cambridge: +44 7964 598 147; cag1@cam.ac.uk

Marcel Meyer, University of Cambridge: mm2086@cam.ac.uk

Matthew Hort, UK Met Office: +44 (0)1392 886242; matthew.hort@metoffice.gov.uk

Dave Hodson, CIMMYT-Ethiopia: d.hodson@cgiar.org

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.

Summary

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.

Acknowledgement

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.

Reference

Shamanin, V., Salina, E., Wanyera, R. et al. Euphytica (2016) 212: 287. https://doi.org/10.1007/s10681-016-1769-0

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