- Rust Issues: Both stem and yellow rust are serious constraints to wheat production. In 1993/94 the popular variety Enkoy broke down to stem rust and epidemics occurred. In 2010/11 severe yellow rust epidemics were observed on widely grown cultivars e.g., Kubsa and Galema. Yr27 virulent yellow rust races were implicated in the 2010/11 epidemics. In 2013/14 and 2014/15 severe localized stem rust epidemics occurred on Digalu, caused by race TKTTF.
- Ug99 Status: Ug99 (race TTKSK) was first confirmed in 2005 and continued to be the predominant pathotype until 2014 when the non-Ug99 race TKTTF (Digalu) became dominant. Three additional variants of Ug99 have been detected in Ethiopia (Races: TTTSK, PTKSK, PTKST).
- Rust Screening: Rust screening is undertaken at the EIAR wheat research stations of Debre Zeit and Kulumsa. Debre Zeit is the principle BGRI site for Durum Wheat screening against stem rust.
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.
Race analysis undertaken by EIAR, Ambo, GRRC, Denmark and USDA-ARS CDL on samples collected in 2015 from Ethiopia and Kenya indicates that stem rust populations in East Africa are changing. The detection of race TKTTF (“Digalu” race) in Ethiopia in 2012 and the subsequent epidemics in 2013, 2014 and 2015 (see Olivera et al 2015) appears to have profoundly influenced the stem rust populations in East Africa. For over a decade the Ug99 race group has dominated in both Ethiopia and Kenya, however the latest results indicate that this situation is now changing.
A total of 214 stem rust samples from Ethiopia in 2015 were analysed by the 3 different laboratories. The results indicated that the original Digalu race (TKTTF) dominated throughout the country, with 86% (n=185) of samples being this race. Other presumed variants of the Digalu race were also detected – TTTTF (n=9), TTTTC (n=3), TRTTF (n=3), PKPTF (n=4), PKPTC (n=2), PTTTF (n=1), PTPTF (n=1). Other races included: SJPQC (n=1), JRCSF (n=1), JRCQC (n=1). Ug99 (race TTKSK) was still present at very low frequency, only 2 samples out of 214.
In Kenya, only 17 isolates were analysed by USDA-ARS CDL however the results indicated that the Digalu group of races were also emerging. A total of 7 races were identified in Kenya. Races presumed to be variants of the Digalu race pre-dominated. The most frequent race was PTTTF (n=7), with PKPTC (n=3) and PKPTF (n=1) also detected. Interestingly, the original Digalu race (TKTTF) was not detected in the Kenya samples. Three Ug99 races were also detected in the Kenya 2015 samples: Races TTKSK (n=4), TTKTT (n=1) and TTKTT (n=1).
Analysis of dead, single pustule stem rust pathogen samples (D-samples) using molecular diagnostic SNP assay at the USDA-ARS Cereals Disease Lab, Minnesota has detected a race TKTTF (“Digalu” race) genotype in Kenya for the first time. Five samples from 2014 and 7 samples from 2015, all collected by Ruth Wanyera and the pathology team from KALRO, Njoro, tested positive for race TKTTF genotype. These results indicated that a single genotype (clade IV-B) was present in Kenya. Clade IV-B is the predominant genotype in Ethiopia.
The D-sample results indicate that race TKTTF is distributed (probably at low frequency) throughout the major wheat growing regions of Kenya. The 2014 positive samples were collected from North Rift (n=2), Central Rift (n=1) and Mount Kenya (n=2). In 2015, positive samples were collected from South Rift (n=1), Central Rift (n=1) and Mount Kenya (n=5). Most of the TKTTF genotype positive samples were collected from the cultivar ‘Robin’ (n=9), but ‘KS Mwamba’ (n=1), ‘Kwale’ (n=1) and an unknown barley variety (n=1) also produced positive results for TKTTF genotype.
At present no race analysis studies on live samples collected in Kenya have detected the presence of race TKTTF. Testing of the SNP assay against known isolates of TKTTF and negative controls has proven 100% reliable, but until there is confirmation by race analysis the D-sample results are considered indicative.
Race TKTTF now totally dominates the stem rust pathogen population in all the wheat growing regions of neighbouring Ethiopia, so its presence in Kenya is not unexpected.
Following the localized stem rust epidemics in Ethiopia on the cultivar “Digalu” in 2013/14 (see report 23rd Dec 2013); continued, severe stem rust outbreaks have been observed in the 2014/15 main season. Once again the popular cultivar “Digalu” has been seriously affected in several areas. Overall, at least 20 districts were considered to be affected to some extent by the Digalu epidemic. Complete crop loss has occurred in the worst affected areas. Race TKTTF (known as the “Digalu” race in Ethiopia) has been identified as the causal race for the 2014/15 outbreaks (the same as in 2013/14). Virtually all samples analyzed from 2014/15 have proven to be race TKTTF and this race now totally dominates the stem rust population in Ethiopia. This race is NOT related to the Ug99 race group; it was first detected in Ethiopia in Aug 2012 (1 sample only, trace levels) but then went undetected until it caused severe localized epidemics during Nov 2013 to Jan 2014. The same race is known from several countries in the Middle East and that region is a presumed likely origin. Virulence on the resistance gene SrTmp is considered the main factor behind the complete susceptibility of the cultivar “Digalu”.
The first stem rust outbreaks in Ethiopia were recorded in West Shewa (about 100 km to the west of Addis Ababa) in early September 2014. Digalu exhibited very high stem rust incidence and severity (both up to 100%) and severe losses resulted on unsprayed fields. Two districts were initially affected, but over time the outbreak spread to cover 5-7 districts in this area. Subsequent outbreaks were recorded in October to December 2014 and these have continued into Jan 2015, with the Arsi Robe area and Bale zone (notably Sinana district) experiencing severe outbreaks with complete crop loss in many fields.
Yellow rust also caused localized problems during the 2014/15 season. In Amhara region, 4 zones (East Gojam, South Gonder, North and South Wollo) were affected, with South Wollo experiencing the worst outbreaks. Local triticale’s and the known susceptible variety Kubsa were the most badly affected. Aggressive yellow rust outbreaks also occurred in Bale zone, with some newly released varieties showing susceptibility. Analysis is on-going to determine the causal race.
An overview of the stem and yellow rust outbreaks in Ethiopia during 2014/15 is given in Map 1.
A broad spectrum of different agencies, both national and international, worked tirelessly to control and mitigate the rust outbreaks in Ethiopia in 2014/15. These efforts were successful in many areas and very good crop performance was observed. However, in some areas no, or limited, control was achieved and serious losses resulted (see photos). The 2014/15 situation in Ethiopia is a stark reminder of the extreme difficulties in trying to successfully control stem rust when large areas are planted to highly susceptible cultivars, a virulent pathogen is present and environmental conditions are suitable. Replacement of the highly susceptible cultivars is now the highest priority for Ethiopia.
The huge stem rust inoculum load generated in Ethiopia during 2014/15 is a threat and concern for neighbouring countries and also for future seasons in Ethiopia. Spore dispersal modelling undertaken by the Epidemiological Modelling Group at Cambridge University, UK indicated that most spores were likely to be distributed in a south-westerly direction towards Kenya, Uganda and possibly Rwanda. These countries should be vigilant for the incursion of race TKTTF and any varieties protected by the SrTmp gene should be closely monitored.
This report gives an update on the previously reported stem rust outbreak in southern Ethiopia (see http://rusttracker.cimmyt.org/?p=5473). Thanks to extensive surveillance and sampling, more details are now available regarding the areas affected and also the likely causal race.
Based on surveys and information received, up to 17 woredas (districts) in Oromia and SNNPR regions may have been affected to some degree by the stem rust epidemic (see overview map). Based on Ethiopian Central Statistical Agency (CSA) data from 2001, total wheat area in these woredas is approximately 91,000 ha. Based on field observations it is not unrealistic to assume that the susceptible cultivar Digelu might occupy 20-40% of the areas planted. A very rough, approximate, estimate of the area that may have been affected to some degree by stem rust is therefore 18,000 – 36,000 ha (i.e., approximately 1-2% of the total Ethiopian wheat area). More precise area estimates will hopefully be available in the future. Detailed crop loss assessments for the Bale zone are in progress, but no results are available yet.
Survey and sampling data currently available indicate the first outbreaks occurred in the general area of Agarfa/Gasera / Arsi Robe, most likely in late September 2013, then there appeared to be spread in a south-westerly direction into SNNPR region. Such movements would correspond to the previous predictions for spore dispersal made by the Cambridge University modelling group. The potential source of the initial outbreak is unknown.
Surveys in Arsi Robe/Diksis/Sude on 21st Jan 2014 revealed widespread high incidence (100%) and severity (up to 80%) of stem rust on Digelu. The situation was somewhat better than that observed in Agarfa/Gasera in Nov 2013, in the respect that no fields with 100% crop loss were observed. However, disease pressure continued to be very high in this area. The cultivar Danda’a was observed to have much lower severity of stem rust compared to Digelu.
The stem rust race implicated in the epidemic has been tentatively identified as race TKTT-, using North American nomenclature. This race is NOT part of the Ug99 race group. At present there is some uncertainty around the effectiveness of gene Sr38 in respect to this race, hence the last letter of the race code is currently blank. Further tests are on-going to resolve this issue. The race has confirmed virulence on the following resistance genes: Sr5, 21, 9e, 7b, 6, 8a, 9g, 36, 9b, 30, 17, 9a, 9d, 10, Tmp, McN. It is confirmed avirulent on: Sr11, 24, 31. The virulence on SrTmp is believed to be the key factor for the susceptibility of Digelu. Further analysis is on-going to definitively confirm this as the causal race.
This race, prior to Sep/Oct 2013, had not been detected in Ethiopia. The assumption therefore is that this is either a foreign incursion (most likely by wind) or a mutation in-country. The same (or similar) race is already known from other countries: Turkey (in 2007, 2008, 2011, 2012); Lebanon (in 2012); Egypt (in 2013); Germany (in 2013). Studies are underway to determine how related the races in different countries might be through DNA fingerprinting.
No reports of race TKTT- have yet been confirmed from any the countries neighbouring Ethiopia. However, survey and sampling activities are taking place in several countries to monitor potential spore movements.
(NB: This report was updated with new information on 10th March 2014)