- Rust Issues: Stem rust is a serious constraint to wheat production, requiring chemical control in many areas.
- Ug99 Status: Ug99 was first identified in in Kenya in 2001, although it may have been present for a longer period of time. Currently, 8 variants of Ug99 have been detected in Kenya (Races: TTKST, TTKST, TTTSK, PTKSK, PTKST, TTKTT, TTKTK, TTHSK) with Sr24 variants (Races: TTKST, PTKST) being the predominant pathotypes.
- Rust Screening: The main BGRI bread wheat stem rust screening nursery is located at KALRO, Njoro in the Rift Valley.
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.
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
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.
Combined results from race analysis undertaken at several different labs indicate that five new variants in the Ug99 lineage were detected from samples collected in East Africa during 2013 or 2014. Probably most significant were the two new SrTmp variants (Races TTKTK and TTKTT) previously reported (see “16 April 2015: BGRI report two new Ug99 variants with virulence to SrTmp detected in Kenya” and Patpour et al. 2015). Further analysis has revealed the presence of three additional new Ug99 lineage races. Details of these additional new races are:
- Race TTHST: Similar to race TTKST (Ug99 + Sr24 vir) but avirulent on Detected in Kenya in 2013 (1 isolate). Source lab: USDA-ARS Cereals Disease Lab, USA (Newcomb et al in prep)
- Race TTHSK: Similar to race TTKSK (Ug99) but avirulent on Detected in Kenya in 2014 (2 isolates). Source lab: AAFC Morden Research Centre, Canada (Fetch et al 2016)
- Race PTKTK: Similar to race PTKSK (Ug99 but avir on Sr21) but virulent on SrTmp. Detected in Kenya in 2014 (5 isolates). Source lab: AAFC Morden Research Centre, Canada (Fetch et al 2016)
These latest results bring the total of known variants within the Ug99 lineage to 13, with yet another SrTmp variant being detected in Kenya. All five of the new variants were detected in Kenya, but as previously reported race TTKTK was also detected in Uganda, Rwanda, Eritrea and Egypt in 2014. The results indicate that the Ug99 race group continues to evolve at a rapid rate.