Latest Survey Data

  • 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.

Situation Updates:

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

May 30th, 2016: Race Analysis Data from 2015 Indicates a Possible Shift in Stem Rust Populations in East Africa


Digalu crop destroyed by race TKTTF. Ethiopia 2013

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).

Jan 12, 2016: Molecular diagnostics indicate presence of race TKTTF (“Digalu” race) in Kenya

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.

Dec 20, 2015: Five new variants of Ug99 confirmed from 2013/2014 samples in East Africa

stem rust bannerCombined 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:

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.

Sep 2, 2015: Emergence and spread of virulence to SrTmp in the Ug99 race group in Africa – note published in Plant Disease

Mehran Patpour (Global Rust Reference Center in Denmark) and co-authors have just published details of the emergence and spread of virulence to SrTmp in the Ug99 race group in Africa. The note is now available as a First Look in Plant Disease  (see The report details the results of combined race analysis undertaken by the GRRC, Denmark and the USDA-ARS Cereals Disease Lab, Minnesota on 84 stem rust samples collected in 2014 from Kenya, Uganda, Rwanda and Egypt.

Seedling reaction of Race TTKTK on selected differentials (Photo: GRRC, Denmark)

Seedling reaction of Race TTKTK on selected differentials (Photo: GRRC, Denmark)

The presence of two new Ug99 race group variants – race TTKTK (Ug99 + virulent on SrTmp) and race TTKTT (Ug99 + virulent on SrTmp and Sr24) were confirmed in Kenya. Race TTKTK was also confirmed in Uganda, Rwanda and Egypt. Detection of these new variants in the Ug99 race group across several countries in a single year indicates the relevance of coordinated surveillance activities and also indicates potentially very rapid geographical dispersal of race TTKTK.