Latest Survey Data

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  • Rust Issues: Stem and yellow rust are serious constraints to wheat production.
  • Ug99 Status: Ug99 (Race TTKSK) was first detected in 1998, but formally identified in 1999 (Pretorius et al., 2000). Ug99 race group members – TTKST, TTTSK and TTKSF identified in 2012

Situation Updates:

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.

Oct. 19th, 2012: Molecular diagnostics provide updated knowledge on Ugandan stem rust races: Four Ug99 race group members (TTKSK, TTKST, TTTSK and TTKSF) postulated

Credit: W. Khoury (IFAD)

New molecular diagnostic assays are providing rapid and useful information on the Ug99 race group in Africa. The assays have been developed by the group led by Dr Les Szabo at the USDA-ARS Cereals Disease Laboratory in St Paul, Minnesota, USA. Dr Szabo explains that “The assay consists of two-stages, the first determines if the sample belongs to the Ug99 race group and the second stage predicts the race phenotype based on genotype of a select set of SNP markers”. These assays have been refined over the last 2-3 years and have been validated and correlated against known stem rust isolates. They have been shown to reliably distinguish members of the Ug99 race group (stage 1 assay) and postulate with a high degree of accuracy specific races in the Ug99 race group (stage 2 assay). These molecular diagnostic assays are now being applied to stem rust samples from the field.

A survey team from Buginyanya Zonal Agricultural Research and Development Institute, Uganda led by Dr William Wagoire undertook surveys in the eastern and south-western wheat growing of Uganda during the periods Jan-Feb 2012 and Oct 2012. DNA samples from stem rust recorded on surveys were collected, sent to the Cereals Disease Laboratory and analysed using the molecular diagnostic assays. A total of 53 samples were tested and 62% tested positive for the Ug99 race group. Of the samples that tested positive, it was possible to identify 29 samples that belonged to the following races: TTKSK, TTKST, TTTSK and TTKSF. The results indicated that race TTKST (Ug99 Sr24 variant) predominated with 15 samples, race TTKSK (the original Ug99) was second with 9 samples, race TTTSK (Ug99 Sr36 variant) was third with 3 samples and race TTKSF (Sr31 avirulent) was fourth with 2 samples. Since the original Ug99 isolate (race TTKSK) was first detected in Uganda in 1998/99, little has been known about the stem rust populations now present in Uganda. The latest results from the molecular assays indicate that at least 4 variants of the Ug99 race group are now present in Uganda and the Sr24 variant (race TTKST) predominates. This mirrors the known situation in neighbouring Kenya. Presence of race TTKSF is noteworthy as this Sr31 avirulent race, which dominates in southern Africa, has never been recorded before in East Africa. It must be recognized however that the molecular assays are currently unable to differentiate race TTKSF from the closely related variant TTKSF+ recently identified in South Africa and Zimbabwe (Pretorius et al., 2012).

May 1, 2012: Uganda – High severity of stem rust in both the eastern and south-west regions, yellow rust in both regions

During the period 12th January 2012 to 7th February 2012 Buginyanya ZARDI staff – W.W. Wagoire (Team Leader), A. Wasukira (Pathologist), B. Chemayek and S. Wobibi with the cooperation of field staff from the wheat growing districts, undertook a wheat rust survey in Uganda’s main wheat growing areas.   The survey route included sites in Kapchorwa, Kween and Bukwo in the east and, Kabale and Kisoro in the south west.  In the east, the wheat crop was mainly at post dough stage while in the southwest just a few fields with mature small grains could be accessed as this period did not constitute the main wheat growing season.  A total of 30 fields were surveyed using the standard BGRI survey methodology.  And all survey locations were geo-referenced using GPS. All the 16 fields surveyed in the east were bread wheat, whereas in the west of the 14 fields surveyed 5 were bread wheat, 3 Triticale, 5 barley and 1 other ( a grass). Stem rust predominated, being recorded in 23 out of the 30 fields surveyed (77%) and was widespread in both the east and the south-west. High (>40%) or moderate (20-40%) severity was recorded in 11 of the fields surveyed. Compared to previous surveys undertaken in 2010 higher incidence and severity of stem rust was recorded in the eastern region. Yellow rust was recorded in 10 of the 30 fields surveyed (33%), occurring in both the east and the south-west. High (>40%) or moderate (20-40%) severity of yellow rust was recorded in 6 of the fields surveyed. Similar to stem rust, higher incidence and severity of yellow rust was recorded in the eastern region compared to the previous surveys undertaken in 2010. Leaf rust was the least common rust observed on the surveys, present in only 5 fields (17%).  A total of 25 stem rust samples were collected for DNA analysis and sent to the Cereals Disease Lab, Minnesota for further analysis.

July 23, 2010: Survey Updates – East Africa

Survey updates – East Africa

Kenya: Stem rust incidence and severity is very high in Kenya. Recent surveys (June 2010) by KARI,Njoro staff in the Narok region recorded stem rust in 80% of the 109 fields surveyed. Stem rust severity was recorded as moderate (20-40%) or high (>40%) in 33% of the survey fields. Extremely susceptible reactions (80-100S) were recorded in 5% of the survey fields. From the survey, 90% of the fields were considered to have received some fungicide application. Reports from the field indicate that farmers who have not sprayed, sprayed late, or used incorrect dosages are experiencing crop losses. Following above normal rainfall in recent months, conditions appear conducive for disease development.

Uganda: Surveys were undertaken by Buginyanya Zonal Agricultural Research and Development Institute and FAO in July 2010. A total of 25 fields were surveyed in Kapchorwa district (east) and Kabale / Kisoro districts (south-west), Uganda. Stem rust was recorded in 64% of the fields surveyed. Highest incidence and severity was recorded in Kabale district, with only trace amounts and low incidence detected in Kapchorwa district. Bread wheat, barley and triticale were all observed with susceptible reactions; however any losses would be minimal due to the advanced stage of most crops. Current race composition in Uganda is unknown, but samples were collected for future race analysis.