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).