Leaf rust is a common wheat disease in South Africa. Annual surveys conducted by the Agricultural Research Council - Small Grain Institute (ARC-SGI) during the last 35 years used infection type (IT) data on a defined differential set to identify individual field isolates. Results from these surveys confirmed that the South African Pt population is affected by both local evolution and foreign introductions. A good correlation was found between avirulence/virulence phenotypes and simple sequence repeat (SSR) genotypes in the South African Pt population. We therefore evaluated whether identification of field isolates by SSR analysis would complement the traditional IT analysis using 47 field isolates collected during the 2013 growing season. Of the 39 phenotyped isolates, 35 were correctly genotyped while three were incorrectly genotyped only because the corresponding race was not included as a control. Five isolates that could not be phenotyped due to non-viable spores were successfully genotyped. The dominant race 3SA145 (North American race annotation CCPS) was represented by nine different genotypes sharing 82% genetic similarity. The SSR data further showed that the field isolates formed part of two distinct lineages with little admixture between them. This study confirmed the supporting value of SSR genotyping to traditional race analysis in monitoring the South African Pt population.
