PCR-based simple sequence repeat markers for diagnostic identification of major clonal lineages of Puccinia striiformis f. sp. tritici and related stripe rust pathogens in Australia

Abstract

Puccinia striiformis f. sp. tritici (Pst) is the specialised form of the stripe rust pathogen that primarily infects wheat. It was first detected in Australia in 1979 (Pst-104 lineage) with a subsequent incursion in 2002 (Pst-134 lineage). The threat of further incursions of exotic isolates of this pathogen continues to be a concern to the cereals industries. Diagnostic tools that allow rapid and efficient pathogen identification are needed to minimise risk and time constraints associated with initial incursion management. In this study, nine microsatellite, or simple sequence repeat (SSR), markers were developed and evaluated for their application to DNA isolated from urediniospores and rust infected leaf tissue. The SSR primers were shown to be robust, reproducible, and amplify polymerase chain reaction (PCR) products even when working with limited DNA quantities, typical of diagnostic scenarios. In addition, PCR products were conveniently and easily visualised using 3 % agarose gel electrophoresis.