Hypervariable RAPD, ISSR and SSR markers generate robust taxonomic groups among Puccinia striiformis formae speciales of importance to Australian agriculture

Puccinia striiformis is the causal pathogen for stripe (yellow) rust of cereals. Puccinia striiformis f. sp. tritici causing wheat stripe rust and a variant of P. striiformis causing barley grass stripe rust (BGYR) are endemic to Australia. Puccinia striiformis f. sp. hordei causing barley stripe rust is exotic and a potential threat to the Australian barley industry. Sequence identity of 100% was detected among Puccinia striiformis f. sp. hordei Puccinia striiformis f. sp. tritici and BGYR in the internal transcribed spacers regions of rRNA. In the intergenic regions of rRNA, Puccinia striiformis f. sp. tritici and BGYR were identical with Puccinia striiformis f. sp. hordei showing 64% sequence identity to the former. A robust dendrogram with isolates of P. striiformis f. sp. tritici, BGYR and P. striiformis f. sp. hordei forming distinct clusters was generated using variation detected by Random Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeat (ISSR) and Simple Sequence Repeat (SSR) markers. Size variation in the intergenic region of rRNA and variation in the SSR RJ24 profile are recommended as diagnostic tools to distinguish P. striiformis f. sp. hordei from P. striiformis f. sp. tritici and BGYR in a sample of stripe rust on barley. An incursion of P. striiformis f. sp. hordei should still be regarded as a significant threat to the Australian barley industry.