SPECIES-SPECIFIC DETECTION OF Phytophthora inundata BY SIMPLE AND NESTED-PCR

Phytophthora inundata has been recently described and depicted as a ‘difficult’ taxon for identification due to its morphology and unusually high upper temperature limit for growth which has been mistaken for other non-papillate and high temperature tolerant plant pathogenic Phytophthora species. A simple as well as a nested-PCR based method was developed for the identification of P. inundata. A collection of isolates from different hosts representing diversity of species were examined for unique regions of coding as well as non-coding gene sequences. Based on internal transcribed spacers 1, 2 and 5.8S gene of rDNA (ITS), heat shock protein 90 gene (HSP), triosephosphate isomerase/glyceraldehyde-3-phosphate dehydrogenase fusion protein (TIG), and 60S ribosomal protein L10 gene (RPL) ten PCR primers specific for P. inundata were designed. Annealing temperatures and extension times were optimized for each set of primers for maximum specificity and efficiency. To evaluate the specificity of the method, 28 morphologically and molecularly characterized Phytophthora species were tested. In most cases neither set of primers amplified purified DNA from these non-homologous Phytophthora species. Analysis showed that the best candidate for identification of P. inundata isolates is ITS-I1 set which is a combination of ITS-IF1 and ITS-IR1. The optimized annealing temperature for this set was 69 °C and the best extension time was 40 sec. It seems that nested-PCR by ITS-I1 set together with universal ITS6 and ITS4 as external primers is at least 50 times more sensitive than conventional PCR.