Differentiation of European and North American genotypes of Phytophthora ramorum by real-time polymerase chain reaction primer extension.

Phytophthora ramorum, the organism responsible for sudden oak death, causes severe damage to oak (Quercus spp.) and tanoak (Lithocarpus densiflorus) trees in California and Oregon. There are now >100 host plants that can be affected by this pathogen in nurseries and in the wild in Europe and North America. Molecular diagnosis and genotyping are important tools to monitor and prevent spread of this pathogen, to enforce quarantines, and to support eradication programs. By amplifying and sequencing DNA in a worldwide panel of strains of P. ramorum, we discovered single-nucleotide polymorphisms (SNP) in two genes (β -tubulin and cellulose binding elicitor lectin (CBEL)) that differ in the European and the North American P. ramorum isolates. Using these SNPs in diagnostic assays and distinguishing among strains of different geographic origins, we developed primer extension assays in real-time polymerase chain reaction using allele-specific oligonucleotides. All European isolates genotyped were homozygous for t...