DisplayTitle

​​​

The proccess of Simple Sequence Repeat (SSR) or microsatellite identification can be streamlined in non-model organisms due to increased availability of genomes and transcriptomes. SSRs derived from transcripts in particular show promise as useful markers due to their high polymorphism and transferability across species. Informative molecular markers are needed for understanding more about the population structure of <i>Pseudoperonospora cubensis</i>, the foliar pathogen causing cucurbit downy mildew. This study aimed to identify SSRs found in expressed regions of the <i>P. cubensis</i> genome. The MIcroSAtellite identification tool (MISA) was used to extract locations and frequencies of 2-6 bp repeats and reported that 10% of the 23,522 sequences examined contained SSRs. Primer3 identified 2,088 primers to amplify detected SSRs. A subset representative of the SSR motifs found was screened against a diverse panel of <i>P. cubensis</i> isolates from commercial and non-commercial cucurbit hosts as well as two <i>P. humuli</i> (hop downy mildew) isolates. Of the 100 SSRs tested, sixteen SSR loci were polymorphic across downy mildew isolates and nine differentiated <i>P. cubensis</i> isolates from <i>P. humuli</i> isolates. Markers displaying polymorphism were further investigated via fragment analysis. These results demonstrate that MISA and publically available transcriptomes provide a vast source of genetic markers that can be used to characterize populations of <i>P. cubensis</i> and possibly other downy midlews.