Abstract

Phytophthora capsici is a devastating oomycete that affects solanaceous, cucurbitaceous, fabaceous, and other crops in the United States (US) and worldwide. The release of the P. capsici genome allows for design of robust markers for genetic studies. We surveyed and characterized simple sequence repeats (SSRs) in the P. capsici transcriptome using an in silico approach. Identifying SSRs associated with transcript sequences is of interest since they constitute annotated markers with a predicted function. SSRs are also desirable markers due to their high polymorphism and transferability across species. A total of 1,855 SSRs were identified, representing 9.36% of the total number of sequences examined. Trinucleotide repeats were the most abundant and accounted for 71% of all repeats. A total of 1,620 primer pairs were successfully designed to amplify the SSRs. A subset of SSR primers was evaluated in a diverse set of P. capsici isolates, and fragment analysis revealed variations in the repeats of 20 SSR primers. P. capsici isolates from North Carolina were also evaluated for virulence, fungicide resistance, and mating type. The identified SSRs will facilitate the genetic characterization of P. capsici populations, which may assist in deployment of disease management strategies.