ASHS 2025 Conference

Phytophthora capsici is a devastating pathogen in peppers (Capsicum annuum L.), responsible for root, stem, and fruit rot, often leading to yield losses of 40% to 60% in outbreak conditions. Marker-assisted selection (MAS) offers a precise strategy for accelerating resistance breeding. While high-throughput genotyping approaches such as genome-wide resequencing (WGRS) are increasingly adopted, SSR markers remain a practical and informative tool for initial diversity assessment, especially in large and diverse germplasm collections. In this study, 485 globally sourced pepper accessions including 473 accessions from C. annuum and 12 accessions from seven wild Capsicum species were evaluated using 31 SSR markers previously reported to be linked with Phytophthora resistance. Eighteen markers showing robust and reproducible amplification were selected for full-panel genotyping. To ensure consistent and accurate allele calling, SSR allele binning was performed using TANDEM software. The resulting dataset revealed substantial allelic richness, reflecting the broad genetic diversity of the collection. Gradient PCR was also performed to optimize amplification of the 13 initially non-amplifying markers, resulting in six additional markers now suitable for further screening. Downstream diversity analyses, including PCA, STRUCTURE, and phylogenetic clustering, are currently in progress. Additionally, WGRS is planned for this germplasm panel, and integration of SSR and SNP datasets will allow for a comprehensive assessment of genetic relationships, population structure, and resistance allele distribution. Together, these efforts will support the identification of novel resistance sources and inform strategic breeding for improved Phytophthora resistance in pepper.