Development and Characterization of New SSR Markers in Sclerotinia sclerotiorum Using Genomic and Variant Analysis

<i>Sclerotinia sclerotiorum</i> is a globally distributed fungal pathogen responsible for significant agricultural losses across a wide range of crops. This study aimed to develop polymorphic simple sequence repeat (SSR) markers by whole-genome resequencing of three Korean isolates and a public reference genome. A total of 16,885 SSR motifs were identified, of which 368 overlapped with polymorphic insertion-deletion (InDel) sites across the four genomes. From these, 12 SSR markers were selected based on polymorphism information content and amplification quality. Validation across the 28 isolates in Korea revealed high levels of genotypic diversity, suggesting that each isolate is a unique haplotype, although <i>S. sclerotiorum</i> is homothallic and clonally propagated. This multi-genome approach provides robust resources for genotyping, molecular diagnostics, and epidemiological surveillance of <i>S. sclerotiorum</i>.