Development and application of SNP markers to discriminate Korean Perilla (Perilla frutescens) varieties using genomic sequence variations

Perilla [Perilla frutescens (L.) Britton] is an annual herbaceous species of the Lamiaceae family native to Northeast Asia, cultivated for both seed oil production and as a leafy vegetable. We developed and validated Kompetitive Allele-Specific PCR (KASP) markers for accurate identification of Korean Perilla cultivars. Whole-genome resequencing of 16 representative cultivars yielded 9686,199 SNPs, with 6183 high-confidence SNPs identified after stringent filtering. From these, 237 KASP markers were designed, and 150 polymorphic markers were validated across 48 cultivars. Principal coordinate analysis (PCoA) and phylogenetic analyses mostly distinguished seed-type from leaf-type Perilla. Minimal KASP marker sets (five for seed Perilla, six for leaf Perilla) were established, sufficient to distinguish widely cultivated Korean cultivars. These markers, encoded by a binary barcode system, enabled rapid and precise cultivar identification. Application tests demonstrated their utility for evaluating seed purity by quantifying contamination. This work provides substantial genomic resources for cultivar authentication, genetic purity assessment, and molecular breeding. The new KASP system offers a cost-effective, high-throughput, and reliable approach for managing and enhancing Perilla genetic resources, ultimately advancing breeding programs and improving seed industry processes.