Mapping of major QTLs for flowering time, seed weight, and oil content in a recombinant inbred line population of perilla

Perilla [Perilla frutescens (L.) Britton] is an important oilseed crop, which is valued for its high nutritional and medicinal properties. In the Republic of Korea, perilla breeding programs are generally divided into two distinct directions as seed-type for oil production and leaf-type for vegetable use, with key agronomic traits, such as flowering time, seed weight, and oil content, playing critical roles in differentiating these types. Therefore, understanding the genetic basis of these traits is essential for developing improved perilla cultivars. To investigate the genetic basis of key agronomic traits, we developed a recombinant inbred line (RIL) population derived from a cross between the representative seed-type cultivar ‘Daesil’ (DS) and the leaf-type cultivar ‘Ipdeulkkae1’ (IDK1). A high-density linkage map was constructed using molecular markers generated via genotyping-by-sequencing (GBS). This map enabled the identification of major quantitative trait loci (QTLs), namely qFT1, qSW17, and qOil5, which significantly influence flowering time, seed weight, and oil content, respectively. Significant single-nucleotide polymorphisms (SNP) associated with these QTLs were used to develop kompetitive allele specific PCR (KASP) markers, offering practical tools for marker-assisted selection (MAS). By integrating phenotypic evaluation with marker segregation analysis, we identified favorable alleles contributing to variation in flowering time, seed weight, and oil content. These trait-linked molecular markers will facilitate highly efficient selection in the early generations of perilla breeding programs. Furthermore, this work enhances our understanding of the genetic control of key agronomic traits and paves the way for the accelerated development of superior perilla cultivars with optimized seed quality and agronomic performance.