nSSR 마커 수 감소에 따른

무궁화 품종 수준 유전구조 추론의 안정성 분석

문영범*, 신한나

(국립산림과학원 임목자원연구과)

Structural Robustness of Cultivar-Level Genetic Inference

under nSSR Maker Reduction in Hibiscus syriacus L.

Young-bum Moon*, Hanna Shin

(Department of Forest Bio-resources, National Institute of Forest Science)

Abstract: Reducing the number of molecular markers while maintaining reliable genetic inference remains a central challenge in practical cultivar-level analyses. In this study, we evaluated the extent to which genetic structure and marker-based classification decisions are preserved following marker reduction in Hibiscus syriacus L., using a dataset of 168 cultivars. A reduced panel of six nuclear simple sequence repeat (nSSR) markers was derived from an initial marker set and systematically compared with a reference panel of ten markers. Comparative analyses included genetic diversity indices, population structure inferred by principal coordinate analysis (PCoA), discriminant analysis of principal components (DAPC), and phylogenetic relationships reconstructed using BioNJ trees. Although marker reduction resulted in lower allelic diversity and polymorphism information content, the reduced marker panel consistently recovered the major genetic structure patterns observed with the reference panel across multiple analytical frameworks. Quantitative assessments of classification concordance, including the adjusted Rand index, overall classification accuracy, and leave-one-out cross-validation, demonstrated a high level of agreement between the two marker sets. Nevertheless, a subset of cultivars exhibited ambiguous classification or phenotypic divergence despite high genetic similarity, delineating the practical resolution limits of the reduced panel. These results indicate that marker reduction can be implemented without substantial loss of structural interpretability, while underscoring the importance of clearly defining analytical boundaries when resolving closely related cultivars.

Acknowledgement: This study was supported by the Research Program of National Institute of Forest Science (Grant number FG0403-2023-02-2025).

Keywords: Hibiscus syriacus, nuclear SSR (nSSR), marker reduction, genetic structure, cultivar classification