Expanded SSR profile database for forensic discrimination and phylogenetic analysis in cultivars of spring orchid...

Cymbidium goeringii is one of the most widely cultivated and traded ornamental orchids in East Asia. Due to its high horticultural value and phenotypic variability, accurate cultivar identification is essential but challenging, as their flowers bloom only briefly in spring.

We have developed a forensic tool for rapid and exact cultivar discrimination by applying 12 simple sequence repeat (SSR) profiles in C. goeringii. This study was performed to establish an expanded SSR dataset for cultivar identification and phylogenetics in C. goeringii.

We examined a total of 6,051 samples from 269 cultivars, including 92 Korean cultivars with ≥ 10 samples each. Among these, representative combined genotypes (CG1) were determined, and their frequencies (CG1%) were used to assess genetic concordance among samples. Phylogenetic trees were constructed using both Euclidean and codominant genetic distances, and cultivar distributions were visualized using Principal Coordinate Analysis (PCoA) and t-SNE.

Approximately 72.8% of the samples matched their dominant combined genotype (CG1), suggesting that nearly 30% of cultivated orchids may exhibit genotype discordance. Phylogenetics and PCoA showed a weak or no correlation between phenotypes, while they revealed relatively clear clustering between Korean and Japanese origins.

These results highlight the value of integrating multiple analytical methods to enhance interpretability. The expanded SSR genotype dataset presented here offers a robust resource for cultivar identification, verifying genotype concordance, phylogenetic analysis, and ecological genetics research. This study will be an important milestone in the forensic application of plants with diverse cultivars exhibiting a wide range of horticultural and commercial values.