Application of ISSR markers reveals extensive genetic variability in the tropical lycophyte Selaginella ciliaris

Abstract. Jafron, Sutarno, Pangastuti A, Solichatun, Sugiyarto, Sunarto, Setyawan AD. 2025. Application of ISSR markers reveals extensive genetic variability in the tropical lycophyte Selaginella ciliaris. Asian J Trop Biotechnol 22: 80-93. Genetic information on early-diverging vascular plants remains limited, despite their ecological importance and emerging relevance in biotechnology. This study assessed genetic variability in the tropical lycophyte Selaginella ciliaris uses Inter-Simple Sequence Repeat (ISSR) markers as a cost-effective molecular approach for non-model plants. A total of 27 samples were analyzed using selected ISSR primers, generating clear and reproducible banding patterns. A total of 49 loci were scored, all of which were polymorphic (100% polymorphism), indicating a very high level of genetic variability. Dice genetic similarity coefficients were consistently low, ranging from 0.0000 to 0.0816, with the majority of pairwise comparisons falling below 0.05. Dice genetic similarity values were consistently low, and the frequency distribution of similarity classes was strongly skewed toward very low similarity ranges, reflecting pronounced multilocus differentiation. UPGMA cluster analysis further revealed the absence of dominant genetic groups, with samples forming small clusters and numerous singletons. These results demonstrate substantial genetic heterogeneity within S. ciliaris at a regional scale. The study confirms the effectiveness of ISSR markers for detecting genetic variability in non-model tropical plants lacking genomic resources. From an applied perspective, the high genetic diversity observed highlights the potential of S. ciliaris as a valuable genetic resource for early-stage germplasm screening, conservation planning, and future biotechnological research. This work provides baseline molecular insights into an understudied lycophyte and underscores the utility of ISSR markers as an accessible tool bridging biodiversity assessment and tropical plant biotechnology.