Multivariate analysis highlights genetic structure in Olive (Olea Europaea L.) germplasm using Resource-Efficient RAPD marker system.

Olive (Olea europaea L.) is a genetically diverse, clonally propagated species with a long history of domestication, outcrossing, and germplasm exchange. In regions where access to high-throughput genotyping is limited, cost-effective methods for diversity analysis are needed. This study aimed to extract maximum genetic information from low-cost RAPD markers, complemented by robust multivariate statistical approaches, to assess diversity and structure in olive germplasm. Twenty-four olive varieties were analyzed using an initial screen of 22 RAPD primers and finally selecting 10 polymorphic primers. Marker informativeness was evaluated using Polymorphic Information Content (PIC), Marker Index (MI), and Diversity Detection Index (DDI). Genetic relationships were examined through Principal Coordinate Analysis (PCoA), hierarchical clustering, Discriminant Analysis of Principal Components (DAPC) and Analysis of Molecular Variance (AMOVA) using R software. A total of 142 bands were amplified, of which 140 were polymorphic. The average PIC, MI, and DDI values were 0.27, 3.81, and 0.16, respectively, indicating moderate marker informativeness. Multivariate analyses revealed high intra-group diversity, limited correlation with geographic origin, and eight distinct genetic clusters. DAPC provided clearer resolution of genetic structure compared to distance-based methods, while AMOVA confirmed that the majority of variation resided within groups. The integration of RAPD markers with multivariate analysis successfully captured complex genetic patterns in olive germplasm. This approach offers a cost-effective yet informative framework for diversity analysis, especially relevant for breeding and conservation programs in resource-limited conditions.