Molecular Profiling of Greek Native Germplasm Collection of Rosa Canina L. for Enhanced Fruit Extract Production: a Comprehensive Approach Utilizing Neutral, Gene, and Exon-Based Markers

The genus Rosa L. is globally distributed and Rosa canina L. is a distinguished member of multifaceted interest. Apart from the traditional uses of R. canina in folk medicine, food and cosmetic industries, or its ornamental applications, its rose hips are renowned for their functional bioactive components. Thus, identifying the genetic diversity within this species is crucial for any plant breeding project. This study employed three molecular markers namely inter simple sequence repeats; (ISSRs), start codon-targeted (SCoTs), and exon-based amplified polymorphisms; (EBAPs) to conduct the first comprehensive genetic analysis of 12 R. canina genotypes. DNA extraction, marker selection, and sequences' amplification were performed following established protocols. The resulting genetic data were analyzed for polymorphism, diversity indices, and population structure using various statistical methods including principal component analysis (PCA), unweighted pair group method with arithmetic mean (UPGMA) clustering, and STRUCTURE analysis. The ISSR analysis revealed a high level of polymorphism (81.82%) and identified two major clusters in the UPGMA dendrogram. SCoT and EBAP markers also exhibited substantial polymorphism (74.56% and 82.11%, respectively) and formed three distinct clusters. PCA indicated a consistent pattern across markers suggesting reliable genetic grouping. STRUCTURE analysis supported the presence of three genetically uniform subpopulations (K = 3) within the studied R. canina germplasm collection. This study provided a comprehensive genetic characterization of the Greek native R. canina genebank collection. The observed genetic diversity and population structure offered valuable insights for future breeding programs targeting specific R. canina genetic clusters.