Unraveling olive germplasm diversity through integrated phenotypic and SSR-based characterization under temperate Himalayan conditions

Introduction Olive ( Olea europaea L.) cultivation is expanding beyond its traditional Mediterranean production regions; however, information on cultivar performance, phenotypic diversity, and molecular relationships under temperate Himalayan conditions remains limited. This study aimed to characterize olive germplasm using integrated morpho-pomological and simple sequence repeat (SSR) approaches. Methods Thirteen olive accessions, comprising eleven named cultivars and two local selections (S1 and S2), were evaluated using 24 morpho-pomological descriptors of fruits, stones, and leaves. Analysis of variance, correlation analysis, principal component analysis, hierarchical clustering, and multiple regression were used to assess phenotypic variation and relationships. Molecular characterization was performed using three polymorphic SSR loci (UDO99-019, EMO3, and EMO88), and allele-presence profiles were analysed using Jaccard similarity and unweighted pair-group method with arithmetic mean (UPGMA) clustering. Results Analysis of variance revealed highly significant ( P ≤ 0.001) differences among accessions for all quantitative traits. Fruit weight ranged from 2.13 to 7.95 g, while the flesh-to-stone ratio varied from 2.16 to 6.06. Fruit weight was strongly correlated with fruit diameter ( r = 0.859), flesh-to-stone ratio ( r = 0.764), fruit length ( r = 0.716), and stone weight ( r = 0.699). The first two principal components explained 68.3% of the total phenotypic variation, with fruit size-related traits contributing most strongly to the multivariate structure. Hierarchical clustering separated the accessions into four phenotypic clusters. Multiple regression identified fruit length and flesh-to-stone ratio as significant positive predictors of fruit weight, whereas leaf length showed a significant negative conditional association. The three SSR loci generated 11 alleles, averaging 3.67 alleles per locus, with polymorphism information content (PIC) values ranging from 0.31 to 0.43 (mean 0.36), indicating moderate marker-level diversity. UPGMA clustering separated the accessions into three major groups based on Jaccard similarity of SSR allele-presence profiles. Discussion S1, S2, and Carolea exhibited comparatively favourable fruit characteristics, including higher fruit weight, flesh-to-stone ratio, and desirable fruit dimensions. The integrated morpho-pomological and SSR approaches provided complementary information for phenotypic characterization, cultivar discrimination, and germplasm documentation, establishing a baseline for further multi-environment and higher-resolution molecular evaluation of olive germplasm under Himalayan conditions.