Genetic diversity and population structure of Liangshan olive collection revealed by simple sequence repeat (SSR) markers and phenotypic traits

Genetic The investigation of genetic diversity is a prerequisite for the conservation and utilization of germplasm resources. This study assessed the genetic diversity and population structure of 103 olive (Olea europaea) varieties in Liangshan region, Sichuan province, China, based on fruit phenotypic traits and 48 simple sequence repeat (SSR) markers. There was a high positive correlation among various fruit phenotypic indicators, while a few indicators showed negative correlations (e.g., stone longitudinal diameter was significantly negatively correlated with fruit shape index and kernel shape index). Fresh fruit oil content was significantly negatively correlated with fruit longitudinal diameter, stone transverse diameter, stone longitudinal diameter, and fruit volume. The number of allelic variations at SSR loci in the population ranged from 2 to 22, with an average of 10.7. The mean number of effective alleles was 3.931, indicating relatively high genetic diversity. The estimated number of effective alleles (Ne) ranged from 1.178 to 9.227, with an average of 3.931 across all evaluated SSR loci. The Shannon’s information index for the SSR loci examined in this study ranges from 0.285 to 2.380, with an average of 1.529. Structure analysis exhibited that the ΔK value peaked at K = 2, suggesting that the 103 olive samples originated from two ancestral groups. These results were consistent with both principal component analysis and principal coordinates analysis. Phylogenetic analysis based on SSR markers classified the 103 olive varieties into three clusters: Group I (51 varieties), Group II (15 varieties), and Group III (37 varieties). This study systematically analyzes the genetic composition of 103 olive varieties in the Liangshan region, establishing SSR fingerprint profiles for each variety, facilitating their identification and resource management, thereby laying the foundation for marker-assisted molecular breeding of olive varieties.Keywords Olea europaea · genetic diversity · population structure · simple sequence repeat (S