Genetic Diversity and Population Structure of Olive Germplasm from Liangshan Based on SSR Markers and Phenotypic Traits

Vollständiger Abstract

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Investigating genetic diversity is a prerequisite for the management and utilization of germplasm resources. This study assessed the genetic diversity and population structure of 103 olive (Olea europaea) varieties in the Liangshan region, Sichuan Province, China, based on fruit phenotypic traits and 48 simple sequence repeat (SSR) markers. There were high positive correlations between various fruit phenotypic indicators, while a few indicators showed negative correlations (e.g., stone longitudinal diameter was significantly negatively correlated with the 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 Shannon’s information index (I), observed heterozygosity (Ho), and expected heterozygosity (He) of the 103 varieties were 1.529, 0.54, and 0.685, respectively, indicating relatively high genetic diversity between these olive varieties. Structure analysis, PCA, and PCoA consistently classified the varieties into two ancestral populations, with mean fixation index (FST) = 0.052 and gene flow (Nm) = 4.544, suggesting moderate genetic differentiation and extensive gene flow between the populations. Based on phenotypic clustering and phylogenetic analysis, eight varieties exhibiting synonymy or homonymy were successfully identified. Furthermore, molecular fingerprint profiles were established using seven pairs of SSR primers, which could effectively identify all varieties. This study provides a valuable reference for the management and breeding of olive germplasm resources in the Liangshan region.