## 3 Results
### Genetic Diversity  
The genetic diversity of the six varieties was assessed using ten highly informative SSR loci selected from the literature. The main genetic indexes of diversity are reported in Table 3. \begin{table}
\begin{tabular}{c c c c} \hline \hline \begin{tabular}{c} **Principal** \\ **Component** \\ \end{tabular} & **Eigenvalue** & \
\begin{tabular}{c} **Variance Explained** \\ **(\%)** \\ \end{tabular} &
\begin{tabular}{c} **Cumulated Variance** \\ **Explained (\%)** \\ \end{tabular} \\ \hline Dim. 1 & 14.74 & 61.4 & 61.4 \\ Dim. 2 & 5.98 & 24.9 & 86.3 \\ Dim. 3 & 2.27 & 9.5 & 95.8 \\ Dim. 4 & 0.63 & 2.6 & 98.4 \\ Dim. 5 & 0.38 & 1.6 & 100.0 \\ \hline \hline \end{tabular}
\end{table} 
Table 2: Eigenvalue, percent of explained variance, and cumulated percentage of explained variance by the five principal components (Dim.) extracted. Figure 4: Principal Component Analysis (PCA) plot of the olive varieties based on the morphological measurements. Each data point represents a variety, indicated by a different color and symbol. The first principal component (PC1) explains 61.4 of the variance in the data, while the second principal component (PC2) explains 24.9. The ten loci were all polymorphic, and the size of the alleles was within the variation reported in the literature (Supplementary Table S1). We detected fifty-two alleles (for an average of 5.2 alleles per locus), ranging from a minimum of three alleles for DCA5 to a maximum of seven alleles for UDO31. There was a strong positive correlation between the number of alleles and the Shannon Index of Diversity (r = 0.90, \(p\) < 0.001; Pearson). The genotypes were highly heterozygotes. The observed heterozygosity was maximum (i.e., one) at four loci but did not significantly correlate with the number of alleles (r = 0.15, \(p\) > 0.05; Pearson). The Polymorphic Information Content (PIC), a measure of the informativeness of genetic markers based on allelic frequency, was on average high (0.72) and, as expected, was positively correlated with the number of alleles (r = 0.77, \(p\) < 0.01; Pearson). Considering the effective number of alleles, a measure of genetic diversity that takes into account the squared frequencies of different alleles at a given locus, the most informative loci were GAPU47 and UDO31. DCA17 was the marker that detected more diversity, taking into consideration the number of genotypes and their relative frequencies (i.e., the evenness, E5). The ten SSRs were able to provide a unique profile for each variety. To identify relationships and visualize possible patterns of genetic variation among varieties using the whole marker set, we performed a PCA (Figure 5). \begin{table}
\begin{tabular}{c c c c c c} \hline
**Locus** & **Na** & **ASR (bp)** & **I** & **Ho** & **PIC** & **E5** \\ \hline DCA3 & 5 & 228–250 & 1.31 & 0.83 & 0.67 & 0.73 \\ DCA4 & 5 & 128–160 & 1.42 & 0.83 & 0.72 & 0.82 \\ DCA5 & 3 & 198–206 & 0.72 & 0.50 & 0.40 & 0.64 \\ DCA9 & 5 & 162–206 & 1.55 & 1.00 & 0.78 & 0.95 \\ DCA16 & 6 & 124–176 & 1.47 & 0.83 & 0.69 & 0.68 \\ DCA17 & 5 & 102–140 & 1.59 & 1.00 & 0.79 & 0.97 \\ DCA18 & 6 & 171–185 & 1.63 & 0.83 & 0.78 & 0.85 \\ GAPU47 & 6 & 187–203 & 1.70 & 1.00 & 0.81 & 0.92 \\ GAPU71b & 4 & 124–144 & 1.31 & 1.00 & 0.71 & 0.90 \\ UDO31 & 7 & 106–150 & 1.79 & 0.67 & 0.81 & 0.83 \\ \hline \end{tabular}
\end{table} 
Table 3: Main genetic indexes of diversity. Na: number of different alleles; ASR: allelic size range in bp; I: Shannon Index of Diversity; Ho: observed heterozygosity; PIC: polymorphic information content; E5: evenness. Figure 5: Principal Component Analysis (PCA) plot of the olive varieties based on the molecular markers. Each data point represents a variety, indicated by a different color and symbol. The first principal component (PC1) explains 40.88 of the variance in the data, while the second principal component (PC2) explains 20.38. This analysis showed a clear separation between the different varieties, indicating that the genetic markers used were effective at distinguishing the germplasm.