Naturally growing populations of olive trees are found in the Mediterranean garrigue and maquis in Israel. Here, we used the Simple Sequence Repeat (SSR) genetic marker technique to investigate whether these represent wild var. sylvestris. Leaf samples were collected from a total of 205 trees at six sites of naturally growing olive populations in Israel. The genetic analysis included a multi-locus lineage (MLL) analysis, Rousset’s genetic distances, Fst values, private alleles, other diversity values and a Structure analysis. The analyses also included scions and suckers of old cultivated olive trees, for which the dominance of one clone in scions (MLL1) and a second in suckers (MLL7) had been shown earlier. The majority of trees from a Judean Mts. population and from one population from the Galilee showed close genetic similarity to scions of old cultivated trees. Different from that, site-specific and a high number of single occurrence MLLs were found in four olive populations from the Galilee and Carmel which also were genetically more distant from old cultivated trees, had relatively high genetic diversity values and higher numbers of private alleles. Whereas in two of these populations MLL7 (and partly MLL1) were found in low frequency, the two other populations did not contain these MLLs and were very similar in their genetic structure to suckers of old cultivated olive trees that originated from sexual reproduction. The genetic distinctness from old cultivated olive trees, particularly of one population from Galilee and one from Carmel, suggests that trees at these sites might represent wild var. sylvestris. The similarity in genetic structure of these two populations with the suckers of old cultivated trees implies that wild trees were used as rootstocks. Alternatively, trees at these two sites may be remnants of old cultivated trees in which the scion-derived trunk died and was replaced by suckers. However, considering landscape and topographic environment at the two sites this second interpretation is less likely.

A previous multi-locus lineage (MLL) analysis of SSR-microsatellite data of old olive trees in the southeast Mediterranean area had shown the predominance of the Souri cultivar (MLL1) among grafted trees. The MLL analysis had also identified an MLL (MLL7) that was more common among rootstocks than other MLLs. We here present a comparison of the MLL combinations MLL1 (scion)/MLL7 (rootstock) and MLL1/MLL1 in order to investigate the possible influence of rootstock on scion phenotype. A linear regression analysis demonstrated that the abundance of MLL1/MLL7 trees decreases and of MLL1/MLL1 trees increases along a gradient of increasing aridity. Hypothesizing that grafting on MLL7 provides an advantage under certain conditions, Akaike information criterion (AIC) model selection procedure was used to assess the influence of different environmental conditions on phenotypic characteristics of the fruits and oil of the two MLL combinations. The most parsimonious models indicated differential influences of environmental conditions on parameters of olive oil quality in trees belonging to the MLL1/MLL7 and MLL1/MLL1 combinations, but a similar influence on fruit characteristics and oil content. These results suggest that in certain environments grafting of the local Souri cultivar on MLL7 rootstocks and the MLL1/MLL1 combination result in improved oil quality. The decreasing number of MLL1/MLL7 trees along an aridity gradient suggests that use of this genotype combination in arid sites was not favoured because of sensitivity of MLL7 to drought. Our results thus suggest that MLL1/MLL7 and MLL1/MLL1 combinations were selected by growers in traditional rain-fed cultivation under Mediterranean climate conditions in the southeast Mediterranean area.