Uncovering Hidden Genetic Diversity in Ancient Palestinian Olive Rootstocks and Insights into Levantine Domestication

The Levant is a primary cradle of olive (Olea europaea L.) domestication. While canopy diversity is well-documented, historical grafting obscures an untapped genetic reservoir within ancient rootstocks. This study utilized a dual-sampling approach, genotyping 142 canopy and rootstock samples across the West Bank using 10 SSR loci, benchmarked against 695 global cultivars. Molecular analysis uncovered 41 distinct grafting events among 49 paired trees, indicating a historical grafting practice where ‘Baladi’ canopies were combined with 45 unique rootstock genotypes and in five cases with the ‘Safrawi’ cultivar. Parentage analysis suggested that these rootstocks formed a putatively interbreeding population. The eastern founder ‘Safrawi’ was identified as candidate parent for several rootstocks, whereas ‘Baladi’ scions remained genetically distinct. Bayesian structure analysis (K = 3) showed the West Bank population belongs predominantly to the ancestral Eastern Mediterranean pool (POP3), remaining isolated from central and western breeding loops. The local germplasm exhibited high allelic richness and observed heterozygosity (Ho up to 0.97), rivaling global collections. These findings provide direct molecular evidence of historical agricultural practices, establishing the West Bank as an important reservoir of the Eastern Mediterranean gene pool. These putative resilient genotypes could offer valuable traits for future breeding programs, making their conservation a priority.