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Historical Genomics of the Mediterranean Olive tree

Final Report Summary - GENOLIVE (Historical genomics of the mediterranean olive tree)

The olive tree (Olea europaea subsp. europaea L. Oleaceae) is the emblematic species of the Mediterranean Basin and it represents one of the first domesticated trees. The history of this species and particularly the location of refugees and its post-glacial recolonisation remains unidentified until now. The domestication of the tree after the Holocene was associated to the dispersal of cultivars and feral forms everywhere in the Mediterranean Basin, and this probably strongly obliterates the initial genetic imprints of recolonisation. More recently, the species was also introduced in new ranges and escaped from culture to become a major weed in Australia and Pacific Islands. In this project, the main objective was to reconstruct a phylogeography of the olive tree on a comprehensive sampling in both native and invasive ranges to depict its history. Both chloroplast (cpDNA) and nuclear genome informations were used.

During the course of this project, several datasets have been constituted. First, eight complete cpDNA genomes have been released, and a method for characterising a maximum of cpDNA polymorphisms (60 loci) has been developed. More than 2 000 genotypes were analysed with these markers. Several nuclear genome datasets (i.e. nSSRs, sequences of five nuclear genes) were also generated on a subsample of diploid trees from the whole range (i.e. 1 200 individuals for 11 nSSRs, 90 for five nuclear gene sequences). Preliminary analyses showed that hotspots of cpDNA diversity match with supposed LGM refugees for the wild olive tree. Three well differentiated regions have been identified: Morocco-Andalusia, Aegean islands, and Levantine region including Cyprus. In addition, the main origin of the cultivated olive in the Levantine area has been strongly supported by this study. Finally, this study has brought much new information on the olive history and several biogeographic analyses are in progress. The origin of invasive olive has been depicted more in details revealing frequent hybridisations between subspp. europaea and cuspidata in Australia, and the generated data also allow comparisons of gene dispersal patterns in different wild populations, and particularly in subspecies guanchica, cerasiformis, maroccana and laperrinei from Macaronesia and Saharan mountains.

In conclusion, this project permits to generate huge genetic information for investigating the diversification of the olive tree at different time scales and in different geographic areas. The datasets will be released and will constitute reference information for further studies. In this way, our cpDNA markers are presently tested for forensic analyses on olive oil (Coroba University), but they could have other applications such as the characterisation of archaeological material. In addition, considering the management of genetic resources of this Mediterranean species, our study pointed out that cpDNA hotspots generally match with areas under strong human pressures and the endangered wild olive germplasm needs to be urgently prospected in several regions (i.e. Southern Spain, Northern Morocco, Middle Atlas mountains, Aegean region and Peloponese, Levantine region).