Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.)

Abstract

Background Olive tree (Olea europaea L. subsp. europaea, Oleaceae) has been the most emblematic perennial crop for Mediterranean countries since its domestication around 6000 years ago in the Levant. Two taxonomic varieties are currently recognized: cultivated (var. europaea) and wild (var. sylvestris) trees. However, it remains unclear whether olive cultivars derive from a single initial domestication event followed by secondary diversification, or whether cultivated lineages are the result of more than a single, independent primary domestication event. To shed light into the recent evolution and domestication of the olive tree, here we analyze a group of newly sequenced and available genomes using a phylogenomics and population genomics framework. Results We improved the assembly and annotation of the reference genome, newly sequenced the genomes of twelve individuals: ten var. europaea, one var. sylvestris, and one outgroup taxon (subsp. cuspidata)—and assembled a dataset comprising whole genome data from 46 var. europaea and 10 var. sylvestris. Phylogenomic and population structure analyses support a continuous process of olive tree domestication, involving a major domestication event, followed by recurrent independent genetic admixture events with wild populations across the Mediterranean Basin. Cultivated olives exhibit only slightly lower levels of genetic diversity than wild forms, which can be partially explained by the occurrence of a mild population bottleneck 3000–14,000 years ago during the primary domestication period, followed by recurrent introgression from wild populations. Genes associated with stress response and developmental processes were positively selected in cultivars, but we did not find evidence that genes involved in fruit size or oil content were under positive selection. This suggests that complex selective processes other than directional selection of a few genes are in place. Conclusions Altogether, our results suggest that a primary domestication area in the eastern Mediterranean basin was followed by numerous secondary events across most countries of southern Europe and northern Africa, often involving genetic admixture with genetically rich wild populations, particularly from the western Mediterranean Basin.

Olive Fruit Development and Ripening: Break on through to the “-Omics” Side

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Climate Change and Major Pests of Mediterranean Olive Orchards: Are We Ready to Face the Global Heating?

“…Additionally, southern Mediterranean countries are expected to be the most afflicted by heatwaves and drought, and a huge backlash on agriculture productivity is predictable [ 18 , 19 ]. Olea europaea L. is one of the oldest permanent crops of the Mediterranean, where it has an essential socioeconomic and ecological relevance [ 19 , 20 , 21 , 22 , 23 , 24 ]. Nearly all (95%) of global olive oil demand is satisfied by the southern European countries; among them, Spain is the most devoted to oil production, followed by Italy, Greece and Portugal [ 23 , 25 ].…”

Olive (Olea europaea L.) Genetic Transformation: Current Status and Future Prospects

“…In this regard, olive is a recalcitrant species to in vitro manipulation [ 14 ]; however, in the last two decades, a small number of studies reported the development of olive genetic transformation protocols, which have been used for obtaining transgenic plants expressing reporter genes and even transgenes of interest, although in most cases transformed explants were of juvenile origin. The importance of this technology will increase in the near future with the advancement in the olive genome sequence projects that are currently underway [ 15 , 16 , 17 ], which could allow the identification of genes of interest for future breeding programs. In addition, protocols for the regeneration of somatic embryos (SE)from explants of adult origin are needed to develop new cultivars or rootstocks useful for breeders.…”