Genomic evidence for recurrent genetic admixture during domestication mediterranean olive trees (Olea europaea)

Abstract

BackgroundThe olive tree (Olea europaea L. subsp. europaea, Oleaceae) has been the most economic perennial crop for Mediterranean countries since its domestication around 6,000 years ago. Two taxonomic varieties are currently recognized: cultivated (var. europaea) and wild (var. sylvestris) trees. To shed light into the recent evolution and domestication of the olive tree, we sequenced the genomes of twelve individuals: ten var. europaea, one var. sylvestris, and one outgroup taxon (subsp. cuspidata). All of them were analysed together with an improved assembly of var. europaea reference genome and the available assembly of var. sylvestris.ResultsOur analyses show that cultivated olives exhibit slightly lower levels of overall genetic diversity than wild forms, and that this can be partially explained by the occurrence of a mild population bottleneck 5000-7000 years ago during the primary domestication period. We also provide the first phylogenetic analysis of genome-wide sequences, which supports a continuous process of domestication of the olive tree. This, together with population structure and introgression analyses highlights genetic admixture with wild populations across the Mediterranean Basin in the course of domestication.ConclusionsAltogether, 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. Based on selection tests and a search for selective sweeps, we found that genes associated with stress response and developmental processes were positively selected in cultivars. However, we did not find evidence that genes involved in fruit size or oil content were under positive selection.

Conservation of Native Wild Ivory-White Olives from the MEDES Islands Natural Reserve to Maintain Virgin Olive Oil Diversity

“…Sylvestris (also named oleaster) and the cultivated tree var. europaea [ 6 , 7 ], some of which produce ivory-white fruit. Oleasters are usually located in isolated areas far from cultivated zones and are characterized by small fruits with a thin mesocarp [ 7 , 8 ].…”

A genomic approach to the evolution, diversification and domestication of the genus Citrus

“…These results indicate that, despite the great degree of relatedness that exists among commercial mandarins (Wu et al, 2018), the major transcriptomic differences between wild and domesticated mandarins accumulate in the admixed regions of the genome. The role of interspecific hybridization as a major driver in domestication has been thoroughly confirmed in several tree species (Myles et al, 2011;Duan et al, 2017;Flowers et al, 2019;Julca et al, 2020), including…”

“…These Citrus wild species. However, like in other tree species (Duan et al, 2017;Julca et al, 2020), the domestication of the genus Citrus was profoundly shaped by interspecific crosses that, in parallel with the selection of desirable traits, gave rise to the current admixtures and commercial cultivars. The great phenotypic diversity found within Citrus possibly paved the way for these interspecific hybridizations.…”

“…Instead, many domesticated perennials appear to be the product of recurrent selections of somatic mutants vegetatively propagated (Gaut et al, 2015). Accordingly, sexual reproduction in perennial crops is a relatively rare event, involving a moderately low number of interspecific crosses between cultivated and wild individuals, as observed in grapevine, olive, apple or cocoa (Myles et al, 2011;Duan et al, 2017;Cornejo et al, 2018;Julca et al, 2020). As a consequence of the vegetative propagation of perennial trees, the genomic structure of hybrids and admixtures is conserved across generations, frozen in time, which allows for interspecific hybrids to be maintained without allele segregation.…”

“…The importance of interspecific hybridizations between genetically distant individuals or species has been repeatedly reported as a major force in the domestication of many tree species including olive (Julca et al, 2020), date palm (Flowers et al, 2019), apple (Duan et al, 2017) or grapevine (Myles et al, 2011). Even in annual crops such as maize, admixed regions have proven their relevance in driving the adaptation of this species from the tropical latitudes of Mexico to Northern latitudes, affecting the flowering time and cold resistance of the European and North American landraces (Brandenburg et al, 2017).…”