Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication.

Muriel Gros‐Balthazard,Guillaume Besnard,Sylvain Glémin,Julie Leclercq,Daniel Wegmann,Gautier Sarah,Sylvain Santoni,Bouchaib Khadari,Yan Holtz

doi:10.1111/tpj.14435

Abstract

SummaryThe olive (Olea europaea L. subsp. europaea) is one of the oldest and most socio‐economically important cultivated perennial crop in the Mediterranean region. Yet, its origins are still under debate and the genetic bases of the phenotypic changes associated with its domestication are unknown. We generated RNA‐sequencing data for 68 wild and cultivated olive trees to study the genetic diversity and structure both at the transcription and sequence levels. To localize putative genes or expression pathways targeted by artificial selection during domestication, we employed a two‐step approach in which we identified differentially expressed genes and screened the transcriptome for signatures of selection. Our analyses support a major domestication event in the eastern part of the Mediterranean basin followed by dispersion towards the West and subsequent admixture with western wild olives. While we found large changes in gene expression when comparing cultivated and wild olives, we found no major signature of selection on coding variants and weak signals primarily affected transcription factors. Our results indicated that the domestication of olives resulted in only moderate genomic consequences and that the domestication syndrome is mainly related to changes in gene expression, consistent with its evolutionary history and life history traits.

Highlights

The olive tree (Olea europaea L. subsp. europaea var. europaea) constitutes a cornerstone of Mediterranean culture by its multiple past and present uses and its omnipresence in traditional agrosystems (Loumou and Giourga, 2003)
We examined population structure in our olive transcriptomic data using principal component analysis (PCAs) (Figure 1) and NGSadmix (Figure 2)
To identify SNPs related to domestication, but not to the geographic differentiation, we focused on the top 1% hits associated to PC2 only

Summary

Introduction

The olive tree (Olea europaea L. subsp. europaea var. europaea) constitutes a cornerstone of Mediterranean culture by its multiple past and present uses and its omnipresence in traditional agrosystems (Loumou and Giourga, 2003). Europaea) constitutes a cornerstone of Mediterranean culture by its multiple past and present uses and its omnipresence in traditional agrosystems (Loumou and Giourga, 2003). Olives were restricted to the Mediterranean basin, but current cultivation includes the Americas and Australia. By 2017, more than 10 million hectares were devoted to olive cultivation globally, with more than 90% in the Mediterranean area (FAO, 2018). The olive tree is one of the most important oil-producing plant species, and demand for its oil is still increasing due to its nutritional quality (Kalua et al, 2007). Over 20 million tonnes of olives were harvested in 2017, and the production is in constant growth (FAO, 2018)

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