@article{7d01156d4f094779a079ba4ab8c330b6,
title = "Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication",
abstract = "The 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.",
keywords = "Olea europaea (olive tree), RNA-sequencing, artificial selection, differential expression analysis, domestication, perennial crop, transcriptomics",
author = "Muriel Gros-Balthazard and Guillaume Besnard and Gautier Sarah and Yan Holtz and Julie Leclercq and Sylvain Santoni and Daniel Wegmann and Sylvain Gl{\'e}min and Bouchaib Khadari",
note = "Funding Information: This work was supported by Agropolis Fondation through the program OliveMed under the reference ID 1403-026, ?Investissements d'avenir? program (Labex Agro:ANR-10-LABX-0001-01). MGB has received the support of the EU in the framework of the Marie-Curie FP7 COFUND People Programme, through the award of an AgreenSkills fellowship under grant agreement no. 267196. G.B. is member of the EDB laboratory supported by the excellence projects Labex CEBA (ANR-10LABX-25-01) and Labex TULIP (ANR-10LABX-0041), managed by the French ANR. We thank Sylvia Lochon-Menseau, Daniel Bielmann, Bruno Bernazeau (CBNMed collection at Porquerolles, France), Hayat Zaher, Abdelmajid Moukhli, Sikaoui lhassane (Word Olive Germplasm Bank of Marrakech, Morocco), and the staff of the experimental field of the Platform {"}Terrains d'Exp?riences{"} of the LabEx CeMEB (Montpellier, France); Mohammed Ater, Melek Gurbuz, Mehmet Ulas and Mehmet Hakan for helping us in the wild olive sampling from in situ areas; Audrey Veber for helping with the RNA extraction and library preparation for sequencing; Christine Tollon for chloroplast DNA genotyping; Bertrand Pitollat, St?phanie Sidibe-Bocs and Ga?tan Droc for their support in the bioinformatic analyses; Yann Bourgeois, Athanasios Kousathanas, Fran?ois Sabot, Baptiste Guitton, Jean-Jacques Kelner, R?my Tournebize, Yves Vigouroux, Olivier Fran?ois and Eric Frichot for constructive discussions; Michael Blum, Keurcien Luu and Nicolas Duforet-Frebourt for their help with PCAdapt software; Christopher Sauvage for providing with scripts for gene expression analysis and helpful discussions; Emeline Pobelle for graphic design and Philip P. Rodenbough for proofreading.",
year = "2019",
month = oct,
day = "1",
doi = "10.1111/tpj.14435",
language = "English (US)",
volume = "100",
pages = "143--157",
journal = "Plant Journal",
issn = "0960-7412",
publisher = "Wiley-Blackwell",
number = "1",
}