Population genomics of apricots unravels domestication history and adaptive events

Alexis Groppi, Shuo Liu, Amandine Cornille, Stéphane Decroocq, Quynh Trang Bui, David Tricon, Corinne Cruaud, Sandrine Arribat, Caroline Belser, William Marande, Jérôme Salse, Cécile Huneau, Nathalie Rodde, Wassim Rhalloussi, Stéphane Cauet, Benjamin Istace, Erwan Denis, Sébastien Carrère, Jean-Marc Audergon, Guillaume Roch, Patrick Lambert, Tetyana Zhebentyayeva, Wei-Sheng Liu, Olivier Bouchez, Céline Lopez-Roques, Rémy-Félix Serre, Robert Debuchy, Joseph Tran, Patrick Wincker, Xilong Chen, Pierre Pétriacq, Aurélien Barre, Macha Nikolski, Jean-Marc Aury, Albert Glenn Abbott, Tatiana Giraud () and Véronique Decroocq ()
Additional contact information
Alexis Groppi: Univ. Bordeaux, Centre de Bioinformatique de Bordeaux (CBiB)
Shuo Liu: Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie
Amandine Cornille: Université Paris Saclay, INRAE, CNRS, AgroParisTech, UMR GQE-Le Moulon
Stéphane Decroocq: Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie
Quynh Trang Bui: Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie
David Tricon: Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie
Corinne Cruaud: Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay
Sandrine Arribat: French Plant Genomic Resource Center, INRAE-CNRGV
Caroline Belser: Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay
William Marande: French Plant Genomic Resource Center, INRAE-CNRGV
Jérôme Salse: Laboratory PaleoEVO Paleogenomics & Evolution
Cécile Huneau: Laboratory PaleoEVO Paleogenomics & Evolution
Nathalie Rodde: French Plant Genomic Resource Center, INRAE-CNRGV
Wassim Rhalloussi: French Plant Genomic Resource Center, INRAE-CNRGV
Stéphane Cauet: French Plant Genomic Resource Center, INRAE-CNRGV
Benjamin Istace: Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay
Erwan Denis: Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay
Sébastien Carrère: LIPME, Université de Toulouse, INRAE, CNRS
Jean-Marc Audergon: INRAE UR1052 GAFL, Domaine Saint Maurice
Guillaume Roch: INRAE UR1052 GAFL, Domaine Saint Maurice
Patrick Lambert: INRAE UR1052 GAFL, Domaine Saint Maurice
Tetyana Zhebentyayeva: The Pennsylvania State University
Wei-Sheng Liu: Liaoning Institute of Pomology
Olivier Bouchez: INRAE, US 1426, GeT-PlaGe, Genotoul
Céline Lopez-Roques: INRAE, US 1426, GeT-PlaGe, Genotoul
Rémy-Félix Serre: INRAE, US 1426, GeT-PlaGe, Genotoul
Robert Debuchy: Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)
Joseph Tran: EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV
Patrick Wincker: Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay
Xilong Chen: Université Paris Saclay, INRAE, CNRS, AgroParisTech, UMR GQE-Le Moulon
Pierre Pétriacq: Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie
Aurélien Barre: Univ. Bordeaux, Centre de Bioinformatique de Bordeaux (CBiB)
Macha Nikolski: Univ. Bordeaux, Centre de Bioinformatique de Bordeaux (CBiB)
Jean-Marc Aury: Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay
Albert Glenn Abbott: University of Kentucky
Tatiana Giraud: Université Paris-Saclay AgroParisTech
Véronique Decroocq: Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie

Nature Communications, 2021, vol. 12, issue 1, 1-16

Abstract: Abstract Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding.

Date: 2021
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DOI: 10.1038/s41467-021-24283-6

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