Population genomics of apricots unravels domestication history and adaptive events

Alexis Groppi; Shuo Liu; Amandine Cornille; Stephane Decroocq; Quynh Trang Bui; David Tricon; Corinne Cruaud; Sandrine Arribat; Caroline Belser; William Marande; Jerome Salse; Cecile Huneau; Nathalie Rodde; Wassim Rhalloussi; Stephane Cauet; Benjamin Istace; Erwan Denis; Sebastien Carrere; Jean-Marc Audergon; Guillaume Roch; Patrick Lambert; Tetyana Zhebentyayeva; Wei-Sheng Liu; Olivier Bouchez; Celine Lopez-Roques; Remy-Felix Serre; Robert Debuchy; Joseph Tran; Patrick Wincker; Xilong Chen; Pierre Petriacq; Aurelien Barre; Macha Nikolski; Jean-Marc Aury; Albert Glenn Abbott; Tatiana Giraud; Veronique Decroocq

doi:10.1038/s41467-021-24283-6

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Population genomics of apricots unravels domestication history and adaptive events

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Population genomics of apricots unravels domestication history and adaptive events

Alexis Groppi, Shuo Liu, Amandine Cornille, Stephane Decroocq, Quynh Trang Bui, David Tricon, Corinne Cruaud, Sandrine Arribat, Caroline Belser, William Marande, …

Nature communications, Vol.12(1), pp.3956-16

25/06/2021

DOI: https://doi.org/10.1038/s41467-021-24283-6

PMID: 34172741

Résumé

Multidisciplinary Sciences

Science & Technology

Science & Technology - Other Topics

The evolutionary and domestication history of apricots is poorly understood. Here, the authors provide four apricot high-quality genome assemblies, the genomes of 578 accessions from natural and cultivated populations, and show that Chinese and European apricots constitute two different gene pools, resulting from independent domestication events. 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.

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Titre: Population genomics of apricots unravels domestication history and adaptive events
Créateurs - sans rôle: Alexis Groppi - Univ Bordeaux, Ctr Bioinformat Bordeaux CBiB, F-33076 Bordeaux, France
Shuo Liu - Univ Bordeaux, INRAE, UMR 1332 Biol Fruit & Pathol, 71 Av E Bourlaux, F-33140 Villenave Dornon, France
Amandine Cornille - Univ Paris Saclay, INRAE, CNRS, AgroParisTech,UMR GQE Le Moulon, F-91190 Gif Sur Yvette, France
Stephane Decroocq - Univ Bordeaux, INRAE, UMR 1332 Biol Fruit & Pathol, 71 Av E Bourlaux, F-33140 Villenave Dornon, France
Quynh Trang Bui - Univ Bordeaux, INRAE, UMR 1332 Biol Fruit & Pathol, 71 Av E Bourlaux, F-33140 Villenave Dornon, France
David Tricon - Univ Bordeaux, INRAE, UMR 1332 Biol Fruit & Pathol, 71 Av E Bourlaux, F-33140 Villenave Dornon, France
Corinne Cruaud - Univ Paris Saclay, Genoscope, Inst Francois Jacob, Commissariat Energie Atom CEA, 2 Rue Gaston Cremieux, F-91057 Evry, France
Sandrine Arribat - French Plant Genom Resource Ctr, INRAE CNRGV, Castanet Tolosan, France
Caroline Belser - Univ Paris Saclay, Genoscope, Inst Francois Jacob, Commissariat Energie Atom CEA, 2 Rue Gaston Cremieux, F-91057 Evry, France
William Marande - French Plant Genom Resource Ctr, INRAE CNRGV, Castanet Tolosan, France
Jerome Salse - INRAE, UBP UMR 1095, GDEC Genet Diversite & Ecophysiol Cereales, Lab PaleoEVO Paleogen & Evolut, 5 Chemin Beaulieu, F-63100 Clermont Ferrand, France
Cecile Huneau - INRAE, UBP UMR 1095, GDEC Genet Diversite & Ecophysiol Cereales, Lab PaleoEVO Paleogen & Evolut, 5 Chemin Beaulieu, F-63100 Clermont Ferrand, France
Nathalie Rodde - French Plant Genom Resource Ctr, INRAE CNRGV, Castanet Tolosan, France
Wassim Rhalloussi - French Plant Genom Resource Ctr, INRAE CNRGV, Castanet Tolosan, France
Stephane Cauet - French Plant Genom Resource Ctr, INRAE CNRGV, Castanet Tolosan, France
Benjamin Istace - Univ Paris Saclay, Genoscope, Inst Francois Jacob, Commissariat Energie Atom CEA, 2 Rue Gaston Cremieux, F-91057 Evry, France
Erwan Denis - Univ Paris Saclay, Genoscope, Inst Francois Jacob, Commissariat Energie Atom CEA, 2 Rue Gaston Cremieux, F-91057 Evry, France
Sebastien Carrere - Univ Toulouse, CNRS, INRAE, LIPME, Castanet Tolosan, France
Jean-Marc Audergon - INRAE UR1052 GAFL, Domaine St Maurice,CS60094, F-84143 Montfavet, France
Guillaume Roch - INRAE UR1052 GAFL, Domaine St Maurice,CS60094, F-84143 Montfavet, France
Patrick Lambert - INRAE UR1052 GAFL, Domaine St Maurice,CS60094, F-84143 Montfavet, France
Tetyana Zhebentyayeva - Penn State Univ, Schatz Ctr Tree Mol Genet, Dept Ecosyst Sci & Management, University Pk, PA 16802 USA
Wei-Sheng Liu - Liaoning Inst Pomol, Tiedong St, Yingkou City 115009, Liaoning, Peoples R China
Olivier Bouchez - INRAE, US 1426, GeT PlaGe, F-31326 Castanet Tolosan, France
Celine Lopez-Roques - INRAE, US 1426, GeT PlaGe, F-31326 Castanet Tolosan, France
Remy-Felix Serre - INRAE, US 1426, GeT PlaGe, F-31326 Castanet Tolosan, France
Robert Debuchy - Univ Paris Saclay, CEA, CNRS, Inst Integrat Biol Cell I2BC, F-91198 Gif Sur Yvette, France
Joseph Tran - Univ Bordeaux, ISVV, INRAE, EGFV,Bordeaux Sci Agro, F-33882 Villenave Dornon, France
Patrick Wincker - Univ Paris Saclay, Genoscope, Inst Francois Jacob, Commissariat Energie Atom CEA, 2 Rue Gaston Cremieux, F-91057 Evry, France
Xilong Chen - Univ Paris Saclay, INRAE, CNRS, AgroParisTech,UMR GQE Le Moulon, F-91190 Gif Sur Yvette, France
Pierre Petriacq - Univ Bordeaux, INRAE, UMR 1332 Biol Fruit & Pathol, 71 Av E Bourlaux, F-33140 Villenave Dornon, France
Aurelien Barre - Univ Bordeaux, Ctr Bioinformat Bordeaux CBiB, F-33076 Bordeaux, France
Macha Nikolski - Univ Bordeaux, Ctr Bioinformat Bordeaux CBiB, F-33076 Bordeaux, France
Jean-Marc Aury - Univ Paris Saclay, Genoscope, Inst Francois Jacob, Commissariat Energie Atom CEA, 2 Rue Gaston Cremieux, F-91057 Evry, France
Albert Glenn Abbott - Univ Kentucky, Forest Hlth Res & Educ Ctr, Lexington, KY USA
Tatiana Giraud - Univ Paris Saclay, CNRS, Ecol Systemat & Evolut, AgroParisTech, F-91400 Orsay, France
Veronique Decroocq - Univ Bordeaux, INRAE, UMR 1332 Biol Fruit & Pathol, 71 Av E Bourlaux, F-33140 Villenave Dornon, France
Détails de publication: Nature communications, Vol.12(1), pp.3956-16
Éditeur: NATURE PORTFOLIO
Nombre de pages: 16
Note de subvention: ABRIWG project (ANR CHEX 2012-2014) by Genoscope; Agence Nationale de la Recherche (ANR); Agence nationale pour le developpement de la recherche en sante (ANDRS) 0001455 / Institut Carnot Plant2Pro INRAE Biology and Plant Breeding division (WildArm project) Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA); CEA ANR-10-INBS09 / France Genomique National infrastructure as part of 'Investissement d'avenir' program by Agence Nationale pour la Recherche; Agence Nationale de la Recherche (ANR); Agence nationale pour le developpement de la recherche en sante (ANDRS); Agence Nationale Des Plantes Medicinales Et Aromatiques, ANPMA, Morocco ANR-10-INBS-09-08 / France Genomique Bordeaux University (ATT ABXING) 00002146 / ISITE CAP2025 Chinese Scholarship Council by the ATIP CNRS Inserm funding Bordeaux University (G2P SWAGMAN)
Identifiants: 99162817809311
Unité académique: Institut de Recherche en Cancérologie de Montpellier - IRCM
Langue: English
Type de ressource: Journal article