TY - JOUR
T1 - Population genomics of apricots unravels domestication history and adaptive events
AU - Groppi, Alexis
AU - Liu, Shuo
AU - Cornille, Amandine
AU - Decroocq, Stéphane
AU - Bui, Quynh Trang
AU - Tricon, David
AU - Cruaud, Corinne
AU - Arribat, Sandrine
AU - Belser, Caroline
AU - Marande, William
AU - Salse, Jérôme
AU - Huneau, Cécile
AU - Rodde, Nathalie
AU - Rhalloussi, Wassim
AU - Cauet, Stéphane
AU - Istace, Benjamin
AU - Denis, Erwan
AU - Carrère, Sébastien
AU - Audergon, Jean Marc
AU - Roch, Guillaume
AU - Lambert, Patrick
AU - Zhebentyayeva, Tetyana
AU - Liu, Wei Sheng
AU - Bouchez, Olivier
AU - Lopez-Roques, Céline
AU - Serre, Rémy Félix
AU - Debuchy, Robert
AU - Tran, Joseph
AU - Wincker, Patrick
AU - Chen, Xilong
AU - Pétriacq, Pierre
AU - Barre, Aurélien
AU - Nikolski, Macha
AU - Aury, Jean Marc
AU - Abbott, Albert Glenn
AU - Giraud, Tatiana
AU - Decroocq, Véronique
N1 - Funding Information:
Most of the computational resources and infrastructure used in present publication were provided by the Bordeaux Bioinformatics Center (CBiB). Additional computer time for this study was provided by MCIA (Mesocentre de Calcul Intensif Aquitain) of the Universities of Bordeaux and of Pau and des Pays de l’Adour. We are also grateful to the Genotoul bioinformatics platform, Toulouse, for providing help, computing and/or storage resources (http://bioinfo.genotoul.fr/index.php) and the URGI platform (https://urgi.versailles.inra.fr/Tools/REPET), for help in running the REPET package v2.5. We acknowledge valuable contribution of Dr Peter Civan (INRAE GDEC, Clermont-Ferrand) for chloroplastic phylogenomics and admixture analysis and Dr Ricardo Rodriguez de la Vega (Université Paris-Saclay, ESE, Orsay) for help in ‘managing’ the BEAST. We thank the INRAE BFP technical team: Aurélie Chague for the extraction of Prunus genomic DNA for ILLUMINA sequencing, Mélodie Caballero for the extraction of RNA, Jean-Philippe Eyquard and Pascal Briard for the care of the plants. S.L. was supported by the Chinese Scholarship Council (2015-2019), X.C. by the ATIP CNRS Inserm funding. This research was supported by the ABRIWG project (ANR CHEX 2012-2014), by Genoscope, the Commissariat à l’Energie Atomique et aux Énergies Alternatives (CEA), France Génomique (ANR-10-INBS-09–08, SWAG project), Bordeaux University (G2P SWAGMAN and ATT ABXING), INRAE Biology and Plant Breeding division (WildArm project). This work was performed in collaboration with the GeT core facility, Toulouse, France (http://get.genotoul.fr), and was supported by France Génomique National infrastructure, funded as part of ‘Investissement d’avenir’ program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09) and by the GET-PACBIO program (« Programme opérationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020 »). The ancestral karyotype reconstruction approach was supported by the Institut Carnot Plant2Pro (#0001455 project SyntenyViewer 2017) and the ISITE CAP2025 (#00002146 SRESRI 2015 ‘Pack Ambition Recherche Project’ TransBlé 2018). The Bergeron x Bakour genetic maps were constructed in the frame of the ABRIWG CHEX ANR (2012-2014) and of the Resibac CASDAR (2013-2016) projects. The Liaoning pomology institute benefited from Grant/Award Number: 2019YFD1000600 from the National Key Research and Development Program of China.
Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12/1
Y1 - 2021/12/1
N2 - 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.
AB - 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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U2 - 10.1038/s41467-021-24283-6
DO - 10.1038/s41467-021-24283-6
M3 - Article
C2 - 34172741
AN - SCOPUS:85109211899
VL - 12
JO - Nature Communications
JF - Nature Communications
SN - 2041-1723
IS - 1
M1 - 3956
ER -