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Population genomics of apricots unravels domestication history and adaptive events.

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.

SUBMITTER: Groppi A

PROVIDER: S-EPMC8233370 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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Population genomics of apricots unravels domestication history and adaptive events.

Groppi Alexis A Liu Shuo S Cornille Amandine A Decroocq Stéphane S Bui Quynh Trang QT Tricon David D Cruaud Corinne C Arribat Sandrine S Belser Caroline C Marande William W Salse Jérôme J Huneau Cécile C Rodde Nathalie N Rhalloussi Wassim W Cauet Stéphane S Istace Benjamin B Denis Erwan E Carrère Sébastien S Audergon Jean-Marc JM Roch Guillaume G Lambert Patrick P Zhebentyayeva Tetyana T Liu Wei-Sheng WS Bouchez Olivier O Lopez-Roques Céline C Serre Rémy-Félix RF Debuchy Robert R Tran Joseph J Wincker Patrick P Chen Xilong X Pétriacq Pierre P Barre Aurélien A Nikolski Macha M Aury Jean-Marc JM Abbott Albert Glenn AG Giraud Tatiana T Decroocq Véronique V

Nature communications 20210625 1

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 genom ...[more]

PMID: 34172741

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Project description:BackgroundRhodomyrtus tomentosa (Ait.) Hassk. is useful for its ornamental, medicinal, and ecological characteristics, and is considered a "Neglected and Underutilized Crop Species". However, our understanding of the geographic structure and evolutionary history of its wild populations is limited. To address this gap, we investigated genomic data from 284 samples of R. tomentosa from 28 wild populations in southern China.ResultsThe genetic diversity of populations in different regions revealed the similar trends using whole-genome and RAD-seq data, and Hainan Island having a higher genetic diversity than other regions. The 28 populations clustered into three distinct groups: (a) GROUP1 on the eastern mainland within Guangdong, Fujian, and Hunan Provinces; (b) GROUP2 on the western mainland within Guangxi and Yunnan Provinces; and (c) GROUP3 on Hainan Island. Mantel tests and redundancy analyses revealed population differentiation was affected by distance and environmental factors such as annual average radiation. Demographic history and gene flow analyses indicated the mainland populations and the Hainan Island populations diverged around 0.93 MYA, with gene flow primarily occurring from Hainan Island and the coastal regions (such as Zhanjiang in Guangdong and Fangchenggang in Guangxi) towards the mainland, reflecting an expansion trend within the species. PSMC' analyses indicated that the populations of the three groups underwent a bottleneck during the Pleistocene due to glacial-interglacial cycles and geological events. Niche analysis revealed that the ice ages caused habitat contraction for the species, and populations with higher genetic diversity are generally distributed in areas with more suitable habitats.ConclusionsThis study elucidates the current genetic distribution of the species within China and suggests that drastic Pleistocene climate change and geographical events caused population divergence and fluctuations in effective population size, shaping the current genetic distribution of R. tomentosa. These findings provide a theoretical basis for the genetic conservation and improvement of R. tomentosa.

Dataset Information

Population genomics of apricots unravels domestication history and adaptive events.

Publications

Population genomics of apricots unravels domestication history and adaptive events.

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