Population genomics of apricots unravels domestication history and adaptive events

Alexis Groppi,Jérôme Salse,Véronique Decroocq,Stéphane Decroocq,Quynh Trang Bui,Cécile Huneau,Joseph Tran,Stéphane Cauet,Pierre Pétriacq,Sébastien Carrère,Erwan Denis,Jean Marc Audergon ,Macha Nikolski,Shuo Liu,Xilong Chen,Sandrine Arribat,Benjamin Istace,David Torgerson ,Tatiana Giraud,Rémy Félix Serre ,William Marande,Nathalie Rodde,Jean‐Marc Aury ,Amandine Cornille,Robert Debuchy,Wassim Rhalloussi,Caroline Belser,Tetyana Zhebentyayeva,Aurélien Barré ,Albert G Abbott ,Guillaume Roch,Corinne Cruaud,Wei Sheng Liu ,Céline Roques ,Patrick Lambert,Patrick Wincker,Olivier Bouchez

doi:10.1038/s41467-021-24283-6

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.

Highlights

1234567890():,; Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes
We find that a relatively small part of their genomes is affected by selection, as expected for perennial crops, and that different genomic regions are affected by selection in European and Chinese cultivated apricots despite convergent phenotypic traits
We looked for signatures of positive selection in the genomes of the two cultivated populations, the European cultivars originating from Northern Central Asian wild apricots, and the Chinese cultivars originating from Southern Central Asian populations

Summary

Introduction

1234567890():,; Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Independent domestication events have occurred in some crops, fungi and animals with selection on the same traits, resulting in convergent adaptation[6,7], such as the loss of seed shattering, minimization of seed dormancy and increase in seed size and number in annual crops[8]. These independent domestication events having led to similar derived traits provide opportunities to address the question of whether such convergent adaptation occurs through changes in the same or different genomic regions. Refers to both the wild progenitor and the cultivated species ( called ‘common apricot’) It is a deciduous tree grown for its edible fruits with an annual worldwide production of ~4.1 million tons (FAO, 2019). The four other related species are P. sibirica L., P. mandshurica (Maxim.)

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Results

Conclusion