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.

Evidence of an additional wild contributor, Malus orientalis Uglitzk., to the genome of cultivated apple varieties in the Caucasus and Iran

“…Our study revealed the role of gene flow and human practices in natural and anthropogenic divergence processes of an emblematic fruit tree in the Caucasus and Iran. Our results are consistent with those reported for other woody perennials, including apricot (Groppi et al, 2021; Liu et al, 2019), olive (Besnard et al, 2018; Diez et al, 2015), pear (Volk & Cornille, 2019; Wu et al, 2018), and date palm (Flowers et al, 2019). This study also supports the view that domestication of fruit trees was likely a geographically diffuse and protracted process, involving multiple, geographically disparate origins of domestication (Groppi et al, 2021; Wu et al, 2018).…”

“…Studies of the regions under selection during domestication in the Iranian and European cultivated apple genomes will likely provide insights into whether multiple de novo domestication events occurred. Independent selection regimes in each of the cultivated genetic groups would be a hallmark of multiple domestications, as shown in apricot and pear trees (Groppi et al, 2021; Wu et al, 2018). In addition, coalescent-based methods combined with ABC-RF provided a powerful statistical framework for inferring the apple domestication history in the Caucasus and Iran.…”

“…The occurrence of independent domestication events in many crop species is a source of ongoing debate (Besnard et al, 2018; Choi et al, 2017; Gros-Balthazard & Flowers, 2021). In apricot and pear trees, there is evidence of independent domestication events in Europe and Asia, with distinct cultivated gene pools of different ancestries which display different genomic regions showing footprints of selection (Groppi et al, 2021; Liu et al, 2019; Wu et al, 2018). Here, our data shows that there are distinct cultivated apple populations, with different geographic origins and which are derived from distinct ancestral gene pools.…”

Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature

“…Pear ( Pyrus ) originated in southwestern China domestication went toward the two directions of both east and west, and then Asian and European pears were formed separately ( Wu et al, 2018 ). Apricot ( Prunus armeniaca ), which had long been considered to have originated from China, form two different gene pools of Chinese and European apricots, but now the European cultivated apricots were found to originate from the Northern Central Asian wild population, while the Chinese cultivars originated from Southern Central Asian ( Groppi et al, 2021 ).…”

Variation of Fruit Quality Traits in Apricot as Sources for Nutraceutical Breeding

“…More recently, a population genomics study using 600 apricot genomes pointed two independent domestication events from distinct wild Central Asian populations as the origin of Chinese and European apricots ca. 2,000-3,000 years ago (Groppi et al, 2021). According to these authors, Chinese cultivated apricots had higher genetic diversity than the European ones, that could be explained by their lower fraction of self-compatible accessions or/and the gene flow with wild relatives.…”