Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement

• DOI: 10.1038/s41467-017-00336-7
• Publication Date: 2017-08-07T15:52:43Z
• Authors: Naibin Duan; Yang Bai; Honghe Sun; Nan Wang; Yumin Ma; Mingjun Li; Xin Wang; Chen Jiao; Noah Legall; Linyong Mao; Sibao Wan; Kun Wang; Tianming He; Shouqian Feng; Zongying Zhang; Zhiquan Mao; Xiang Shen; Xiaoliu Chen; Yuanmao Jiang; Shujing Wu; Chengmiao Yin; Shunfeng Ge; Long Yang; Shenghui Jiang; Haifeng Xu; Jingxuan Liu; Deyun Wang; Changzhi Qu; Yicheng Wang; Weifang Zuo; Li Xiang; Chang Liu; Daoyuan Zhang; Yuan Gao; Yimin Xu; Kenong Xu; Thomas Chao; Gennaro Fazio; Huairui Shu; Gan-Yuan Zhong; Lailiang Cheng; Zhangjun Fei; Xuesen Chen
• Keywords: 0301 basic medicine; 2. Zero hunger; China; Science; Q; Sequence Analysis, DNA; Breeding; 15. Life on land; Polymorphism, Single Nucleotide; Article; Evolution, Molecular; 03 medical and health sciences; Phenotype; Fruit; Malus; Genome, Plant

AbstractHuman selection has reshaped crop genomes. Here we report an apple genome variation map generated through genome sequencing of 117 diverse accessions. A comprehensive model of apple speciation and domestication along the Silk Road is proposed based on evidence from diverse genomic analyses. Cultivated apples likely originate fromMalus sieversiiin Kazakhstan, followed by intensive introgressions fromM. sylvestris.M. sieversiiin Xinjiang of China turns out to be an “ancient” isolated ecotype not directly contributing to apple domestication. We have identified selective sweeps underlying quantitative trait loci/genes of important fruit quality traits including fruit texture and flavor, and provide evidences supporting a model of apple fruit size evolution comprising two major events with one occurring prior to domestication and the other during domestication. This study outlines the genetic basis of apple domestication and evolution, and provides valuable information for facilitating marker-assisted breeding and apple improvement.