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

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 () and Xuesen Chen ()
Additional contact information
Naibin Duan: Shandong Agricultural University
Yang Bai: Cornell University
Honghe Sun: Cornell University
Nan Wang: Shandong Agricultural University
Yumin Ma: Shandong Academy of Agricultural Sciences
Mingjun Li: Northwest A&F University
Xin Wang: Cornell University
Chen Jiao: Cornell University
Noah Legall: Cornell University
Linyong Mao: Cornell University
Sibao Wan: Cornell University
Kun Wang: Chinese Academy of Agricultural Sciences
Tianming He: Xinjiang Agricultural University
Shouqian Feng: Shandong Agricultural University
Zongying Zhang: Shandong Agricultural University
Zhiquan Mao: Shandong Agricultural University
Xiang Shen: Shandong Agricultural University
Xiaoliu Chen: Shandong Agricultural University
Yuanmao Jiang: Shandong Agricultural University
Shujing Wu: Shandong Agricultural University
Chengmiao Yin: Shandong Agricultural University
Shunfeng Ge: Shandong Agricultural University
Long Yang: Shandong Agricultural University
Shenghui Jiang: Shandong Agricultural University
Haifeng Xu: Shandong Agricultural University
Jingxuan Liu: Shandong Agricultural University
Deyun Wang: Shandong Agricultural University
Changzhi Qu: Shandong Agricultural University
Yicheng Wang: Shandong Agricultural University
Weifang Zuo: Shandong Agricultural University
Li Xiang: Shandong Agricultural University
Chang Liu: Mudanjiang Branch of Heilongjiang Academy of Agricultural Science
Daoyuan Zhang: Chinese Academy of Sciences
Yuan Gao: Chinese Academy of Agricultural Sciences
Yimin Xu: Cornell University
Kenong Xu: Cornell University
Thomas Chao: Plant Genetic Resources Unit
Gennaro Fazio: Plant Genetic Resources Unit
Huairui Shu: Shandong Agricultural University
Gan-Yuan Zhong: Plant Genetic Resources Unit
Lailiang Cheng: Cornell University
Zhangjun Fei: Cornell University
Xuesen Chen: Shandong Agricultural University

Nature Communications, 2017, vol. 8, issue 1, 1-11

Abstract: Abstract Human 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 from Malus sieversii in Kazakhstan, followed by intensive introgressions from M. sylvestris. M. sieversii in 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.

Date: 2017
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DOI: 10.1038/s41467-017-00336-7

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