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Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops

Ke Cao12, Zhijun Zheng34, Lirong Wang12*, Xin Liu356, Gengrui Zhu1, Weichao Fang1, Shifeng Cheng356, Peng Zeng3, Changwen Chen1, Xinwei Wang1, Min Xie3, Xiao Zhong3, Xiaoli Wang1, Pei Zhao1, Chao Bian3, Yinling Zhu3, Jiahui Zhang1, Guosheng Ma1, Chengxuan Chen3, Yanjun Li3, Fengge Hao1, Yong Li1, Guodong Huang3, Yuxiang Li3, Haiyan Li1, Jian Guo1, Xun Xu356 and Jun Wang3*

Author Affiliations

1 Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou 450009, China

2 The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou 450009, China

3 BGI-Shenzhen, Shenzhen 518083, China

4 MetaGene Genomics Institute, Hangzhou 310011, China

5 State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China

6 Key Laboratory of Genomics, Ministry of Agriculture, BGI-Shenzhen, Shenzhen 518083, China

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Genome Biology 2014, 15:415  doi:10.1186/s13059-014-0415-1

Published: 31 July 2014



Recently, many studies utilizing next generation sequencing have investigated plant evolution and domestication in annual crops. Peach, Prunus persica, is a typical perennial fruit crop that has ornamental and edible varieties. Unlike other fruit crops, cultivated peach includes a large number of phenotypes but few polymorphisms. In this study, we explore the genetic basis of domestication in peach and the influence of humans on its evolution.


We perform large-scale resequencing of 10 wild and 74 cultivated peach varieties, including 9 ornamental, 23 breeding, and 42 landrace lines. We identify 4.6 million SNPs, a large number of which could explain the phenotypic variation in cultivated peach. Population analysis shows a single domestication event, the speciation of P. persica from wild peach. Ornamental and edible peach both belong to P. persica, along with another geographically separated subgroup, Prunus ferganensis.

We identify 147 and 262 genes under edible and ornamental selection, respectively. Some of these genes are associated with important biological features. We perform a population heterozygosity analysis in different plants that indicates that free recombination effects could affect domestication history. By applying artificial selection during the domestication of the peach and facilitating its asexual propagation, humans have caused a sharp decline of the heterozygote ratio of SNPs.


Our analyses enhance our knowledge of the domestication history of perennial fruit crops, and the dataset we generated could be useful for future research on comparative population genomics.