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

• Published in: Genome biology 2014-07, Vol.15 (7), p.415-415, Article 415
• Main Authors: Cao, Ke, Zheng, Zhijun, Wang, Lirong, Liu, Xin, Zhu, Gengrui, Fang, Weichao, Cheng, Shifeng, Zeng, Peng, Chen, Changwen, Wang, Xinwei, Xie, Min, Zhong, Xiao, Wang, Xiaoli, Zhao, Pei, Bian, Chao, Zhu, Yinling, Zhang, Jiahui, Ma, Guosheng, Chen, Chengxuan, Li, Yanjun, Hao, Fengge, Li, Yong, Huang, Guodong, Li, Yuxiang, Li, Haiyan, Guo, Jian, Xu, Xun, Wang, Jun
• Format: Article
• Language: English
• Subjects: Crops, Agricultural - classification; Crops, Agricultural - genetics; Evolution, Molecular; Genetic Variation; Genome, Plant; Homozygote; Humans; Linkage Disequilibrium; Metagenomics - methods; Molecular Sequence Data; Phylogeny; Polymorphism, Single Nucleotide; Prunus; Prunus - classification; Prunus - genetics; Prunus persica; Selection, Genetic; Sequence Analysis, DNA
• ISSN: 1474-760X; 1465-6906; 1474-760X; 1465-6914
• DOI: 10.1186/s13059-014-0415-1

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. 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.