Dataset Information

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

ABSTRACT: BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.

SUBMITTER: Cao K

PROVIDER: S-EPMC4174323 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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

Cao Ke K Zheng Zhijun Z Wang Lirong L Liu Xin X Zhu Gengrui G Fang Weichao W Cheng Shifeng S Zeng Peng P Chen Changwen C Wang Xinwei X Xie Min M Zhong Xiao X Wang Xiaoli X Zhao Pei P Bian Chao C Zhu Yinling Y Zhang Jiahui J Ma Guosheng G Chen Chengxuan C Li Yanjun Y Hao Fengge F Li Yong Y Huang Guodong G Li Yuxiang Y Li Haiyan H Guo Jian J Xu Xun X Wang Jun J

Genome biology 20140731 7

<h4>Background</h4>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.<h4>Results</h4>We perform large-s ...[more]

PMID: 25079967

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Project description:MicroRNAs (miRNAs) are a group of non-coding RNAs that have functions in post-transcriptional gene regulation in plants. Although the most important economic component of peach trees (Prunus persica) is the fruit, not much is known about miRNAs in this organ. In this study, miRNAs and their targets were identified and characterized from libraries of small RNAs of peach fruit through Solexa based-sequencing and bioinformatics approaches. A total of 557 known peach miRNAs belonging to 34 miRNA families were identified, and some of these miRNAs were found to be highly conserved in at least four other plant species. Using the most current criteria for miRNA annotation, 275 putative novel miRNAs were predicted, and the sequencing frequencies of these novel miRNAs were less than those of the conserved miRNAs. In total, 3959 and 1614 target genes for 349 known and 193 novel miRNAs, respectively, were predicted with the criteria that a single target gene can be targeted by different miRNAs and that a single miRNA can also have a large number of target genes. Three targets were even found to be targeted by 13 novel miRNAs that contained the same complete miRNA sequence at different locations and had different scaffolds. The proteins predicted to be targeted by the miRNAs identified in this study encompass a wide range of transcription factors and are involved in many biological processes and pathways, including development, metabolism, stress responses and signal transduction. A total of 115 and 101 target genes were identified to be cleaved by 60 known miRNAs and 27 novel miRNAs through degradome sequencing, respectively. These miRNAs induce cleavage of their targets precisely at the position between nucleotides 10 and 11 of the miRNA sequences from the 5' to the 3' end. Thirty conserved miRNAs and 19 novel miRNAs exhibited differential expression profiles in the peach, and the expression patterns of some miRNAs appeared to be tissue- or developmental stage-specific. The findings of this study provide an important basis for the analysis of miRNAs, their targets and the functions of these targets in peach fruit.

Dataset Information

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

Publications

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

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