Genome re-sequencing reveals the evolutionary history of peach fruit edibility

Yang Yu, Jun Fu, Yaoguang Xu, Jiewei Zhang, Fei Ren, Hongwei Zhao, Shilin Tian, Wei Guo, Xiaolong Tu, Jing Zhao, Dawei Jiang, Jianbo Zhao, Weiying Wu, Gaochao Wang, Rongcai Ma, Quan Jiang (), Jianhua Wei () and Hua Xie ()
Additional contact information
Yang Yu: Beijing Academy of Agricultural and Forestry Sciences
Jun Fu: Beijing 8omics Gene Technology Co. Ltd
Yaoguang Xu: Beijing Academy of Agricultural and Forestry Sciences
Jiewei Zhang: Beijing Academy of Agricultural and Forestry Sciences
Fei Ren: Beijing Academy of Agricultural and Forestry Sciences
Hongwei Zhao: Beijing 8omics Gene Technology Co. Ltd
Shilin Tian: Novogene Bioinformatics Institute
Wei Guo: Beijing 8omics Gene Technology Co. Ltd
Xiaolong Tu: Beijing Academy of Agricultural and Forestry Sciences
Jing Zhao: Novogene Bioinformatics Institute
Dawei Jiang: Novogene Bioinformatics Institute
Jianbo Zhao: Beijing Academy of Agricultural and Forestry Sciences
Weiying Wu: Beijing Academy of Agricultural and Forestry Sciences
Gaochao Wang: Beijing 8omics Gene Technology Co. Ltd
Rongcai Ma: Beijing Academy of Agricultural and Forestry Sciences
Quan Jiang: Beijing Academy of Agricultural and Forestry Sciences
Jianhua Wei: Beijing Academy of Agricultural and Forestry Sciences
Hua Xie: Beijing Academy of Agricultural and Forestry Sciences

Nature Communications, 2018, vol. 9, issue 1, 1-13

Abstract: Abstract Peach (Prunus persica) is an economically important fruit crop and a well-characterized model for studying Prunus species. Here we explore the evolutionary history of peach using a large-scale SNP data set generated from 58 high-coverage genomes of cultivated peach and closely related relatives, including 44 newly re-sequenced accessions and 14 accessions from a previous study. Our analyses suggest that peach originated about 2.47 Mya in southwest China in glacial refugia generated by the uplift of the Tibetan plateau. Our exploration of genomic selection signatures and demographic history supports the hypothesis that frugivore-mediated selection occurred several million years before the eventual human-mediated domestication of peach. We also identify a large set of SNPs and/or CNVs, and candidate genes associated with fruit texture, taste, size, and skin color, with implications for genomic-selection breeding in peach. Collectively, this study provides valuable information for understanding the evolution and domestication of perennial fruit tree crops.

Date: 2018
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DOI: 10.1038/s41467-018-07744-3

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