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Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses

Author

Listed:
  • Zhenchang Liang

    (Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Shengchang Duan

    (Yunnan Agricultural University
    Nowbio Biotechnology Company)

  • Jun Sheng

    (Yunnan Agricultural University
    Yunnan Research Institute for Local Plateau Agriculture and Industry
    Yunnan Agricultural University)

  • Shusheng Zhu

    (Yunnan Agricultural University
    Yunnan Agricultural University)

  • Xuemei Ni

    (BGI-Shenzhen
    BGI-Shenzhen)

  • Jianhui Shao

    (Yunnan Agricultural University)

  • Chonghuai Liu

    (Chinese Academy of Agricultural Sciences)

  • Peter Nick

    (Karlsruhe Institute of Technology)

  • Fei Du

    (Yunnan Agricultural University)

  • Peige Fan

    (Chinese Academy of Sciences)

  • Ruzhi Mao

    (Yunnan Agricultural University)

  • Yifan Zhu

    (Yunnan Agricultural University
    Yunnan Agricultural University)

  • Weiping Deng

    (Yunnan Agricultural University)

  • Min Yang

    (Yunnan Agricultural University)

  • Huichuan Huang

    (Yunnan Agricultural University)

  • Yixiang Liu

    (Yunnan Agricultural University)

  • Yiqing Ding

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Xianju Liu

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Jianfu Jiang

    (Chinese Academy of Agricultural Sciences)

  • Youyong Zhu

    (Yunnan Agricultural University
    Yunnan Research Institute for Local Plateau Agriculture and Industry
    Yunnan Agricultural University)

  • Shaohua Li

    (Chinese Academy of Sciences)

  • Xiahong He

    (Yunnan Agricultural University
    Yunnan Agricultural University)

  • Wei Chen

    (Yunnan Agricultural University
    Yunnan Research Institute for Local Plateau Agriculture and Industry)

  • Yang Dong

    (Yunnan Agricultural University
    Yunnan Research Institute for Local Plateau Agriculture and Industry)

Abstract

Understanding the Vitis species at the genomic level is important for cultivar improvement of grapevine. Here we report whole-genome genetic variation at single-base resolution of 472 Vitis accessions, which cover 48 out of 60 extant Vitis species from a wide geographic distribution. The variation helps to identify a recent dramatic expansion and contraction of effective population size in the domesticated grapevines and that cultivars from the pan-Black Sea region have a unique demographic history in comparison to the other domesticated cultivars. We also find selective sweeps for berry edibility and stress resistance improvement. Furthermore, we find associations between candidate genes and important agronomic traits, such as berry shape and aromatic compounds. These results demonstrate resource value of the resequencing data for illuminating the evolutionary biology of Vitis species and providing targets for grapevine genetic improvement.

Suggested Citation

  • Zhenchang Liang & Shengchang Duan & Jun Sheng & Shusheng Zhu & Xuemei Ni & Jianhui Shao & Chonghuai Liu & Peter Nick & Fei Du & Peige Fan & Ruzhi Mao & Yifan Zhu & Weiping Deng & Min Yang & Huichuan H, 2019. "Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-09135-8
    DOI: 10.1038/s41467-019-09135-8
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    Cited by:

    1. Sylvain Aubry, 2023. "Genebanking plant genetic resources in the postgenomic era," Agriculture and Human Values, Springer;The Agriculture, Food, & Human Values Society (AFHVS), vol. 40(3), pages 961-971, September.

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