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Analyzes of pan-genome and resequencing atlas unveil the genetic basis of jujube domestication

Author

Listed:
  • Mingxin Guo

    (Luoyang Normal University)

  • Qun Lian

    (Chinese Academy of Agricultural Sciences
    University College Dublin)

  • Ye Mei

    (Chinese Academy of Agricultural Sciences)

  • Wangwang Yang

    (Luoyang Normal University)

  • Suna Zhao

    (Luoyang Normal University)

  • Siyuan Zhang

    (Luoyang Normal University)

  • Xinfeng Xing

    (Luoyang Normal University)

  • Haixiang Zhang

    (Luoyang Normal University)

  • Keying Gao

    (Luoyang Normal University)

  • Wentong He

    (Bureau of Natural Resources and Planning of Cangxian County)

  • Zhitong Wang

    (Bureau of Natural Resources and Planning of Cangxian County)

  • Huan Wang

    (Chinese Academy of Agricultural Sciences)

  • Jun Zhou

    (North Minzu University)

  • Lin Cheng

    (Chinese Academy of Agricultural Sciences
    Gembloux Agro-Bio Tech)

  • Zhigui Bao

    (Chinese Academy of Agricultural Sciences)

  • Sanwen Huang

    (Chinese Academy of Agricultural Sciences)

  • Jianbin Yan

    (Chinese Academy of Agricultural Sciences)

  • Xusheng Zhao

    (Luoyang Normal University)

Abstract

Jujube (Ziziphus jujuba Mill.), belonging to the Rhamnaceae family, is gaining increasing prominence as a perennial fruit crop with significant economic and medicinal values. Here, we conduct de novo assembly of four reference-grade genomes, encompassing one wild and three cultivated jujube accessions. We present insights into the population structure, genetic diversity, and genomic variations within a diverse collection of 1059 jujube accessions. Analyzes of the jujube pan-genome, based on our four assemblies and four previously released genomes, reveal extensive genomic variations within domestication-associated regions, potentially leading to the discovery of a candidate gene that regulates flowering and fruit ripening. By leveraging the pan-genome and a large-scale resequencing population, we identify two candidate genes involved in domestication traits, including the seed-setting rate, the bearing-shoot length and the leaf size in jujube. These genomic resources will accelerate evolutionary and functional genomics studies of jujube.

Suggested Citation

  • Mingxin Guo & Qun Lian & Ye Mei & Wangwang Yang & Suna Zhao & Siyuan Zhang & Xinfeng Xing & Haixiang Zhang & Keying Gao & Wentong He & Zhitong Wang & Huan Wang & Jun Zhou & Lin Cheng & Zhigui Bao & Sa, 2024. "Analyzes of pan-genome and resequencing atlas unveil the genetic basis of jujube domestication," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-53718-z
    DOI: 10.1038/s41467-024-53718-z
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