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Genome sequencing of ‘Fuji’ apple clonal varieties reveals genetic mechanism of the spur-type morphology

Author

Listed:
  • Yudong Cai

    (Northwest A&F University
    Northwest A&F University)

  • Xiuhua Gao

    (Northwest A&F University)

  • Jiangping Mao

    (Northwest A&F University)

  • Yu Liu

    (Northwest A&F University)

  • Lu Tong

    (Northwest A&F University)

  • Xilong Chen

    (Northwest A&F University)

  • Yandong Liu

    (Northwest A&F University)

  • Wenyan Kou

    (Northwest A&F University)

  • Chuanjun Chang

    (Northwest A&F University)

  • Toshi Foster

    (Private Bag 92169)

  • Jialong Yao

    (Private Bag 92169)

  • Amandine Cornille

    (GQE-Le Moulon)

  • Muhammad Mobeen Tahir

    (Northwest A&F University)

  • Zhi Liu

    (Liaoning Institute of Polomogy)

  • Zhongye Yan

    (Liaoning Institute of Polomogy)

  • Siyi Lin

    (Northwest A&F University)

  • Fengwang Ma

    (Northwest A&F University)

  • Juanjuan Ma

    (Northwest A&F University)

  • Libo Xing

    (Northwest A&F University)

  • Na An

    (Northwest A&F University)

  • Xiya Zuo

    (Northwest A&F University)

  • Yanrong Lv

    (Northwest A&F University)

  • Zhengyang Zhao

    (Northwest A&F University)

  • Wenqiang Li

    (China Apple Research System Xian Guoyou Association)

  • Qianjin Li

    (Apple Industry R&D Center of Luochuan County)

  • Caiping Zhao

    (Northwest A&F University)

  • Yanan Hu

    (Northwest A&F University)

  • Hangkong Liu

    (Northwest A&F University)

  • Chao Wang

    (Northwest A&F University)

  • Xueyan Shi

    (Northwest A&F University)

  • Doudou Ma

    (Northwest A&F University)

  • Zhangjun Fei

    (Cornell University
    Robert W. Holley Center for Agriculture and Health)

  • Yu Jiang

    (Northwest A&F University)

  • Dong Zhang

    (Northwest A&F University)

Abstract

Somatic variations can give rise to bud sports with advantageous traits, serving as the foundation for bud sport breeding in perennial plants. Here, we report a fully phased genome assembly of ‘Fuji’ apple, enabling comprehensive identification of somatic variants across 74 clonally propagated ‘Fuji’ varieties. Phylogenetic analysis indicates that spur-type and early-maturation traits in ‘Fuji’ sport varieties arise from multiple independent events. Several putative functional somatic variants have been identified, including a spur-type-specific deletion in the promoter of the TCP transcription factor gene MdTCP11. DNA methylation level of the deletion-associated miniature inverted-repeat transposable element is lower in spur-type varieties compared to standard-type varieties, while the expression of MdTCP11 is significantly higher. Overexpression of MdTCP11 in apple decreases plant height, highlighting its important role in the development of spur-type apple varieties. This study sheds light on the cloning history of ‘Fuji’ and provides valuable resources for apple breeding.

Suggested Citation

  • Yudong Cai & Xiuhua Gao & Jiangping Mao & Yu Liu & Lu Tong & Xilong Chen & Yandong Liu & Wenyan Kou & Chuanjun Chang & Toshi Foster & Jialong Yao & Amandine Cornille & Muhammad Mobeen Tahir & Zhi Liu , 2024. "Genome sequencing of ‘Fuji’ apple clonal varieties reveals genetic mechanism of the spur-type morphology," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-54428-2
    DOI: 10.1038/s41467-024-54428-2
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    References listed on IDEAS

    as
    1. Nick Patterson & Alkes L Price & David Reich, 2006. "Population Structure and Eigenanalysis," PLOS Genetics, Public Library of Science, vol. 2(12), pages 1-20, December.
    2. Hannes P. Eggertsson & Snaedis Kristmundsdottir & Doruk Beyter & Hakon Jonsson & Astros Skuladottir & Marteinn T. Hardarson & Daniel F. Gudbjartsson & Kari Stefansson & Bjarni V. Halldorsson & Pall Me, 2019. "GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs," Nature Communications, Nature, vol. 10(1), pages 1-8, December.
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