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

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, Zhongye Yan, Siyi Lin, Fengwang Ma, Juanjuan Ma, Libo Xing, Na AnXiya Zuo, Yanrong Lv, Zhengyang Zhao, Wenqiang Li, Qianjin Li, Caiping Zhao, Yanan Hu, Hangkong Liu, Chao Wang, Xueyan Shi, Doudou Ma, Zhangjun Fei, Yu Jiang, Dong Zhang

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Article number10082
JournalNature communications
Volume15
Issue number1
DOIs
StatePublished - Dec 2024

ASJC Scopus subject areas

  • General Chemistry
  • General Biochemistry, Genetics and Molecular Biology
  • General Physics and Astronomy

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