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 An, Xiya 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 () and Dong Zhang ()
Additional contact information
Yudong Cai: 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
Yu Jiang: Northwest A&F University
Dong Zhang: Northwest A&F University

Nature Communications, 2024, vol. 15, issue 1, 1-14

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-54428-2

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