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

IF 14.7 1区综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES Nature Communications Pub Date : 2024-11-21 DOI:10.1038/s41467-024-54428-2

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, Dong Zhang

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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.

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富士 "苹果克隆品种的基因组测序揭示了距型形态的遗传机制

体细胞变异可产生具有优势性状的芽变，是多年生植物芽变育种的基础。在这里，我们报告了'富士'苹果的全阶段基因组组装，从而能够全面鉴定 74 个克隆繁殖的'富士'品种的体细胞变异。系统发育分析表明，'富士'运动品种的距型和早熟性状来自多个独立事件。已鉴定出几种推定的功能性体细胞变异，包括 TCP 转录因子基因 MdTCP11 启动子中的距型特异性缺失。与标准型品种相比，马刺型品种中与缺失相关的微型倒位重复转座元件的DNA甲基化水平较低，而MdTCP11的表达量则明显较高。苹果中过量表达 MdTCP11 会降低植株高度，凸显了其在距型苹果品种发展中的重要作用。这项研究揭示了 "富士 "的克隆历史，为苹果育种提供了宝贵的资源。

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来源期刊

Nature Communications Biological Science Disciplines-

CiteScore

24.90

自引率

2.40%

发文量

6928

审稿时长

3.7 months

期刊介绍： Nature Communications, an open-access journal, publishes high-quality research spanning all areas of the natural sciences. Papers featured in the journal showcase significant advances relevant to specialists in each respective field. With a 2-year impact factor of 16.6 (2022) and a median time of 8 days from submission to the first editorial decision, Nature Communications is committed to rapid dissemination of research findings. As a multidisciplinary journal, it welcomes contributions from biological, health, physical, chemical, Earth, social, mathematical, applied, and engineering sciences, aiming to highlight important breakthroughs within each domain.