Genome sequencing of ‘Fuji’ apple clonal varieties reveals genetic mechanism of the spur-type morphology
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.
Authors
- Na An (ORCID: https://orcid.org/0000-0002-7855-4447)
- Lu Tong (ORCID: https://orcid.org/0009-0009-9142-3327)
- Muhammad Mobeen Tahir (ORCID: https://orcid.org/0000-0001-7511-0608)
- Caiping Zhao (ORCID: https://orcid.org/0000-0001-6190-7931)
- Amandine Cornille (ORCID: https://orcid.org/0000-0002-5348-7081)
- Toshi Foster (ORCID: https://orcid.org/0000-0002-2829-4384)
- Hangkong Liu
- Fengwang Ma (ORCID: https://orcid.org/0000-0003-3890-2125)
- Juanjuan Ma (ORCID: https://orcid.org/0000-0002-6936-4772)
- Jiangping Mao (ORCID: https://orcid.org/0000-0002-1267-581X)
- Xiuhua Gao (ORCID: https://orcid.org/0000-0003-0267-0887)
- Xilong Chen (ORCID: https://orcid.org/0000-0003-1588-6564)
- Yanrong Lv
- Yu Jiang (ORCID: https://orcid.org/0000-0003-4821-3585)
- Libo Xing (ORCID: https://orcid.org/0000-0002-8918-7128)
- Xiya Zuo (ORCID: https://orcid.org/0000-0002-7707-7829)
- Zhangjun Fei (ORCID: https://orcid.org/0000-0001-9684-1450)
- Jia‐Long Yao (ORCID: https://orcid.org/0000-0003-2570-8139)
- Qianjin Li (ORCID: https://orcid.org/0000-0002-6498-7284)
- Zhengyang Zhao (ORCID: https://orcid.org/0000-0002-8017-3635)
- Wenyan Kou
- Yu Liu (ORCID: https://orcid.org/0009-0004-8411-1310)
- Wenqiang Li (ORCID: https://orcid.org/0000-0002-0833-246X)
- Dong Zhang (ORCID: https://orcid.org/0000-0003-1392-2971)
- Chao Wang (ORCID: https://orcid.org/0000-0002-6251-7908)
- Yudong Cai (ORCID: https://orcid.org/0000-0001-5902-0901)
- Zhi Liu (ORCID: https://orcid.org/0000-0002-8973-6561)
- Siyi Lin
- Chuanjun Chang (ORCID: https://orcid.org/0009-0009-7746-1247)
- Yandong Liu (ORCID: https://orcid.org/0000-0002-3035-9618)
- Xueyan Shi
- Yanan Hu (ORCID: https://orcid.org/0009-0004-6194-0693)
- Doudou Ma
- Zhongye Yan
Institutions
- Centre National de la Recherche Scientifique (FR)
- Plant & Food Research (NZ)
- Cornell University (US)
- AgroParisTech (FR)
- Université Paris-Saclay (FR)
- North West Agriculture and Forestry University (CN)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Génétique Quantitative et Évolution Le Moulon (FR)
- Robert W. Holley Center for Agriculture & Health (US)
- Northwest A&F University (CN)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-11-21
- DOI
- https://doi.org/10.1038/s41467-024-54428-2
- Citations
- 12
- Primary Topic
- Plant Reproductive Biology
- Type
- article
- Field-Weighted Citation Impact
- 2.81
Funders
- Cyrus Tang Foundation
- National Natural Science Foundation of China
- Shandong Agricultural University
- Northwest A and F University
- Huazhong Agricultural University
- Nanjing University
- Shenyang Agricultural University
- Xinjiang Production and Construction Corps
- National Key Research and Development Program of China