Genome sequencing of ‘Fuji’ apple clonal varieties reveals genetic mechanism of the spur-type morphology
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 propaga...
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Nature Portfolio
2024-11-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-54428-2 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Yudong Cai |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-5cf25860e9b44f278a3e9d9ff64ef9fa |
| institution | OA Journals |
| issn | 2041-1723 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-5cf25860e9b44f278a3e9d9ff64ef9fa2025-08-20T02:33:31ZengNature PortfolioNature Communications2041-17232024-11-0115111410.1038/s41467-024-54428-2Genome sequencing of ‘Fuji’ apple clonal varieties reveals genetic mechanism of the spur-type morphologyYudong Cai0Xiuhua Gao1Jiangping Mao2Yu Liu3Lu Tong4Xilong Chen5Yandong Liu6Wenyan Kou7Chuanjun Chang8Toshi Foster9Jialong Yao10Amandine Cornille11Muhammad Mobeen Tahir12Zhi Liu13Zhongye Yan14Siyi Lin15Fengwang Ma16Juanjuan Ma17Libo Xing18Na An19Xiya Zuo20Yanrong Lv21Zhengyang Zhao22Wenqiang Li23Qianjin Li24Caiping Zhao25Yanan Hu26Hangkong Liu27Chao Wang28Xueyan Shi29Doudou Ma30Zhangjun Fei31Yu Jiang32Dong Zhang33College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Animal Science and Technology, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityThe New Zealand Institute for Plant and Food Research Ltd, Private Bag 92169The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92169Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE-Le MoulonCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityLiaoning Institute of PolomogyLiaoning Institute of PolomogyCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityChina Apple Research System Xian Guoyou AssociationApple Industry R&D Center of Luochuan CountyCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityBoyce Thompson Institute, Cornell UniversityCollege of Animal Science and Technology, Northwest A&F UniversityCollege of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Northwest A&F UniversityAbstract 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.https://doi.org/10.1038/s41467-024-54428-2 |
| spellingShingle | 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 Genome sequencing of ‘Fuji’ apple clonal varieties reveals genetic mechanism of the spur-type morphology Nature Communications |
| title | Genome sequencing of ‘Fuji’ apple clonal varieties reveals genetic mechanism of the spur-type morphology |
| title_full | Genome sequencing of ‘Fuji’ apple clonal varieties reveals genetic mechanism of the spur-type morphology |
| title_fullStr | Genome sequencing of ‘Fuji’ apple clonal varieties reveals genetic mechanism of the spur-type morphology |
| title_full_unstemmed | Genome sequencing of ‘Fuji’ apple clonal varieties reveals genetic mechanism of the spur-type morphology |
| title_short | Genome sequencing of ‘Fuji’ apple clonal varieties reveals genetic mechanism of the spur-type morphology |
| title_sort | genome sequencing of fuji apple clonal varieties reveals genetic mechanism of the spur type morphology |
| url | https://doi.org/10.1038/s41467-024-54428-2 |
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