Nature Communications (Nov 2024)
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,
- Dong Zhang
Affiliations
- Yudong Cai
- College 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 University
- Xiuhua Gao
- College 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 University
- Jiangping Mao
- College 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 University
- Yu Liu
- College 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 University
- Lu Tong
- College 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 University
- Xilong Chen
- College 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 University
- Yandong Liu
- College 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 University
- Wenyan Kou
- College of Animal Science and Technology, Northwest A&F University
- Chuanjun Chang
- College 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 University
- Toshi Foster
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92169
- Jialong Yao
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92169
- Amandine Cornille
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon
- Muhammad Mobeen Tahir
- College 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 University
- Zhi Liu
- Liaoning Institute of Polomogy
- Zhongye Yan
- Liaoning Institute of Polomogy
- Siyi Lin
- College 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 University
- Fengwang Ma
- College 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 University
- Juanjuan Ma
- College 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 University
- Libo Xing
- College 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 University
- Na An
- College 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 University
- Xiya Zuo
- College 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 University
- Yanrong Lv
- College 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 University
- Zhengyang Zhao
- College 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 University
- Wenqiang Li
- China Apple Research System Xian Guoyou Association
- Qianjin Li
- Apple Industry R&D Center of Luochuan County
- Caiping Zhao
- College 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 University
- Yanan Hu
- College 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 University
- Hangkong Liu
- College 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 University
- Chao Wang
- College 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 University
- Xueyan Shi
- College 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 University
- Doudou Ma
- College 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 University
- Zhangjun Fei
- Boyce Thompson Institute, Cornell University
- Yu Jiang
- College of Animal Science and Technology, Northwest A&F University
- Dong Zhang
- College 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 University
- DOI
- https://doi.org/10.1038/s41467-024-54428-2
- Journal volume & issue
-
Vol. 15,
no. 1
pp. 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.
