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.
Original language | English (US) |
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Article number | 10082 |
Journal | Nature communications |
Volume | 15 |
Issue number | 1 |
DOIs | |
State | Published - Dec 2024 |
ASJC Scopus subject areas
- General Chemistry
- General Biochemistry, Genetics and Molecular Biology
- General Physics and Astronomy