Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
文献类型： 外文期刊
作者： Hu, Shaoqiang 1 ; Zeng, Xiangguo 2 ; Liu, Yuguo 1 ; Li, Yongping 4 ; Qu, Minghao 5 ; Jiao, Wen-Biao 1 ; Han, Yongchao 2 ; Kang, Chunying 1 ;
作者机构： 1.Huazhong Agr Univ, Natl Key Lab Germplasm Innovat Utilizat Hort Crops, Wuhan 430070, Peoples R China
2.Hubei Acad Agr Sci, Inst Ind Crops, Hubei Key Lab Vegetable Germplasm Enhancement & Ge, Wuhan 430063, Peoples R China
3.Hubei Hongshan Lab, Wuhan 430070, Peoples R China
4.Hainan Univ, Sch Breeding & Multiplicat, Sanya 572025, Peoples R China
5.Chinese Acad Sci, Innovat Acad Seed Design, Plant Germplasm Res Ctr, Key Lab Plant Germplasm Enhancement & Specialty Ag, Wuhan 430074, Hubei, Peoples R China
期刊名称：GENOME RESEARCH （ 影响因子：5.5； 五年影响因子：7.3 ）
ISSN： 1088-9051
年卷期： 2024 年 34 卷 10 期
页码：
收录情况： SCI
摘要： Somatic mutations arise and accumulate during tissue culture and vegetative propagation, potentially affecting various traits in horticultural crops, but their characteristics are still unclear. Here, somatic mutations in regenerated woodland strawberry derived from tissue culture of shoot tips under different conditions and 12 cultivated strawberry individuals are analyzed by whole genome sequencing. The mutation frequency of single nucleotide variants is significantly increased with increased hormone levels or prolonged culture time in the range of 3.3 x 10-8-3.0 x 10-6 mutations per site. CG methylation shows a stable reduction (0.71%-8.03%) in regenerated plants, and hypoCG-DMRs are more heritable after sexual reproduction. A high-quality haplotype-resolved genome is assembled for the strawberry cultivar "Beni hoppe." The 12 "Beni hoppe" individuals randomly selected from different locations show 4731-6005 mutations relative to the reference genome, and the mutation frequency varies among the subgenomes. Our study has systematically characterized the genetic and epigenetic variants in regenerated woodland strawberry plants and different individuals of the same strawberry cultivar, providing an accurate assessment of somatic mutations at the genomic scale and nucleotide resolution in plants.
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