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 × 10⁻⁸–3.0 × 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.

中文翻译：

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草莓营养繁殖过程中体细胞突变和 DNA 甲基化变化的全局表征


体细胞突变在组织培养和无性繁殖过程中产生和积累，可能影响园艺作物的各种性状，但其特征尚不清楚。在这里，通过全基因组测序分析了来自不同条件下笋尖组织培养的再生林地草莓和 12 个栽培草莓个体的体细胞突变。单核苷酸变异的突变频率随着激素水平的增加或培养时间的延长而显著增加，每个位点 3.3 × ^10-8-3.0 × ^10-6 个突变。CG 甲基化在再生植物中显示稳定降低 （0.71%–8.03%），并且 hypoCG-DMRs 在有性繁殖后更具遗传性。为草莓栽培品种 “Beni hoppe” 组装了一个高质量的单倍型分辨基因组。从不同位置随机选择的 12 个“Beni hoppe”个体相对于参考基因组显示出 4731-6005 个突变，并且突变频率因亚基因组而异。我们的研究系统地表征了再生林地草莓植物和同一草莓品种的不同个体的遗传和表观遗传变异，在基因组尺度和核苷酸分辨率上提供了对植物体细胞突变的准确评估。