Apple bud sports enable a rich resource for clonal selection of numerous elite cultivars. The accumulation of somatic mutations as plants develop may potentially impact the emergence of bud sport. Previous studies focused on the somatic mutation in the essential genes associated with the bud sport. However, the rate and function of genome-wide somatic mutations that accumulate when bud sport arises remain unclear. In this study, we identified a bud sport as a branch from a ten-year-old tree of the apple cultivar ‘Oregon Spur II’. The mutant branch showed reduced red coloration on fruit skin. Using these plant materials, we assembled a high-quality haplotype reference genome consisting of 649.61 Mb sequences with a contig N50 value of 2.04 Mb. We then estimated the somatic mutation rate of the apple tree being 4.56×10-8 per base per year, and further identified 253 somatic SNPs, including five nonsynonymous SNPs, between original type and mutant samples. Transcriptome analyses identified 69 differentially expressed genes (DEGs) between original type and mutant fruit skin were highly correlated with anthocyanin content. DNA methylation in the promoter of five anthocyanin associated genes was increased in the mutant compared to the original type as determined using DNA methylation profiling. Among genetic and epigenetic factors that directly and indirectly influence anthocyanin content in the mutant apple fruit skin, the hypermethylated promoter of MdMYB10 is an important factor. This study indicated that numerous somatic mutations accumulated at the emergence of bud sport from a genome-wide perspective, some of which contribute to the low coloration bud sport.

中文翻译：

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多组学分析揭示 MdMYB10 高甲基化是苹果果实颜色芽运动的原因

苹果芽运动为众多精英品种的克隆选择提供了丰富的资源。随着植物发育，体细胞突变的积累可能会影响芽运动的出现。先前的研究重点是与芽运动相关的必需基因的体细胞突变。然而，芽运动出现时积累的全基因组体细胞突变的速率和功能仍不清楚。在这项研究中，我们将芽运动鉴定为苹果品种“Oregon Spur II”的一棵十年树的树枝。突变枝条的果皮红色着色减少。使用这些植物材料，我们组装了一个高质量的单倍型参考基因组，由 649.61 Mb 序列组成，重叠群 N50 值为 2.04 Mb。然后我们估计苹果树的体细胞突变率为每年每个碱基4.56×10-8，并进一步在原始类型和突变样本之间鉴定了253个体细胞SNP，其中包括5个非同义SNP。转录组分析发现，原始果皮和突变果皮之间的 69 个差异表达基因 (DEG) 与花青素含量高度相关。根据 DNA 甲基化分析确定，与原始类型相比，突变体中五个花青素相关基因的启动子中的 DNA 甲基化有所增加。在直接和间接影响突变苹果果皮花青素含量的遗传和表观遗传因素中，MdMYB10启动子的高甲基化是一个重要因素。这项研究表明，从全基因组的角度来看，芽运动出现时积累了许多体细胞突变，其中一些突变导致了芽运动的低着色。