Methylome and transcriptome analyses of apple fruit somatic mutations reveal the difference of red phenotype
Methylome and transcriptome analyses of apple fruit somatic mutations reveal the difference of red phenotype
复制标题
苹果果实体细胞突变的甲基化组和转录组分析揭示了红色表型的差异
DOI：
10.1186/s12864-019-5499-2
复制
发表时间：
2019-02-07
期刊：
影响因子：
4.4
通讯作者：
Chen, Xue-Sen
中科院分区：
文献类型：
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作者：
Jiang, Sheng-Hui;Sun, Qing-Guo;Chen, Xue-Sen
果皮颜色是果实品质的重要农艺性状。胞嘧啶甲基化在基因调控中发挥着重要作用。虽然单个基因的DNA甲基化水平对突变的表型有重要影响，但植物及其突变体的DNA甲基化差异还存在很大的未知数苹果突变体（盐辐3号，YF 3;盐辐8号，YF 8;山农红，SNH）和它们的浅色亲本（Nagafu 2，NF 2; Yanfu 3，YF 3; Ralls，RL）来探索与花青素苷浓度相关的甲基化模式的不同变化。我们在NF 2/YF 3、YF 3/YF 8和RL/SNH比较中分别鉴定了13，405、13，384和10，925个差异甲基化区域（DMR）和1987、956和1180个差异表达基因（DEG）。我们还发现两个与DMR相关的DEG参与了花青素途径：ANS（MD 06 G1071600）和F3 H（MD 05 G1074200）。这些基因在苹果突变体中表现出上调表达，并且在其启动子的甲基化模式中观察到差异。这些结果表明，调控基因和结构基因都可能被花青素途径中的DNA甲基化修饰。然而，结构基因的甲基化不是表达水平变化的主要原因。结构基因的表达可能受到转录因子和甲基化变化的协同调控。此外，转录因子MYB 114（MD 17 G1261100）在深红皮苹果中表达上调。结论通过甲基化和转录水平分析，未发现基因表达与DNA甲基化之间存在相关性。然而，我们观察到苹果突变体中ANS（MD 06 G1071600）和F3 H（MD 05 G1074200）的表达上调导致花青素含量增加。此外，MYB 114（MD 17 G1261100）可能是另一个参与苹果着色的调控基因。这些结果为苹果颜色突变体形成的差异提供了新的认识。
BackgroundFruit peel colour is an important agronomic trait for fruit quality. Cytosine methylation plays an important role in gene regulation. Although the DNA methylation level of a single gene is important to affect the phenotype of mutation, there are large unknown of difference of the DNA methylation in plant and its mutants.ResultsUsing bisulfite sequencing (BS-Seq) and RNA-sequencing (RNA-Seq), we analysed three deep-red-skinned apple (Malus×domestica) mutants (Yanfu 3, YF3; Yanfu 8, YF8; Shannonghong, SNH) and their lighter-skinned parents (Nagafu 2, NF2; Yanfu 3, YF3; Ralls, RL) to explore the different changes in methylation patterns associated with anthocyanin concentrations. We identified 13,405, 13,384, and 10,925 differentially methylated regions (DMRs) and 1987, 956, and 1180 differentially expressed genes (DEGs) in the NF2/YF3, YF3/YF8, and RL/SNH comparisons, respectively. And we found two DMR-associated DEGs involved in the anthocyanin pathway:ANS(MD06G1071600) andF3H(MD05G1074200). These genes exhibited upregulated expression in apple mutants, and differences were observed in the methylation patterns of their promoters. These results suggested that both the regulatory and structural genes may be modified by DNA methylation in the anthocyanin pathway. However, the methylation of structural genes was not the primary reason for expression-level changes. The expression of structural genes may be synergistically regulated by transcription factors and methylation changes. Additionally, the expression of the transcription factor geneMYB114(MD17G1261100) was upregulated in the deep-red-skinned apple.ConclusionThrough the analysis of global methylation and transcription, we did not find the correlation between gene expression and the DNA methylation. However, we observed that the upregulated expression ofANS(MD06G1071600) andF3H(MD05G1074200) in apple mutants results in increased anthocyanin contents. Moreover, MYB114 (MD17G1261100) is likely another regulatory gene involved in apple coloration. Our data provided a new understanding about the differences in formation of apple colour mutants.