College of Horticulture Science and Engineering, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China.
State Key Laboratory of Crop Biology, Shandong Agricultural University, 61 Daizong Road, Tai'an, 271018, China.
BMC Genomics. 2019 Feb 7;20(1):117. doi: 10.1186/s12864-019-5499-2.
Fruit 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.
Using 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) and F3H (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 gene MYB114 (MD17G1261100) was upregulated in the deep-red-skinned apple.
Through 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 of ANS (MD06G1071600) and F3H (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.
果皮颜色是果实品质的一个重要农艺性状。胞嘧啶甲基化在基因调控中起着重要作用。虽然单个基因的 DNA 甲基化水平对突变表型的影响很重要，但植物及其突变体的 DNA 甲基化差异很大，还有很多未知之处。
利用亚硫酸氢盐测序（BS-Seq）和 RNA 测序（RNA-Seq），我们分析了三个深红色果皮苹果（Malus × domestica）突变体（Yanfu 3，YF3；Yanfu 8，YF8；Shannonghong，SNH）及其浅色果皮亲本（Nagafu 2，NF2；Yanfu 3，YF3；Ralls，RL），以探讨与花色苷浓度相关的甲基化模式的不同变化。我们在 NF2/YF3、YF3/YF8 和 RL/SNH 比较中分别鉴定了 13405、13384 和 10925 个差异甲基化区域（DMRs）和 1987、956 和 1180 个差异表达基因（DEGs）。我们发现两个与 DMR 相关的 DEGs 参与花色苷途径：ANS（MD06G1071600）和 F3H（MD05G1074200）。这些基因在苹果突变体中表现出上调表达，并且它们启动子的甲基化模式存在差异。这表明花色苷途径中的调节基因和结构基因都可能被 DNA 甲基化修饰。然而，结构基因的甲基化并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，深红色果皮苹果中 MYB114（MD17G1261100）转录因子基因的表达上调。
通过对全局甲基化和转录的分析，我们没有发现基因表达与 DNA 甲基化之间的相关性。然而，我们观察到苹果突变体中 ANS（MD06G1071600）和 F3H（MD05G1074200）的上调表达导致花色苷含量增加。此外，MYB114（MD17G1261100）可能是另一个参与苹果着色的调节基因。我们的数据提供了对苹果颜色突变体形成差异的新认识。
