College of Horticulture, Gansu Agricultural University, 730070, Lanzhou, People's Republic of China.
Planta. 2019 Dec;250(6):1833-1847. doi: 10.1007/s00425-019-03266-4. Epub 2019 Aug 30.
DNA methylation of anthocyanin biosynthesis-related genes and MYB/bHLH transcription factors was associated with apple fruit skin color revealed by whole-genome bisulfite sequencing. DNA methylation is a common feature of epigenetic regulation and is associated with various biological processes. Anthocyanins are among the secondary metabolites that contribute to fruit colour, which is a key appearance and nutrition quality attribute of apple fruit. Although few studies reported that DNA methylation in the promoter of MYB transcription factor was associated with fruit skin color, there is a general lack of understanding of the dynamics of global and genic DNA methylation in apple fruit. Here, whole-genome bisulfite sequencing was carried out in fruit skin of apple (Malus domestica Borkh.) cv. 'Red Delicious' (G0) and its four-generation bud sport mutants, including 'Starking Red' (G1), 'Starkrimson' (G2), 'Campbell Redchief' (G3) and 'Vallee spur' (G4) at color break stage. Correlation and linear-regression analysis between DNA methylation level and anthocyanin content, as well as the transcription levels of genes related to anthocyanin biosynthesis were carried out. The results showed that the number of differentially methylated regions (DMRs) and differentially methylated genes (DMGs) was considerably increased from G1 to G4 versus the number observed in G0. The CHH context was dominant in apple, but the levels of CG and CHG of DMGs were significantly higher than that of the CHH. Genetic variation of bud sport mutants from 'Red Delicious' was associated with differential DNA methylation. Additionally, hypomethylation of CG and CHG contexts in flavonoid biosynthesis pathway genes (PAL, 4CL, CYP98A, PER, CCoAOMT, CHS, and F3'H), CHG context in MYB10 at upstream, led to transcriptional activation and was conductive to anthocyanin accumulation. However, hypermethylation of CG context in bHLH74 at upstream led to transcriptional inhibition, inhibiting anthocyanin accumulation.
利用全基因组重亚硫酸盐测序揭示与苹果果实果皮颜色相关的花色苷生物合成相关基因和 MYB/bHLH 转录因子的 DNA 甲基化。DNA 甲基化是表观遗传调控的常见特征，与各种生物过程有关。花色苷是次生代谢物之一，有助于果实颜色的形成，这是苹果果实外观和营养品质的关键属性。尽管有少数研究报道 MYB 转录因子启动子中的 DNA 甲基化与果皮颜色有关，但人们对苹果果实中全基因组和基因 DNA 甲基化的动态缺乏了解。本研究在苹果（Malus domestica Borkh.）品种‘红元帅’（G0）及其四代芽变突变体果皮（包括‘斯达克红元帅’（G1）、‘斯达克宝石红’（G2）、‘坎贝尔红酋长’（G3）和‘瓦勒 spur’（G4））果实颜色转色期进行了全基因组重亚硫酸盐测序。对 DNA 甲基化水平与花色苷含量以及花色苷生物合成相关基因转录水平之间的相关性和线性回归分析。结果表明，与 G0 相比，G1 到 G4 的差异甲基化区（DMR）和差异甲基化基因（DMG）数量明显增加。苹果中 CHH 为主要的甲基化类型，但 DMG 的 CG 和 CHG 水平显著高于 CHH。‘红元帅’芽变突变体的遗传变异与差异 DNA 甲基化有关。此外，类黄酮生物合成途径基因（PAL、4CL、CYP98A、PER、CCoAOMT、CHS 和 F3'H）中 CG 和 CHG 区的去甲基化以及 MYB10 上游 CHG 区的低甲基化导致转录激活，有助于花色苷积累。然而，bHLH74 上游 CG 区的超甲基化导致转录抑制，抑制花色苷积累。
