DNA methylation is a stable epigenetic mark that plays a crucial role in plant life processes. However, the specific functions of DNA methylation in grape berry development remain largely unknown. In this study, we performed whole-genome bisulfite sequencing on “Kyoho” grape and its early-ripening bud mutant “Fengzao” at different developmental stages. Our results revealed that transposons (TEs) and gene flanking regions exhibited high levels of methylation, particularly in “Fengzao”, attributed to CHH site methylation. Interestingly, the methylation patterns in these two cultivars showed distinct dynamics during berry development. While methylation levels of genes and TEs increased gradually in “Kyoho” throughout berry development, “Fengzao” did not display consistent changes. Notably, “Fengzao” exhibited higher methylation levels in promoters compared to “Kyoho”, suggesting that hypermethylation of promoters may contribute to its early ripening phenotype. Integration of methylome and transcriptome data highlighted differentially methylated genes (DMGs) and expressed genes (DEGs) associated with secondary metabolite biosynthesis, with 38 genes identified as potential candidates involved in grape berry development. Furthermore, the study identified a jasmonate-induced oxygenase gene (JOX1) as a negative regulator of ripening in Arabidopsis and grapes, indicating that hypermethylation of JOX1 may play a role in the early ripening of “Fengzao”. Overall, our findings provide insights into the distinct DNA methylation patterns during grape berry development, shedding light on the epigenetic regulatory mechanisms underlying the early-ripening bud mutant.

中文翻译：

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CHH 高甲基化有助于“巨峰”及其芽突变体的 DNA 甲基化组景观揭示的葡萄的早期成熟


DNA 甲基化是一种稳定的表观遗传标记，在植物生命过程中起着至关重要的作用。然而，DNA 甲基化在葡萄浆果发育中的具体功能在很大程度上仍然未知。本研究对 “巨峰” 葡萄及其早熟芽突变体 “风早” 在不同发育阶段进行了全基因组亚硫酸氢盐测序。我们的结果显示，转座子 （TE） 和基因侧翼区域表现出高水平的甲基化，尤其是在 “Fengzao” 中，这归因于 CHH 位点甲基化。有趣的是，这两个品种的甲基化模式在浆果发育过程中显示出不同的动态。虽然在整个浆果发育过程中，“巨峰”基因和 TE 的甲基化水平逐渐增加，但“丰早”并未表现出一致的变化。值得注意的是，与 “Kyoho” 相比，“Fengzao” 在启动子中表现出更高的甲基化水平，表明启动子的高甲基化可能有助于其早期成熟表型。甲基化组和转录组数据的整合突出了与次生代谢物生物合成相关的差异甲基化基因 （DMG） 和表达基因 （DEG），其中 38 个基因被确定为参与葡萄浆果发育的潜在候选基因。此外，该研究发现茉莉酸钠诱导的加氧酶基因 （JOX1） 是拟南芥和葡萄成熟的负调节因子，表明 JOX1 的高甲基化可能在“风藻”的早期成熟中发挥作用。总体而言，我们的研究结果为葡萄浆果发育过程中不同的 DNA 甲基化模式提供了见解，阐明了早熟芽突变体背后的表观遗传调控机制。