Grain filling is a crucial process for crop yield and quality. Certain studies already gained insight into the molecular mechanism of grain filling. However, it is unclear whether epigenetic modifications are associated with grain filling in foxtail millet. Global DNA methylation and transcriptome analysis were conducted in foxtail millet spikelets during different stages to interpret the epigenetic effects of the grain filling process. The study employed the whole-genome bisulfite deep sequencing and advanced bioinformatics to sequence and identify all DNA methylation during foxtail millet grain filling; the DNA methylation-mediated gene expression profiles and their involved gene network and biological pathway were systematically studied. One context of DNA methylation, namely, CHH methylation, was accounted for the largest percentage, and it was gradually increased during grain filling. Among all developmental stages, the methylation levels were lowest at T2, followed by T4, which mainly occurred in CHG. The distribution of differentially methylated regions (DMR) was varied in the different genetic regions for three contexts. In addition, gene expression was negatively associated with DNA methylation. Evaluation of the interconnection of the DNA methylome and transcriptome identified some stage-specific differentially expressed genes associated with the DMR at different stages compared with the T1 developmental stage, indicating the potential function of epigenetics on the expression regulation of genes related to the specific pathway at different stages of grain development. The results demonstrated that the dynamic change of DNA methylation plays a crucial function in gene regulation, revealing the potential function of epigenetics in grain development in foxtail millet.

中文翻译：

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DNA 甲基化和 RNA 测序分析显示谷子 (Setaria italica L.) 籽粒灌浆过程中的表观遗传功能。

灌浆是作物产量和质量的关键过程。某些研究已经深入了解了籽粒灌浆的分子机制。然而，尚不清楚表观遗传修饰是否与谷子的籽粒灌浆有关。对不同阶段的谷子小穗进行全局 DNA 甲基化和转录组分析，以解释籽粒灌浆过程的表观遗传效应。该研究采用全基因组亚硫酸氢盐深度测序和先进的生物信息学对谷子灌浆过程中的所有 DNA 甲基化进行测序和鉴定；系统地研究了DNA甲基化介导的基因表达谱及其涉及的基因网络和生物学途径。DNA甲基化的一种背景，即CHH甲基化，占最大比例，并在灌浆过程中逐渐增加。在所有发育阶段中，甲基化水平在 T2 时最低，其次是 T4，主要发生在 CHG。差异甲基化区域 (DMR) 的分布在三种情况下的不同遗传区域中有所不同。此外，基因表达与 DNA 甲基化呈负相关。对 DNA 甲基化组和转录组的相互联系的评估确定了与 T1 发育阶段相比在不同阶段与 DMR 相关的一些阶段特异性差异表达基因，表明表观遗传学对特定通路相关基因表达调控的潜在功能。粮食发展的不同阶段。