Starch synthesis is an essential feature of crop filling, but knowledge of the molecular mechanisms regulating the expression of starch synthesis genes (SSGs) is currently limited to transcription factors (TFs). Here, we obtained transcriptome, small RNAome, and DNA methylome data from maize (Zea mays) endosperms during multiple developmental stages and established a regulatory network atlas of starch synthesis. Transcriptome analysis showed a sharp transition at 9–10 days after pollination, when genes involved in starch and sucrose metabolism are upregulated and starch accumulates rapidly. Expression pattern analysis established a comprehensive network between SSGs and TFs. During maize endosperm development, the miRNAs with preferential repression of the expression of TFs, particularly the TFs regulating SSG expression, were extensively downregulated. Specifically, ZmMYB138 and ZmMYB115 affected the transcriptional activities of Du1/Wx and Ae1/Bt2 genes at their respective promoter regions. Remarkably, the two TFs were negatively regulated by the copious expression of Zma‐miR159k‐3p at the post‐transcriptional level. This suggests that miRNAs are important regulators of starch synthesis. Moreover, with the exclusion of the TFs, the expression of both SSGs and miRNAs was globally regulated by DNA methylation. Altogether, the present results (i) establish the regulatory functions of miRNAs and DNA methylation in starch synthesis and (ii) indicate that DNA methylation functions as a master switch.

中文翻译：

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microRNA和DNA甲基化对玉米胚乳淀粉合成的调控

淀粉合成是农作物灌浆的重要特征，但是目前了解淀粉合成基因（SSGs）表达的分子机制知识仅限于转录因子（TFs）。在这里，我们从玉米（Zea mays）获得了转录组，小RNAome和DNA甲基化组数据。）胚乳在多个发育阶段，并建立了淀粉合成的调控网络图集。转录组分析显示，在授粉后9-10天，当淀粉和蔗糖代谢相关基因被上调并且淀粉迅速积累时，急剧转变。表达模式分析在SSG和TF之间建立了一个全面的网络。在玉米胚乳发育过程中，优先抑制TFs表达的miRNA，特别是调节SSG表达的TFs，被广泛下调。具体来说，ZmMYB138和ZmMYB115影响Du1 / Wx和Ae1 / Bt2的转录活性基因在其各自的启动子区域。值得注意的是，两个TF在转录后水平上受到Zma-miR159k-3p大量表达的负调控。这表明miRNA是淀粉合成的重要调节剂。此外，排除TF，SSG和miRNA的表达均受DNA甲基化的调节。总而言之，目前的结果（i）建立了miRNA的调控功能和淀粉合成中的DNA甲基化，并且（ii）表明DNA甲基化起着主开关的作用。