Main conclusion Maize has a set of dark response genes, expression of which is influenced by multiple factor and varies with maize inbred lines but without germplasm specificity. Abstract The response to photoperiod is a common biological issue across the species kingdoms. Dark is as important as light in photoperiod. However, further in-depth understanding of responses of maize ( Zea mays ) to light and dark transition under photoperiod is hindered due to the lack of understanding of dark response genes. With multiple public “-omic” datasets of temperate and tropical/subtropical maize, 16 maize dark response genes, ZmDRG s, were found and had rhythmic expression under dark and light–dark cycle. ZmDRG s 6 – 8 were tandemly duplicated. ZmDRG s 2 , 13 , and 14 had a chromosomal collinearity with other maize genes. ZmDRG s 1 – 11 and 13 – 16 had copy-number variations. ZmDRG s 2 , 9 , and 16 showed 5′-end sequence deletion mutations. Some ZmDRG s had chromatin interactions and underwent DNA methylation and/or m6A mRNA methylation. Chromosomal histones associated with 15 ZmDRG s were methylated and acetylated. ZmDRG s 1 , 2 , 4 , 9 , and 13 involved photoperiodic phenotypes. ZmDRG16 was within flowering-related QTLs. ZmDRG s 1 , 3 , and 6 – 11 were present in cis- acting expression QTLs (eQTLs). ZmDRG s 1 , 4 , 6 – 9 , 11 , 12 , and 14 – 16 showed co-expression with other maize genes. Some of ZmDRG -encoded ZmDRGs showed obvious differences in abundance and phosphorylation. Conclusion: Sixteen ZmDRG s 1 – 16 are associated with the dark response of maize. In the process of post-domestication and/or breeding, the ZmDRG s undergo the changes without germplasm specificity, including epigenetic modifications, gene copy numbers, chromatin interactions, and deletion mutations. In addition to effects by these factors, ZmDRG expression is influenced by promoter elements, cis -acting eQTLs, and co-expression networks.

中文翻译：

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暗反应基因：玉米中的一组内源性钟摆/计时参与者？

主要结论 玉米具有一组暗反应基因，其表达受多种因素影响，随玉米自交系而异，但无种质特异性。摘要 对光周期的反应是跨物种界的共同生物学问题。在光周期中，黑暗与光一样重要。然而，由于缺乏对暗反应基因的了解，进一步深入了解玉米在光周期下对明暗转变的反应受到阻碍。利用温带和热带/亚热带玉米的多个公共“组学”数据集，发现了 16 个玉米暗反应基因 ZmDRG s，并在暗和明暗循环下具有节律性表达。ZmDRG s 6 – 8 被串联复制。ZmDRG s 2 、 13 和 14 与其他玉米基因具有染色体共线性。ZmDRG s 1 – 11 和 13 – 16 有拷贝数变异。ZmDRG s 2 、 9 和 16 显示出 5'-末端序列缺失突变。一些 ZmDRG 具有染色质相互作用并经历 DNA 甲基化和/或 m6A mRNA 甲基化。与 15 个 ZmDRG 相关的染色体组蛋白被甲基化和乙酰化。ZmDRG s 1 、 2 、 4 、 9 和 13 涉及光周期表型。ZmDRG16 在开花相关的 QTL 内。ZmDRG s 1、3 和 6-11 存在于顺式表达 QTL (eQTL) 中。ZmDRG s 1 、 4 、 6 – 9 、 11 、 12 和 14 – 16 显示与其他玉米基因的共表达。一些 ZmDRG 编码的 ZmDRG 在丰度和磷酸化方面表现出明显的差异。结论：16 个 ZmDRG s 1 – 16 与玉米的暗反应有关。在驯化和/或繁殖后的过程中，ZmDRG 经历了没有种质特异性的变化，包括表观遗传修饰、基因拷贝数、染色质相互作用和缺失突变。除了这些因素的影响外，ZmDRG 表达还受到启动子元件、顺式作用 eQTL 和共表达网络的影响。