Deng Yang, Zhang Haolin, Wang Hailong, Xing Guofang, Lei Biao, Kuang Zheng, Zhao Yongxin, Li Congcong, Dai Shaojun, Yang Xiaozeng, Wei Jianhua, Zhang Jiewei
Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing, China.
Front Plant Sci. 2022 May 6;13:848474. doi: 10.3389/fpls.2022.848474. eCollection 2022.
MicroRNA (miRNA) is an essential endogenous post-transcriptional regulatory factor, and foxtail millet ( L.) is an ideal C4 model cereal that is a highly valuable crop in semiarid and arid areas. The Research on comprehensive and high confidence identification and annotation of foxtail millet miRNAs needs to be strengthened, and to our knowledge, there is no information on the regulatory network of foxtail millet miRNA. In this study, 136 high confidence miRNAs were identified through high-throughput sequencing of the small RNAs in seven tissues at the shooting and grain filling stages of foxtail millet. A total of 2,417 target genes were obtained by combining computational biology software and degradome sequencing methods. Furthermore, an analysis using transcriptome sequencing revealed the relationships between miRNAs and their target genes and simultaneously explored key regulatory modules in panicles during the grain filling stage. An miRNA regulatory network was constructed to explore the functions of miRNA in more detail. This network, centered on miRNAs and combining upstream transcriptional factors and downstream target genes, is primarily composed of feed forward loop motifs, which greatly enhances our knowledge of the potential functions of miRNAs and uncovers numerous previously unknown regulatory links. This study provides a solid foundation for research on the function and regulatory network of miRNAs in foxtail millet.
微小RNA（miRNA）是一种重要的内源性转录后调控因子，而谷子（Setaria italica (L.)）是一种理想的C4模式谷物，在半干旱和干旱地区是一种极具价值的作物。目前对谷子miRNA进行全面且高可信度的鉴定和注释的研究仍需加强，据我们所知，尚无关于谷子miRNA调控网络的信息。在本研究中，通过对谷子拔节期和灌浆期七个组织中的小RNA进行高通量测序，鉴定出136个高可信度的miRNA。结合计算生物学软件和降解组测序方法，共获得了2417个靶基因。此外，通过转录组测序分析揭示了miRNA与其靶基因之间的关系，并同时探索了灌浆期穗部的关键调控模块。构建了一个miRNA调控网络以更详细地探究miRNA的功能。这个以miRNA为中心，结合上游转录因子和下游靶基因的网络主要由前馈环基序组成，极大地增进了我们对miRNA潜在功能的了解，并揭示了许多以前未知的调控联系。本研究为谷子miRNA的功能和调控网络研究提供了坚实的基础。
