Wang Mengyao, Wang Jianbo
State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.
Front Plant Sci. 2022 Sep 26;13:990656. doi: 10.3389/fpls.2022.990656. eCollection 2022.
Heterosis has been used widespread in agriculture, but its molecular mechanism is inadequately understood. Plants have a large number of non-coding RNAs (ncRNAs), among them, functional ncRNAs that have been studied widely containing long non-coding RNA (lncRNA) and circular RNA (circRNA) that play a role in varied biological processes, as well as microRNA (miRNA), which can not only regulate the post-transcriptional expression of target genes, but also target lncRNA and circRNA then participate the competing endogenous RNA (ceRNA) regulatory network. However, the influence of these three ncRNAs and their regulatory relationships on heterosis is unknown in rice. In this study, the expression profile of ncRNAs and the ncRNA regulatory network related to heterosis were comprehensively analyzed in inter-subspecific hybrid rice. A total of 867 miRNAs, 3,278 lncRNAs and 2,521 circRNAs were identified in the hybrid and its parents. Analysis of the global profiles of these three types of ncRNAs indicated that significant differences existed in the distribution and sequence characteristics of the corresponding genes. The numbers of miRNA and lncRNA in hybrid were higher than those in its parents. A total of 784 ncRNAs (169 miRNAs, 573 lncRNAs and 42 circRNAs) showed differentially expressed in the hybrid, and their target/host genes were vital in stress tolerance, growth and development in rice. These discoveries suggested that the expression plasticity of ncRNA has an important role of inter-subspecific hybrid rice heterosis. It is worth mentioning that miRNAs exhibited substantially more variations between hybrid and parents compared with observed variation for lncRNA and circRNA. Non-additive expression ncRNAs and allele-specific expression genes-related ncRNAs in hybrid were provided in this study, and multiple sets of ncRNA regulatory networks closely related to heterosis were obtained. Meanwhile, heterosis-related regulatory networks of ceRNA (lncRNA and circRNA) and miRNA were also demonstrated.
杂种优势在农业中已被广泛应用，但其分子机制尚未得到充分了解。植物含有大量非编码RNA（ncRNA），其中，已被广泛研究的功能性ncRNA包括在各种生物学过程中发挥作用的长链非编码RNA（lncRNA）和环状RNA（circRNA），以及微小RNA（miRNA），miRNA不仅可以调节靶基因的转录后表达，还可以靶向lncRNA和circRNA，进而参与竞争性内源RNA（ceRNA）调控网络。然而，这三种ncRNA及其调控关系对水稻杂种优势的影响尚不清楚。在本研究中，对亚种间杂交水稻中ncRNA的表达谱及其与杂种优势相关的调控网络进行了综合分析。在杂种及其亲本中总共鉴定出867个miRNA、3278个lncRNA和2521个circRNA。对这三种类型ncRNA的整体图谱分析表明，相应基因的分布和序列特征存在显著差异。杂种中miRNA和lncRNA的数量高于其亲本。共有784个ncRNA（169个miRNA、573个lncRNA和42个circRNA）在杂种中差异表达，它们的靶标/宿主基因对水稻的胁迫耐受性、生长和发育至关重要。这些发现表明，ncRNA的表达可塑性对亚种间杂交水稻杂种优势具有重要作用。值得一提的是，与lncRNA和circRNA相比，杂种与亲本之间miRNA表现出更多的差异。本研究提供了杂种中非加性表达的ncRNA和与等位基因特异性表达基因相关的ncRNA，并获得了多套与杂种优势密切相关的ncRNA调控网络。同时，还展示了ceRNA（lncRNA和circRNA）与miRNA的杂种优势相关调控网络。
