National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China.
Int J Mol Sci. 2022 Aug 22;23(16):9472. doi: 10.3390/ijms23169472.
The discovery of long noncoding RNAs (lncRNAs) has filled a great gap in our understanding of posttranscriptional gene regulation in a variety of biological processes related to plant stress responses. However, systematic analyses of the lncRNAs expressed in rice seeds that germinate under cold stress have been elusive. In this study, we performed strand-specific whole transcriptome sequencing in germinated rice seeds under cold stress and normal temperature. A total of 6258 putative lncRNAs were identified and expressed in a stage-specific manner compared to mRNA. By investigating the targets of differentially expressed (DE) lncRNAs of LT-I (phase I of low temperature)/NT-I (phase I of normal temperature), it was shown that the auxin-activated signaling pathway was significantly enriched, and twenty-three protein-coding genes with most of the members of the SAUR family located in chromosome 9 were identified as the candidate target genes that may interact with five lncRNAs. A seed vigor-related lncRNA, SVR, which interplays with the members of the SAUR gene family in cis was eventually identified. The CRISPR/Cas 9 engineered mutations in SVR cause delay of germination. The findings provided new insights into the connection between lncRNAs and the auxin-activated signaling pathway in the regulation of rice seed vigor.
长链非编码 RNA（lncRNA）的发现填补了我们对植物应激反应相关多种生物学过程中转录后基因调控理解的空白。然而，系统分析在冷胁迫下萌发的水稻种子中表达的 lncRNA 仍然难以捉摸。在这项研究中，我们在冷胁迫和正常温度下对萌发的水稻种子进行了链特异性全转录组测序。与 mRNA 相比，总共鉴定出了 6258 个假定的 lncRNA，它们具有特定于阶段的表达模式。通过研究 LT-I（低温第一阶段）/NT-I（正常温度第一阶段）中差异表达（DE）lncRNA 的靶标，表明生长素激活的信号通路显著富集，并且鉴定出了 23 个与 SAUR 家族大多数成员位于 9 号染色体上的蛋白质编码基因作为可能与五个 lncRNA 相互作用的候选靶基因。最终鉴定出了一个与 SAUR 基因家族顺式相互作用的种子活力相关的 lncRNA SVR。SVR 的 CRISPR/Cas 9 工程突变导致萌发延迟。这些发现为 lncRNA 与生长素激活的信号通路在调控水稻种子活力中的联系提供了新的见解。
