Food Science and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China.
National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan.
Mol Biol Rep. 2023 Sep;50(9):7381-7392. doi: 10.1007/s11033-023-08648-2. Epub 2023 Jul 14.
Alkaline-salt is one of the abiotic stresses that slows plant growth and developmental processes and threatens crop yield. Long non-coding RNAs (lncRNAs) are endogenous RNA found in plants that engage in a variety of cellular functions and stress responses.
lncRNAs act as competing endogenous RNAs (ceRNA) and constitute a new set of gene control. The precise regulatory mechanism by which lncRNAs function as ceRNAs in response to alkaline-salt stress remains unclear. We identified alkaline-salt responsive lncRNAs using transcriptome-wide analysis of two varieties including alkaline-salt tolerant [WD20342 (WD)] and alkaline-salt sensitive [Caidao (CD)] rice cultivar under control and alkaline-salt stress treated [WD20342 (WDT, and Caidao (CDT)] conditions.
Investigating the competitive relationships between mRNAs and lncRNAs, we next built a ceRNA network involving lncRNAs based on the ceRNA hypothesis. Expression profiles revealed that a total of 65, 34, and 1549 differentially expressed (DE) lncRNAs, miRNAs, and mRNAs were identified in alkaline-salt tolerant WD (Control) vs. WDT (Treated). Similarly, 75 DE-lncRNAs, 34 DE-miRNAs, and 1725 DE-mRNAs (including up-regulated and down-regulated) were identified in alkaline-salt sensitive CD (Control) vs. CDT (Treated), respectively. An alkaline-salt stress ceRNA network discovered 321 lncRNA-miRNA-mRNA triplets in CD and CDT, with 32 lncRNAs, 121 miRNAs, and 111 mRNAs. Likewise, 217 lncRNA-miRNA-mRNA triplets in WD and WDT revealed the NONOSAT000455-osa_miR5809b-LOC_Os11g01210 triplet with the highest degree as a hub node with the most significant positive correlation in alkaline-salt stress response.
The results of our investigation indicate that osa-miR5809b is dysregulated and plays a part in regulating the defense response of rice against alkaline-salt stress. Our study highlights the regulatory functions of lncRNAs acting as ceRNAs in the mechanisms underlying alkaline-salt resistance in rice.
碱性盐是一种非生物胁迫，它会减缓植物的生长和发育过程，威胁作物产量。长链非编码 RNA（lncRNA）是植物中发现的内源性 RNA，参与多种细胞功能和应激反应。
lncRNA 作为竞争性内源 RNA（ceRNA），构成了一组新的基因调控因子。lncRNA 作为 ceRNA 响应碱性盐胁迫的确切调控机制尚不清楚。我们使用包括耐碱性盐[WD20342（WD）]和碱性盐敏感[Caidao（CD）]水稻品种在内的转录组全分析，在对照和碱性盐胁迫处理[WD20342（WDT 和 Caidao（CDT）]条件下，鉴定了碱性盐响应的 lncRNA。
在研究 mRNAs 和 lncRNAs 之间的竞争关系后，我们根据 ceRNA 假说构建了一个基于 lncRNA 的 ceRNA 网络。表达谱分析显示，在碱性盐耐受 WD（对照）与 WDT（处理）之间，共鉴定出 65、34 和 1549 个差异表达（DE）lncRNA、miRNA 和 mRNA。同样，在碱性盐敏感 CD（对照）与 CDT（处理）之间，分别鉴定出 75 个 DE-lncRNA、34 个 DE-miRNA 和 1725 个 DE-mRNA（包括上调和下调）。在 CD 和 CDT 中，碱性盐胁迫 ceRNA 网络发现了 321 个 lncRNA-miRNA-mRNA 三联体，其中包括 32 个 lncRNA、121 个 miRNA 和 111 个 mRNA。同样，在 WD 和 WDT 中，217 个 lncRNA-miRNA-mRNA 三联体揭示了 NONOSAT000455-osa_miR5809b-LOC_Os11g01210 三联体作为一个具有最高度的节点，与碱性盐胁迫反应中最显著的正相关。
我们的研究结果表明，osa-miR5809b 是失调的，并在调节水稻对碱性盐胁迫的防御反应中发挥作用。我们的研究强调了 lncRNA 作为 ceRNA 在水稻耐碱性盐机制中的调控作用。
