College of Agriculture, Yangtze University, Jingzhou, 434000, Hubei, China.
State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
BMC Plant Biol. 2024 Jun 12;24(1):534. doi: 10.1186/s12870-024-05234-x.
Waterlogging stress (WS) negatively impacts crop growth and productivity, making it important to understand crop resistance processes and discover useful WS resistance genes. In this study, rye cultivars and wild rye species were subjected to 12-day WS treatment, and the cultivar Secale cereale L. Imperil showed higher tolerance. Whole transcriptome sequencing was performed on this cultivar to identify differentially expressed (DE) messenger RNAs (DE-mRNAs) and long non-coding RNAs (DE-lncRNAs) involved in WS response.
Among the 6 species, Secale cereale L. Imperil showed higher tolerance than wild rye species against WS. The cultivar effectively mitigated oxidative stress, and regulated hydrogen peroxide and superoxide anion. A total of 728 DE-mRNAs and 60 DE-lncRNAs were discovered. Among these, 318 DE-mRNAs and 32 DE-lncRNAs were upregulated, and 410 DE-mRNAs and 28 DE-lncRNAs were downregulated. GO enrichment analysis discovered metabolic processes, cellular processes, and single-organism processes as enriched biological processes (BP). For cellular components (CC), the enriched terms were membrane, membrane part, cell, and cell part. Enriched molecular functions (MF) terms were catalytic activity, binding, and transporter activity. LncRNA and mRNA regulatory processes were mainly related to MAPK signaling pathway-plant, plant hormone signal transduction, phenylpropanoid biosynthesis, anthocyanin biosynthesis, glutathione metabolism, ubiquitin-mediated proteolysis, ABC transporter, Cytochrome b6/f complex, secondary metabolite biosynthesis, and carotenoid biosynthesis pathways. The signalling of ethylene-related pathways was not mainly dependent on AP2/ERF and WRKY transcription factors (TF), but on other factors. Photosynthetic activity was active, and carotenoid levels increased in rye under WS. Sphingolipids, the cytochrome b6/f complex, and glutamate are involved in rye WS response. Sucrose transportation was not significantly inhibited, and sucrose breakdown occurs in rye under WS.
This study investigated the expression levels and regulatory functions of mRNAs and lncRNAs in 12-day waterlogged rye seedlings. The findings shed light on the genes that play a significant role in rye ability to withstand WS. The findings from this study will serve as a foundation for further investigations into the mRNA and lncRNA WS responses in rye.
水淹胁迫（WS）会对作物生长和生产力产生负面影响，因此了解作物的抗性过程并发现有用的 WS 抗性基因非常重要。在这项研究中，对黑麦品种和野生黑麦种进行了 12 天的 WS 处理，品种 Secale cereale L. Imperil 表现出更高的耐受性。对该品种进行了全转录组测序，以鉴定参与 WS 反应的差异表达（DE）信使 RNA（DE-mRNA）和长非编码 RNA（DE-lncRNA）。
在 6 个物种中，Secale cereale L. Imperil 对 WS 的耐受性高于野生黑麦种。该品种有效缓解了氧化应激，调节了过氧化氢和超氧阴离子。共发现 728 个 DE-mRNA 和 60 个 DE-lncRNA。其中，318 个 DE-mRNA 和 32 个 DE-lncRNA 上调，410 个 DE-mRNA 和 28 个 DE-lncRNA 下调。GO 富集分析发现，代谢过程、细胞过程和单细胞过程是富含生物过程（BP）的过程。对于细胞成分（CC），富集的术语是膜、膜部分、细胞和细胞部分。富集的分子功能（MF）术语是催化活性、结合和转运活性。LncRNA 和 mRNA 调节过程主要与 MAPK 信号通路-植物、植物激素信号转导、苯丙烷生物合成、花青素生物合成、谷胱甘肽代谢、泛素介导的蛋白水解、ABC 转运体、细胞色素 b6/f 复合体、次生代谢物生物合成和类胡萝卜素生物合成途径有关。乙烯相关途径的信号转导并不主要依赖于 AP2/ERF 和 WRKY 转录因子（TF），而是依赖于其他因素。在 WS 下，黑麦的光合作用活性增强，类胡萝卜素水平升高。鞘脂类、细胞色素 b6/f 复合体和谷氨酸参与了黑麦 WS 反应。蔗糖运输没有受到显著抑制，WS 下黑麦的蔗糖分解发生。
本研究调查了 12 天水淹黑麦幼苗中 mRNA 和 lncRNA 的表达水平和调控功能。研究结果揭示了在黑麦耐 WS 能力中起重要作用的基因。本研究结果将为进一步研究黑麦中 mRNA 和 lncRNA 的 WS 反应奠定基础。
