Abstract Oxygen limitation under submerged condition induces hypoxic stress and causes a metabolic shift from aerobic respiration to anaerobic fermentation. Submergence stress often limits plant growth and causes substantial yield loss. The present small RNA (sRNA) transcriptome study aims to identify and characterise submergence responsive miRNAs to delineate the response mechanisms of maize seedlings to complete submergence. In this study, we constructed two sRNA libraries from control and submerged maize roots. Deep sequencing revealed 524 known (conserved and non-conserved) and 48 novel miRNAs from two libraries. Out of 188 commonly expressed known miRNAs, 45 miRNAs were found to be differentially expressed (43 down- and 2 up-regulated) in maize roots upon submergence. Submergence responsive miRNAs were found to be associated with diverse biological processes such as plant growth and development (miR172a, miR393b-3p), hormone signalling pathways (miR159c,f, miR160f-5p, miR167d-3p, miR172a, miR393a-5p), redox homeostasis (miR164a,b,c-5p, miR166h, a-3p, miR167e-3p.1), miRNA biogenesis (miR168a, miR168a-5p), chromatin remodeling (miR156a,g, miR159f, miR827-3p), and protein transport (miR156d-3p, miR159c,f, miR169c-3p). Moreover, dynamic correlations between selected miRNAs and their target genes were validated by qRT-PCR. The miR172a mediated upregulation of ERTF RAP2-7 ISOFORM X2 might be a pre-requisite for shifting of aerobic respiration to a less efficient anaerobic fermentation leading to restricted plant growth under flooded condition. To further understand the overall modulation of antioxidant defense system and metabolic adaptation strategy, fine tuning of ascorbate–glutathione cycle, anaerobic fermentation pathway genes, membrane damage, in vivo ROS detection and root MDA accumulation under flooding stress were also investigated in details. Taken together, our findings indicate that deregulation of ROS scavenging system might be the determining factor of meagre performance of maize seedlings under submerged condition. In a nutshell, our study adds new insights into the stress response mechanisms of maize seedlings towards submergence stress at post-transcriptional level.

中文翻译：

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玉米根sRNA转录组比较分析揭示miRNA在淹没胁迫响应机制中的调控作用

摘要 淹没条件下的氧气限制会引起缺氧应激，并导致代谢从有氧呼吸转变为厌氧发酵。淹水胁迫通常会限制植物生长并导致大量的产量损失。目前的小 RNA (sRNA) 转录组研究旨在鉴定和表征淹没响应 miRNA，以描绘玉米幼苗完全淹没的响应机制。在这项研究中，我们从对照和沉水玉米根构建了两个 sRNA 文库。深度测序揭示了来自两个文库的 524 个已知（保守和非保守）和 48 个新 miRNA。在 188 种常见表达的已知 miRNA 中，发现 45 种 miRNA 在浸水后在玉米根中差异表达（43 种下调和 2 种上调）。发现淹没响应 miRNA 与多种生物过程相关，例如植物生长和发育（miR172a、miR393b-3p）、激素信号通路（miR159c、f、miR160f-5p、miR167d-3p、miR172a、miR393a-5p）、氧化还原稳态（miR164a、b、c-5p、miR166h、a-3p、miR167e-3p.1）、miRNA 生物发生（miR168a、miR168a-5p）、染色质重塑（miR156a、g、miR159f、miR827-3p）、 （miR156d-3p、miR159c、f、miR169c-3p）。此外，通过 qRT-PCR 验证了所选 miRNA 与其靶基因之间的动态相关性。miR172a 介导的 ERTF RAP2-7 ISOFORM X2 上调可能是将有氧呼吸转变为效率较低的厌氧发酵的先决条件，从而导致水淹条件下植物生长受限。为了进一步了解抗氧化防御系统和代谢适应策略的整体调节，还详细研究了抗坏血酸-谷胱甘肽循环的微调、厌氧发酵途径基因、膜损伤、体内 ROS 检测和洪水胁迫下的根 MDA 积累。综上所述，我们的研究结果表明，ROS 清除系统的失调可能是淹没条件下玉米幼苗性能不佳的决定因素。简而言之，我们的研究为玉米幼苗在转录后水平对淹没胁迫的胁迫反应机制增加了新的见解。还详细研究了洪水胁迫下体内 ROS 检测和根 MDA 积累。综上所述，我们的研究结果表明，ROS 清除系统的失调可能是淹没条件下玉米幼苗性能不佳的决定因素。简而言之，我们的研究为玉米幼苗在转录后水平对淹没胁迫的胁迫反应机制增加了新的见解。还详细研究了洪水胁迫下体内 ROS 检测和根 MDA 积累。综上所述，我们的研究结果表明，ROS 清除系统的失调可能是淹没条件下玉米幼苗性能不佳的决定因素。简而言之，我们的研究为玉米幼苗在转录后水平对淹没胁迫的胁迫反应机制增加了新的见解。