Abstract Seed-flooding stress is one of the most important constraints that affects the yield and quality of soybean. However, very little is known about the molecular mechanisms underlying seed-flooding tolerance. Hence, the present study investigated the transcriptome profile in root tissues of two contrasting soybean genotypes viz., PI342618B/SFT-tolerant, and NN86-4/SFS-sensitive under seed-flooding stress using RNA-Seq approach. A total of 1563 and 1958 differentially expressed genes (DEGs) were identified in SFT-tolerant and SFS-sensitive, respectively suggesting that the former is less affected by flooding stress. Both Gene ontology (GO) enrichment and MapMan pathway analyses revealed that response to seed-flooding stress was mostly enriched in the DEGs that are involved in the cell wall, antioxidant activity, catalytic and transcription factor activities as well as protein metabolism and signaling. Based on gene annotation, GO enrichment and protein-protein interaction (PPI) network analysis, a total of 807 DEGs were screened from the above terms related to the stress including response to stress, defense response and response to stimulus for candidate gene prediction analysis. Out of them, 51 genes revealing significant opposite gene expression pattern between tolerant and sensitive genotypes along with GmERFVII1, GmERFVII2 & GmERFVII3 and MAPK1 were predicted as the possible candidate genes for further analysis. Using quantitative real-time RT-PCR (qRT-PCR) and sequencing analysis, five of the randomly selected ten genes viz., Glyma.01G231200, Glyma.08G083300, Glyma.06G045400, Glyma.05G215900, and Glyma.15G015100 revealed both significant opposite expression pattern and nucleotide differences, respectively between SFT-tolerant and SFS-sensitive. Hence, these genes will be of great value for breeding seed-flooding tolerance in soybean after their proper functional validation. Overall, the transcriptome profiling indicates that all the three major processes viz., biological process (BP), cellular components (CC), and molecular functions (MF) are altered in the soybean in response to seed-flooding stress. In conclusion, these findings provide in-depth insights that will be of great utility for the exploration of candidate gene functions for seed-flooding tolerance in soybean.

中文翻译：

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基于 RNA-Seq 的转录组学分析揭示了与野生大豆 (Glycine soja Sieb. & Zucc.) 种子淹水耐受性相关的基因

摘要 种子淹水胁迫是影响大豆产量和品质的最重要的制约因素之一。然而，人们对种子淹水耐受性的分子机制知之甚少。因此，本研究使用 RNA-Seq 方法研究了种子洪水胁迫下两种对比大豆基因型（PI342618B/SFT 耐受型和 NN86-4/SFS 敏感型）根组织中的转录组谱。在 SFT 耐受和 SFS 敏感中分别鉴定了 1563 和 1958 个差异表达基因（DEG），表明前者受洪水胁迫的影响较小。基因本体论 (GO) 富集和 MapMan 通路分析都表明，对种子淹没胁迫的反应主要富集在参与细胞壁、抗氧化活性、催化和转录因子活性以及蛋白质代谢和信号传导。基于基因注释、GO富集和蛋白质-蛋白质相互作用（PPI）网络分析，从上述应激反应、防御反应和刺激反应等与应激相关的术语中，共筛选出807个DEG，用于候选基因预测分析。其中，51 个基因在耐受和敏感基因型之间显示出显着相反的基因表达模式，以及 GmERFVII1、GmERFVII2 & GmERFVII3 和 MAPK1 被预测为可能的候选基因进行进一步分析。使用定量实时 RT-PCR (qRT-PCR) 和测序分析，随机选择的十个基因中的五个，即 Glyma.01G231200、Glyma.08G083300、Glyma.06G045400、Glyma.05G215900 和 Glyma。15G015100 分别揭示了 SFT 耐受和 SFS 敏感之间显着相反的表达模式和核苷酸差异。因此，这些基因经过适当的功能验证后，对于培育大豆耐种子泛滥具有重要价值。总体而言，转录组分析表明，大豆中的所有三个主要过程，即生物过程 (BP)、细胞成分 (CC) 和分子功能 (MF) 都因种子淹水胁迫而发生改变。总之，这些发现提供了深入的见解，对于探索大豆耐种子淹水的候选基因功能将非常有用。这些基因经过适当的功能验证后，对于培育大豆耐种子泛滥具有重要价值。总体而言，转录组分析表明，大豆中的所有三个主要过程，即生物过程 (BP)、细胞成分 (CC) 和分子功能 (MF) 都因种子淹水胁迫而发生改变。总之，这些发现提供了深入的见解，对于探索大豆耐种子淹水的候选基因功能将非常有用。这些基因经过适当的功能验证后，对于培育大豆耐种子泛滥具有重要价值。总体而言，转录组分析表明，大豆中的所有三个主要过程，即生物过程 (BP)、细胞成分 (CC) 和分子功能 (MF) 都因种子淹水胁迫而发生改变。总之，这些发现提供了深入的见解，对于探索大豆耐种子淹水的候选基因功能将非常有用。