Cotton (Gossypium hirsutum) is considered a fairly salt tolerant crop however, salinity can still cause significant economic losses by affecting the yield and deteriorating the fiber quality. We studied a salt-tolerant upland cotton cultivar under temporal salt stress to unfold the salt tolerance molecular mechanisms. Biochemical response to salt stress (400 mM) was measured at 0 h, 3 h, 12 h, 24 h and 48 h post stress intervals and single-molecule long-read sequencing technology from Pacific Biosciences (PacBio) combined with the unique molecular identifiers approach was used to identify differentially expressed genes (DEG). Antioxidant enzymes including, catalase (CAT), peroxidase (POD), superoxide dismutase (SOD) were found significantly induced under temporal salt stress, suggesting that reactive oxygen species scavenging antioxidant machinery is an essential component of salt tolerance mechanism in cotton. We identified a wealth of novel transcripts based on the PacBio long reads sequencing approach. Prolonged salt stress duration induces high number of DEGs. Significant numbers of DEGs were found under key terms related to stress pathways such as “response to oxidative stress”, “response to salt stress”, “response to water deprivation”, “cation transport”, “metal ion transport”, “superoxide dismutase”, and “reductase”. Key DEGs related to hormone (abscisic acid, ethylene and jasmonic acid) biosynthesis, ion homeostasis (CBL-interacting serine/threonine-protein kinase genes, calcium-binding proteins, potassium transporter genes, potassium channel genes, sodium/hydrogen exchanger or antiporter genes), antioxidant activity (POD, SOD, CAT, glutathione reductase), transcription factors (myeloblastosis, WRKY, Apetala 2) and cell wall modification were found highly active in response to salt stress in cotton. Expression fold change of these DEGs showed both positive and negative responses, highlighting the complex nature of salt stress tolerance mechanisms in cotton. Collectively, this study provides a good insight into the regulatory mechanism under salt stress in cotton and lays the foundation for further improvement of salt stress tolerance.

中文翻译：

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陆地棉中PacBio长读RNA测序揭示了时态盐胁迫诱导的转录组改变和调控机制

棉花（陆地棉）被认为是相当耐盐的作物，但是盐分仍然会通过影响产量和使纤维质量恶化而造成重大的经济损失。我们研究了在盐胁迫下耐盐的陆地棉品种，以揭示其耐盐分子机制。在胁迫间隔后0小时，3小时，12小时，24小时和48小时测量了对盐胁迫（400 mM）的生化响应，采用了太平洋生物科学公司（PacBio）的单分子长读测序技术，并结合了独特的分子标识符方法用于鉴定差异表达基因（DEG）。发现抗氧化酶包括过氧化氢酶（CAT），过氧化物酶（POD），超氧化物歧化酶（SOD）在短暂的盐胁迫下被显着诱导，这表明清除活性氧的抗氧化剂机制是棉花耐盐机理的重要组成部分。我们基于PacBio长读测序方法鉴定了许多新颖的转录本。延长的盐胁迫持续时间会诱导大量的DEG。在与应力途径相关的关键术语下发现了大量的DEG，例如“对氧化胁迫的响应”，“对盐胁迫的响应”，“对缺水的响应”，“阳离子迁移”，“金属离子迁移”，“超氧化物歧化酶” ”和“还原酶”。与激素（脱落酸，乙烯和茉莉酸）生物合成，离子稳态（CBL相互作用的丝氨酸/苏氨酸蛋白激酶基因，钙结合蛋白，钾转运蛋白基因，钾通道基因，钠/氢交换子或反转运蛋白基因）相关的关键DEG ），发现抗氧化活性（POD，SOD，CAT，谷胱甘肽还原酶），转录因子（成纤维细胞增多症，WRKY，Apetala 2）和细胞壁修饰对棉花的盐胁迫响应非常活跃。这些DEG的表达倍数变化既显示阳性反应，也显示阴性反应，突出了棉花盐胁迫耐受机制的复杂性。总体而言，本研究为棉花盐胁迫下的调控机制提供了很好的见识，并为进一步提高盐胁迫耐受性奠定了基础。突出了棉花盐胁迫耐受机制的复杂性。总体而言，本研究为棉花盐胁迫下的调控机制提供了很好的见识，并为进一步提高盐胁迫耐受性奠定了基础。突出了棉花盐胁迫耐受机制的复杂性。总体而言，本研究为棉花盐胁迫下的调控机制提供了很好的见识，并为进一步提高盐胁迫耐受性奠定了基础。