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Integrated bioinformatics analysis reveals the response of Arabidopsis roots to salt stress through multiple gene expression omnibus datasets
Journal of Plant Interactions ( IF 3.2 ) Pub Date : 2020-09-30 , DOI: 10.1080/17429145.2020.1824027
Meili Guo 1 , Xin Liu 2 , Lei Li 3 , Yusu Jiang 1 , Xuejuan Yu 1 , Tao Meng 1 , Chunxi Zhou 4
Affiliation  

ABSTRACT

Plant growth and crop productivity has been adversely affected by salt stress around the world. Arabidopsis root is an important model to demonstrate how the glycophyte adapts to salt stress. To better understand the salt-responsive genes in Arabidopsis root, a rank aggregation method has been applied to disclose 836 dysregulated genes including 449 upregulated and 387 down-regulated genes out of more than 20,000 genes in NaCl-treated Arabidopsis root from the Gene Expression Omnibus (GEO) database. Then, the integrated approaches of PANTHER, DAVID, KEGG, Cytoscape and STRING have been used for bioinformatic analysis. Our results showed that these salt-responsive genes were involved in various gene ontology enrichments (transcription, oxidative stress, cell wall organization), differential pathways (MAPK signaling pathway, hormone signal transduction), and complicated interactions (cross-talking with wounding stress, abscisic acid stress, heat stress, water deprivation stress, cold stress). Furthermore, the activities of the oxidative stress related gene, peroxidase, were determined under salt stress, cold stress and water deprivation stress, which validated the bioinformatic outcome of cross-tolerance to different stresses. Our work will throw new lights on the response of Arabidopsis roots to salt stress, and provide potential salt-targets to improve plant growth and increase crop output.



中文翻译:

综合的生物信息学分析揭示了拟南芥根对盐胁迫的响应,通过多种基因表达综合数据集

摘要

全世界的盐胁迫对植物生长和农作物生产力造成了不利影响。拟南芥根是证明糖原植物如何适应盐胁迫的重要模型。为了更好地了解拟南芥根中的盐响应基因,已采用秩聚合法公开了836个失调基因,包括在NaCl处理的拟南芥中的20,000多个基因中的449个上调基因和387个下调基因。根来自基因表达综合(GEO)数据库。然后,将PANTHER,DAVID,KEGG,Cytoscape和STRING的集成方法用于生物信息学分析。我们的结果表明,这些盐反应性基因参与了各种基因本体的丰富(转录,氧化应激,细胞壁组织),差异途径(MAPK信号传导途径,激素信号传导)以及复杂的相互作用(与创伤应激的串扰,脱落酸胁迫,热胁迫,缺水胁迫,冷胁迫)。此外,在盐胁迫,冷胁迫和缺水胁迫下测定了氧化应激相关基因过氧化物酶的活性,这证明了交叉耐受的生物信息学结果。我们的工作将对拟南芥根源于盐胁迫,并提供潜在的盐目标,以改善植物生长和增加作物产量。

更新日期:2020-09-30
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