Integrated bioinformatics analysis reveals the response of Arabidopsis roots to salt stress through multiple gene expression omnibus datasets

Abstract

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.