In-depth investigation on abiotic stress-responsive differentially expressed genes in Arabidopsis roots through GEO database

Abiotic stresses limit the plant growth and productivity. Plants have developed various responsive mechanisms to survive these adverse environmental conditions. To better understand plants how to adapt environmental stress, we retrieved the Arabidopsis root responsive genes related to eight abiotic...

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Bibliographic Details
Published inJournal of plant interactions Vol. 15; no. 1; pp. 294 - 302
Main Authors Guo, Meili, Liu, Xin, Wang, Jiahui, Li, Lei, Jiang, Yusu, Yu, Xuejuan, Meng, Tao
Format Journal Article
LanguageEnglish
Published Philadelphia Taylor & Francis 01.01.2020
Taylor & Francis Ltd
Taylor & Francis Group
Subjects
Abiotic stress
Algorithms
antioxidant activity
Arabidopsis
Arabidopsis root
Bioinformatics
Biomarkers
DNA microarrays
Drought
Environmental conditions
Environmental stress
Enzymatic activity
Enzyme activity
experimental validation
Gene expression
Gene regulation
Genes
Heavy metals
integrated bioinformatics analysis
Molecular modelling
Oxidative stress
Plant growth
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Summary:Abiotic stresses limit the plant growth and productivity. Plants have developed various responsive mechanisms to survive these adverse environmental conditions. To better understand plants how to adapt environmental stress, we retrieved the Arabidopsis root responsive genes related to eight abiotic stresses (salt, cold, drought, osmotic, UV, wounding, heat, and heavy metal stresses) from the Gene Expression Omnibus (GEO) database. After quantile normalization of microarray data, a robust rank aggregation (RRA) algorithm was applied to determine the differentially expressed genes (DEGs). The resultant 213 DEGs, including 139 up-regulated and 74 down-regulated genes out of more than 20,000 genes, were further analyzed by the integrated bioinformatics approaches of PUBMED, PANTHER, DAVID, and STRING. The results indicated that the up-regulated DEGs were more positively involved in response to oxidative stress, regulation of transcription, and structure organization than the down-regulated DEGs. The former also had more complicated PPI interactions than the latter. Furthermore, qRT-PCR and enzyme activity have been done to validate the outcome of integrated bioinformatics analysis. Our work will facilitate to demonstrate the common molecular mechanisms responsive to differential abiotic stresses and these DEGs might be potential biomarkers for future abiotic stress-resistance studies.
ISSN:1742-9145
1742-9153
DOI:10.1080/17429145.2020.1812742