The Open Bioinformatics Journal

ISSN: 1875-0362 ― Volume 12, 2019

Investigation of Drought and Salinity Tolerance Related Genes and their Regulatory Mechanisms in Arabidopsis (Arabidopsis thaliana)

Nikwan Shariatipour, Bahram Heidari*
Department of Crop Production and Plant Breeding, School of Agriculture, 7144165186, Shiraz University, Shiraz, Iran



The development of genome microarrays of the model plant; Arabidopsis thaliana, with increasing repositories of publicly available data and high-throughput data analysis tools, has opened new avenues to genome-wide systemic analysis of plant responses to environmental stresses.


To identify differentially expressed genes and their regulatory networks in Arabidopsis thaliana under harsh environmental condition.


Two replications of eight microarray data sets were derived from two different tissues (root and shoot) and two different time courses (control and 24 hours after the beginning of stress occurrence) for comparative data analysis through various bioinformatics tools.


Under drought stress, 2558 gene accessions in root and 3691 in shoot tissues had significantly differential expression with respect to control condition. Likewise, under salinity stress 9078 gene accessions in root and 5785 in shoot tissues were discriminated between stressed and non-stressed conditions. Furthermore, the transcription regulatory activity of differentially expressed genes was mainly due to hormone, light, circadian and stress responsive cis-acting regulatory elements among which ABRE, ERE, P-box, TATC-box, CGTCA-motif, GARE-motif, TGACG-motif, GAG-motif, GA-motif, GATA- motif, TCT-motif, GT1-motif, Box 4, G-Box, I-box, LAMP-element, Sp1, MBS, TC-rich repeats, TCA-element and HSE were the most important elements in the identified up-regulated genes.


The results of the high-throughput comparative analyses in this study provide more options for plant breeders and give an insight into genes and cis-acting regulatory elements involved in plant response to drought and salinity stresses in strategic crops such as cereals.

Keywords: Bioinformatics, Microarray, Gene expression, Gene ontology, Cis-acting regulatory element, Abiotic stress.

Article Information

Identifiers and Pagination:

Year: 2018
Volume: 11
First Page: 12
Last Page: 28
Publisher Id: TOBIOIJ-11-12
DOI: 10.2174/1875036201811010012

Article History:

Received Date: 22/10/2017
Revision Received Date: 12/02/2018
Acceptance Date: 19/02/2018
Electronic publication date: 07/03/2018
Collection year: 2018

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© 2018 Shariatipour and Heidari.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: ( This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this author at the Department of Crop Production and Plant Breeding, School of Agriculture, Shiraz University, Bahram Heidari, Shiraz, Iran; Tel: +98-9177070889; E-mail:


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