The Open Bioinformatics Journal

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Meta-Analysis of Expression of the Stress Tolerance Associated Genes and Uncover their Cis-Regulatory Elements in Rice (Oryza sativa L.)

Nikwan Shariatipour1, Bahram Heidari1, *
1 Department of Crop Production and Plant Breeding, School of Agriculture, Shiraz University, Shiraz, 7144165186, Iran



Rice contributes to the staple food of more than half of the world’s population. However, its productivity is influenced by various biotic and abiotic stresses. Genetic engineering and plant breeding tools help to overcome the adverse effects of environmental stresses. The advanced bioinformatics tools provide information for a better understanding of the mechanisms underlying stress tolerance, gene expression profiles and functions of the important genes and cis-regulatory elements involved in better performance under abiotic stresses.


To identify the key genes involved in the tolerance mechanism for abiotic stresses and their regulatory networks in rice (Oryza sativa L.).


A total of 152 various microarray datasets associated with nine rice trials were retrieved for expression meta-analysis through various bioinformatics tools.


The results indicated that 29593, 202798, 73224 and 25241 genes represented significant differential expression under cold, drought, salinity and heat stress conditions compared with the control condition, respectively. Twenty three highly overexpressed genes were identified under the evaluated abiotic stresses. The transcription regulatory activity of differentially expressed genes was mainly due to hormone, light and stress-responsive cis-acting regulatory elements among which ABRE, ARE, CGTCA-motif, GARE-motif, TGACG-motif, G-box, G-Box, GAG-motif, GA-motif, TCT-motif, Box 4, Sp1, HSE, MBS and TC-rich repeats were the most important in the promoter sites of the identified up-regulated genes. The results of cis-acting regulatory analysis suggest that 15 cis-acting regulatory elements were contributed to the tolerance mechanisms for abiotic stresses.


The result of expression meta-analysis in this study provides an insight for plant breeders for better understanding the function of the genes and their regulatory mechanism in plants (especially cereals) exposed to different abiotic stresses. The outcome of this study suggests practical approaches for designing unified breeding programmes to breed multi-abiotic stress-tolerant species.

Keywords: Bioinformatics, Gene ontology, Abiotic stress, Rice, High salinity, Novel gene.

Article Information

Identifiers and Pagination:

Year: 2020
Volume: 13
First Page: 39
Last Page: 49
Publisher Id: TOBIOIJ-13-39
DOI: 10.2174/1875036202013010039

Article History:

Received Date: 27/08/2019
Revision Received Date: 29/09/2019
Acceptance Date: 09/10/2019
Electronic publication date: 23/04/2020
Collection year: 2019

© 2020 Shariatipour & 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, Shiraz University, School of Agriculture, Bajgah, Shiraz, Iran; Tel: 989177070889; E-mail:

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