Comparative analysis of cis-regulatory elements associated with salinity and drought tolerance in rice (oryza sativa l.) using in silico analysis

Bui Thi Hai Hoa; Nguyen Huy Duong; Dinh Thi Thu  Le; Trinh Thi Thu Hang; Vu Kim  Thoa; Le Thu Thuy; Bui Van Ngoc

doi:10.15625/vjbt-18581

Author affiliations

Authors

Bui Thi Hai Hoa \(^1\) Institute of Food and Biotechnology - Ha Noi Open University, 101B Nguyen Hien, Hai Ba Trung District, Ha Noi, Vietnam
Nguyen Huy Duong \(^2\) Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi, Vietnam https://orcid.org/0000-0001-8313-3455
Dinh Thi Thu Le \(^1\) Institute of Food and Biotechnology - Ha Noi Open University, 101B Nguyen Hien, Hai Ba Trung District, Ha Noi, Vietnam https://orcid.org/0009-0003-4992-1986
Trinh Thi Thu Hang \(^1\) Institute of Food and Biotechnology - Ha Noi Open University, 101B Nguyen Hien, Hai Ba Trung District, Ha Noi, Vietnam
Vu Kim Thoa \(^1\) Institute of Food and Biotechnology - Ha Noi Open University, 101B Nguyen Hien, Hai Ba Trung District, Ha Noi, Vietnam https://orcid.org/0009-0006-0735-1366
Le Thu Thuy \(^2\) Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi, Vietnam
Bui Van Ngoc \(^2\) Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi, Vietnam
\(^3\) Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi, Vietnam https://orcid.org/0000-0002-4659-7338

DOI:

https://doi.org/10.15625/vjbt-18581

Keywords:

Cis-regulatory elements (cREs), Ion transporters, Rice, Salinity tolerance, In silico analysis

Abstract

The critical roles of cis-regulatory elements (cREs) in the regulation of gene expression in response to environmental stress were reported in previous studies. Although transcription factor families to regulate gene expression in plants are well documented, there is a limited number of cREs related to salinity and drought tolerance in rice to be identified. Therefore, in this study, a comparative analysis and characterization of cREs associated with specific drought and salinity tolerance genes of rice, namely OsNHX1, OsNHX5, OsHKT1;1, OsHKT2;1, and OsSOS1, was performed using the PLACE and PlantPAN 3.0 databases, along with in silico methods. Several cis-elements within the core promoter region, including TATA-box, CAAT-box, G-box, DPE, and Y-Patch were identified. Additionally, eight other cis elements: ABRE, MYBRS, MYCRS, NAC-binding site, ACGTATERD1, GT1GMSCAM4, W-box, and DRE, were discovered and suggested to be potentially involved in drought and salinity tolerance in rice. Comparative analysis revealed that OsNHX1 and OsHKT1;1 exhibit a higher abundance of cREs compared to the other genes studied. The presence of an increased number of cREs suggests a more complex regulatory network, potentially enhancing the ability of these genes to cope with environmental stressors and fine-tune their responses to changing conditions. Furthermore, understanding the distribution and diversity of cREs across different genes can offer practical implications for genetic engineering and crop improvement strategies. Genes with desirable regulatory profiles, especially those associated with specific stress tolerances, may be prime candidates for genetic manipulation.

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