Meta-analysis of microarray and RNAseq data reveal OsbZIP52 to mediate salt stress responses in sensitive, tolerant and halophyte rice varieties
Abstract The development of salt-tolerant rice has become urgent due to climate change and rising global rice consumption. A large-scale analysis using different but related platforms has become imperative to filter out candidate genes responsible for salinity tolerance and salinity stress-responsiv...
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CABI
2023-08-01
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| Series: | CABI Agriculture and Bioscience |
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| Online Access: | https://doi.org/10.1186/s43170-023-00173-3 |
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| author | Dipankor Chatterjee Mohammad Umer Sharif Shohan Nishat Tamanna Zeba I. Seraj |
| author_facet | Dipankor Chatterjee Mohammad Umer Sharif Shohan Nishat Tamanna Zeba I. Seraj |
| author_sort | Dipankor Chatterjee |
| collection | DOAJ |
| description | Abstract The development of salt-tolerant rice has become urgent due to climate change and rising global rice consumption. A large-scale analysis using different but related platforms has become imperative to filter out candidate genes responsible for salinity tolerance and salinity stress-responsive pathways. Such genes can be used to find prospective candidate salt resistance genes in donor rice genotypes and transfer them to high-yielding rice varieties. We performed a meta-analysis to screen out candidate genes using stress-related three microarray and one RNASeq datasets from NCBI. As different genotypes of rice and different salinity stress conditions were considered in our analysis, the sensitivity of the results is expected to be multi-fold higher. Our analysis revealed the differentially expressed genes (DEGs) OsbZIP52 and OsLTP2.5 to be common between leaf and root tissues. These genes were further compared with those of the wild halophytic rice Oryza coarctata expression data in stress conditions to understand the significance of these genes. The OsbZIP52 gene homolog of Oryza coarctata was the only one found to be differentially expressed. The expression level of OsbZIP52 was quantified using RT-qPCR and observed downregulated expression in salt stress in root and leaf tissues of four rice cultivars (2 salt-tolerant and 2 salt-sensitive). Promoter and motif analysis revealed a high number of variations in promoter and motif regions of the gene in IR29 salt-sensitive rice. Expression correlation analysis and Gene Ontology study suggested that OsbZIP52 interacts with genes that are engaged in stress response and participate in stress-responsive pathways. Collectively this study increases our understanding of the differential gene expression in various stress conditions in root and leaf tissues. It also helped identify a critical regulatory transcription factor in assisting the plant in combating salinity stress. |
| format | Article |
| id | doaj-art-48ce08cf2e614103820441c54ff9ba56 |
| institution | Kabale University |
| issn | 2662-4044 |
| language | English |
| publishDate | 2023-08-01 |
| publisher | CABI |
| record_format | Article |
| series | CABI Agriculture and Bioscience |
| spelling | doaj-art-48ce08cf2e614103820441c54ff9ba562025-02-03T09:35:57ZengCABICABI Agriculture and Bioscience2662-40442023-08-014111810.1186/s43170-023-00173-3Meta-analysis of microarray and RNAseq data reveal OsbZIP52 to mediate salt stress responses in sensitive, tolerant and halophyte rice varietiesDipankor Chatterjee0Mohammad Umer Sharif Shohan1Nishat Tamanna2Zeba I. Seraj3Department of Biochemistry and Molecular Biology, University of DhakaDepartment of Biochemistry and Molecular Biology, University of DhakaDepartment of Biochemistry and Molecular Biology, University of DhakaDepartment of Biochemistry and Molecular Biology, University of DhakaAbstract The development of salt-tolerant rice has become urgent due to climate change and rising global rice consumption. A large-scale analysis using different but related platforms has become imperative to filter out candidate genes responsible for salinity tolerance and salinity stress-responsive pathways. Such genes can be used to find prospective candidate salt resistance genes in donor rice genotypes and transfer them to high-yielding rice varieties. We performed a meta-analysis to screen out candidate genes using stress-related three microarray and one RNASeq datasets from NCBI. As different genotypes of rice and different salinity stress conditions were considered in our analysis, the sensitivity of the results is expected to be multi-fold higher. Our analysis revealed the differentially expressed genes (DEGs) OsbZIP52 and OsLTP2.5 to be common between leaf and root tissues. These genes were further compared with those of the wild halophytic rice Oryza coarctata expression data in stress conditions to understand the significance of these genes. The OsbZIP52 gene homolog of Oryza coarctata was the only one found to be differentially expressed. The expression level of OsbZIP52 was quantified using RT-qPCR and observed downregulated expression in salt stress in root and leaf tissues of four rice cultivars (2 salt-tolerant and 2 salt-sensitive). Promoter and motif analysis revealed a high number of variations in promoter and motif regions of the gene in IR29 salt-sensitive rice. Expression correlation analysis and Gene Ontology study suggested that OsbZIP52 interacts with genes that are engaged in stress response and participate in stress-responsive pathways. Collectively this study increases our understanding of the differential gene expression in various stress conditions in root and leaf tissues. It also helped identify a critical regulatory transcription factor in assisting the plant in combating salinity stress.https://doi.org/10.1186/s43170-023-00173-3SalinityRiceMicroarrayRNASeqSalt-stressOsbZIP52 |
| spellingShingle | Dipankor Chatterjee Mohammad Umer Sharif Shohan Nishat Tamanna Zeba I. Seraj Meta-analysis of microarray and RNAseq data reveal OsbZIP52 to mediate salt stress responses in sensitive, tolerant and halophyte rice varieties CABI Agriculture and Bioscience Salinity Rice Microarray RNASeq Salt-stress OsbZIP52 |
| title | Meta-analysis of microarray and RNAseq data reveal OsbZIP52 to mediate salt stress responses in sensitive, tolerant and halophyte rice varieties |
| title_full | Meta-analysis of microarray and RNAseq data reveal OsbZIP52 to mediate salt stress responses in sensitive, tolerant and halophyte rice varieties |
| title_fullStr | Meta-analysis of microarray and RNAseq data reveal OsbZIP52 to mediate salt stress responses in sensitive, tolerant and halophyte rice varieties |
| title_full_unstemmed | Meta-analysis of microarray and RNAseq data reveal OsbZIP52 to mediate salt stress responses in sensitive, tolerant and halophyte rice varieties |
| title_short | Meta-analysis of microarray and RNAseq data reveal OsbZIP52 to mediate salt stress responses in sensitive, tolerant and halophyte rice varieties |
| title_sort | meta analysis of microarray and rnaseq data reveal osbzip52 to mediate salt stress responses in sensitive tolerant and halophyte rice varieties |
| topic | Salinity Rice Microarray RNASeq Salt-stress OsbZIP52 |
| url | https://doi.org/10.1186/s43170-023-00173-3 |
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