Unboxing the bZIP transcription factor family exhibiting their role under cold and salt stresses in indica rice
Basic leucine zipper (bZIP) extensively studied transcription factor family and has been implicated in abiotic stress resistance in eukaryotes. Genes encoded by bZIP govern changes in molecular, physiological, and biological processes in response to abiotic stimuli. Developments in molecular knowled...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2023-12-01
|
| Series: | Plant Stress |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667064X23001665 |
| _version_ | 1797422537761619968 |
|---|---|
| author | Ammara Hussain Rezwan Tariq Ali Aslam Huma Saleem Huma Mumtaz Imran Khan Muhammad Sajid Huseyin Basim |
| author_facet | Ammara Hussain Rezwan Tariq Ali Aslam Huma Saleem Huma Mumtaz Imran Khan Muhammad Sajid Huseyin Basim |
| author_sort | Ammara Hussain |
| collection | DOAJ |
| description | Basic leucine zipper (bZIP) extensively studied transcription factor family and has been implicated in abiotic stress resistance in eukaryotes. Genes encoded by bZIP govern changes in molecular, physiological, and biological processes in response to abiotic stimuli. Developments in molecular knowledge and easy access to the drafted genome of indica rice open ways to explore bZIP and related features within the indica rice genome. We identified 82 TFs encoding bZIPs in the indica rice genome. The identified 82 bZIPs are unevenly distributed across all 12 chromosomes. The identified bZIP family expansion in the indica rice genome is mainly by segmental duplication relative to tandem duplication. The gene structure analysis exhibited that most genes are intron-less and distributed among all phylogenetic groups. We identified 20 different conserved motifs, supporting that bZIPs regulate the different biological processes in rice. The comparative phylogenetic analysis of indica rice bZIPs with Arabidopsis categorized the genes into 11 different groups, having several orthologs and paralogs. Apart from the comparative analysis, gene ontology (GO) analysis illustrated the involvement of bZIPs in different biological processes and the interaction between different processes are important for the metabolic activity of a living organism.Moreover, KEGG pathway analysis identified the 23 bZIPs involved in pathogen infection, carotenoid biosynthesis, and phenylalanine metabolism. Among 23 genes, 12 genes were selected for the expression analysis under salt and cold stress treatments in the Khusboo-95 indica rice variety. In this research, LOC_Os01g17260.2, LOC_Os02g52780.1, and LOC_Os09g10840.1 showed upregulated expression under salt stress conditions. This genome-wide analysis allows researchers to functionally characterize the genes, involved in different abiotic stresses that could be beneficial to improve plant performance under challenging conditions. |
| first_indexed | 2024-03-09T07:33:44Z |
| format | Article |
| id | doaj.art-eccc4ac925034165aec80675cebdf365 |
| institution | Directory Open Access Journal |
| issn | 2667-064X |
| language | English |
| last_indexed | 2024-03-09T07:33:44Z |
| publishDate | 2023-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Plant Stress |
| spelling | doaj.art-eccc4ac925034165aec80675cebdf3652023-12-03T05:43:42ZengElsevierPlant Stress2667-064X2023-12-0110100299Unboxing the bZIP transcription factor family exhibiting their role under cold and salt stresses in indica riceAmmara Hussain0Rezwan Tariq1Ali Aslam2Huma Saleem3Huma Mumtaz4Imran Khan5Muhammad Sajid6Huseyin Basim7Department of Biotechnology, University of Okara, Punjab 56300, PakistanCenter for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi ArabiaFaculty of Agriculture and Veterinary Sciences, Superior University, Lahore, PakistanDepartment of Plant Breeding and Genetics, University of Agriculture Faisalabad, PakistanDepartment of Biotechnology, University of Okara, Punjab 56300, PakistanState Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, ChinaDepartment of Biotechnology, University of Okara, Punjab 56300, PakistanDepartment of Plant Protection, Akdeniz University, Antalya 07070, Turkey; Corresponding author.Basic leucine zipper (bZIP) extensively studied transcription factor family and has been implicated in abiotic stress resistance in eukaryotes. Genes encoded by bZIP govern changes in molecular, physiological, and biological processes in response to abiotic stimuli. Developments in molecular knowledge and easy access to the drafted genome of indica rice open ways to explore bZIP and related features within the indica rice genome. We identified 82 TFs encoding bZIPs in the indica rice genome. The identified 82 bZIPs are unevenly distributed across all 12 chromosomes. The identified bZIP family expansion in the indica rice genome is mainly by segmental duplication relative to tandem duplication. The gene structure analysis exhibited that most genes are intron-less and distributed among all phylogenetic groups. We identified 20 different conserved motifs, supporting that bZIPs regulate the different biological processes in rice. The comparative phylogenetic analysis of indica rice bZIPs with Arabidopsis categorized the genes into 11 different groups, having several orthologs and paralogs. Apart from the comparative analysis, gene ontology (GO) analysis illustrated the involvement of bZIPs in different biological processes and the interaction between different processes are important for the metabolic activity of a living organism.Moreover, KEGG pathway analysis identified the 23 bZIPs involved in pathogen infection, carotenoid biosynthesis, and phenylalanine metabolism. Among 23 genes, 12 genes were selected for the expression analysis under salt and cold stress treatments in the Khusboo-95 indica rice variety. In this research, LOC_Os01g17260.2, LOC_Os02g52780.1, and LOC_Os09g10840.1 showed upregulated expression under salt stress conditions. This genome-wide analysis allows researchers to functionally characterize the genes, involved in different abiotic stresses that could be beneficial to improve plant performance under challenging conditions.http://www.sciencedirect.com/science/article/pii/S2667064X23001665Gene ontologyClimatic challengeBiosynthetic processAbiotic stressExpression profilingPathway |
| spellingShingle | Ammara Hussain Rezwan Tariq Ali Aslam Huma Saleem Huma Mumtaz Imran Khan Muhammad Sajid Huseyin Basim Unboxing the bZIP transcription factor family exhibiting their role under cold and salt stresses in indica rice Plant Stress Gene ontology Climatic challenge Biosynthetic process Abiotic stress Expression profiling Pathway |
| title | Unboxing the bZIP transcription factor family exhibiting their role under cold and salt stresses in indica rice |
| title_full | Unboxing the bZIP transcription factor family exhibiting their role under cold and salt stresses in indica rice |
| title_fullStr | Unboxing the bZIP transcription factor family exhibiting their role under cold and salt stresses in indica rice |
| title_full_unstemmed | Unboxing the bZIP transcription factor family exhibiting their role under cold and salt stresses in indica rice |
| title_short | Unboxing the bZIP transcription factor family exhibiting their role under cold and salt stresses in indica rice |
| title_sort | unboxing the bzip transcription factor family exhibiting their role under cold and salt stresses in indica rice |
| topic | Gene ontology Climatic challenge Biosynthetic process Abiotic stress Expression profiling Pathway |
| url | http://www.sciencedirect.com/science/article/pii/S2667064X23001665 |
| work_keys_str_mv | AT ammarahussain unboxingthebziptranscriptionfactorfamilyexhibitingtheirroleundercoldandsaltstressesinindicarice AT rezwantariq unboxingthebziptranscriptionfactorfamilyexhibitingtheirroleundercoldandsaltstressesinindicarice AT aliaslam unboxingthebziptranscriptionfactorfamilyexhibitingtheirroleundercoldandsaltstressesinindicarice AT humasaleem unboxingthebziptranscriptionfactorfamilyexhibitingtheirroleundercoldandsaltstressesinindicarice AT humamumtaz unboxingthebziptranscriptionfactorfamilyexhibitingtheirroleundercoldandsaltstressesinindicarice AT imrankhan unboxingthebziptranscriptionfactorfamilyexhibitingtheirroleundercoldandsaltstressesinindicarice AT muhammadsajid unboxingthebziptranscriptionfactorfamilyexhibitingtheirroleundercoldandsaltstressesinindicarice AT huseyinbasim unboxingthebziptranscriptionfactorfamilyexhibitingtheirroleundercoldandsaltstressesinindicarice |