Deciphering salt-responsive NB-ARC genes in rice transcriptomic data: A bioinformatics approach with gene expression validation
The salt-tolerant rice can be developed by finding exotic germplasm that possesses tolerant traits through a series of selections. Determination of functional marker genes is essential to perform a concise and fast method for selection. This research focuses on pinpointing candidate genes suitable f...
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| Format: | Article |
| Language: | English |
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De Gruyter
2024-12-01
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| Series: | Open Agriculture |
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| Online Access: | https://doi.org/10.1515/opag-2022-0389 |
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| author | Saputro Triono Bagus Wardhani Fila Oxi Sholihah Nur Fadlilatus Ermavitalini Dini Purnama Putut Rakhmad Nurhidayati Tutik |
| author_facet | Saputro Triono Bagus Wardhani Fila Oxi Sholihah Nur Fadlilatus Ermavitalini Dini Purnama Putut Rakhmad Nurhidayati Tutik |
| author_sort | Saputro Triono Bagus |
| collection | DOAJ |
| description | The salt-tolerant rice can be developed by finding exotic germplasm that possesses tolerant traits through a series of selections. Determination of functional marker genes is essential to perform a concise and fast method for selection. This research focuses on pinpointing candidate genes suitable for functional markers. We conducted an in silico analysis of the NB-ARC gene family across three transcriptomic datasets of rice under salt stress. This included examining cis-regulatory elements in the promoter regions, protein domains/motifs, and predicting subcellular localizations to narrow down our gene selection. From 19 different rice varieties evaluated under salt stress, we identified the most tolerant and susceptible ones for further investigation. Two varieties with contrasting tolerance levels were selected for validation. Real-time polymerase chain reaction was employed to determine the gene expression for validation. Among the 139 NB-ARC genes studied, 28 exhibited differential expression in all 3 transcriptome datasets. The candidate genes LOC_Os04g43440, LOC_Os11g15700, and LOC_Os11g39310 were selected, primarily based on their predicted subcellular localization within the nucleus. Out of 19 varieties, Inpari 35, FL478, and Siak Raya are considered salt-tolerant varieties. Notably, among the three salt-tolerant varieties – Inpari 35, FL478, and Siak Raya – Inpari 35 emerged as the most resilient, displaying robust growth parameters during the seedling stage. Conversely, IR29 was found to be the most susceptible. Expression analysis revealed that LOC_Os04g43440 in Inpari 35 showed increased expression at 24 h of salt stress exposure, while LOC_Os11g15700 exhibited upregulation after 48 h. Remarkably, LOC_Os11g39310 displayed a remarkable 21.78-fold increase at 24 h, followed by a decline at 48 h. LOC_Os11g39310 stands out as a promising marker essential for guiding selection in breeding programs aimed at cultivating salt-tolerant rice varieties. |
| format | Article |
| id | doaj-art-a70715756baa4162af806dedea3f708a |
| institution | Kabale University |
| issn | 2391-9531 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Open Agriculture |
| spelling | doaj-art-a70715756baa4162af806dedea3f708a2025-01-14T13:23:23ZengDe GruyterOpen Agriculture2391-95312024-12-019111310.1515/opag-2022-0389Deciphering salt-responsive NB-ARC genes in rice transcriptomic data: A bioinformatics approach with gene expression validationSaputro Triono Bagus0Wardhani Fila Oxi1Sholihah Nur Fadlilatus2Ermavitalini Dini3Purnama Putut Rakhmad4Nurhidayati Tutik5Department of Biology, Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember Surabaya, Surabaya, Jawa Timur, IndonesiaDepartment of Biology, Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember Surabaya, Surabaya, Jawa Timur, IndonesiaDepartment of Biology, Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember Surabaya, Surabaya, Jawa Timur, IndonesiaDepartment of Biology, Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember Surabaya, Surabaya, Jawa Timur, IndonesiaDepartment of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Surabaya, Ketintang, Surabaya, East Java 60231, IndonesiaDepartment of Biology, Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember Surabaya, Surabaya, Jawa Timur, IndonesiaThe salt-tolerant rice can be developed by finding exotic germplasm that possesses tolerant traits through a series of selections. Determination of functional marker genes is essential to perform a concise and fast method for selection. This research focuses on pinpointing candidate genes suitable for functional markers. We conducted an in silico analysis of the NB-ARC gene family across three transcriptomic datasets of rice under salt stress. This included examining cis-regulatory elements in the promoter regions, protein domains/motifs, and predicting subcellular localizations to narrow down our gene selection. From 19 different rice varieties evaluated under salt stress, we identified the most tolerant and susceptible ones for further investigation. Two varieties with contrasting tolerance levels were selected for validation. Real-time polymerase chain reaction was employed to determine the gene expression for validation. Among the 139 NB-ARC genes studied, 28 exhibited differential expression in all 3 transcriptome datasets. The candidate genes LOC_Os04g43440, LOC_Os11g15700, and LOC_Os11g39310 were selected, primarily based on their predicted subcellular localization within the nucleus. Out of 19 varieties, Inpari 35, FL478, and Siak Raya are considered salt-tolerant varieties. Notably, among the three salt-tolerant varieties – Inpari 35, FL478, and Siak Raya – Inpari 35 emerged as the most resilient, displaying robust growth parameters during the seedling stage. Conversely, IR29 was found to be the most susceptible. Expression analysis revealed that LOC_Os04g43440 in Inpari 35 showed increased expression at 24 h of salt stress exposure, while LOC_Os11g15700 exhibited upregulation after 48 h. Remarkably, LOC_Os11g39310 displayed a remarkable 21.78-fold increase at 24 h, followed by a decline at 48 h. LOC_Os11g39310 stands out as a promising marker essential for guiding selection in breeding programs aimed at cultivating salt-tolerant rice varieties.https://doi.org/10.1515/opag-2022-0389ricemarker genenb-arc familysalt stresstranscriptomicqrt-pcr |
| spellingShingle | Saputro Triono Bagus Wardhani Fila Oxi Sholihah Nur Fadlilatus Ermavitalini Dini Purnama Putut Rakhmad Nurhidayati Tutik Deciphering salt-responsive NB-ARC genes in rice transcriptomic data: A bioinformatics approach with gene expression validation Open Agriculture rice marker gene nb-arc family salt stress transcriptomic qrt-pcr |
| title | Deciphering salt-responsive NB-ARC genes in rice transcriptomic data: A bioinformatics approach with gene expression validation |
| title_full | Deciphering salt-responsive NB-ARC genes in rice transcriptomic data: A bioinformatics approach with gene expression validation |
| title_fullStr | Deciphering salt-responsive NB-ARC genes in rice transcriptomic data: A bioinformatics approach with gene expression validation |
| title_full_unstemmed | Deciphering salt-responsive NB-ARC genes in rice transcriptomic data: A bioinformatics approach with gene expression validation |
| title_short | Deciphering salt-responsive NB-ARC genes in rice transcriptomic data: A bioinformatics approach with gene expression validation |
| title_sort | deciphering salt responsive nb arc genes in rice transcriptomic data a bioinformatics approach with gene expression validation |
| topic | rice marker gene nb-arc family salt stress transcriptomic qrt-pcr |
| url | https://doi.org/10.1515/opag-2022-0389 |
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