Comprehensive <i>In Silico</i> Analysis of the <i>NHX</i> (Na<sup>+</sup>/H<sup>+</sup> Antiporter) Gene in Rice (<i>Oryza sativa</i> L.)
The Na<sup>+</sup>/H<sup>+</sup> antiporter (<i>NHX</i>) gene family plays a pivotal role in plant salt tolerance in regulating intracellular Na<sup>+</sup> and H<sup>+</sup> homeostasis. In this study, seven candidate <i>OsNHX</i&...
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2025-01-01
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| author | Hoa Hai Thi Bui Duong Huy Nguyen Le Thu Thi Dinh Hang Thu Thi Trinh Thoa Kim Vu Van Ngoc Bui |
| author_facet | Hoa Hai Thi Bui Duong Huy Nguyen Le Thu Thi Dinh Hang Thu Thi Trinh Thoa Kim Vu Van Ngoc Bui |
| author_sort | Hoa Hai Thi Bui |
| collection | DOAJ |
| description | The Na<sup>+</sup>/H<sup>+</sup> antiporter (<i>NHX</i>) gene family plays a pivotal role in plant salt tolerance in regulating intracellular Na<sup>+</sup> and H<sup>+</sup> homeostasis. In this study, seven candidate <i>OsNHX</i> genes (<i>OsNHX1</i> to <i>OsNHX7</i>) were identified in the rice genome and classified into three phylogenetic clusters (Vac, Endo, and PM) based on their predicted subcellular localization. Five <i>OsNHX</i> gene pairs (<i>OsNHX1/OsNHX2</i>, <i>OsNHX1/OsNHX3</i>, <i>OsNHX1/OsNHX4</i>, <i>OsNHX2/OsNHX6</i>, and <i>OsNHX5/OsNHX6</i>) were found to have arisen from dispersed duplication events and exhibited purifying selection, indicating functional conservation. Analysis of <i>cis</i>-regulatory elements (CREs) revealed a diverse range of elements associated with tissue-specific expression, hormone signaling, and stress responses, particularly to dehydration and salinity. Notably, CREs associated with tissue/organelle-specific expression and stress responses were the most abundant, suggesting a potential role for <i>OsNHX</i> genes in regulating growth, development, and stress tolerance in rice. Importantly, expression profiling revealed that <i>OsNHX1</i>, <i>OsNHX2</i>, <i>OsNHX3</i>, and <i>OsNHX5</i> were upregulated under salt stress, with significantly higher expression levels in the salt-tolerant rice cultivar Pokkali compared to the salt-sensitive cultivar IR64. Our findings provide a comprehensive analysis of the evolutionary, structural, and functional features of the <i>OsNHX</i> gene family and highlights their critical role in rice salt tolerance, offering insights into potential applications for crop improvement. |
| format | Article |
| id | doaj-art-aef4d5cbff1342ada9cfdadc7751a3f2 |
| institution | DOAJ |
| issn | 2037-0164 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | MDPI AG |
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| series | International Journal of Plant Biology |
| spelling | doaj-art-aef4d5cbff1342ada9cfdadc7751a3f22025-08-20T02:42:34ZengMDPI AGInternational Journal of Plant Biology2037-01642025-01-01161610.3390/ijpb16010006Comprehensive <i>In Silico</i> Analysis of the <i>NHX</i> (Na<sup>+</sup>/H<sup>+</sup> Antiporter) Gene in Rice (<i>Oryza sativa</i> L.)Hoa Hai Thi Bui0Duong Huy Nguyen1Le Thu Thi Dinh2Hang Thu Thi Trinh3Thoa Kim Vu4Van Ngoc Bui5Institute of Biological and Food Technology, Hanoi Open University, 101B Nguyen Hien Street, Hai Ba Trung District, Hanoi 10072, VietnamInstitute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi 10072, VietnamInstitute of Biological and Food Technology, Hanoi Open University, 101B Nguyen Hien Street, Hai Ba Trung District, Hanoi 10072, VietnamInstitute of Biological and Food Technology, Hanoi Open University, 101B Nguyen Hien Street, Hai Ba Trung District, Hanoi 10072, VietnamInstitute of Biological and Food Technology, Hanoi Open University, 101B Nguyen Hien Street, Hai Ba Trung District, Hanoi 10072, VietnamInstitute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi 10072, VietnamThe Na<sup>+</sup>/H<sup>+</sup> antiporter (<i>NHX</i>) gene family plays a pivotal role in plant salt tolerance in regulating intracellular Na<sup>+</sup> and H<sup>+</sup> homeostasis. In this study, seven candidate <i>OsNHX</i> genes (<i>OsNHX1</i> to <i>OsNHX7</i>) were identified in the rice genome and classified into three phylogenetic clusters (Vac, Endo, and PM) based on their predicted subcellular localization. Five <i>OsNHX</i> gene pairs (<i>OsNHX1/OsNHX2</i>, <i>OsNHX1/OsNHX3</i>, <i>OsNHX1/OsNHX4</i>, <i>OsNHX2/OsNHX6</i>, and <i>OsNHX5/OsNHX6</i>) were found to have arisen from dispersed duplication events and exhibited purifying selection, indicating functional conservation. Analysis of <i>cis</i>-regulatory elements (CREs) revealed a diverse range of elements associated with tissue-specific expression, hormone signaling, and stress responses, particularly to dehydration and salinity. Notably, CREs associated with tissue/organelle-specific expression and stress responses were the most abundant, suggesting a potential role for <i>OsNHX</i> genes in regulating growth, development, and stress tolerance in rice. Importantly, expression profiling revealed that <i>OsNHX1</i>, <i>OsNHX2</i>, <i>OsNHX3</i>, and <i>OsNHX5</i> were upregulated under salt stress, with significantly higher expression levels in the salt-tolerant rice cultivar Pokkali compared to the salt-sensitive cultivar IR64. Our findings provide a comprehensive analysis of the evolutionary, structural, and functional features of the <i>OsNHX</i> gene family and highlights their critical role in rice salt tolerance, offering insights into potential applications for crop improvement.https://www.mdpi.com/2037-0164/16/1/6conserved motifsevolutionary relationship<i>NHX</i> gene familyricesalt stress |
| spellingShingle | Hoa Hai Thi Bui Duong Huy Nguyen Le Thu Thi Dinh Hang Thu Thi Trinh Thoa Kim Vu Van Ngoc Bui Comprehensive <i>In Silico</i> Analysis of the <i>NHX</i> (Na<sup>+</sup>/H<sup>+</sup> Antiporter) Gene in Rice (<i>Oryza sativa</i> L.) International Journal of Plant Biology conserved motifs evolutionary relationship <i>NHX</i> gene family rice salt stress |
| title | Comprehensive <i>In Silico</i> Analysis of the <i>NHX</i> (Na<sup>+</sup>/H<sup>+</sup> Antiporter) Gene in Rice (<i>Oryza sativa</i> L.) |
| title_full | Comprehensive <i>In Silico</i> Analysis of the <i>NHX</i> (Na<sup>+</sup>/H<sup>+</sup> Antiporter) Gene in Rice (<i>Oryza sativa</i> L.) |
| title_fullStr | Comprehensive <i>In Silico</i> Analysis of the <i>NHX</i> (Na<sup>+</sup>/H<sup>+</sup> Antiporter) Gene in Rice (<i>Oryza sativa</i> L.) |
| title_full_unstemmed | Comprehensive <i>In Silico</i> Analysis of the <i>NHX</i> (Na<sup>+</sup>/H<sup>+</sup> Antiporter) Gene in Rice (<i>Oryza sativa</i> L.) |
| title_short | Comprehensive <i>In Silico</i> Analysis of the <i>NHX</i> (Na<sup>+</sup>/H<sup>+</sup> Antiporter) Gene in Rice (<i>Oryza sativa</i> L.) |
| title_sort | comprehensive i in silico i analysis of the i nhx i na sup sup h sup sup antiporter gene in rice i oryza sativa i l |
| topic | conserved motifs evolutionary relationship <i>NHX</i> gene family rice salt stress |
| url | https://www.mdpi.com/2037-0164/16/1/6 |
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