Using WGCNA and transcriptome profiling to identify hub genes for salt stress tolerance in germinating soybean seeds
Salinized soil can significantly hinder soybean growth, leading to a reduction in overall yield. To address this issue, identifying key genes related to salt tolerance in soybeans is essential for improving their resistance to salinity and ensuring sustainable development of soybean production. Whil...
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| Language: | English |
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Frontiers Media S.A.
2025-08-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2025.1569565/full |
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| author | Lijun Pan Yifan Chen Zeyu Ren Dalia Mohamedkheir Khojely Dalia Mohamedkheir Khojely Siyu Wang Yueming Li Seifeldin Elrayah Ibrahim Seifeldin Elrayah Ibrahim Sujie Fan Yang Song Zhuo Zhang Jian Wei |
| author_facet | Lijun Pan Yifan Chen Zeyu Ren Dalia Mohamedkheir Khojely Dalia Mohamedkheir Khojely Siyu Wang Yueming Li Seifeldin Elrayah Ibrahim Seifeldin Elrayah Ibrahim Sujie Fan Yang Song Zhuo Zhang Jian Wei |
| author_sort | Lijun Pan |
| collection | DOAJ |
| description | Salinized soil can significantly hinder soybean growth, leading to a reduction in overall yield. To address this issue, identifying key genes related to salt tolerance in soybeans is essential for improving their resistance to salinity and ensuring sustainable development of soybean production. While current research predominantly focuses on salt tolerance during the seedling stage, there is still a lack of comprehensive studies on the genes involved in salt tolerance during the germination stage. This study established the optimal screening criteria by phenotyping the salt-tolerant variety R063 and the salt-sensitive variety W82 during the germination stage under salt stress. RNA-seq analysis was performed on 24 samples from both varieties at 36 and 48 hours under two different salt concentrations (0 and 150 mM/L NaCl). Differential expression analysis revealed that the salt-tolerant variety R063 exhibited the fewest differentially expressed genes (DEGs) compared to its control after 48 hours of salt stress. A total of 305 DEGs were commonly identified between the salt-tolerant variety R063 and the salt-sensitive variety W82 under salt stress at both time points. Additionally, 187 DEGs were commonly identified between R063 under salt stress and its corresponding control group across the two time points. Gene ontology (GO) enrichment analysis revealed that the differentially expressed genes were significantly enriched in ADP binding, monooxygenase activity, oxidoreductase activity, defense response, and protein phosphorylation signaling pathways. The weighted gene co-expression network analysis (WGCNA) method was employed to identify modules strongly correlated with salt tolerance during soybean germination. Candidate genes associated with soybean sprouting salt tolerance were identified by evaluating the connectivity and expression profiles of genes within these modules. These findings provide a theoretical foundation for further elucidating the molecular mechanisms underlying salt tolerance during soybean germination and present new genetic resources for studying this trait. |
| format | Article |
| id | doaj-art-7b238c85d8e648ad9ea480aba0cd6c2c |
| institution | DOAJ |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj-art-7b238c85d8e648ad9ea480aba0cd6c2c2025-08-20T02:55:06ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-08-011610.3389/fpls.2025.15695651569565Using WGCNA and transcriptome profiling to identify hub genes for salt stress tolerance in germinating soybean seedsLijun Pan0Yifan Chen1Zeyu Ren2Dalia Mohamedkheir Khojely3Dalia Mohamedkheir Khojely4Siyu Wang5Yueming Li6Seifeldin Elrayah Ibrahim7Seifeldin Elrayah Ibrahim8Sujie Fan9Yang Song10Zhuo Zhang11Jian Wei12Plant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, ChinaPlant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, ChinaPlant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, ChinaPlant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, ChinaGezira Research Station, Agricultural Research Corporation (ARC), Wad Madani, SudanPlant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, ChinaPlant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, ChinaPlant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, ChinaGezira Research Station, Agricultural Research Corporation (ARC), Wad Madani, SudanPlant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, ChinaPlant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, ChinaPlant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, ChinaPlant Biotechnology Center, College of Agronomy, Jilin Agriculture University, Changchun, Jilin, ChinaSalinized soil can significantly hinder soybean growth, leading to a reduction in overall yield. To address this issue, identifying key genes related to salt tolerance in soybeans is essential for improving their resistance to salinity and ensuring sustainable development of soybean production. While current research predominantly focuses on salt tolerance during the seedling stage, there is still a lack of comprehensive studies on the genes involved in salt tolerance during the germination stage. This study established the optimal screening criteria by phenotyping the salt-tolerant variety R063 and the salt-sensitive variety W82 during the germination stage under salt stress. RNA-seq analysis was performed on 24 samples from both varieties at 36 and 48 hours under two different salt concentrations (0 and 150 mM/L NaCl). Differential expression analysis revealed that the salt-tolerant variety R063 exhibited the fewest differentially expressed genes (DEGs) compared to its control after 48 hours of salt stress. A total of 305 DEGs were commonly identified between the salt-tolerant variety R063 and the salt-sensitive variety W82 under salt stress at both time points. Additionally, 187 DEGs were commonly identified between R063 under salt stress and its corresponding control group across the two time points. Gene ontology (GO) enrichment analysis revealed that the differentially expressed genes were significantly enriched in ADP binding, monooxygenase activity, oxidoreductase activity, defense response, and protein phosphorylation signaling pathways. The weighted gene co-expression network analysis (WGCNA) method was employed to identify modules strongly correlated with salt tolerance during soybean germination. Candidate genes associated with soybean sprouting salt tolerance were identified by evaluating the connectivity and expression profiles of genes within these modules. These findings provide a theoretical foundation for further elucidating the molecular mechanisms underlying salt tolerance during soybean germination and present new genetic resources for studying this trait.https://www.frontiersin.org/articles/10.3389/fpls.2025.1569565/fullsoybeangerminationsalt stress tolerancetranscriptome profilingWGCNA |
| spellingShingle | Lijun Pan Yifan Chen Zeyu Ren Dalia Mohamedkheir Khojely Dalia Mohamedkheir Khojely Siyu Wang Yueming Li Seifeldin Elrayah Ibrahim Seifeldin Elrayah Ibrahim Sujie Fan Yang Song Zhuo Zhang Jian Wei Using WGCNA and transcriptome profiling to identify hub genes for salt stress tolerance in germinating soybean seeds Frontiers in Plant Science soybean germination salt stress tolerance transcriptome profiling WGCNA |
| title | Using WGCNA and transcriptome profiling to identify hub genes for salt stress tolerance in germinating soybean seeds |
| title_full | Using WGCNA and transcriptome profiling to identify hub genes for salt stress tolerance in germinating soybean seeds |
| title_fullStr | Using WGCNA and transcriptome profiling to identify hub genes for salt stress tolerance in germinating soybean seeds |
| title_full_unstemmed | Using WGCNA and transcriptome profiling to identify hub genes for salt stress tolerance in germinating soybean seeds |
| title_short | Using WGCNA and transcriptome profiling to identify hub genes for salt stress tolerance in germinating soybean seeds |
| title_sort | using wgcna and transcriptome profiling to identify hub genes for salt stress tolerance in germinating soybean seeds |
| topic | soybean germination salt stress tolerance transcriptome profiling WGCNA |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2025.1569565/full |
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