Time-course RNA-seq analysis provides an improved understanding of genetic regulation in response to cold stress from white clover (Trifolium repens L.)
AbstractWhite clover (Trifolium repens L.) is an important legume forage, which is widely distributed in cool-season regions. Therefore, cold stress is a major environmental factor limiting its growth and production, while little is known about the its cold tolerance at molecular level. In the prese...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2022-12-01
|
| Series: | Biotechnology & Biotechnological Equipment |
| Subjects: | |
| Online Access: | https://www.tandfonline.com/doi/10.1080/13102818.2022.2108339 |
| _version_ | 1797974105988792320 |
|---|---|
| author | Xueqi Zhang Huanhuan Yang Manman Li Chao Chen Yan Bai Donglin Guo Changhong Guo Yongjun Shu |
| author_facet | Xueqi Zhang Huanhuan Yang Manman Li Chao Chen Yan Bai Donglin Guo Changhong Guo Yongjun Shu |
| author_sort | Xueqi Zhang |
| collection | DOAJ |
| description | AbstractWhite clover (Trifolium repens L.) is an important legume forage, which is widely distributed in cool-season regions. Therefore, cold stress is a major environmental factor limiting its growth and production, while little is known about the its cold tolerance at molecular level. In the present study, we performed time-course RNA-seq analysis under cold stress. RNA-seq results suggested that genes associated with “oxidoreductase activity” and “transcription regulator activity” are more likely related to the response of white clover to cold stress. To identify the specific gene modules and the hub genes of white clover in response to cold stress, we applied weighted gene co-expression network analyses (WGCNA) to transcriptome data. We also found that gene modules that focus on protein kinase activity, DNA-binding transcription factor activity and oxidoreductase activity, are more likely to be involved in the response of white clover to cold stress. Especially, we identified several AP2/ERF TF genes and CDPK genes as pivotal genes in white clover in response to cold stress, which would provide helpful insights into the molecular mechanisms underlying the response of white clover to cold stress. |
| first_indexed | 2024-04-11T04:14:48Z |
| format | Article |
| id | doaj.art-14295da46f044312adc559ba4cfd9b0e |
| institution | Directory Open Access Journal |
| issn | 1310-2818 1314-3530 |
| language | English |
| last_indexed | 2024-04-11T04:14:48Z |
| publishDate | 2022-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Biotechnology & Biotechnological Equipment |
| spelling | doaj.art-14295da46f044312adc559ba4cfd9b0e2022-12-31T18:03:16ZengTaylor & Francis GroupBiotechnology & Biotechnological Equipment1310-28181314-35302022-12-0136174575210.1080/13102818.2022.2108339Time-course RNA-seq analysis provides an improved understanding of genetic regulation in response to cold stress from white clover (Trifolium repens L.)Xueqi Zhang0Huanhuan Yang1Manman Li2Chao Chen3Yan Bai4Donglin Guo5Changhong Guo6Yongjun Shu7Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, PR ChinaKey Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, PR ChinaKey Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, PR ChinaKey Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, PR ChinaKey Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, PR ChinaKey Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, PR ChinaKey Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, PR ChinaKey Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, PR ChinaAbstractWhite clover (Trifolium repens L.) is an important legume forage, which is widely distributed in cool-season regions. Therefore, cold stress is a major environmental factor limiting its growth and production, while little is known about the its cold tolerance at molecular level. In the present study, we performed time-course RNA-seq analysis under cold stress. RNA-seq results suggested that genes associated with “oxidoreductase activity” and “transcription regulator activity” are more likely related to the response of white clover to cold stress. To identify the specific gene modules and the hub genes of white clover in response to cold stress, we applied weighted gene co-expression network analyses (WGCNA) to transcriptome data. We also found that gene modules that focus on protein kinase activity, DNA-binding transcription factor activity and oxidoreductase activity, are more likely to be involved in the response of white clover to cold stress. Especially, we identified several AP2/ERF TF genes and CDPK genes as pivotal genes in white clover in response to cold stress, which would provide helpful insights into the molecular mechanisms underlying the response of white clover to cold stress.https://www.tandfonline.com/doi/10.1080/13102818.2022.2108339Trifolium repensoxidoreductaseWGCNAAP2/ERFCDPK |
| spellingShingle | Xueqi Zhang Huanhuan Yang Manman Li Chao Chen Yan Bai Donglin Guo Changhong Guo Yongjun Shu Time-course RNA-seq analysis provides an improved understanding of genetic regulation in response to cold stress from white clover (Trifolium repens L.) Biotechnology & Biotechnological Equipment Trifolium repens oxidoreductase WGCNA AP2/ERF CDPK |
| title | Time-course RNA-seq analysis provides an improved understanding of genetic regulation in response to cold stress from white clover (Trifolium repens L.) |
| title_full | Time-course RNA-seq analysis provides an improved understanding of genetic regulation in response to cold stress from white clover (Trifolium repens L.) |
| title_fullStr | Time-course RNA-seq analysis provides an improved understanding of genetic regulation in response to cold stress from white clover (Trifolium repens L.) |
| title_full_unstemmed | Time-course RNA-seq analysis provides an improved understanding of genetic regulation in response to cold stress from white clover (Trifolium repens L.) |
| title_short | Time-course RNA-seq analysis provides an improved understanding of genetic regulation in response to cold stress from white clover (Trifolium repens L.) |
| title_sort | time course rna seq analysis provides an improved understanding of genetic regulation in response to cold stress from white clover trifolium repens l |
| topic | Trifolium repens oxidoreductase WGCNA AP2/ERF CDPK |
| url | https://www.tandfonline.com/doi/10.1080/13102818.2022.2108339 |
| work_keys_str_mv | AT xueqizhang timecoursernaseqanalysisprovidesanimprovedunderstandingofgeneticregulationinresponsetocoldstressfromwhiteclovertrifoliumrepensl AT huanhuanyang timecoursernaseqanalysisprovidesanimprovedunderstandingofgeneticregulationinresponsetocoldstressfromwhiteclovertrifoliumrepensl AT manmanli timecoursernaseqanalysisprovidesanimprovedunderstandingofgeneticregulationinresponsetocoldstressfromwhiteclovertrifoliumrepensl AT chaochen timecoursernaseqanalysisprovidesanimprovedunderstandingofgeneticregulationinresponsetocoldstressfromwhiteclovertrifoliumrepensl AT yanbai timecoursernaseqanalysisprovidesanimprovedunderstandingofgeneticregulationinresponsetocoldstressfromwhiteclovertrifoliumrepensl AT donglinguo timecoursernaseqanalysisprovidesanimprovedunderstandingofgeneticregulationinresponsetocoldstressfromwhiteclovertrifoliumrepensl AT changhongguo timecoursernaseqanalysisprovidesanimprovedunderstandingofgeneticregulationinresponsetocoldstressfromwhiteclovertrifoliumrepensl AT yongjunshu timecoursernaseqanalysisprovidesanimprovedunderstandingofgeneticregulationinresponsetocoldstressfromwhiteclovertrifoliumrepensl |