Dynamic DNA methylation modification in peanut seed development
Summary: Cytosine methylation is an important epigenetic modification involved in regulation of plant development. However, the epigenetic mechanisms governing peanut seed development remain unclear. Herein, we generated DNA methylation profiles of developmental seeds of peanut H2014 and its smaller...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-07-01
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| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004223011392 |
| _version_ | 1797774571163615232 |
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| author | Zhongfeng Li Qian Liu Kai Zhao Di Cao Zenghui Cao Kunkun Zhao Qian Ma Gaidan Zhai Sasa Hu Zhan Li Kuopeng Wang Fangping Gong Xingli Ma Xingguo Zhang Rui Ren Ding Qiu Yu Zhao Dongmei Yin |
| author_facet | Zhongfeng Li Qian Liu Kai Zhao Di Cao Zenghui Cao Kunkun Zhao Qian Ma Gaidan Zhai Sasa Hu Zhan Li Kuopeng Wang Fangping Gong Xingli Ma Xingguo Zhang Rui Ren Ding Qiu Yu Zhao Dongmei Yin |
| author_sort | Zhongfeng Li |
| collection | DOAJ |
| description | Summary: Cytosine methylation is an important epigenetic modification involved in regulation of plant development. However, the epigenetic mechanisms governing peanut seed development remain unclear. Herein, we generated DNA methylation profiles of developmental seeds of peanut H2014 and its smaller seed mutant H1314 at 15 and 60 days after pegging (DAP, S1, S4). Accompanying seed development, globally elevated methylation was observed in both lines. The mutant had a higher methylation level of 31.1% than wild type at S4, and 27.1–35.9% of the differentially methylated regions (DMRs) between the two lines were distributed in promoter or genic regions at both stages. Integrated methylome and transcriptome analysis revealed important methylation variations closely associated with seed development. Furthermore, some genes showed significantly negative correlation of expression with the methylation level within promoter or gene body. The results provide insights into the roles of DNA methylation in peanut seed development. |
| first_indexed | 2024-03-12T22:23:01Z |
| format | Article |
| id | doaj.art-c4a95a24ee9f45ab8f5dab4001164135 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-03-12T22:23:01Z |
| publishDate | 2023-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-c4a95a24ee9f45ab8f5dab40011641352023-07-23T04:55:23ZengElsevieriScience2589-00422023-07-01267107062Dynamic DNA methylation modification in peanut seed developmentZhongfeng Li0Qian Liu1Kai Zhao2Di Cao3Zenghui Cao4Kunkun Zhao5Qian Ma6Gaidan Zhai7Sasa Hu8Zhan Li9Kuopeng Wang10Fangping Gong11Xingli Ma12Xingguo Zhang13Rui Ren14Ding Qiu15Yu Zhao16Dongmei Yin17College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, ChinaNational Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei Province, ChinaCollege of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, ChinaCollege of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, ChinaCollege of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, ChinaCollege of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, ChinaCollege of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, ChinaCollege of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, ChinaCollege of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, ChinaCollege of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, ChinaCollege of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, ChinaCollege of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, ChinaCollege of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, ChinaCollege of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, ChinaCollege of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, ChinaCollege of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, ChinaNational Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China; Corresponding authorCollege of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan Province, China; Corresponding authorSummary: Cytosine methylation is an important epigenetic modification involved in regulation of plant development. However, the epigenetic mechanisms governing peanut seed development remain unclear. Herein, we generated DNA methylation profiles of developmental seeds of peanut H2014 and its smaller seed mutant H1314 at 15 and 60 days after pegging (DAP, S1, S4). Accompanying seed development, globally elevated methylation was observed in both lines. The mutant had a higher methylation level of 31.1% than wild type at S4, and 27.1–35.9% of the differentially methylated regions (DMRs) between the two lines were distributed in promoter or genic regions at both stages. Integrated methylome and transcriptome analysis revealed important methylation variations closely associated with seed development. Furthermore, some genes showed significantly negative correlation of expression with the methylation level within promoter or gene body. The results provide insights into the roles of DNA methylation in peanut seed development.http://www.sciencedirect.com/science/article/pii/S2589004223011392EpigeneticsPlant developmentTranscriptomics |
| spellingShingle | Zhongfeng Li Qian Liu Kai Zhao Di Cao Zenghui Cao Kunkun Zhao Qian Ma Gaidan Zhai Sasa Hu Zhan Li Kuopeng Wang Fangping Gong Xingli Ma Xingguo Zhang Rui Ren Ding Qiu Yu Zhao Dongmei Yin Dynamic DNA methylation modification in peanut seed development iScience Epigenetics Plant development Transcriptomics |
| title | Dynamic DNA methylation modification in peanut seed development |
| title_full | Dynamic DNA methylation modification in peanut seed development |
| title_fullStr | Dynamic DNA methylation modification in peanut seed development |
| title_full_unstemmed | Dynamic DNA methylation modification in peanut seed development |
| title_short | Dynamic DNA methylation modification in peanut seed development |
| title_sort | dynamic dna methylation modification in peanut seed development |
| topic | Epigenetics Plant development Transcriptomics |
| url | http://www.sciencedirect.com/science/article/pii/S2589004223011392 |
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