Genome Biology
Abstract
Background
In addition to genetic variation, epigenetic variation plays an important role in determining various biological processes. The importance of natural genetic variation to crop domestication and improvement has been widely investigated. However, the contribution of epigenetic variation in crop domestication at population level has rarely been explored.
Results
To understand the impact of epigenetics on crop domestication, we investigate the variation of DNA methylation during soybean domestication and improvement by whole-genome bisulfite sequencing of 45 soybean accessions, including wild soybeans, landraces, and cultivars. Through methylomic analysis, we identify 5412 differentially methylated regions (DMRs). These DMRs exhibit characters distinct from those of genetically selected regions. In particular, they have significantly higher genetic diversity. Association analyses suggest only 22.54% of DMRs can be explained by local genetic variations. Intriguingly, genes in the DMRs that are not associated with any genetic variation are enriched in carbohydrate metabolism pathways.
Conclusions
This study provides a valuable map of DNA methylation across diverse accessions and dissects the relationship between DNA methylation variation and genetic variation during soybean domestication, thus expanding our understanding of soybean domestication and improvement.
| 论文编号: | DOI:10.1186/s13059-018-1516-z |
| 论文题目: | DNA Methylation Footprints during Soybean Domestication and Improvement |
| 英文论文题目: | DNA Methylation Footprints during Soybean Domestication and Improvement |
| 第一作者: | Yanting Shen, Jixiang Zhang, Yucheng Liu, Shulin Liu, Zhi Liu, Zongbiao Duan, Zheng Wang, Baoge Zhu, Ya-Long Guo and Zhixi Tian |
| 英文第一作者: | Yanting Shen, Jixiang Zhang, Yucheng Liu, Shulin Liu, Zhi Liu, Zongbiao Duan, Zheng Wang, Baoge Zhu, Ya-Long Guo and Zhixi Tian |
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| 发表年度: | 2018-09-12 |
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| 摘要: | Background In addition to genetic variation, epigenetic variation plays an important role in determining various biological processes. The importance of natural genetic variation to crop domestication and improvement has been widely investigated. However, the contribution of epigenetic variation in crop domestication at population level has rarely been explored. Results To understand the impact of epigenetics on crop domestication, we investigate the variation of DNA methylation during soybean domestication and improvement by whole-genome bisulfite sequencing of 45 soybean accessions, including wild soybeans, landraces, and cultivars. Through methylomic analysis, we identify 5412 differentially methylated regions (DMRs). These DMRs exhibit characters distinct from those of genetically selected regions. In particular, they have significantly higher genetic diversity. Association analyses suggest only 22.54% of DMRs can be explained by local genetic variations. Intriguingly, genes in the DMRs that are not associated with any genetic variation are enriched in carbohydrate metabolism pathways. Conclusions This study provides a valuable map of DNA methylation across diverse accessions and dissects the relationship between DNA methylation variation and genetic variation during soybean domestication, thus expanding our understanding of soybean domestication and improvement. |
| 英文摘要: | Background In addition to genetic variation, epigenetic variation plays an important role in determining various biological processes. The importance of natural genetic variation to crop domestication and improvement has been widely investigated. However, the contribution of epigenetic variation in crop domestication at population level has rarely been explored. Results To understand the impact of epigenetics on crop domestication, we investigate the variation of DNA methylation during soybean domestication and improvement by whole-genome bisulfite sequencing of 45 soybean accessions, including wild soybeans, landraces, and cultivars. Through methylomic analysis, we identify 5412 differentially methylated regions (DMRs). These DMRs exhibit characters distinct from those of genetically selected regions. In particular, they have significantly higher genetic diversity. Association analyses suggest only 22.54% of DMRs can be explained by local genetic variations. Intriguingly, genes in the DMRs that are not associated with any genetic variation are enriched in carbohydrate metabolism pathways. Conclusions This study provides a valuable map of DNA methylation across diverse accessions and dissects the relationship between DNA methylation variation and genetic variation during soybean domestication, thus expanding our understanding of soybean domestication and improvement. |
| 刊物名称: | Genome Biology |
| 英文刊物名称: | Genome Biology |
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| 其它备注: | Yanting Shen, Jixiang Zhang, Yucheng Liu, Shulin Liu, Zhi Liu, Zongbiao Duan, Zheng Wang, Baoge Zhu, Ya-Long Guo and Zhixi Tian. DNA Methylation Footprints during Soybean Domestication and Improvement. Genome Biology. DOI:10.1186/s13059-018-1516-z |
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