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| DNA methylation footprints during soybean domestication and improvement | |
Shen, Yanting; Zhang, Jixiang; Liu, Yucheng; Liu, Shulin; Liu, Zhi; Duan, Zongbiao; Wang, Zheng; Zhu, Baoge; Guo, Ya-Long ; Tian, Zhixi2
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| 2018 | |
| Source Publication | GENOME BIOLOGY
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| ISSN | 1474-760X |
| Volume | 19 |
| 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. |
| Keyword | DNA methylation Domestication Soybean |
| Subject Area | Biotechnology & Applied Microbiology ; Genetics & Heredity |
| DOI | 10.1186/s13059-018-1516-z |
| Indexed By | SCI |
| Language | 英语 |
| WOS Keyword | GENOME-WIDE ASSOCIATION ; NATURAL EPIGENETIC VARIATION ; ARABIDOPSIS-THALIANA ; AGRONOMIC TRAITS ; TRANSPOSABLE ELEMENTS ; EPIGENOMIC DIVERSITY ; ANALYSIS TOOLKIT ; SEQUENCING DATA ; PLANT ; POPULATION |
| WOS ID | WOS:000444255100001 |
| Publisher | BMC |
| Subtype | Article |
| Publication Place | LONDON |
| Funding Organization | National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [91531304, 31525018, 31788103] ; Strategic Priority Research Program of the Chinese Academy of SciencesChinese Academy of Sciences [XDA08000000] |
| Corresponding Author Email | zxtian@genetics.ac.cn |
| OA | gold, Green Published |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.ibcas.ac.cn/handle/2S10CLM1/20339 |
| Collection | 系统与进化植物学国家重点实验室 |
| Affiliation | 1.Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Plant Cell & Chromosome Engn, Beijing 100101, Peoples R China 2.Chinese Acad Sci, State Key Lab Systemat & Evolutionary Bot, Inst Bot, Beijing 100093, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100039, Peoples R China |
| Recommended Citation GB/T 7714 | Shen, Yanting,Zhang, Jixiang,Liu, Yucheng,et al. DNA methylation footprints during soybean domestication and improvement[J]. GENOME BIOLOGY,2018,19. |
| APA | Shen, Yanting.,Zhang, Jixiang.,Liu, Yucheng.,Liu, Shulin.,Liu, Zhi.,...&Tian, Zhixi.(2018).DNA methylation footprints during soybean domestication and improvement.GENOME BIOLOGY,19. |
| MLA | Shen, Yanting,et al."DNA methylation footprints during soybean domestication and improvement".GENOME BIOLOGY 19(2018). |
| Files in This Item: | ||||||
| File Name/Size | DocType | Version | Access | License | ||
| Shen-2018-DNA methyl（1815KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View Application Full Text | |
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