IB-CAS  > 系统与进化植物学国家重点实验室
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
2018
Source PublicationGENOME BIOLOGY
ISSN1474-760X
Volume19
AbstractBackground: 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.
KeywordDNA methylation Domestication Soybean
Subject AreaBiotechnology & Applied Microbiology ; Genetics & Heredity
DOI10.1186/s13059-018-1516-z
Indexed BySCI
Language英语
WOS KeywordGENOME-WIDE ASSOCIATION ; NATURAL EPIGENETIC VARIATION ; ARABIDOPSIS-THALIANA ; AGRONOMIC TRAITS ; TRANSPOSABLE ELEMENTS ; EPIGENOMIC DIVERSITY ; ANALYSIS TOOLKIT ; SEQUENCING DATA ; PLANT ; POPULATION
WOS IDWOS:000444255100001
PublisherBMC
SubtypeArticle
Publication PlaceLONDON
Funding OrganizationNational 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 Emailzxtian@genetics.ac.cn
OAgold, Green Published
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Cited Times:27[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ibcas.ac.cn/handle/2S10CLM1/20339
Collection系统与进化植物学国家重点实验室
Affiliation1.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).
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