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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
2018
发表期刊GENOME BIOLOGY
ISSN1474-760X
卷号19
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.
关键词DNA methylation Domestication Soybean
学科领域Biotechnology & Applied Microbiology ; Genetics & Heredity
DOI10.1186/s13059-018-1516-z
收录类别SCI
语种英语
WOS关键词GENOME-WIDE ASSOCIATION ; NATURAL EPIGENETIC VARIATION ; ARABIDOPSIS-THALIANA ; AGRONOMIC TRAITS ; TRANSPOSABLE ELEMENTS ; EPIGENOMIC DIVERSITY ; ANALYSIS TOOLKIT ; SEQUENCING DATA ; PLANT ; POPULATION
WOS记录号WOS:000444255100001
出版者BMC
文献子类Article
出版地LONDON
资助机构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]
作者邮箱zxtian@genetics.ac.cn
作品OA属性gold, Green Published
引用统计
被引频次:48[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.ibcas.ac.cn/handle/2S10CLM1/20339
专题系统与进化植物学国家重点实验室
作者单位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
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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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