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Gene body demethylation increases expression and is associated with self-pruning during grape genome duplication
Zou, Luming1,2; Liu, Wenwen1,2; Zhang, Zhan1,2,3; Edwards, Everard J.; Gathunga, Elias Kirabi1,2; Fan, Peige1; Duan, Wei1; Li, Shaohua1,2; Liang, Zhenchang1,5
AbstractA colchicine-induced autotetraploid grapevine exhibiting potentially valuable agronomic traits for grape production and breeding, including self-pruning, was identified. This study investigated DNA methylation variation and its role in gene expression during self-pruning in the autotetraploid grapevine. We used RNA-Seq to estimate differentially expressed genes between diploid and autotetraploid grapevine shoot tips. The genes showing increases in the autotetraploid were mainly related to stress response pathways, whereas those showing decreases in the autotetraploid were related to biological metabolism and biosynthesis. Whole-genome bisulfite sequencing was performed to produce single-base methylomes for the diploid and autotetraploid grapevines. Comparison between the methylomes revealed that they were conserved in CG and CHG contexts. In the autotetraploid grapevine, hypodifferentially methylated regions (DMRs) and hyper-DMRs in the gene body increased or decreased gene expression, respectively. Our results indicated that a hypo-DMR in the ACO1 gene body increased its expression and might promote self-pruning. This study reports that hypo-DMRs in the gene body increase gene expression in plants and reveals the mechanism underlying the changes in the modifications affecting gene expression during genome duplication. Overall, our results provide valuable information for understanding the relationships between DNA methylation, gene expression, and autotetraploid breeding in grape.
Subject AreaPlant Sciences ; Genetics & Heredity ; Horticulture
Indexed BySCI
WOS Research AreaPlant Sciences ; Genetics & Heredity ; Agriculture
WOS IDWOS:000538044000006
Publication PlaceNANJING
Funding OrganizationNational Key Research and Development Program of China [2018YFD1000105] ; National Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31772266] ; Agricultural Breeding Project of Ningxia Hui Autonomous Region [NXNYYZ20150203] ; STS Project of the Chinese Academy of Sciences [KFJ-STS-ZDTP-025]
Corresponding Author Emailshhli@ibcas.ac.cn ; zl249@ibcas.ac.cn
OAGreen Published, gold
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Cited Times:3[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Affiliation1.Chinese Acad Sci, Inst Bot, Beijing Key Lab Grape Sci & Enol, Beijing 100093, Peoples R China
2.Chinese Acad Sci, Inst Bot, CAS Key Lab Plant Resources, Beijing 100093, Peoples R China
3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
4.Shaanxi Normal Univ, Coll Life Sci, Xian 041004, Shanxi, Peoples R China
5.Edwards, Everard J.] CSIRO Agr & Food, Locked Bag 2, Glen Osmond, SA 5064, Australia
6.Chinese Acad Sci, Sino Africa Joint Res Ctr, Wuhan 430074, Peoples R China
Recommended Citation
GB/T 7714
Zou, Luming,Liu, Wenwen,Zhang, Zhan,et al. Gene body demethylation increases expression and is associated with self-pruning during grape genome duplication[J]. HORTICULTURE RESEARCH,2020,7(1).
APA Zou, Luming.,Liu, Wenwen.,Zhang, Zhan.,Edwards, Everard J..,Gathunga, Elias Kirabi.,...&Liang, Zhenchang.(2020).Gene body demethylation increases expression and is associated with self-pruning during grape genome duplication.HORTICULTURE RESEARCH,7(1).
MLA Zou, Luming,et al."Gene body demethylation increases expression and is associated with self-pruning during grape genome duplication".HORTICULTURE RESEARCH 7.1(2020).
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