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Sun Q, Qiao J, Zhang S, He S, Shi Y, Yuan Y, Zhang X, Cai Y. Changes in DNA methylation assessed by genomic bisulfite sequencing suggest a role for DNA methylation in cotton fruiting branch development. PeerJ 2018; 6:e4945. [PMID: 29915693 PMCID: PMC6004305 DOI: 10.7717/peerj.4945] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/18/2018] [Indexed: 12/20/2022] Open
Abstract
Cotton plant architecture, including fruit branch formation and flowering pattern, influences plant light exploitation, cotton yield and planting cost. DNA methylation has been widely observed at different developmental stages in both plants and animals and is associated with regulation of gene expression, chromatin remodelling, genome protection and other functions. Here, we investigated the global epigenetic reprogramming during the development of fruiting branches and floral buds at three developmental stages: the seedling stage, the pre-squaring stage and the squaring stage. We first identified 22 cotton genes which potentially encode DNA methyltransferases and demethylases. Among them, the homologous genes of CMT, DRM2 and MET1 were upregulated at pre-squaring and squaring stages, suggesting that DNA methylation is involved in the development of floral buds and fruit branches. Although the global methylation at all of three developmental stages was not changed, the CHG-type methylation of non-expressed genes was higher than those of expressed genes. In addition, we found that the expression of the homologous genes of the key circadian rhythm regulators, including CRY, LHY and CO, was associated with changes of DNA methylation at three developmental stages.
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Affiliation(s)
- Quan Sun
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China.,Chongqing University of Posts and Telecommunications, College of Bioinformation, ChongQing, China
| | - Jing Qiao
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China
| | - Sai Zhang
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China
| | - Shibin He
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China
| | - Yuzhen Shi
- Cotton Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Youlu Yuan
- Cotton Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Xiao Zhang
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China.,Cotton Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Yingfan Cai
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China
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