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Multi‐omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation process

Li, J.; Wang, M.; Li, Y.; Zhang, Q.; Lindsey, K.; Daniell, H.; Jin, S.; Zhang, X.

Multi‐omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation process Thumbnail


Authors

J. Li

M. Wang

Y. Li

Q. Zhang

H. Daniell

S. Jin

X. Zhang



Abstract

Plant regeneration via somatic embryogenesis is time‐consuming and highly genotype‐dependent. The plant somatic embryogenesis process provokes many epigenetics changes including DNA methylation and histone modification. Recently, an elite cotton Jin668, with an extremely high regeneration ability, was developed from its maternal inbred Y668 cultivar using a Successive Regeneration Acclimation (SRA) strategy. To reveal the underlying mechanism of SRA, we carried out a genome‐wide single‐base resolution methylation analysis for non‐embryogenic calluses (NECs), ECs, somatic embryos (SEs) during the somatic embryogenesis procedure and the leaves of regenerated offspring plants. Jin668 (R4) regenerated plants were CHH hypomethylated compared with the R0 regenerated plants of SRA process. The increase of CHH methylation from NEC to EC were demonstrated to be associated with the RNA‐dependent DNA methylation (RdDM) and the H3K9me2‐dependent pathway. Intriguingly, the hypomethylated CHH differentially methylated regions (DMRs) of promoter activated some hormone‐related and WUSCHEL‐related homeobox genes during the somatic embryogenesis process. Inhibiting DNA methylation using zebularine treatment in NEC increased the number of embryos. Our multi‐omics data provide new insights into the dynamics of DNA methylation during the plant tissue culture and regenerated offspring plants. This study also reveals that induced hypomethylation (SRA) may faciliate the higher plant regeneration ability and optimize maternal genetic cultivar.

Journal Article Type Article
Acceptance Date Jul 10, 2018
Online Publication Date Jul 12, 2018
Publication Date Feb 28, 2019
Deposit Date Jul 13, 2018
Publicly Available Date Jul 13, 2018
Journal Plant Biotechnology Journal
Print ISSN 1467-7644
Electronic ISSN 1467-7652
Publisher Association of Applied Biologists
Peer Reviewed Peer Reviewed
Volume 17
Issue 2
Pages 435-450
DOI https://doi.org/10.1111/pbi.12988
Public URL https://durham-repository.worktribe.com/output/1321271

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Publisher Licence URL
http://creativecommons.org/licenses/by/4.0/

Copyright Statement
© 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.






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