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

Plant Biotechnology Journal
Jianying LiXianlong 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 nonembryogenic 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 in CHH methylation from NEC to EC was 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. ...Continue Reading

References

Jul 13, 2001·Plant Science : an International Journal of Experimental Plant Biology·S Peraza-EcheverriaA -J. Kay
Jul 23, 2004·Nature·Zachary LippmanRob Martienssen
May 25, 2007·Nature·Ian R Henderson, Steven E Jacobsen
Jun 17, 2008·Plant Molecular Biology·Sanjeev Kumar SharmaGlenn J Bryan
Sep 4, 2008·Proceedings of the National Academy of Sciences of the United States of America·Qianwen Sun, Dao-Xiu Zhou
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Dec 17, 2008·PLoS Biology·Milos TanurdzicRobert A Martienssen
Oct 13, 2009·Plant Signaling & Behavior·Dolores Abarca, Carmen Díaz-Sala
Feb 5, 2010·Trends in Plant Science·Rebecca A Mosher, Charles W Melnyk
Feb 10, 2010·Nature Reviews. Genetics·Julie A Law, Steven E Jacobsen
Apr 16, 2011·Bioinformatics·Felix Krueger, Simon R Andrews
May 28, 2011·Journal of Experimental Botany·Célia Miguel, Liliana Marum
Dec 28, 2012·Genome Research·Jonathan I GentR Kelly Dawe
Feb 6, 2013·Journal of Experimental Botany·Xiyan YangXianlong Zhang
Jun 12, 2013·Nature Reviews. Genetics·Z Jeffrey Chen
Dec 18, 2013·Nature Structural & Molecular Biology·Hume StroudSteven E Jacobsen
Jan 28, 2014·The Arabidopsis Book·Joseph J Kieber, G Eric Schaller
May 9, 2014·Nature Reviews. Genetics·Marjori A Matzke, Rebecca A Mosher
Aug 22, 2015·Nature Reviews. Molecular Cell Biology·Jiamu DuDinshaw J Patel
Sep 9, 2015·Frontiers in Plant Science·Clelia De-la-PeñaVíctor M Loyola-Vargas
Sep 10, 2015·Nature·Meilina Ong-AbdullahRobert A Martienssen
Oct 12, 2015·Current Opinion in Plant Biology·Momoko IkeuchiKeiko Sugimoto
May 5, 2016·Development·Momoko IkeuchiKeiko Sugimoto
Jul 29, 2016·The Plant Cell·Marcelinus R HatoranganClaudia Köhler
Mar 4, 2017·The Plant Journal : for Cell and Molecular Biology·Falk ZakrzewskiThomas Schmidt

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Citations

Apr 1, 2020·International Journal of Molecular Sciences·Barbara WójcikowskaMałgorzata D Gaj
Jul 6, 2019·Frontiers in Plant Science·Taras Pasternak, Denes Dudits
Oct 20, 2018·International Journal of Molecular Sciences·Pedro Osorio-MontalvoClelia De-la-Peña
Jan 23, 2021·Journal of Cellular Physiology·Sijia LiangShuangxia Jin
Mar 18, 2021·Journal of Biological Research·Renata Orłowska
Mar 6, 2021·The Plant Journal : for Cell and Molecular Biology·Yanfei PeiTianzhen Zhang
Apr 13, 2021·Theoretical and Experimental Plant Physiology·Milton C Lima NetoJoaquim A G Silveira
Jun 24, 2021·The Plant Journal : for Cell and Molecular Biology·Meng ZhangShuxun Yu
Aug 11, 2021·Plants·Camille SalaünBertrand Dubreucq

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Datasets Mentioned

BETA
PRJNA380842

Methods Mentioned

BETA
genetic modifications
transgenic
PCR
immunoprecipitation
Illumina sequencing

Software Mentioned

customized
Trimmomatic
NGSQC
Cuffdiff
Perl scripts
bismark
Bowtie2
Blast2GO
MACS
genome

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