Dynamic Changes of DNA Methylation During Wild Strawberry (Fragaria nilgerrensis) Tissue Culture

Tissue culture is an important tool for asexual propagation and genetic transformation of strawberry plants. In plant tissue culture, variation of DNA methylation is a potential source of phenotypic variation in regenerated plants. However, the genome wide dynamic methylation patterns of strawberry...

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Autores principales:	Qiang Cao, Yuxi Feng, Xiongwei Dai, Lin Huang, Jiamin Li, Pang Tao, M. James C. Crabbe, Ticao Zhang, Qin Qiao
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	Fragaria nilgerrensis tissue culture somaclonal variations DNA methylation gene expression Plant culture SB1-1110
Acceso en línea:	https://doaj.org/article/75b9f0c2d80f404eba70aa014f0cf564
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spelling	oai:doaj.org-article:75b9f0c2d80f404eba70aa014f0cf5642021-12-01T16:59:47ZDynamic Changes of DNA Methylation During Wild Strawberry (Fragaria nilgerrensis) Tissue Culture1664-462X10.3389/fpls.2021.765383https://doaj.org/article/75b9f0c2d80f404eba70aa014f0cf5642021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fpls.2021.765383/fullhttps://doaj.org/toc/1664-462XTissue culture is an important tool for asexual propagation and genetic transformation of strawberry plants. In plant tissue culture, variation of DNA methylation is a potential source of phenotypic variation in regenerated plants. However, the genome wide dynamic methylation patterns of strawberry tissue culture remain unclear. In this study, we used whole-genome bisulfite sequencing (WGBS) to study genomic DNA methylation changes of a wild strawberry Fragaria nilgerrensis at six stages: from explants of shoot tips to outplanting and acclimation. Global methylation levels showed that CG sites exhibited the highest methylation level in all stages with an average of 49.5%, followed by CHG (33.2%) and CHH (12.4%). Although CHH accounted for the lowest proportion of total cytosine methylation, it showed the most obvious methylation change and the most of these changes occurred in the transposable element regions. The overall methylation levels alternately decreased and increased during the entire tissue culture process and the distribution of DNA methylation was non-uniform among different genetic regions. Furthermore, much more differentially methylated regions (DMRs) were detected in dedifferentiation and redifferentiation stages and most of them were transposable elements, suggesting these processes involved activating or silencing of amounts of transposons. The functional enrichment of the DMR-related genes indicated that genes involved in hormone metabolic processes, plant development and the stress response changed methylation throughout the tissue culture process. Finally, the quantitative real-time PCR (qRT-PCR) was conducted to examine the association of methylation and gene expression of a set of different methylated genes. Our findings give deeper insight into the epigenetic regulation of gene expression during the plant tissue cultures process, which will be useful in the efficient control of somaclonal variations and in crop improvement.Qiang CaoYuxi FengXiongwei DaiLin HuangJiamin LiPang TaoM. James C. CrabbeM. James C. CrabbeM. James C. CrabbeTicao ZhangQin QiaoFrontiers Media S.A.articleFragaria nilgerrensistissue culturesomaclonal variationsDNA methylationgene expressionPlant cultureSB1-1110ENFrontiers in Plant Science, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Fragaria nilgerrensis tissue culture somaclonal variations DNA methylation gene expression Plant culture SB1-1110
spellingShingle	Fragaria nilgerrensis tissue culture somaclonal variations DNA methylation gene expression Plant culture SB1-1110 Qiang Cao Yuxi Feng Xiongwei Dai Lin Huang Jiamin Li Pang Tao M. James C. Crabbe M. James C. Crabbe M. James C. Crabbe Ticao Zhang Qin Qiao Dynamic Changes of DNA Methylation During Wild Strawberry (Fragaria nilgerrensis) Tissue Culture
description	Tissue culture is an important tool for asexual propagation and genetic transformation of strawberry plants. In plant tissue culture, variation of DNA methylation is a potential source of phenotypic variation in regenerated plants. However, the genome wide dynamic methylation patterns of strawberry tissue culture remain unclear. In this study, we used whole-genome bisulfite sequencing (WGBS) to study genomic DNA methylation changes of a wild strawberry Fragaria nilgerrensis at six stages: from explants of shoot tips to outplanting and acclimation. Global methylation levels showed that CG sites exhibited the highest methylation level in all stages with an average of 49.5%, followed by CHG (33.2%) and CHH (12.4%). Although CHH accounted for the lowest proportion of total cytosine methylation, it showed the most obvious methylation change and the most of these changes occurred in the transposable element regions. The overall methylation levels alternately decreased and increased during the entire tissue culture process and the distribution of DNA methylation was non-uniform among different genetic regions. Furthermore, much more differentially methylated regions (DMRs) were detected in dedifferentiation and redifferentiation stages and most of them were transposable elements, suggesting these processes involved activating or silencing of amounts of transposons. The functional enrichment of the DMR-related genes indicated that genes involved in hormone metabolic processes, plant development and the stress response changed methylation throughout the tissue culture process. Finally, the quantitative real-time PCR (qRT-PCR) was conducted to examine the association of methylation and gene expression of a set of different methylated genes. Our findings give deeper insight into the epigenetic regulation of gene expression during the plant tissue cultures process, which will be useful in the efficient control of somaclonal variations and in crop improvement.
format	article
author	Qiang Cao Yuxi Feng Xiongwei Dai Lin Huang Jiamin Li Pang Tao M. James C. Crabbe M. James C. Crabbe M. James C. Crabbe Ticao Zhang Qin Qiao
author_facet	Qiang Cao Yuxi Feng Xiongwei Dai Lin Huang Jiamin Li Pang Tao M. James C. Crabbe M. James C. Crabbe M. James C. Crabbe Ticao Zhang Qin Qiao
author_sort	Qiang Cao
title	Dynamic Changes of DNA Methylation During Wild Strawberry (Fragaria nilgerrensis) Tissue Culture
title_short	Dynamic Changes of DNA Methylation During Wild Strawberry (Fragaria nilgerrensis) Tissue Culture
title_full	Dynamic Changes of DNA Methylation During Wild Strawberry (Fragaria nilgerrensis) Tissue Culture
title_fullStr	Dynamic Changes of DNA Methylation During Wild Strawberry (Fragaria nilgerrensis) Tissue Culture
title_full_unstemmed	Dynamic Changes of DNA Methylation During Wild Strawberry (Fragaria nilgerrensis) Tissue Culture
title_sort	dynamic changes of dna methylation during wild strawberry (fragaria nilgerrensis) tissue culture
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/75b9f0c2d80f404eba70aa014f0cf564
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Dynamic Changes of DNA Methylation During Wild Strawberry (Fragaria nilgerrensis) Tissue Culture

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