Dynamic Changes of DNA Methylation During Wild Strawberry (Fragaria nilgerrensis) Tissue Culture.
Dynamic Changes of DNA Methylation During Wild Strawberry (Fragaria nilgerrensis) Tissue Culture.
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野草莓组织培养过程中DNA甲基化的动态变化
DOI：
10.3389/fpls.2021.765383
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发表时间：
2021
影响因子：
5.6
通讯作者：
Qiao Q
中科院分区：
文献类型：
--
作者：
Cao Q;Feng Y;Dai X;Huang L;Li J;Tao P;Crabbe MJC;Zhang T;Qiao Q
组织培养是草莓无性繁殖和遗传转化的重要手段。在植物组织培养中，DNA甲基化变异是再生植株表型变异的潜在来源。然而，草莓组织培养的全基因组动态甲基化模式仍不清楚。本研究采用全基因组亚硫酸氢盐测序（WGBS）技术，研究了野生草莓草莓从茎尖外植体到出圃驯化6个阶段基因组DNA甲基化的变化。总体甲基化水平显示，CG位点在所有阶段均表现出最高的甲基化水平，平均为49.5%，其次是CHG（33.2%）和CHH（12.4%）。虽然CHH在总胞嘧啶甲基化中所占比例最低，但其甲基化变化最明显，且大部分发生在转座因子区域。在整个组织培养过程中，甲基化水平呈交替下降和上升的趋势，且不同遗传区域间甲基化水平的分布不均匀。此外，在去分化和再分化阶段检测到更多的差异甲基化区域（DMR），其中大部分是转座因子，表明这些过程涉及大量转座子的激活或沉默。DMR相关基因的功能富集表明，在整个组织培养过程中，参与激素代谢过程，植物发育和胁迫反应的基因改变甲基化。最后，进行定量实时PCR（qRT-PCR）以检查一组不同甲基化基因的甲基化和基因表达的关联。我们的研究结果提供了更深入的了解植物组织培养过程中基因表达的表观遗传调控，这将有助于有效地控制体细胞克隆变异和作物改良。
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.
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影响因子：
4.5
作者：
Fukai E;Umehara Y;Sato S;Endo M;Kouchi H;Hayashi M;Stougaard J;Hirochika H
通讯作者：
Hirochika H
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
3.9
作者：
Anastasiadi D;Esteve-Codina A;Piferrer F
通讯作者：
Piferrer F
影响因子：
3.1
作者：
Cheng, Chaoyang;Daigen, Masaaki;Hirochika, Hirohiko
通讯作者：
Hirochika, Hirohiko
DOI：
10.1038/nrg2719
发表时间：
2010-03
期刊：
Nature reviews. Genetics
影响因子：
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作者：
通讯作者：
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