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Open AccessArticle

Integrated Methylome and Transcriptome Analysis between the CMS-D2 Line ZBA and Its Maintainer Line ZB in Upland Cotton

1
State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang 455000, China
2
Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(23), 6070; https://doi.org/10.3390/ijms20236070
Received: 17 September 2019 / Revised: 1 November 2019 / Accepted: 27 November 2019 / Published: 2 December 2019
(This article belongs to the Special Issue Plant Fertility and Sexual Reproduction)
DNA methylation is an important epigenetic modification involved in multiple biological processes. Altered methylation patterns have been reported to be associated with male sterility in some plants, but their role in cotton cytoplasmic male sterility (CMS) remains unclear. Here, integrated methylome and transcriptome analyses were conducted between the CMS-D2 line ZBA and its near-isogenic maintainer line ZB in upland cotton. More methylated cytosine sites (mCs) and higher methylation levels (MLs) were found among the three sequence contexts in ZB compared to ZBA. A total of 4568 differentially methylated regions (DMRs) and 2096 differentially methylated genes (DMGs) were identified. Among the differentially expressed genes (DEGs) associated with DMRs (DMEGs), 396 genes were upregulated and 281 genes were downregulated. A bioinformatics analysis of these DMEGs showed that hyper-DEGs were significantly enriched in the “oxidative phosphorylation” pathway. Further qRT-PCR validation indicated that these hypermethylated genes (encoding the subunits of mitochondrial electron transport chain (ETC) complexes I and V) were all significantly upregulated in ZB. Our biochemical data revealed a higher extent of H2O2 production but a lower level of adenosine triphosphate (ATP) synthesis in CMS-D2 line ZBA. On the basis of the above results, we propose that disrupted DNA methylation in ZBA may disrupt the homeostasis of reactive oxygen species (ROS) production and ATP synthesis in mitochondria, triggering a burst of ROS that is transferred to the nucleus to initiate programmed cell death (PCD) prematurely, ultimately leading to microspore abortion. This study illustrates the important role of DNA methylation in cotton CMS. View Full-Text
Keywords: upland cotton; cytoplasmic male sterility; DNA methylation; oxidative phosphorylation; transcriptome upland cotton; cytoplasmic male sterility; DNA methylation; oxidative phosphorylation; transcriptome
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Zhang, M.; Guo, L.; Qi, T.; Zhang, X.; Tang, H.; Wang, H.; Qiao, X.; Zhang, B.; Feng, J.; Zuo, Z.; Li, T.; Shahzad, K.; Wu, J.; Xing, C. Integrated Methylome and Transcriptome Analysis between the CMS-D2 Line ZBA and Its Maintainer Line ZB in Upland Cotton. Int. J. Mol. Sci. 2019, 20, 6070.

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