Abstract
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.
Highlights
Cotton (Gossypium hirsutum L.), as a vital resource for plant fiber and oil, is widely cultivated worldwide [1]
We found the overall genomic methylation degree of the methylated cytosine sites (mCs) was significantly higher in ZB (31.59%) than in ZBA (28.58%), and the methylation levels (MLs) in CG, CHG, and CHH contexts presented similar comparative trends (Figure 2b)
The global DNA methylation pattern was profiled in anthers of the cytoplasmic male sterility (CMS)-D2 line ZBA and its near-isogenic maintainer line ZB using Whole-genome bisulfite sequencing (WGBS)
Summary
Cotton (Gossypium hirsutum L.), as a vital resource for plant fiber and oil, is widely cultivated worldwide [1]. The utilization of heterosis can effectively increase yield and improve quality in cotton fiber [2,3,4]. As an economical and ideal pollination system, cytoplasmic male sterility (CMS) plays an important role in the production of hybrid seeds [5], and it has been widely used to facilitate the utilization of heterosis in major crops [6]. Different types of cotton CMS lines, such as DBA/ZBA (CMS-D2) [7,8], Zhong41A (CMS-D8) [9], P30A (interspecific hybridization), [10] and H276A (exogenous gene transfer) [11], have been developed and improved. The molecular mechanism of CMS in cotton remains obscure
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