Genome-Wide Analysis of DNA Methylation During Ovule Development of Female-Sterile Rice fsv1

Abstract

The regulation of female fertility is an important field of rice sexual reproduction research. DNA methylation is an essential epigenetic modification that dynamically regulates gene expression during development processes. However, few reports have described the methylation profiles of female-sterile rice during ovule development. In this study, ovules were continuously acquired from the beginning of megaspore mother cell meiosis until the mature female gametophyte formation period, and global DNA methylation patterns were compared in the ovules of a high-frequency female-sterile line (fsv1) and a wildtype rice line (Gui99) using whole-genome bisulfite sequencing (WGBS). Profiling of the global DNA methylation revealed hypo-methylation, and 3471 significantly differentially methylated regions (DMRs) were observed in fsv1 ovules compared with Gui99. Based on functional annotation and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis of differentially methylated genes (DMGs), we observed more DMGs enriched in cellular component, reproduction regulation, metabolic pathway, and other pathways. In particular, many ovule development genes and plant hormone-related genes showed significantly different methylation patterns in the two rice lines, and these differences may provide important clues for revealing the mechanism of female gametophyte abortion. Rice (Oryza sativa L.) not only feeds half of the global population, but it is also useful for basic molecular and genetic studies because of its relatively small genome size and complete genome information (Goff 1999;Delseny et al. 2001). As an important participant in the sexual reproduction of rice, the fertility of male and female gametes is directly related to rice yield. In recent years, attention has been focused on the mechanism of male fertility regulation, while few studies have been conducted to elucidate the mechanism of female fertility in rice. The rice ovule is an important sexual reproductive organ, and previous studies have demonstrated the inseparability of ovule development and female gametophyte formation (Reiser and Fischer 1993). Generally, the process of female gametophyte formation is mainly divided into three stages: meiotic division of the megaspore mother cell (MMC), mitotic stage of functional megaspore cells, and mature stage of embryo sac. In detail, the MMC originating from a sporogenous cell derives from below the epidermis of the nucellus and divides into the linear tetrad type after meiosis. Subsequently, the megaspore near the chalaza becomes the functional megaspore, and the remaining three megaspores die during ovule development. The functional megaspore undergoes three rounds of mitotic division and finally forms the female gametophyte with eight nuclei (Yadegari and Drews 2004;Pagnussat et al. 2005). The ovule sporophyte tissue provides the necessary nutritional and mechanical support for the formation of the female gametophyte, and communication between the ovule sporophyte and the female gametophyte has bee...

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