Genome-Wide Methylation Landscape Uncovers the Role of DNA Methylation in Ramie (Boehmeria nivea L.) Bast Fiber Growth

Abstract

Ramie is one of the most important fiber crops in China, with fibers extracted from stem barks having been used as textile materials for thousands of years. DNA methylation is an important epigenetic modification involved in plant growth and development. However, the role of methylation in ramie fiber growth remains poorly understood. In the present study, we investigated the DNA methylation landscape of the nuclear genome in bark sections taken from the top (TPS) and the middle (MPS) of the stems of ramie plants, which represent different stages of fiber growth, using whole-genome bisulfite sequencing. We detected 7,709,555 and 8,508,326 5-methylcytosines in the TPS and MPS genomes, respectively. The distribution of methylation across three sequence contexts, CG, CHG, and CHH, varied greatly among gene elements, with methylation at CHH being the most prevalent. Comparison of methylation levels between the TPS and MPS genomes revealed 23.162 Mb of differentially methylated genomic regions, encompassing 9485 genes. Among these differentially methylated genes, 841 exhibited altered expression in the MPS genome. Notably, an SND2 ortholog Bni05G006779 showed a negative correlation between its expression and methylation levels. Overexpression of Bni05G006779 in Arabidopsis dramatically increased the number of xylem fibers and the secondary wall thickness of the fibers in the stems of transgenic plants. These findings provide important insights into the involvement of DNA methylation in regulating ramie fiber growth.