Atlas of Age- and Tissue-Specific DNA Methylation during Early Development of Barley (Hordeum vulgare)

The barley (Hordeum vulgare) genome comprises over 32,000 genes, with differentiated cells expressing only a subset of genes; the remainder being silent. Mechanisms by which tissue-specific genes are regulated are not entirely understood, although DNA methylation is likely to be involved. To shed light on the dynamic of DNA methylation during development and its variation between organs, methylation-sensitive genotyping by sequencing (ms-GBS) was used to generate methylation profiles for roots, leaf-blades and leaf-sheaths from five barley varieties, using seedlings at the three-leaf stage. Robust differentially methylated markers (DMMs) were characterised by pairwise comparisons of roots, leaf-blades and leaf-sheaths of three different ages. While very many DMMs were found between roots and leaf parts, only a few existed between leaf-blades and leaf-sheaths, with differences decreasing with leaf rank. Organ-specific DMMs appeared to target mainly repeat regions, implying that organ differentiation partially relies on the spreading of DNA methylation from repeats to promoters of adjacent genes. Identified DMMs indicate that different organs do possess diagnostic methylation profiles and suggest that DNA methylation is important for both tissue differentiation and organ function and will provide the basis to the understanding of the role of DNA methylation in plant organ differentiation and development.