Abstract

Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo, exhibits extensive localized DNA demethylation on maternally-inherited chromosomes, which mediates parent-of-origin-specific (imprinted) gene expression. Endosperm DNA in rice and maize is likewise locally hypomethylated. We have shown that localized hypomethylation in rice endosperm occurs solely on the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini, and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. Our data indicate that localized hypomethylation of maternal endosperm DNA is conserved in flowering plants. By examining divergent rice cultivars, we also identified genes the imprinting of which has changed in the course of rice evolution. In some cases, this variation is genetic, with gene expression differences caused by underlying sequence changes, such as transposon insertions. In other cases, methylation differences that control gene expression exist in the absence of significant genetic polymorphism. The results suggest that epigenetic variation contributes to short term plant evolution and may influence traits selected by crop breeders.