Rice epigenomics and epigenetics: challenges and opportunities

•Features of rice genome-wide DNA methylation and histone modification landscape.•Rice epigenetic regulators display specific developmental and stress–responsive functions.•Importance of epigenetic variation as a resource for trait variations and epiallele discovery in rice. During recent years rice genome-wide epigenomic information such as DNA methylation and histone modifications, which are important for genome activity has been accumulated. The function of a number of rice epigenetic regulators has been studied, many of which are found to be involved in a diverse range of developmental and stress–responsive pathways. Analysis of epigenetic variations among different rice varieties indicates that epigenetic modification may lead to inheritable phenotypic variation. Characterizing phenotypic consequences of rice epigenomic variations and the underlining chromatin mechanism and identifying epialleles related to important agronomic traits may provide novel strategies to enhance agronomically favorable traits and grain productivity in rice.