Cereals and grains are the most important source of calories and nutrition for humans and an essential feed for animal production. The genome sequences of these crops continue to be produced at a frenetic pace, with the potential to significantly contribute to breeding activities and crop improvement. Our work has demonstrated the potential for DNA methylation technologies to accelerate the molecular understanding of DNA methylation and yield determinants. Here we present avenues to use epigenomic technologies in crop genome research. DNA methylation is a DNA modification, and variation in DNA methylation can be associated with phenotypic variation. These variants, or ‘epialleles’, could provide markers for selection and can provide information not captured by conventional genetic markers such as SNPs. In addition, despite the advances in genome sequencing and assembly, detailed annotation of plant genomes is now a bottleneck in genomic analysis and an impediment to realizing the full potential of association studies or genome editing for crop improvement. Here, we describe our recently developed approach that uses DNA methylation profiling of a single tissue (e.g. a leaf) to distill a genome down to the relatively small fraction of regions that are functionally valuable for trait variation throughout development. We are using this approach in sorghum, wheat, barley and maize to better annotate these genomes and select gene regulatory regions as targets for gene editing for trait improvement to accelerate the transition from discovery to trait modification.