Epigenetic and developmental regulation in plant polyploids

•Polyploidy is a common evolutionary feature in all eukaryotes especially in plants.•Ploidy and intergenomic hybridization induce genetic and epigenetic changes.•DNA methylation and histone modifications affect homoeologous gene expression.•Gene expression networks are reprogrammed by environmental and developmental cues.•Studies of polyploidy at sequence and single-cell levels will reveal mechanistic insights. Polyploidy or whole-genome duplication occurs in some animals and many flowering plants, including many important crops such as wheat, cotton and oilseed rape. The prevalence of polyploidy in the plant kingdom suggests it as an important evolutionary feature for plant speciation and crop domestication. Studies of natural and synthetic polyploids have revealed rapid and dynamic changes in genomic structure and gene expression after polyploid formation. Growing evidence suggests that epigenetic modifications can alter homoeologous gene expression and reprogram gene expression networks, which allows polyploids to establish new cytotypes, grow vigorously and promote adaptation in local environments. Sequence and gene expression changes in polyploids have been well documented and reviewed elsewhere. This review is focused on developmental regulation and epigenetic changes including DNA methylation and histone modifications in polyploids.