Genome-wide approaches to the study of hybrid vigor have identified epigenetic changes in the hybrid nucleus in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa). DNA methylation associated with 24-nucleotide small interfering RNAs exhibits transallelic effects in hybrids of Arabidopsis and other species. Some of the transmethylation changes are inherited and some affect gene expression. Hybrids have larger leaves than those of the parents and have increases in cell size and number. The increased leaf size results in a greater photosynthetic capacity, which may support the increased vegetative and reproductive yields of the F1 hybrids. Genes and metabolic pathways that have altered expression relative to the parents include loci involved in responses to hormones and to biotic and abiotic stress. Whereas epigenetically induced changes in gene expression may contribute to hybrid vigor, the link between the transcriptional changes and the hybrid phenotype is not confirmed. Recurrent selection of high yielding F1 lines from the F2/F3 of a number of crops has fixed heterosis yields in pure breeding lines. These hybrid-like lines may have valuable applications in crop systems.