DNA methylation modification in heterosis initiation through analyzing rice hybrid contemporary seeds

Abstract Heterosis is an important biological phenomenon and widely applied in agriculture. Although many studies have been performed by using vegetative organs of F1 hybrid plants, how heterosis (or hybrid vigor) is initiated and formed, particularly the underlying molecular mechanism, remain elusive. Hybrid contemporary seeds of rice indica varieties 9311 and PA64 were innovatively used and analysis of DNA methylome of embryo and endosperm at early developing stages revealed the globally decreased DNA methylation. Genes, especially those relate to hormones function and transcriptional regulation present non-additive methylation. Previously identified heterosis-related superior genes are non-additively methylated in early developing hybrid contemporary seeds, suggesting that key genes/loci responsible for heterosis are epigenetically modified even in early developing hybrid seeds and hypomethylation of hybrid seeds after cross-pollination finally result in the long-term transcriptional change of F1 hybrid vegetative tissues after germination, demonstrating that altered DNA methylation in hybrid seeds is essential for initiation regulation and maintenance of heterosis exhibiting in F1 hybrid plants. Notably, a large number of genes show non-additive methylation in the endosperm of reciprocal hybrids, suggesting that endosperm might also contribute to heterosis.