IC4R009-Epigenomic-2013-23562565

Project Title

Rice is one of the most important food crops in the world and has been established as a model for plant genome study. Genomic sequences of two of the three subspecies of rice are available [1,2]. With its accurate genomic sequences, abundant genetic resources and availability of highly efficient reverse genetic tools, rice has become a model for cereal epigenomics and epigenetics as well. Epigenomics refers to genome-wide chromatin modification profiles mainly including DNA methylation and histone modifications, which control chromatin accessibility to DNA replication and repair and transcription machineries, thereby modulating the genome activities. Epigenetics studies mechanisms that are involved in variation and inheritance of epigenomic modifications. A wealth of trait variations among different rice species, subspecies and cultivars related to epigenomic variations, which may have been accumulated during the long history of rice evolution, domestication and selection, provides unique opportunities for crop epigenetic study. The researchers summarize and discuss features of rice epigenomes and epigenetic variations and its possible implication in heterosis and genetic improvement.

DNA cytosine methylation is a hallmark of inactivation of repetitive sequences and transposable elements in plants and is associated with heterochromatin formation. DNA cytosine methylation in plants occurs in CG, CHG and CHH contexts (where H is A, C or T). Extensive genome-wide DNA methylation data have been recently generated in rice. Genome-wide histone modifications (e.g. H3K4me2 H3K4me3, H3K9ac, H4K12ac, H3K27me3 and H3K36me3) have been defined in rice seedlings.

The chromatin modification machinery is generally conserved between rice and other plant species (www.chromdb.org). Analysis of loss-of-function mutants and RNAi or over-expression transgenic plants revealed that rice chromatin regulators are involved in various developmental pathways and in diverse responses to environment (Table 1).

Table 1 Chromatin modifiers reported in rice.

DNA methylation may contribute to rice phenotypic variation at both epigenetic and genetic levels. Epigenetic variation can be induced by trans-acting effect (e.g. siRNA), cis-acting sequence variation (e.g. nearby transposon insertions, or repeated sequences) and environment challenges or be spontaneous due to stochastic activity of chromatin modifiers. Epigenetic change may have important implications in crop production, as it was recently shown that natural variation of DNA methylation may contribute to trait variation in maize inbreds . However, the extent to which epigenetic variation contributes to variation of phenotypic traits in rice is not clear at present.

Epigenetic processes were suggested to be involved in parental genome interaction leading to distinct expression patterns in the hybrid. As discussed above hybrid parent lines Nipponbare and 93-11 display substantial differences in abundance and in positions regarding to DNA methylation. In the hybrid, a substantial number of loci show non-additive DNA methylation. This non-additive methylation may be of trans-acting effects mediated by RNA-dependent DNA methylation (RdDM) involving siRNA. However, the majority of gene expression changes in the hybrid are not associated with cis-acting DNA methylation changes, suggesting that other factors may be more important in non-additive gene expression related to heterosis. Variation of histone modification was found among a number of genes with non-additive expression. Regulation of histone acetylation by the histone deacetylase OsHDT1/HDT701 seems to play a role in non-additive expression of a subset of genes involved in flowering time control.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
Institut de Biologie des Plantes, Universite´ Paris sud, 91405 Orsay, France