Rice Papers

Plant Cell Advance Online Publication
Published on January 19, 2010; 10.1105/tpc.109.072041

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

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The behavior of transcriptomes and epigenomes in hybrids of heterotic parents is of fundamental interest. Here, we report highly integrated maps of the epigenome, mRNA, and small RNA transcriptomes of two rice (Oryza sativa) subspecies and their reciprocal hybrids. We found that gene activity was correlated with DNA methylation and both active and repressive histone modi铿乧ations in transcribed regions. Differential epigenetic modi铿乧ations correlated with changes in transcript levels among hybrids and parental lines. Distinct patterns in gene expression and epigenetic modi铿乧ations in reciprocal hybrids were observed. Through analyses of single nucleotide polymorphisms from our sequence data, we observed a high correlation of allelic bias of epigenetic modi铿乧ations or gene expression in reciprocal hybrids with their differences in the parental lines. The abundance of distinct small RNA size classes differed between the parents, and more small RNAs were downregulated聽 than聽 upregulated聽 in聽 the聽 reciprocal聽 hybrids.聽 Together,聽 our聽 data聽 reveal聽 a聽 comprehensive聽 overview聽 of transcriptional and epigenetic trends in heterotic rice crosses and provide a useful resource for the rice community.