SRA

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 subspecies and their reciprocal hybrids. We found that gene activity was correlated with DNA methylation and both active and repressive histone modifications in transcribed regions. Differential epigenetic modifications correlated with changes in transcript levels among hybrids and parental lines. Distinct patterns in gene expression and epigenetic modifications 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 modifications 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 down-regulated than up-regulated in the reciprocal hybrids. Together, our data reveals a comprehensive overview of transcriptional and epigenetic trends in heterotic rice crosses, and provides a very useful resource for the rice community. Overall design: Genome-wide integrated mapping of mRNA transcripts, DNA methylation and three select histone modifications (H3K4me3, H3K9ac and H3K27me3), using shoots of four-leaf stage seedlings of two rice subspecies (Oryza sativa L. ssp. japonica cv. Nipponbare and Oryza sativa L. ssp. indica cv. 93-11) and their reciprocal hybrids (Nipponbare/93-11 and 93-11/Nipponbare).