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

TLDR

Transcriptomes and epigenomes in hybrids of heterotic rice parents are of fundamental interest. The study reports integrated epigenomic, mRNA, and small RNA maps for two rice subspecies and their reciprocal hybrids. The authors generated integrated epigenomic, mRNA, and small RNA maps for the two subspecies and their reciprocal hybrids. Gene activity correlated with DNA methylation and histone marks, differential epigenetic changes aligned with transcript shifts, reciprocal hybrids displayed distinct expression and epigenetic patterns tied to parental differences, and small RNA profiles differed with more downregulation, offering a comprehensive resource for rice.

Abstract

Abstract 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 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 downregulated than upregulated in the reciprocal hybrids. Together, our data reveal a comprehensive overview of transcriptional and epigenetic trends in heterotic rice crosses and provide a useful resource for the rice community.