title: Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids.
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.
authors.affiliation: Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China.
authors.forename: Guangming
authors.initials: G
authors.lastname: He
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Zhu
authors.forename: Axel A
authors.initials: AA
authors.lastname: Elling
authors.forename: Liangbi
authors.initials: L
authors.lastname: Chen
authors.forename: Xiangfeng
authors.initials: X
authors.lastname: Wang
authors.forename: Lan
authors.initials: L
authors.lastname: Guo
authors.forename: Manzhong
authors.initials: M
authors.lastname: Liang
authors.forename: Hang
authors.initials: H
authors.lastname: He
authors.forename: Huiyong
authors.initials: H
authors.lastname: Zhang
authors.forename: Fangfang
authors.initials: F
authors.lastname: Chen
authors.forename: Yijun
authors.initials: Y
authors.lastname: Qi
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
authors.forename: Xing-Wang
authors.initials: XW
authors.lastname: Deng
mesh_terms: D002678:Chimera; D002874:Chromosome Mapping; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D018745:Genome, Plant; D006657:Histones / Q000378:metabolism; D012275:Oryza / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D006657:Histones; D012333:RNA, Messenger; D018749:RNA, Plant