Heterosis refers to the superior performance of the hybrid over the inbred parental lines. Besides genetic variation, epigenetic difference between the parental lines has been suggested to be involved in heterosis. However, precise nature and extent of parental epigenome difference and reprograming in hybrids governing heterotic gene expression remain unclear. In this work, we analyzed DNA methylomes and transcriptomes of the widely cultivated and genetically studied elite hybrid rice SY63, the reciprocal hybrid, and the parental varieties ZS97 and MH63, of which the high-quality reference genomic sequences are available. We show that the parental varieties display important variation in genic methylation at CG and CHG (H=A, C, or T) sequences. Compared with the parents the hybrids display dynamic methylation variation during development. However, many parental differentially methylated regions (DMR) at CG and CHG sites are maintained in the hybrid. Only a small fraction of the DMRs display non-additive DNA methylation variation which, however, shows no overall correlation with gene expression variation. By contrast, most of the allelic-specific expression (ASE) genes in the hybrid are associated with DNA methylation and the ASE negatively correlates with allelic-specific methylation (ASM) at CHG but positively at CG sites. The results reveal a specific DNA methylation reprogramming pattern in the hybrid rice and point to a role of parental CG and CHG methylation divergence in allelic specific expression that has been associated with phenotype variation and hybrid vigor in several plant species.

中文翻译：

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亲本CG和CHG甲基化变异与优良杂交水稻等位基因特异性表达相关

杂种优势是指杂种在近交亲本系中的优异表现。除遗传变异外，已提出亲本系之间的表观遗传差异也涉及杂种优势。但是，尚不清楚父母表观基因组差异的确切性质和程度以及控制杂种基因表达的杂种中的重编程。在这项工作中，我们分析了广泛栽培和遗传研究的优良杂交水稻SY63，倒数杂种以及亲本品种ZS97和MH63的DNA甲基基因组和转录组，其中高质量的参考基因组序列可用。我们表明，亲本品种在CG和CHG（H = A，C或T）序列上显示出重要的甲基化变异。与亲本相比，杂种在发育过程中表现出动态的甲基化变化。然而，在杂种中，在CG和CHG位点保留了许多亲本差异甲基化区域（DMR）。仅一小部分DMR表现出非加性DNA甲基化变异，但是，该变异与基因表达变异没有整体相关性。相比之下，杂种中的大多数等位基因特异性表达（ASE）基因与DNA甲基化相关，并且ASE与CHG处的等位基因特异性甲基化（ASM）负相关，而在CG位点正相关。结果揭示了杂交水稻中的一种特定的DNA甲基化重编程模式，并指出了亲本CG和CHG甲基化差异在等位基因特异性表达中的作用，该表达与几种植物物种的表型变异和杂交活力有关。