Parental variation in CHG methylation is associated with allelic-specific expression in elite hybrid rice
Parental variation in CHG methylation is associated with allelic-specific expression in elite hybrid rice
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CHG 甲基化亲本变异与优良杂交水稻等位基因特异性表达相关
DOI：
10.1093/plphys/kiab088
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发表时间：
2021-02-23
期刊：
影响因子：
7.4
通讯作者：
Zhou, Dao-Xiu
中科院分区：
文献类型：
--
作者：
Ma, Xuan;Xing, Feng;Zhou, Dao-Xiu
杂种优势是指杂交种优于近交系的亲本。除了遗传变异外，亲本间的表观遗传差异也被认为对杂种优势有贡献。然而，亲本表观基因组与杂交种中控制杂种基因表达的重编程之间差异的确切性质和程度仍不清楚。在这项工作中，我们分析了广泛栽培和遗传研究的精英杂交稻（Oryza sativa） SY63、互惠杂交稻（Oryza sativa）以及亲本品种ZS97和MH63的DNA甲基组和转录组，并为其提供了高质量的参考基因组序列。我们发现亲本品种在CG和CHG （H=A， C或T）序列上显示出实质性的基因甲基化变化。与亲本相比，杂交种在发育过程中表现出动态的甲基化变化。然而，杂交后代在CG和CHG位点保留了许多亲本差异甲基化区（DMRs）。只有一小部分DMRs表现出非加性DNA甲基化变异，但与基因表达变异没有整体相关性。相比之下，杂种中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的等位基因特异性甲基化（ASM）呈负相关。这些结果揭示了杂交水稻中特定的DNA甲基化重编程模式，并指出亲本CHG甲基化差异在ASE中起作用，这与几种植物物种的表型变异和杂交活力有关。
Heterosis refers to the superior performance of hybrid lines over inbred parental lines. Besides genetic variation, epigenetic differences between parental lines are suggested to contribute to heterosis. However, the precise nature and extent of differences between the parental epigenomes and the reprograming in hybrids that govern heterotic gene expression remain unclear. In this work, we analyzed DNA methylomes and transcriptomes of the widely cultivated and genetically studied elite hybrid rice (Oryza sativa) SY63, the reciprocal hybrid, and the parental varieties ZS97 and MH63, for which high-quality reference genomic sequences are available. We showed that the parental varieties displayed substantial variation in genic methylation at CG and CHG (H=A, C, or T) sequences. Compared with their parents, the hybrids displayed dynamic methylation variation during development. However, many parental differentially methylated regions (DMRs) at CG and CHG sites were maintained in the hybrid. Only a small fraction of the DMRs displayed non-additive DNA methylation variation, which, however, showed no overall correlation relationship with gene expression variation. In contrast, most of the allelic-specific expression (ASE) genes in the hybrid were associated with DNA methylation, and the ASE negatively associated with allelic-specific methylation (ASM) at CHG. These results revealed a specific DNA methylation reprogramming pattern in the hybrid rice and pointed to a role for parental CHG methylation divergence in ASE, which is associated with phenotype variation and hybrid vigor in several plant species.