Ma Xuan, Xing Feng, Jia Qingxiao, Zhang Qinglu, Hu Tong, Wu Baoguo, Shao Lin, Zhao Yu, Zhang Qifa, Zhou Dao-Xiu
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China.
College of Life Science, Xinyang Normal University, 464000 Xinyang, China.
Plant Physiol. 2021 Jun 11;186(2):1025-1041. doi: 10.1093/plphys/kiab088.
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.
杂种优势是指杂交种相对于自交亲本表现出的优良性状。除了遗传变异外，亲本之间的表观遗传差异也被认为对杂种优势有贡献。然而，亲本表观基因组之间差异的精确性质和程度以及杂种中控制杂种优势基因表达的重编程仍不清楚。在这项研究中，我们分析了广泛种植且经过基因研究的优良杂交水稻（Oryza sativa）SY63、正反交杂种以及亲本品种ZS97和MH63的DNA甲基化组和转录组，这些品种拥有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）序列的基因甲基化方面表现出显著差异。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，许多亲本在CG和CHG位点的差异甲基化区域（DMRs）在杂种中得以保留。只有一小部分DMRs表现出非加性DNA甲基化变化，不过，这与基因表达变化没有整体的相关性。相反，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）呈负相关。这些结果揭示了杂交水稻中一种特定的DNA甲基化重编程模式，并指出亲本CHG甲基化差异在ASE中发挥作用，而ASE与几种植物物种的表型变异和杂种优势相关。
