State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China.
PLoS One. 2013 Apr 17;8(4):e60668. doi: 10.1371/journal.pone.0060668. Print 2013.
Hybridization, a common process in nature, can give rise to a vast reservoir of allelic variants. Combination of these allelic variants may result in novel patterns of gene action and is thought to contribute to heterosis. In this study, we analyzed genome-wide allele-specific gene expression (ASGE) in the super-hybrid rice variety Xieyou9308 using RNA sequencing technology (RNA-Seq). We identified 9325 reliable single nucleotide polymorphisms (SNPs) distributed throughout the genome. Nearly 68% of the identified polymorphisms were CT and GA SNPs between R9308 and Xieqingzao B, suggesting the existence of DNA methylation, a heritable epigenetic mark, in the parents and their F1 hybrid. Of 2793 identified transcripts with consistent allelic biases, only 480 (17%) showed significant allelic biases during tillering and/or heading stages, implying that trans effects may mediate most transcriptional differences in hybrid offspring. Approximately 67% and 62% of the 480 transcripts showed R9308 allelic expression biases at tillering and heading stages, respectively. Transcripts with higher levels of gene expression in R9308 also exhibited R9308 allelic biases in the hybrid. In addition, 125 transcripts were identified with significant allelic expression biases at both stages, of which 74% showed R9308 allelic expression biases. R9308 alleles may tend to preserve their characteristic states of activity in the hybrid and may play important roles in hybrid vigor at both stages. The allelic expression of 355 transcripts was highly stage-specific, with divergent allelic expression patterns observed at different developmental stages. Many transcripts associated with stress resistance were differently regulated in the F1 hybrid. The results of this study may provide valuable insights into molecular mechanisms of heterosis.
杂交是自然界中常见的过程，可以产生大量的等位基因变异。这些等位基因变异的组合可能导致新的基因作用模式，并被认为有助于杂种优势。在这项研究中，我们使用 RNA 测序技术（RNA-Seq）分析了超级杂交稻品种协优 9308 的全基因组等位基因特异性基因表达（ASGE）。我们鉴定了 9325 个分布在整个基因组中的可靠单核苷酸多态性（SNP）。近 68%的鉴定多态性是 R9308 和协青早 B 之间的 CT 和 GA SNP，这表明在父母及其 F1 杂种中存在 DNA 甲基化，这是一种可遗传的表观遗传标记。在 2793 个具有一致等位基因偏向性的鉴定转录本中，只有 480 个（17%）在分蘖和/或抽穗阶段表现出显著的等位基因偏向性，这意味着在杂种后代中，转录后效应可能介导大多数转录差异。在分蘖和抽穗阶段，大约 67%和 62%的 480 个转录本显示出 R9308 等位基因表达偏向性。在 R9308 中表达水平较高的转录本在杂种中也表现出 R9308 等位基因偏向性。此外，在两个阶段鉴定到 125 个具有显著等位基因表达偏向性的转录本，其中 74%显示出 R9308 等位基因表达偏向性。R9308 等位基因可能倾向于在杂种中保持其活性特征状态，并在两个阶段的杂种优势中发挥重要作用。355 个转录本的等位基因表达具有高度的阶段特异性，在不同的发育阶段观察到不同的等位基因表达模式。许多与应激抗性相关的转录本在 F1 杂种中受到不同的调控。本研究的结果可能为杂种优势的分子机制提供有价值的见解。
