Analysis of Allelic Imbalance in Rice Hybrids Under Water Stress and Association of Asymmetrically Expressed Genes with Drought-Response QTLs.
Analysis of Allelic Imbalance in Rice Hybrids Under Water Stress and Association of Asymmetrically Expressed Genes with Drought-Response QTLs.
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DOI：
10.1186/s12284-016-0123-4
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发表时间：
2016-12
期刊：
影响因子：
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通讯作者：
Leung H
中科院分区：
文献类型：
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作者：
Ereful NC;Liu LY;Tsai E;Kao SM;Dixit S;Mauleon R;Malabanan K;Thomson M;Laurena A;Lee D;Mackay I;Greenland A;Powell W;Leung H
有关胁迫对水稻杂交种等位基因特异性表达（ASE）谱影响的信息有限。更重要的是，等位基因不平衡与重要性状的关联还有待了解。在这里，我们评估了等位基因不平衡（AI）的杂合子状态下的非和水分胁迫处理，并确定相关的不对称表达的基因与产量（戈伊）在干旱胁迫下的硅共定位分析和选择性基因分型。在正常和限水条件下，对基因型IR 64、Apo及其杂种（IR 64 × Apo）进行了研究。我们对所有基因型的总RNA转录物进行测序，然后重建杂合子中的两条染色体。我们能够估计两个亲本特异等位基因在杂交水稻中的转录丰度和差异表达（DE）。AI的大小和方向分为两类：（1）对称或双等位基因和（2）不对称。后者可进一步分类为IR 64-或Apo-偏好基因。分析表明，在非胁迫条件下生长的杂交种中，分别有179和183个有利于Apo和IR 64特异性等位基因。因此，IR 64和Apo偏好基因的数量相对相等。在水分胁迫条件下，179和255有利于载脂蛋白和IR 64特异性等位基因，分别表示，等位基因不平衡的基因数量偏向IR 64。这分别是Apo和IR 64等位基因相对于杂合转录组的近40- 60%的偏好。我们还观察到基因表现出等位基因偏好切换时，暴露于水胁迫条件。对Apo/IR 64 F3：5后代的计算机共定位和选择性基因分型结果显示，干旱胁迫下，几个不对称表达的基因与戈伊显著相关。我们的数据表明，水分胁迫使AI在全基因组范围内向IR 64等位基因（跨特异性母体等位基因）倾斜。在干旱胁迫下，几个不对称表达的基因与戈伊密切相关，这可能暗示与重要性状相关的基因是等位不平衡的。我们的方法整合杂种表达分析和QTL定位分析可能是一个有效的策略，候选基因的筛选基因发现。本文的在线版本（doi：10.1186/s12284-016-0123-4）包含补充材料，可供授权用户使用。
Information on the effect of stress on the allele-specific expression (ASE) profile of rice hybrids is limited. More so, the association of allelically imbalanced genes to important traits is yet to be understood. Here we assessed allelic imbalance (AI) in the heterozygote state of rice under non- and water-stress treatments and determined association of asymmetrically expressed genes with grain yield (GY) under drought stress by in-silico co-localization analysis and selective genotyping. The genotypes IR64, Apo and their F1 hybrid (IR64 × Apo) were grown under normal and water-limiting conditions. We sequenced the total RNA transcripts for all genotypes then reconstructed the two chromosomes in the heterozygote. We are able to estimate the transcript abundance of and the differential expression (DE) between the two parent-specific alleles in the rice hybrids. The magnitude and direction of AI are classified into two categories: (1) symmetrical or biallelic and (2) asymmetrical. The latter can be further classified as either IR64- or Apo-favoring gene. Analysis showed that in the hybrids grown under non-stress conditions, 179 and 183 favor Apo- and IR64-specific alleles, respectively. Hence, the number of IR64- and Apo-favoring genes is relatively equal. Under water-stress conditions, 179 and 255 favor Apo- and IR64-specific alleles, respectively, indicating that the number of allelically imbalanced genes is skewed towards IR64. This is nearly 40–60 % preference for Apo and IR64 alleles, respectively, to the hybrid transcriptome. We also observed genes which exhibit allele preference switching when exposed to water-stress conditions. Results of in-silico co-localization procedure and selective genotyping of Apo/IR64 F3:5 progenies revealed significant association of several asymmetrically expressed genes with GY under drought stress conditions. Our data suggest that water stress skews AI on a genome-wide scale towards the IR64 allele, the cross-specific maternal allele. Several asymmetrically expressed genes are strongly associated with GY under drought stress which may shed hints that genes associated with important traits are allelically imbalanced. Our approach of integrating hybrid expression analysis and QTL mapping analysis may be an efficient strategy for shortlisting candidate genes for gene discovery. The online version of this article (doi:10.1186/s12284-016-0123-4) contains supplementary material, which is available to authorized users.