【作者】 翟荣荣；

【导师】 程式华；

【作者基本信息】 中国农业科学院 ， 作物遗传育种， 2013， 博士

【摘要】 协优9308是农业部推荐的第一批超级稻品种。该品种株型挺拔、根系发达、产量潜力大。本研究以协优9308及双亲协青早B和中恢9308、协优9308衍生的重组自交系（RIL）为材料，深入开展了协优9308根系杂种优势的分子机制研究，主要结果如下：1.以超级杂交稻协优9308衍生的234个重组自交系（RIL）为材料，在正常水分和20%聚乙二醇（PEG-6000）模拟水分胁迫处理下对水稻苗期最大根长（MRL）、总根长（TRL）、根表面积（RSA）、根体积（RV）、根平均直径（RAD）、根尖数（RTN）、根鲜重（RFW）和根冠比（RS）进行QTL定位分析，共检测到影响8个根部性状的21个QTL。其中，在正常水分和胁迫条件下分别检测到7个和14个QTL。两种水分条件下检测到的QTL位点差异很大，表明两种水分条件下的遗传机制不同。在第3和第6染色体上各检测到1个根部性状的QTL簇，尤其在第3染色体RM6283-RM7370区间发现苗期根系性状与抗旱性及产量相关性状之间存在连锁关系，利用这些与QTL紧密连锁的分子标记可望同时对多个相关性状进行遗传改良。除此之外，本研究结果也为挖掘可能与根系发育相关的关键基因及深入研究杂种优势遗传机制提供重要信息。2.基于Illumina HiSeq2000平台，本研究分析了分蘖期和抽穗期超级稻协优9308及双亲根系的转录谱。我们将双端测序产生的约3.91亿条高质量的reads比对到日本晴参考基因组，在已经注释的42081个转录本中，38872（92.4%）个至少有一条测序的read能够比对到日本晴参考基因组。分蘖期和抽穗期分别有829个和4186个在杂种一代（F₁）与亲本之间存在表达差异的转录本(DG_HP)。在分蘖期，F₁中66.59%的DG_HP下调表达，而在抽穗期F₁中约64.41%的DG_HP上调表达。在抽穗期，DG_HP主要集中在碳代谢和植物激素信号转导途径，并且参与这两个途径的多数关键基因在F₁中上调表达；其中涉及上述两个途径的部分DG_HP能够比对到控制产量和根系性状的QTL区间。这些候选基因的表达变化为将来研究根系杂种优势的潜在机制奠定了基础，本研究获得的大量转录组数据也为其他水稻研究团队提供了有用的资源。3.应用RNA-Seq技术分析了超级稻协优9308中的等位基因特异性表达（ASGE），共鉴定9325个可靠的SNP位点，这些SNPs分布于整个基因组。中恢9308与协青早B相比，约68%的SNP类型是CT和GA，表明协优9308和亲本中可能存在DNA甲基化。本研究发现，在分蘖期和抽穗期的2793个等位基因表达偏向性一致的转录本中，仅有480个存在显著的等位基因表达偏向性，约占17%，说明杂交种中亲本等位基因的差异表达多数是由反式作用因子调控。在上述480个转录本中，分蘖期和抽穗期分别有67%和62%转录本的等位基因表达偏向中恢9308。很多转录本在中恢9308中具有高水平表达，在杂交种中它们的等位基因表达也偏向中恢9308。除此之外，在两个时期同时存在等位基因表达偏向性的125个转录本中，约74%的等位基因表达偏向中恢9308。中恢9308的等位基因可能更能维持它们在杂交种中的活性并且对杂种优势作出贡献。355个转录本的等位基因在不同的发育时期表现出不同的表达偏向性，具有很高的时期特异性。杂交种中等位基因表达具有严重偏向性的转录本多与胁迫反应有关，这些转录本可能受到差异调控。本研究结果对深入研究杂种优势的分子机制提供了重要见解。更多还原

【Abstract】 Xieyou9308was one of the super hybrid rice varieties firstly recommended by the ChineseMinistry of Agriculture. Xieyou9308processes straight plant style, vigorous root and high yieldpotential. In this study, Xieyou9308, its maternal line Xieqingzao B, its paternal line R9308, and arecombinant inbred line （RIL） population derived from Xieyou9308were used as materials to conductin-depth research on molecular mechanism of root heterosis. The main results were as follows:1. A recombinant inbred line （RIL） population with234lines derived from a super hybrid riceXieyou9308were treated with normal water condition and20%polyethylene glycol （PEG-6000）. Eightroot traits including the maximum root length （MRL）, total root length （TRL）, root surface area （RSA）,root volume （RV）, root average diameter （RAD）, number of root tip （RTN）, root fresh weight （RFW）and root/shoot ratio （RS） were measured and further used for QTL analysis. A total of21QTLs weredetected. Seven QTLs under normal water condition and14QTLs under drought stress were detected,respectively. The QTLs detected under the two water supply conditions had significant differences,which indicated that there was different genetic mechanism controlling rice root traits at the twodifferent water conditions. Two important QTL clusters on chromosome3and6for root traits weredetected, especially the QTL for seedling root traits detected between RM6283and RM7370onchromosome3had linkage relation with the QTLs for drought resistance and yield related traits. Itwould be possible to improve multiple traits using DNA makers closely linked to these QTLs. Inaddition, the results of our study may provide important information for mining the key genesassociated with root development and for further studying the genetic mechanism underlying rootheterosis.2. Using the Illumina HiSeq2000platform, the root transcriptomes of the super-hybrid rice varietyXieyou9308and its parents were analyzed at tillering and heading stages. Approximately391millionhigh-quality paired-end reads （100-bp in size） were generated and aligned against the Nipponbarereference genome. We found that38,872of42,081（92.4%） annotated transcripts were represented by atleast one sequence read. A total of829and4186transcripts that were differentially expressed betweenthe hybrid and its parents (DG_HP) were identified at tillering and heading stages, respectively. Out of theDG_HP,66.59%were down-regulated at the tillering stage and64.41%were up-regulated at the headingstage. At the heading stage, the DG_HPwere significantly enriched in pathways related to processes suchas carbohydrate metabolism and plant hormone signal transduction, with most of the key genes that areinvolved in the two pathways being up-regulated in the hybrid; several DG_HPinvolved in theabove-mentioned pathways could be mapped to quantitative trait loci （QTLs） for yield and root traits.The changes in the expression of the candidate transcripts may lay a foundation for future studies onmolecular mechanisms underlying root heterosis. An extensive transcriptome dataset was obtained byRNA-Seq, providing a useful resource for the rice research community.3. We analyzed genome-wide allele-specific gene expression （ASGE） in the super-hybrid ricevariety Xieyou9308using RNA sequencing （RNA-Seq） technology. We identified9325reliable single nucleotide polymorphisms （SNPs） distributed throughout the genome. Nearly68%of the identifiedpolymorphisms were CT and GA SNPs between R9308and Xieqingzao B, suggesting the existence ofDNA methylation, a heritable epigenetic mark, in the parents and their F₁hybrid. Of2793identifiedtranscripts with consistent allelic biases, only480（17%） showed significant allelic biases duringtillering and/or heading stages, implying that trans effects may mediate most transcriptional differencesin hybrid offspring. Approximately67%and62%of the480transcripts showed R9308allelicexpression biases at tillering and heading stages, respectively. Transcripts with higher levels of geneexpression in R9308also exhibited R9308allelic biases in the hybrid. In addition,125transcripts wereidentified with significant allelic expression biases at both stages, of which74%showed R9308allelicexpression biases. R9308alleles may tend to preserve their characteristic states of activity in the hybridand may play important roles in hybrid vigor at both stages. The allelic expression of355transcriptswas highly stage-specific, with divergent allelic expression patterns observed at different developmentalstages. Many transcripts associated with stress resistance were differently regulated in the F₁hybrid.The results of this study may provide valuable insights into molecular mechanisms of heterosis.更多还原