超级稻协优9308根系杂种优势的转录组分析
|
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（F_1）与亲本之间存在表达差异的转录本（DG_(HP)）。在分蘖期，F_1中66.59%的DG_(HP)下调表达，而在抽穗期F_1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F_1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。
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_(HP)were 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_(HP)involved 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 F_1hybrid. 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 F_1hybrid.The results of this study may provide valuable insights into molecular mechanisms of heterosis.
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（F_1）与亲本之间存在表达差异的转录本（DG_(HP)）。在分蘖期，F_1中66.59%的DG_(HP)下调表达，而在抽穗期F_1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F_1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。
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_(HP)were 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_(HP)involved 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 F_1hybrid. 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 F_1hybrid.The results of this study may provide valuable insights into molecular mechanisms of heterosis.
引文
1.包文斌，陈国宏，束婧婷，等.基因表达系列分析（SAGE）及其在生命科学中的应用.中国兽医学报，2008，28：106-110
2.陈杰.大规模平行测序技术（MPSS）研究进展.生物化学与生物物理进展，2004，31：761-765
3.陈艳丽.水稻耐低钾胁迫相关性状的QTL定位[硕士学位论文].北京：中国农业科学院，2012
4.程式华.杂交水稻育种材料和方法研究的现状及发展趋势.中国水稻科学，2000，14：165-169
5.冯跃.超级稻协优9308重组自交系群体对氮素水平响应的遗传研究及QTL定位[博士学位论文].沈阳：沈阳农业大学，2010
6.郭玉春，徐惠龙，陈芳育，等.磷高效水稻根系对低磷胁迫响应的差异蛋白分析.应用生态学报，2010，21：3231-3238
7.郝树荣，郭相平，王为木，等.水稻分蘖期水分胁迫及复水对根系生长的影响.干旱地区农业研究，2007，25：149-152
8.黄莉.甘蓝型油菜杂种优势和遗传多样性的研究[硕士学位论文].武汉：华中农业大学，2007
9.黄毅.应用cDNA芯片研究水稻杂种与亲本基因表达谱及杂种优势分子生物学基础[博士学位论文].武汉：华中农业大学，2006
10.景蕊莲，胡荣海，朱志华，等.冬小麦不同基因型幼苗形态性状遗传力和抗旱性的研究.西北植物学报，1997，17：152-157
11.兰进好，李新海，高树仁，等.不同生态环境下玉米产量性状QTL分析.作物学报，2005，31：1253-1259
12.李巧丽.杜氏利什曼原虫两个发育阶段基因表达系列分析文库的构建及HSP90在其阶段转变过程中的作用[博士学位论文].上海：上海交通大学，2009
13.李雪林，杨书化，张泽民，等.植物杂种优势遗传机制的分析遗传学研究进展.河南科技大学学报（农学版），2003，23：62-65
14.李勇超，宋书锋，李建民.杂种优势的分子机理研究进展.湖北农业科学，2009，48：1501-1504
15.李卓坤，彭涛，张卫东，等.利用“永久F2”群体进行小麦幼苗根系性状QTL分析.作物学报，2010，36：442-448
16.梁永书.超级稻协优9308衍生群体根系的遗传研究[博士学位论文].北京：中国农业科学院，2011
17.林建丽，朱正歌，高建伟.植物杂种优势研究进展.华北农学报，2009，24：46-56
18.刘胜群，宋凤斌.玉米不同耐旱性品种根系构型和动态建成研究.扬州大学学报（农业与生命科学版），2007，28：68-78
19.刘桃菊，戚昌瀚，唐建军.水稻根系建成与产量及其构成关系的研究.中国农业科学，2002，35：1416-1419
20.马西青.玉米株高杂种优势遗传基础剖析[硕士学位论文].北京：中国农业大学，2005
21.穆平，李自超，李春平，等.水、旱稻根系性状与抗旱性相关分析及其QTL定位.科学通报，2003，48：2162-2169
22.聂元元.水稻抗旱性相关QTL精细定位[博士学位论文].武汉：华中农业大学，2009
23.牛兆国.水稻杂种优势利用现状及发展对策.现代农业科技，2010，24：93-94，98
24.沈波，庄杰云，樊叶杨，等.不同供水条件下水稻叶绿素含量的QTL分析.浙江大学学报（农业与生命科学版），2007，33：400-406
25.沈希宏，曹立勇，陈深广，等.超级杂交稻协优9308重组自交系群体的穗部性状QTL分析.中国水稻科学，2009，23：354-362
26.沈希宏，陈深广，曹立勇，等.超级杂交稻协优9308重组自交系的分子遗传图谱构建.分子植物育种，2008，6：861-866
27.沈希宏.超级杂交稻协优9308重组自交系构建及若干性状的QTL定位[博士学位论文].北京：中国农业科学院，2008
28.王斌.基于RNA-Seq技术的米曲霉RIB40转录组学研究[博士学位论文].广州：华南理工大学，2010
29.王超. NaHCO3胁迫下柽柳根部组织基因的表达调控研究[博士学位论文].哈尔滨：东北林业大学，2012
30.王经源.杂交稻苗期杂种优势的比较蛋白质组学研究[博士学位论文].福州：福建农林大学，2008
31.王汝慈.两个生育时期水稻耐低磷胁迫相关性状的QTL定位[硕士学位论文].北京：中国农业科学院，2009
32.王曦，汪小我，王丽坤，等.新一代高通量RNA测序数据的处理与分析.生物化学与生物物理进展，2010，37：834-846
33.王志芬，陈学留，余美炎，等.冬小麦生长发育与根系关系的32P示踪研究.核农学报，1997，11：173-178
34.武瑞，连学昭.基因芯片技术在中药研究中的应用.中兽医医药杂志，2005，1：21-23
35.谢晓东.小麦杂交当代和亲本自交种子发育早期的基因表达差异与杂种优势[博士学位论文].北京：中国农业大学，2003
36.徐林娟，徐正浩，李舸，等.不同土壤水分供给下水稻叶水势的变化规律.核农学报，2011，25：0553-0558
37.薛应龙，夏镇澳.植物生理学实验手册.上海：上海科学技术出版社，1982
38.杨玲，孙娜，余有见，等.水分胁迫下水稻叶片相关生理性状的QTL定位.浙江农业学报，2009，21：490-494
39.袁隆平.水稻的雄性不孕性.科学通报，1996，17：185-188
40.袁倩倩，李卓坤，田纪春，等.不同水分胁迫下小麦胚芽鞘和胚根长度的QTL分析.作物学报，2011，37：294-301
41.张耗，黄钻华，王静超，等.江苏中籼水稻品种演化过程中根系形态生理性状的变化及其与产量的关系.作物学报，2011，37：1020-1030
42.张坤普，徐宪斌，田纪春.小麦籽粒产量及穗部相关性状的QTL定位.作物学报，2009，35：270-278
43.张义荣，姚颖垠，彭惠茹，等.植物杂种优势形成的分子遗传机理研究进展.自然科学进展，2009，19：697-703
44.赵秀琴，徐建龙，朱苓华，等.利用回交导入系定位干旱环境下水稻植株水分状况相关QTL.作物学报，2008，34：1696-1703
45.周蓉，陈海峰，王贤智，等.大豆幼苗根系性状的QTL分析.作物学报，2011，37：1151-1158
46.朱军.运用混合线性模型定位复杂数量性状基因的方法.浙江大学学报（自然科学版）,1999,33:327-335
47.庄杰云，樊叶杨，吴建利，等.超显性效应对水稻杂种优势的重要作用.中国科学（C缉），2001，31：106-113
48.庄杰云，樊叶杨，吴建利，等.杂交水稻中超显性效应的分析.遗传，2000，22：205-208
49. Adams M D, Kelly J M, Gocayne J D, et al. Complementary DNA sequencing: expressed sequencetags and human genome project. Science,1991,252:1631-1656
50. Arnold M L. Natural hybridization and the evolution of domesticated, pest and disease organisms.Molecular Ecology,2004:997-1007
51. Ashikawa I. Surveying CpG methylation at5'-CCGG in the genomes of rice cultivars. PlantMolecular Biology,2001,45:31-39
52. Austin D F, Lee M. Detection of quantitative trait loci for grain yield and yield components inmaize across generations in stress and nonstress environments. Crop Science,1998,38:1296-1308
53. Bao J Y, Lee S, Chen C, et al. Serial Analysis of Gene Expression Study of a hybrid rice strain(LYP9) and its parental cultivars. Plant Physiology,2005,138:1216-1231
54. Basu S, Roychoudhury A, Saha P P, et al. Comparative analysis of some biochemical responses ofthree indica rice varieties during polyethylene glycol-mediated water stress exhibits distinctvarietal differences. Acta Physiologiae Plant,2010,32:551-563
55. Birchler J A, Auger D L, Riddle N C, et al. In search of the molecular basis of heterosis. The PlantCell,2003,15:2236-2239
56. Bird A. Perceptions of epigenetics. Nature,2007,447:396-398
57. Bransteitter R, Pham P, Scharff M D, et al. Activation-induced cytidine deaminase deaminatesdeoxycytidine on single-stranded DNA but requires the action of RNase. Proceeding of theNational Academy of Sciences of the United States of America,2003,100:4102-4107
58. Brenner S, Johnson M, Bridgham J, et al. Gene expression analysis by massively parallel signaturesequencing (MPSS) on microbead arrays. Nature Biotechnology,2000,18:630-634
59. Bruce A B. The mendelian theory of heredity and the augmentation of vigor. Science,1910,32627-628
60. Cervera M T, Ruiz-García L, Martínez-Zapater J M. Analysis of DNA methylation in Arabidopsisthaliana based on methylation-sensitive AFLP markers. Molecular Genetic Genomics,2002,268:543-552
61. Cheng S H, Cao LY, Zhuang J Y, et al. Super hybrid rice breeding in China: achievements andprospects. Journal of Intergrative Plant Biology,2007,49:805-810
62. Cho J I, Kim H B, Kim C Y, et al. Identification and characterization of the duplicate rice sucrosesynthase genes OsSUS5and OsSUS7which are associated with the plasma membrane. Molecularand Cells,2011,31:553-561
63. Chodavarapu R K, Feng S, Ding B, et al. Transcriptome and methylome interactions in ricehybrids. Proceedings of the National Academy of Sciences,2012,109:12040-12045
64. Cohen D, Bogeat-Triboulot M B, Tisserant E, et al. Comparative transcriptomics of droughtresponses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves androot apices across two genotypes. BMC Genomics,2010,11:630
65. Coudert Y, Perin C, Courtois B, et al. Genetic control of root development in rice, the modelcereal. Trends in Plant Science,2010,15:219-226
66. Courtosis B, McLaren G, Sinha P K, et al. Mapping QTLs associated with drought avoidance inupland rice. Molecular Breeding,2000,6:55-66
67. Cowles C R, Hirschhorn J N, Altshuler D, et al. Detection of regulatory variation in mouse genes.Nature Genetics,2002,32:432-437
68. Cui K H, Huang J L, Xing Y Z, et al. Mapping QTLs for seedling characteristics under differentwater supply conditions in rice (Oryza sativa). Plant Physiology,2008,132:53-68
69. De Smet I, Signora L, Beeckman T, et al. An abscisic acid-sensitive checkpoint in lateral rootdevelopment of Arabidopsis. The Plant Journal,2003,33:543-555
70. Dolferus R, Ellis M, De Bruxelles G, et al. Strategies of gene action in Arabidopsis during hypoxia.Annals of Botany,1997,79:21-31
71. Duvick D N. Heterosis: feeding people and protecting natural resources. In: Coors J G, Pandey S,eds. The Genetics and Exploitation of Heterosis in Crops. American Society Agronomy, Inc, CropScience Society of America, Inc, Soil Science Society of America, Inc, Madison, WI.1999.19-29
72. East E M. Heterosis. Genetics,1936,21:375-397
73. Edwards M D, Stuber C W, Wendel J F. Molecular-marker-facilitated investigations ofquantitative-trait loci in maize. I. Numbers, genomic distribution and types of gene action.Genetics,1987,116:113-125
74. Eisen M B, Spellman P T, Brown P O, et al. Cluster analysis and display of genome-wideexpression patterns. Proceedings of the National Academy of Sciences,1998,95:14863-14868
75. Ekanayake I J, Garrity D P, Masajo T M, et al. Root pulling resistance in rice: inheritance andassociation with drought tolerance. Euphytica,1985,34:905-913
76. Farrokhi N, Burton R A, Brownfield L, et al. Plant cell wall biosynthesis: genetic, biochemical andfunctional genomics approaches to the identification of key genes. Plant Biotechnology Journal,2006,4:145-167
77. Feng Y, Cao L Y, Wu W M, et al. Mapping QTLs for nitrogen-deficiency tolerance at seedlingstage in rice (Oryza sativa L.). Plant Breeding,2010,129:652-656
78. Fukai S, Cooper M. Development of drought-resistant cultivars using physiomorphological traits inrice. Field Crops Research,1995,40:67-86
79. Gao Y M, Zhu J. Mapping QTLs with digenic epistasis under multiple environments and predictingheterosis based on QTL effects. Theoretical and Applied Genetics,2007,115:325-333
80. Ge X M, Chen W H, Song S H, et al. Transcriptomic profiling of mature embryo from an elitesuper-hybrid rice LYP9and its parental lines. BMC Plant Biology,2008,8:114
81. Gomez S M, Boopathi N M, Kumar S S, et al. Molecular mapping and location of QTLs fordrought-resistance traits in indica rice (Oryza sativa L.) lines adapted to target environments. ActaPhysiologiae Plantarum,2009,32:355-364
82. Gowda V R P, Henry A, Yamauchi A, et al. Root biology and genetic improvement for droughtavoidance in rice. Field Crops Research,2011,122:1-13
83. Griffing B. Use of a controlled-nutrient experiment to test heterosis hypotheses. Genetics,1990,126:753-767
84. Guo D, Liang J, Li L. Abscisic acid (ABA) inhibition of lateral root formation involvesendogenous ABA biosynthesis in Arachis hypogaea L. Plant Growth Regulation,2009,58:173-179
85. Guo M, Rupe M A, Zinselmeier C, et al. Allelic variation of gene expression in maize hybrids. ThePlant Cell,2004,16:1707-1716
86. He G M, Zhu X P, Elling A A, et al. Global epigenetic and transcriptional trends among two ricesubspecies and their reciprocal hybrids. The Plant Cell,2010,22:17-33
87. Hegarty M J, Hiscock S J. Hybrid speciation in plants: new insights from molecular studies. NewPhytologist,2004,165:411-423
88. Hirose T, Scofield G N, Terao T. An expression analysis profile for the entire sucrose synthase genefamily in rice. Plant Science,2008,174:534-543
89. Hoecker N, Keller B, Piepho H P, et al. Manifestation of heterosis during early maize (Zea mays L.)root development. Theoretical and Applied Genetics,2005,112:421-429
90. Hoffman N E, Bent A F, Hanson A D. Induction of lactate dehydrogenase isozymes by oxygendeficit in barley root tissue. Plant Physiology,1986,82:658-663
91. Hu B, Wu P, Liao C Y, et al. QTLs and epistasis underlying activity of acid phosphatase underphosphorus sufficient and defcient condition in rice (Oryza sativa L.). Plant Soil,2001,230:99-105
92. Hu M, Polyak K. Serial analysis of gene expression. Nature Protocols,2006,1:1743-1760
93. Hua J P, Xing Y Z, Wu W R, et al. Single-locus heterosis effects and dominance by dominanceinteraction can adequately explain the genetic basis of heterosis in an elite rice hybrid. Proceedingsof the National Academy of Sciences,2003,100:2574-2579
94. Huang Y, Zhang L, Zhang J, et al. Heterosis and polymorphisms of gene expression in an elite ricehybrid as revealed by a microarray analysis of9198unique ESTs. Plant Molecular Biology,2006,62:579-591
95. Jackson M B. New root formation in plants and cuttings. Netherland: Martinus Nijhoff Press,1986
96. Jiang K, Zhang S, Lee S, et al. Transcription profile analyses identify genes and pathways centralto root cap functions in maize. Plant Molecular Biology,2006,60:343-363
97. Johnston J W, Harding K, Bremner D H, et al. HPLC analysis of plant DNA methylation: a studyof critical methodological factors. Plant Physiology Biochememistry,2005,43:844-853
98. Jones D F. Dominance of linked factors as a means of accounting for heterosis. Genetics,1917,3:310-312
99. Jones J W. Hybrid vigour in rice. American Society of Agronomy,1926,18:423-428
100. Jongeneel C V, Iseli C, Stevenson B J. Comrehensive sampling of gene expression in human celllines with massively parallel signature sequencing. Proceedings of the National Academy ofSciences,2003,100:4702-4705
101. Kao C H, Zeng Z B, Teasdale R D. Multiple interval mapping for quantitative trait loci. Genetics,1999,152:1203-1216
102. Kearsey M J, Pooni H S. The genetical analysis of quantitative traits. London: Chapman&HallPress,1996
103. Kim C M, Park S H, Je B I, et al. OsCSLD1, a cellulose synthase-like D1gene, is required for roothair morphogenesis in rice. Plant Physiology,2007,143:1220-1230
104. Konishi H, Yamane H, Maeshima M, et al. Characterization of fructose-bisphosphate aldolaseregulated by gibberellin in roots of rice seedling. Plant Molecular Biology,2004,56:839-848
105. Kyndt T, Denil S, Haegeman A, et al. Transcriptome analysis of rice mature root tissue and roottips in early development by massive parallel sequencing. Journal of Experimental Botany,2012,63:2141-2157
106. Lander E S, Botstein D. Mapping mendelian factors underlying quantitative traits using RFLPlinkage maps. Genetics,1989,121:85-199
107. Laszlo A, St. Lawrence P. Parallel induction and synthesis of PDC and ADH in anoxic maize roots.Molecular Genetics&Genomics,1983,192:110-117
108. Lee D J, Kim S, Ha Y M, et al. Phosphorylation of Arabidopsis response regulator7(ARR7) at theputative phospho-accepting site is required for ARR7to act as a negative regulator of cytokininsignaling. Planta,2007,227:577-587
109. Li B, Dewey C N. RSEM: accurate transcript quantification from RNA-Seq data with or without areference genome. BMC Bioinformatics,2011,12:323
110. Li J, Swanson R V, Simon M I, et al. The response regulators CheB and CheY exhibit competitivebinding to the kinase CheA. Biochemistry,1995,34:14626-14636
111. Li L Z, Lu K Y, Chen Z M, et al. Dominance, over-dominance and epistasis condition the heterosisin two heterotic rice hybrids. Genetics,2008,180:1725-1742
112. Li X, Mo X R, Shou H X, et al. Cytokinin-mediated cell cycling arrest of pericycle founder cells inlateral root initiation of Arabidopsis. Plant and Cell Physiology,2006,47:1112-1123
113. Li Z K, Luo L J, Mei H W, et al. Overdominant epistatic loci are the primary genetic basis ofinbreeding depression and heterosis in rice.Ⅰ. Biomass and grain yield. Genetics,2001,158:1737-1753
114. Li Z K, Pinson R M, Park W D, et al. Eistasis for three grain yield components in rice (Oryzasativa L.). Genetics,1997,145:453-465
115. Lian X M, Wang S P, Zhang J W, et al. Expression profiles of10,422genes at early stage of lownitrogen stress in rice assayed using a cDNA microarray. Plant Molecular Biology,2006,60:617-631
116. Lian X M, Xiong Y Z, Yan H, et al. QTLs for low nitrogen tolerance at seedling stage identifiedusing a recombinant inbred line population derived from an elite rice hybrid. Theoretical andApplied Genetics,2005,112:85-96
117. Liang Y S, Zhan X D, Gao Z Q, et al. Mapping of QTLs associated with important agronomictraits using three populations derived from a super hybrid rice Xieyou9308. Euphytica,2012,184:1-13
118. Lu C F, Shen L S, He P, et al. Comparative mapping of QTLs for agronomic traits of rice acrossenvironments by using a doubled-haploid population. Theoretcal and Applied Genetics,1997,94:145-150
119. Luo L J, Li Z K, Mei H W, et al. Overdominant epistatic loci are the primary genetic basis ofinbreeding depression and heterosis in rice.Ⅱ.Grain yield components. Genetics,2001,158:1755-1771
120. Luo X J, Fu Y C, Zhang P J, et al. Additive and over-dominant effects resulting from epistatic lociare the primary genetic basis of heterosis in rice. Journal of Integrative Plant Biology,2009,51:393-408
121. Lynch M, Walsh B. Genetics analysis of quantitative traits. Sunderland: Sinauer Associates Press,1998
122. Margulies M, Egholm M, Altman W E, et al. Genome sequencing in microfabricated high-densitypicolitre reactors. Nature,2005,437:376-380
123. Mason M G. Multiple type-B response regulators mediate cytokinin signal transduction inArabidopsis. The Plant Cell,2005,17:3007-3018
124. McCouch S R, Cho Y G, Yano M, et al. Report on QTL nomenclature. Rice Genetics Newsletter,1997,14:11-13
125. Menegus F, Cattaruzza L, Chersi A, et al. Differences in the anaerobic lactate-succinate productionand in the changes of cell sap pH for plants with high and low resistance to anoxia. PlantPhysiology,1989,90:29-32
126. Messmer R, Fracheboud Y, Banziger M, et al. Drought stress and tropical maize:QTL-by-environment interactions and stability of QTLs across environments for yield componentsand secondary traits. Theoretical and Applied Genetics,2009,119:913-930
127. Meyer R C. Heterosis of biomass production in Arabidopsis. Establishment during earlydevelopment. Plant Physiology,2004,134:1813-1823
128. Ming F, Zheng X W, Mi G H, et al. Identification of quantitative trait loci affecting tolerance to lowphosphorus in rice (Oryza sativa L.). Chinese Science Bulletin,2000,45:520-525
129. Mir G N. Development of commercial hybrids for hills-problems, present status and future scope,In: Recent advances in rice production technology in hills, SKUAST-K.2002,107-111
130. Mizuno H, Kawahara Y, Sakai H, et al. Massive parallel sequencing of mRNA in identification ofunannotated salinity stress-inducible transcripts in rice (Oryza sativa L.). BMC Genomics,2010,11:683
131. Morgan H D, Dean W, Coker H A, et al. Activation-induced cytidine deaminase deaminates5-methylcytosine in DNA and is expressed in pluripotent tissues: implications for epigeneticreprogramming. The Journal of Biological Chemistry,2004,279:52353-52360
132. Mortazavi A, Williams B A, McCue K, et al. Mapping and quantifying mammalian transcriptomesby RNA-Seq. Nature Methods,2008,5:621-628
133. Moudal S K, Kour K. Genetic variability and correlation coefficients of some root characteristicsand yield components in bread wheat (Triticum aestivum L.) under rainfed condition. Environmentand Ecology,2004,22:646-648
134. Nguyen H T, Babu R C, Blum A. Breeding for drought resistance in rice: physiology and moleculargenetics considerations. Crop Science,1997,37:1426-1434
135. Ni J J, Wu P, Senadhira D, et al. Mapping QTLs for phosphorus deficiency tolerance in rice (Oryzasativa L.). Theoretical and Applied Genetics,1998,97:1361-1369
136. O'Carra P, Mulcahy P: Lactate dehydrogenase in plants: distribution and function. Phytochemistry1996,42:581-587
137. Ogawa A, Ando F, Toyofuku K, et al. Sucrose metabolism for the development of seminal root inmaize seedlings. Plant Production Science,2009,12:9-16
138. Ogawa A, Yamauchi A. Root osmotic adjustment under osmotic stress in maize seedlings.2. Modeof accumulation of several solutes for osmotic adjustment in the root. Plant Production Science,2006,9:39-46
139. Oono Y, Kawahara Y, Kanamori H, et al. mRNA-Seq reveals a comprehensive transcriptomeprofile of rice under phosphate stress. Rice,2011,4:50-65
140. Pandey A, Mann M. Proteomics to study genes and genomes. Nature,2000,405:837-846
141. Paschold A, Marcon C, Hoecker N, et al. Molecular dissection of heterosis manifestation duringearly maize root development. Theoretical and Applied Genetics,2009,120:383-388
142. Pastinen T. Genome-wide allele-specific analysis: insights into regulatory variation. NatureReviews Genetics,2010,11:533-538
143. Price A H, Steele K A, Moore B J, et al. Upland rice grown in soil-filled chambers and exposed tocontrasting water-deficit regimes: II. Mapping quantitative trait loci for root morphology anddistribution. Field Crop Research,2002,76:25-43
144. Rabin R S, Stewart V. Dual response regulators (NarL and NarP) interact with dual sensors (NarXand NarQ) to control nitrate-and nitrite-regulated gene expression in Escherichia coli K-12. Journalof Bacteriology,1993,175:3259-3268
145. Rebouillat J, Dievart A, Verdeil J L, et al. Molecular genetics of rice root development. Rice,2009,2:15-34
146. Rieseberg L H, Raymond O, Rosenthal D M, et al. Major ecological transitions in wild sunflowersfacilitated by hybridization. Science,2003,301:1211-1216
147. Rieseberg L H. Hybrid origins of plant species. Annual Review Ecology, Evolution, andSystematics,1997,28:359-389
148. Robin S, Pathan M S, Courtois B, et al. Mapping osmotic adjustment in an advanced back-crossinbred population of rice. Theoretical and Applied Genetics,2003,107:1288-1296
149. Robinson M D, McCarthy D J, Smyth G K. edgeR: a Bioconductor package for differentialexpression analysis of digital gene expression data. Bioinformatics,2010,26:139-140
150. Rodriguez H G, Roberts J K M, Jordan W R, et al. Growth, water relations, and accumulation oforganic and inorganic solutes in roots of maize seedlings during salt stress. Plant Physiology,1997,113:881-893
151. Sakthivel K, Girishkumar K, Ramkumar G, et al. Alterations in inheritance pattern and level ofcytosine DNA methylation, and their relationship with heterosis in rice. Euphytica,2010,175:303-314
152. Sanger F, Nicklen S, Chase A R. DNA sequencing with chain termiating inhibitors. Proceedings ofthe National Academy of Sciences,1977,74:5463-5468
153. Santiago J, Dupeux F, Round A, et al. The abscisic acid receptor PYR1in complex with abscisicacid. Nature,2009a,462:665-668
154. Santiago J, Rodrigues A, Saez A, et al. Modulation of drought resistance by the abscisic acidreceptor PYL5through inhibition of clade A PP2Cs. The Plant Journal,2009b,60:575-588
155. Schena M, Shalon D, Davis R W, et al. Quantitative monitoring of gene expression patterns with acomplementary DNA microarray. Science,1995,270:467-470
156. Sharp R E, Silk W K, Hsiao T C. Growth of the maize primary root at low water potentials: I.Spatial distribution of expansive growth. Plant Physiology,1988,87:50-57
157. Shen L, Courtois B, McNally K L, et al. Evaluation of near-isogenic lines of rice introgressed withQTLs for root depth through marker-aided selection. Theoretical and Applied Genetics,2001,103:75-83
158. Shen Y, Catchen J, Garcia T, et al. Identification of transcriptome SNPs between Xiphophorus linesand species for assessing allele specific gene expression within F1interspecies hybrids.Comparative Biochemistry and Physiology Part C: Pharmacology, Toxicology and Endocrinology,2012,155:102-108
159. Shimizu A, Kato K, Komatsu A, et al. Genetic analysis of root elongation induced by phosphorusdeficiency in rice (Oryza sativa L.): fine QTL mapping and multivariate analysis of related traits.Theoretical and Applied Genetics,2008,117:987-996
160. Shimizu A, Yanagihara S, Kawasaki S, et al. Phosphorus deficiency-induced root elongation and itsQTL in rice (Oryza sativa L.). Theoretical and Applied Genetics,2004,109:1361-1368
161. Shull G H. The composition of a field of maize. American Breeders Association Report,1908,4:296-301
162. Singh N, Murata Y, Oda S, et al. Allelic expression changes in Medaka (Oryzias latipes) hybridsbetween inbred strains derived from genetically distant populations. PLoS One,2012,7: e36875
163. Somerville C, Bauer S, Brininstool G, et al. Toward a systems approach to understanding plant cellwalls. Science,2004,306:2206-2211
164. Song G S, Zhai H L, Peng Y G, et al. Comparative transcriptional profiling and preliminary studyon heterosis mechanism of super-hybrid rice. Molecular Plant,2010,3:1012-1025
165. Sourjik V, Schmitt R. Phosphotransfer between CheA, CheY1, and CheY2in the chemotaxis signaltransduction chain of Rhizobium meliloti. Biochemistry,1998,37:2327-2335
166. Springer N M, Stupar R M. Allelic variation and heterosis in maize: How do two halves makemore than a whole? Genome Research,2007a,17:264-275
167. Springer N M, Stupar R M. Allelic-specific expression patterns reveal biases and embryo-specificparent-of-origin effects in hybrid maize. The Plant Cell,2007b,19:2391-2402
168. Stupar R M, Spirnger N M. Cis-transcriptional variation in maize inbred lines B73and Mo17leadsto additive expression patterns in the F1hybrid. Genetics,2006,173:2199-2210
169. Suzuki M M, Bird A. DNA methylation landscapes: provocative insights from epigenomics. NatureReviews Genetics,2008,9:465-476
170. Tirosh I, Reikhav S, Levy A A, et al. A yeast hybrid provides insight into the evolution of geneexpression. Science,2009,324:659-662
171. To J P C, Deruère J, Maxwell B B, et al. Cytokinin regulates type-A Arabidopsis response regulatoractivity and protein stability via two-component phosphorelay. The Plant Cell,2007,19:3901-3914
172. Tsai Y C, Weir N R, Hill K, et al. Characterization of genes involved in cytokinin signaling andmetabolism from rice. Plant Physiology,2012,158:1666-1684
173. Tuberosa R, Sanguineti M C, Landi P, et al. Identification of QTL for root characteristics in maizegrown in hydroponics and analysis of their overlap with QTL for grain yield in the field at twowater regimes. Plant Molecular Biology,2002,48:697-712
174. Tuong T P, Bouman B, Mortimer M. More rice less water-integrated approaches for increasingwater productivity in irrigated rice based systems in Asia. Plant Production Science,2005,8:231-241
175. Velculescu V E, Zhang L, Vogelstein B, et al. Serial analysis of gene expression. Science,1995,270:484-487
176. Vuylsteke M, Van Eeuwijk F, Van Hummelen P, et al. Genetic analysis of variation in geneexpression in Arabidopsis thaliana. Genetics,2005,171:1267-1275
177. Wang D, Pan Y J, Zhao X Q, et al. Genome-wide temporal-spatial gene expression profiling ofdrought responsiveness in rice. BMC Genomics,2011,12:149
178. Wang W W, Meng B, Ge X M, et al. Proteomic profiling of rice embryos from a hybrid ricecultivar and its parental lines. Proteomics,2008,8:4808-4821
179. Wang X, Cnops G, Vanderhaeghen R, et al. AtCSLD3, a cellulose synthase-like gene important forroot hair growth in Arabidopsis. Plant Physiology,2001,126:575-586
180. Wang Y H, Li J Y. Branching in rice. Current Opinion in Plant Biology,2010,14:94-99
181. Wang Z K, Ni Z F, Wu H L, et al. Heterosis in root development and differential gene expressionbetween hybrids and their parental inbreds in wheat (Triticum aestivum L.). Theoretical andApplied Genetics,2006,113:1283-1294
182. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptome. Nature ReviewGenetics,2009,10:57-63
183. Wasaki J, Yonetani R, Kuroda S, et al. Transcriptional analysis of metabolic changes byphosphorus stress in rice plant roots. Plant, Cell and Environment,2003,26:1515-1523
184. Wasinger V C, Cordwell S J, Cerpa-Poljak A, et al. Progress with gene-product mapping of theMollicutes: Mycoplasma genitalium. Electrophoresis,1995,16:1090-1094
185. Wei G, Tao Y, Liu G Z, et al. A transcriptomic analysis of superhybrid rice LYP9and its parents.Proceedings of the National Academy of Sciences,2009,106:7695-7701
186. Wittkopp P J, Haerum B K, Clark A G. Evolutionary changes in cis and trans gene regulation.Nature,2004,430:85-88
187. Wu P, Ni J, Luo A. QTL underlying rice tolerance to low-potassium stress in rice seedlings. Cropscience,1998,38:1458-1462
188. Xiao J, Li J, Yuan L, et al. Dominance is the major genetic basis of heterosis in rice as revealed byQTL analysis using molecular markers. Genetics,1995,140:745-754
189. Xie Z S, Wang J Q, Cao M L, et al. Pedigree analysis of an elite rice hybrid using proteomicapproach. Proteomics,2006,6:474-486
190. Xiong L Z, Xu C G, Saghai-Maroof M A, et al. Patterns of cytosine methylation in an elite ricehybrid and its parental lines detected by a methylation-sensitive amplification polymorphismtechnique. Molecular and General Genetics,1999,261:439-446
191. Xu J C, Li X B, Zhu L H. Comparative mapping of rice root traits in seedlings grown in nutrient ornon-nutrient solution. Process in Natural Science,2004,14:327-331
192. Xu M L, Li X Q, Korban S S. AFLP-based detection of DNA methylation. Plant MolecularBiology Report,2000,18:361-368
193. Yamamoto M, Wakatsuki T, Hada A, et al. Use of serial analysis of gene expression (SAGE)technology. Journal of Immunological Methods,2001,250:45-66
194. Yan H, Yuan W S, Velculescu V E, et al. Allelic variation in human gene expression. Science,2002,297:1143-1143
195. Yao Y Y, Ni Z F, Zhang Y H, et al. Identification of differentially expressed genes in leaf and rootbetween wheat hybrid and its parental inbreds using PCR-based cDNA subtraction. PlantMolecular Biology,2005,58:367-384
196. Ye J, Fang L, Zheng H K, et al. WEGO: a web tool for plotting GO annotations. Nucleic AcidsResearch,2006,34:293-297
197. Yebra M J, Bhagwat A S. A cytosine methyltransferase converts5-methylcytosine in DNA tothymine. Biochemistry,1995,34:14752-14757
198. Yu S B, Li J X, Xu C G, et al. Importance of epistasis as the genetic basis of heterosis in an eliterice hybrid. Proceedings of the National Academy of Sciences,1997,94:9226-9231
199. Yue B, Xue W Y, Xiong L Z, et al. Genetic basis of drought resistance at reproductive stage in rice:separation of drought tolerance from drought avoidance. Genetics,2006,172:1213-1228
200. Zeng Z B. Precision mapping of quantitative trait loci. Genetics,1994,136:1457-468
201. Zhang C, Yin Y, Zhang A, et al. Comparative proteomic study reveals dynamic proteome changesbetween superhybrid rice LYP9and its parents at different developmental stages. Journal of PlantPhysiology,2012a,169:387-398
202. Zhang H Y, He H, Chen L B, et al. A genome-wide transcriptome analysis reveals a closecorrelation of promoter INDEL polymorphism and heterotic gene expression in rice hybrids.Molecular Plant,2008,1:720-731
203. Zhang J W, Xu L, Wu Y R, et al. OsGLU3, a putative membrane-bound endo-1,4-beta-glucanase,is required for root cell elongation and division in rice (Oryza sativa L.). Molecular Plant,2012b,5:176-186
204. Zhang W P, ShenX Y, Wu P, et al. QTLs and epistasis for seminal root length under a differentwater supply in rice (Oryza sativa L.). Theoretical and Applied Genetics,2001,103:118-123
205. Zhang X, Borevitz J O. Global analysis of allele-specific expression in Arabidopsis thaliana.Genetics,2009,182:943-954
206. Zhang Y, Xiao W K, Luo L J, et al. Downregulation of OsPK1, a cytosolic pyruvate kinase, byT-DNA insertion causes dwarfism and panicle enclosure in rice. Planta,2011,235:25-38
207. Zheng B S, Yang L, Zhang W P, et al. Mapping QTLs and candidate genes for rice root traits underdifferent water-supply conditions and comparative analysis across three population. Theoreticaland Applied Genetics,2003,107:1505-1515
208. Zhu J, Weir B S. Mixed model approaches for genetic analysis of quantitative traits. In AdvancedTopics in Biomathematics: Proceedings of International Conference on Mathematical Biology.1998,1:321-330
209. Zhuang Y, Adams K L. Extensive allelic variation in gene expression in populus F1hybrids. NatureGenetics,2007,177:1987-1996
2.陈杰.大规模平行测序技术（MPSS）研究进展.生物化学与生物物理进展，2004，31：761-765
3.陈艳丽.水稻耐低钾胁迫相关性状的QTL定位[硕士学位论文].北京：中国农业科学院，2012
4.程式华.杂交水稻育种材料和方法研究的现状及发展趋势.中国水稻科学，2000，14：165-169
5.冯跃.超级稻协优9308重组自交系群体对氮素水平响应的遗传研究及QTL定位[博士学位论文].沈阳：沈阳农业大学，2010
6.郭玉春，徐惠龙，陈芳育，等.磷高效水稻根系对低磷胁迫响应的差异蛋白分析.应用生态学报，2010，21：3231-3238
7.郝树荣，郭相平，王为木，等.水稻分蘖期水分胁迫及复水对根系生长的影响.干旱地区农业研究，2007，25：149-152
8.黄莉.甘蓝型油菜杂种优势和遗传多样性的研究[硕士学位论文].武汉：华中农业大学，2007
9.黄毅.应用cDNA芯片研究水稻杂种与亲本基因表达谱及杂种优势分子生物学基础[博士学位论文].武汉：华中农业大学，2006
10.景蕊莲，胡荣海，朱志华，等.冬小麦不同基因型幼苗形态性状遗传力和抗旱性的研究.西北植物学报，1997，17：152-157
11.兰进好，李新海，高树仁，等.不同生态环境下玉米产量性状QTL分析.作物学报，2005，31：1253-1259
12.李巧丽.杜氏利什曼原虫两个发育阶段基因表达系列分析文库的构建及HSP90在其阶段转变过程中的作用[博士学位论文].上海：上海交通大学，2009
13.李雪林，杨书化，张泽民，等.植物杂种优势遗传机制的分析遗传学研究进展.河南科技大学学报（农学版），2003，23：62-65
14.李勇超，宋书锋，李建民.杂种优势的分子机理研究进展.湖北农业科学，2009，48：1501-1504
15.李卓坤，彭涛，张卫东，等.利用“永久F2”群体进行小麦幼苗根系性状QTL分析.作物学报，2010，36：442-448
16.梁永书.超级稻协优9308衍生群体根系的遗传研究[博士学位论文].北京：中国农业科学院，2011
17.林建丽，朱正歌，高建伟.植物杂种优势研究进展.华北农学报，2009，24：46-56
18.刘胜群，宋凤斌.玉米不同耐旱性品种根系构型和动态建成研究.扬州大学学报（农业与生命科学版），2007，28：68-78
19.刘桃菊，戚昌瀚，唐建军.水稻根系建成与产量及其构成关系的研究.中国农业科学，2002，35：1416-1419
20.马西青.玉米株高杂种优势遗传基础剖析[硕士学位论文].北京：中国农业大学，2005
21.穆平，李自超，李春平，等.水、旱稻根系性状与抗旱性相关分析及其QTL定位.科学通报，2003，48：2162-2169
22.聂元元.水稻抗旱性相关QTL精细定位[博士学位论文].武汉：华中农业大学，2009
23.牛兆国.水稻杂种优势利用现状及发展对策.现代农业科技，2010，24：93-94，98
24.沈波，庄杰云，樊叶杨，等.不同供水条件下水稻叶绿素含量的QTL分析.浙江大学学报（农业与生命科学版），2007，33：400-406
25.沈希宏，曹立勇，陈深广，等.超级杂交稻协优9308重组自交系群体的穗部性状QTL分析.中国水稻科学，2009，23：354-362
26.沈希宏，陈深广，曹立勇，等.超级杂交稻协优9308重组自交系的分子遗传图谱构建.分子植物育种，2008，6：861-866
27.沈希宏.超级杂交稻协优9308重组自交系构建及若干性状的QTL定位[博士学位论文].北京：中国农业科学院，2008
28.王斌.基于RNA-Seq技术的米曲霉RIB40转录组学研究[博士学位论文].广州：华南理工大学，2010
29.王超. NaHCO3胁迫下柽柳根部组织基因的表达调控研究[博士学位论文].哈尔滨：东北林业大学，2012
30.王经源.杂交稻苗期杂种优势的比较蛋白质组学研究[博士学位论文].福州：福建农林大学，2008
31.王汝慈.两个生育时期水稻耐低磷胁迫相关性状的QTL定位[硕士学位论文].北京：中国农业科学院，2009
32.王曦，汪小我，王丽坤，等.新一代高通量RNA测序数据的处理与分析.生物化学与生物物理进展，2010，37：834-846
33.王志芬，陈学留，余美炎，等.冬小麦生长发育与根系关系的32P示踪研究.核农学报，1997，11：173-178
34.武瑞，连学昭.基因芯片技术在中药研究中的应用.中兽医医药杂志，2005，1：21-23
35.谢晓东.小麦杂交当代和亲本自交种子发育早期的基因表达差异与杂种优势[博士学位论文].北京：中国农业大学，2003
36.徐林娟，徐正浩，李舸，等.不同土壤水分供给下水稻叶水势的变化规律.核农学报，2011，25：0553-0558
37.薛应龙，夏镇澳.植物生理学实验手册.上海：上海科学技术出版社，1982
38.杨玲，孙娜，余有见，等.水分胁迫下水稻叶片相关生理性状的QTL定位.浙江农业学报，2009，21：490-494
39.袁隆平.水稻的雄性不孕性.科学通报，1996，17：185-188
40.袁倩倩，李卓坤，田纪春，等.不同水分胁迫下小麦胚芽鞘和胚根长度的QTL分析.作物学报，2011，37：294-301
41.张耗，黄钻华，王静超，等.江苏中籼水稻品种演化过程中根系形态生理性状的变化及其与产量的关系.作物学报，2011，37：1020-1030
42.张坤普，徐宪斌，田纪春.小麦籽粒产量及穗部相关性状的QTL定位.作物学报，2009，35：270-278
43.张义荣，姚颖垠，彭惠茹，等.植物杂种优势形成的分子遗传机理研究进展.自然科学进展，2009，19：697-703
44.赵秀琴，徐建龙，朱苓华，等.利用回交导入系定位干旱环境下水稻植株水分状况相关QTL.作物学报，2008，34：1696-1703
45.周蓉，陈海峰，王贤智，等.大豆幼苗根系性状的QTL分析.作物学报，2011，37：1151-1158
46.朱军.运用混合线性模型定位复杂数量性状基因的方法.浙江大学学报（自然科学版）,1999,33:327-335
47.庄杰云，樊叶杨，吴建利，等.超显性效应对水稻杂种优势的重要作用.中国科学（C缉），2001，31：106-113
48.庄杰云，樊叶杨，吴建利，等.杂交水稻中超显性效应的分析.遗传，2000，22：205-208
49. Adams M D, Kelly J M, Gocayne J D, et al. Complementary DNA sequencing: expressed sequencetags and human genome project. Science,1991,252:1631-1656
50. Arnold M L. Natural hybridization and the evolution of domesticated, pest and disease organisms.Molecular Ecology,2004:997-1007
51. Ashikawa I. Surveying CpG methylation at5'-CCGG in the genomes of rice cultivars. PlantMolecular Biology,2001,45:31-39
52. Austin D F, Lee M. Detection of quantitative trait loci for grain yield and yield components inmaize across generations in stress and nonstress environments. Crop Science,1998,38:1296-1308
53. Bao J Y, Lee S, Chen C, et al. Serial Analysis of Gene Expression Study of a hybrid rice strain(LYP9) and its parental cultivars. Plant Physiology,2005,138:1216-1231
54. Basu S, Roychoudhury A, Saha P P, et al. Comparative analysis of some biochemical responses ofthree indica rice varieties during polyethylene glycol-mediated water stress exhibits distinctvarietal differences. Acta Physiologiae Plant,2010,32:551-563
55. Birchler J A, Auger D L, Riddle N C, et al. In search of the molecular basis of heterosis. The PlantCell,2003,15:2236-2239
56. Bird A. Perceptions of epigenetics. Nature,2007,447:396-398
57. Bransteitter R, Pham P, Scharff M D, et al. Activation-induced cytidine deaminase deaminatesdeoxycytidine on single-stranded DNA but requires the action of RNase. Proceeding of theNational Academy of Sciences of the United States of America,2003,100:4102-4107
58. Brenner S, Johnson M, Bridgham J, et al. Gene expression analysis by massively parallel signaturesequencing (MPSS) on microbead arrays. Nature Biotechnology,2000,18:630-634
59. Bruce A B. The mendelian theory of heredity and the augmentation of vigor. Science,1910,32627-628
60. Cervera M T, Ruiz-García L, Martínez-Zapater J M. Analysis of DNA methylation in Arabidopsisthaliana based on methylation-sensitive AFLP markers. Molecular Genetic Genomics,2002,268:543-552
61. Cheng S H, Cao LY, Zhuang J Y, et al. Super hybrid rice breeding in China: achievements andprospects. Journal of Intergrative Plant Biology,2007,49:805-810
62. Cho J I, Kim H B, Kim C Y, et al. Identification and characterization of the duplicate rice sucrosesynthase genes OsSUS5and OsSUS7which are associated with the plasma membrane. Molecularand Cells,2011,31:553-561
63. Chodavarapu R K, Feng S, Ding B, et al. Transcriptome and methylome interactions in ricehybrids. Proceedings of the National Academy of Sciences,2012,109:12040-12045
64. Cohen D, Bogeat-Triboulot M B, Tisserant E, et al. Comparative transcriptomics of droughtresponses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves androot apices across two genotypes. BMC Genomics,2010,11:630
65. Coudert Y, Perin C, Courtois B, et al. Genetic control of root development in rice, the modelcereal. Trends in Plant Science,2010,15:219-226
66. Courtosis B, McLaren G, Sinha P K, et al. Mapping QTLs associated with drought avoidance inupland rice. Molecular Breeding,2000,6:55-66
67. Cowles C R, Hirschhorn J N, Altshuler D, et al. Detection of regulatory variation in mouse genes.Nature Genetics,2002,32:432-437
68. Cui K H, Huang J L, Xing Y Z, et al. Mapping QTLs for seedling characteristics under differentwater supply conditions in rice (Oryza sativa). Plant Physiology,2008,132:53-68
69. De Smet I, Signora L, Beeckman T, et al. An abscisic acid-sensitive checkpoint in lateral rootdevelopment of Arabidopsis. The Plant Journal,2003,33:543-555
70. Dolferus R, Ellis M, De Bruxelles G, et al. Strategies of gene action in Arabidopsis during hypoxia.Annals of Botany,1997,79:21-31
71. Duvick D N. Heterosis: feeding people and protecting natural resources. In: Coors J G, Pandey S,eds. The Genetics and Exploitation of Heterosis in Crops. American Society Agronomy, Inc, CropScience Society of America, Inc, Soil Science Society of America, Inc, Madison, WI.1999.19-29
72. East E M. Heterosis. Genetics,1936,21:375-397
73. Edwards M D, Stuber C W, Wendel J F. Molecular-marker-facilitated investigations ofquantitative-trait loci in maize. I. Numbers, genomic distribution and types of gene action.Genetics,1987,116:113-125
74. Eisen M B, Spellman P T, Brown P O, et al. Cluster analysis and display of genome-wideexpression patterns. Proceedings of the National Academy of Sciences,1998,95:14863-14868
75. Ekanayake I J, Garrity D P, Masajo T M, et al. Root pulling resistance in rice: inheritance andassociation with drought tolerance. Euphytica,1985,34:905-913
76. Farrokhi N, Burton R A, Brownfield L, et al. Plant cell wall biosynthesis: genetic, biochemical andfunctional genomics approaches to the identification of key genes. Plant Biotechnology Journal,2006,4:145-167
77. Feng Y, Cao L Y, Wu W M, et al. Mapping QTLs for nitrogen-deficiency tolerance at seedlingstage in rice (Oryza sativa L.). Plant Breeding,2010,129:652-656
78. Fukai S, Cooper M. Development of drought-resistant cultivars using physiomorphological traits inrice. Field Crops Research,1995,40:67-86
79. Gao Y M, Zhu J. Mapping QTLs with digenic epistasis under multiple environments and predictingheterosis based on QTL effects. Theoretical and Applied Genetics,2007,115:325-333
80. Ge X M, Chen W H, Song S H, et al. Transcriptomic profiling of mature embryo from an elitesuper-hybrid rice LYP9and its parental lines. BMC Plant Biology,2008,8:114
81. Gomez S M, Boopathi N M, Kumar S S, et al. Molecular mapping and location of QTLs fordrought-resistance traits in indica rice (Oryza sativa L.) lines adapted to target environments. ActaPhysiologiae Plantarum,2009,32:355-364
82. Gowda V R P, Henry A, Yamauchi A, et al. Root biology and genetic improvement for droughtavoidance in rice. Field Crops Research,2011,122:1-13
83. Griffing B. Use of a controlled-nutrient experiment to test heterosis hypotheses. Genetics,1990,126:753-767
84. Guo D, Liang J, Li L. Abscisic acid (ABA) inhibition of lateral root formation involvesendogenous ABA biosynthesis in Arachis hypogaea L. Plant Growth Regulation,2009,58:173-179
85. Guo M, Rupe M A, Zinselmeier C, et al. Allelic variation of gene expression in maize hybrids. ThePlant Cell,2004,16:1707-1716
86. He G M, Zhu X P, Elling A A, et al. Global epigenetic and transcriptional trends among two ricesubspecies and their reciprocal hybrids. The Plant Cell,2010,22:17-33
87. Hegarty M J, Hiscock S J. Hybrid speciation in plants: new insights from molecular studies. NewPhytologist,2004,165:411-423
88. Hirose T, Scofield G N, Terao T. An expression analysis profile for the entire sucrose synthase genefamily in rice. Plant Science,2008,174:534-543
89. Hoecker N, Keller B, Piepho H P, et al. Manifestation of heterosis during early maize (Zea mays L.)root development. Theoretical and Applied Genetics,2005,112:421-429
90. Hoffman N E, Bent A F, Hanson A D. Induction of lactate dehydrogenase isozymes by oxygendeficit in barley root tissue. Plant Physiology,1986,82:658-663
91. Hu B, Wu P, Liao C Y, et al. QTLs and epistasis underlying activity of acid phosphatase underphosphorus sufficient and defcient condition in rice (Oryza sativa L.). Plant Soil,2001,230:99-105
92. Hu M, Polyak K. Serial analysis of gene expression. Nature Protocols,2006,1:1743-1760
93. Hua J P, Xing Y Z, Wu W R, et al. Single-locus heterosis effects and dominance by dominanceinteraction can adequately explain the genetic basis of heterosis in an elite rice hybrid. Proceedingsof the National Academy of Sciences,2003,100:2574-2579
94. Huang Y, Zhang L, Zhang J, et al. Heterosis and polymorphisms of gene expression in an elite ricehybrid as revealed by a microarray analysis of9198unique ESTs. Plant Molecular Biology,2006,62:579-591
95. Jackson M B. New root formation in plants and cuttings. Netherland: Martinus Nijhoff Press,1986
96. Jiang K, Zhang S, Lee S, et al. Transcription profile analyses identify genes and pathways centralto root cap functions in maize. Plant Molecular Biology,2006,60:343-363
97. Johnston J W, Harding K, Bremner D H, et al. HPLC analysis of plant DNA methylation: a studyof critical methodological factors. Plant Physiology Biochememistry,2005,43:844-853
98. Jones D F. Dominance of linked factors as a means of accounting for heterosis. Genetics,1917,3:310-312
99. Jones J W. Hybrid vigour in rice. American Society of Agronomy,1926,18:423-428
100. Jongeneel C V, Iseli C, Stevenson B J. Comrehensive sampling of gene expression in human celllines with massively parallel signature sequencing. Proceedings of the National Academy ofSciences,2003,100:4702-4705
101. Kao C H, Zeng Z B, Teasdale R D. Multiple interval mapping for quantitative trait loci. Genetics,1999,152:1203-1216
102. Kearsey M J, Pooni H S. The genetical analysis of quantitative traits. London: Chapman&HallPress,1996
103. Kim C M, Park S H, Je B I, et al. OsCSLD1, a cellulose synthase-like D1gene, is required for roothair morphogenesis in rice. Plant Physiology,2007,143:1220-1230
104. Konishi H, Yamane H, Maeshima M, et al. Characterization of fructose-bisphosphate aldolaseregulated by gibberellin in roots of rice seedling. Plant Molecular Biology,2004,56:839-848
105. Kyndt T, Denil S, Haegeman A, et al. Transcriptome analysis of rice mature root tissue and roottips in early development by massive parallel sequencing. Journal of Experimental Botany,2012,63:2141-2157
106. Lander E S, Botstein D. Mapping mendelian factors underlying quantitative traits using RFLPlinkage maps. Genetics,1989,121:85-199
107. Laszlo A, St. Lawrence P. Parallel induction and synthesis of PDC and ADH in anoxic maize roots.Molecular Genetics&Genomics,1983,192:110-117
108. Lee D J, Kim S, Ha Y M, et al. Phosphorylation of Arabidopsis response regulator7(ARR7) at theputative phospho-accepting site is required for ARR7to act as a negative regulator of cytokininsignaling. Planta,2007,227:577-587
109. Li B, Dewey C N. RSEM: accurate transcript quantification from RNA-Seq data with or without areference genome. BMC Bioinformatics,2011,12:323
110. Li J, Swanson R V, Simon M I, et al. The response regulators CheB and CheY exhibit competitivebinding to the kinase CheA. Biochemistry,1995,34:14626-14636
111. Li L Z, Lu K Y, Chen Z M, et al. Dominance, over-dominance and epistasis condition the heterosisin two heterotic rice hybrids. Genetics,2008,180:1725-1742
112. Li X, Mo X R, Shou H X, et al. Cytokinin-mediated cell cycling arrest of pericycle founder cells inlateral root initiation of Arabidopsis. Plant and Cell Physiology,2006,47:1112-1123
113. Li Z K, Luo L J, Mei H W, et al. Overdominant epistatic loci are the primary genetic basis ofinbreeding depression and heterosis in rice.Ⅰ. Biomass and grain yield. Genetics,2001,158:1737-1753
114. Li Z K, Pinson R M, Park W D, et al. Eistasis for three grain yield components in rice (Oryzasativa L.). Genetics,1997,145:453-465
115. Lian X M, Wang S P, Zhang J W, et al. Expression profiles of10,422genes at early stage of lownitrogen stress in rice assayed using a cDNA microarray. Plant Molecular Biology,2006,60:617-631
116. Lian X M, Xiong Y Z, Yan H, et al. QTLs for low nitrogen tolerance at seedling stage identifiedusing a recombinant inbred line population derived from an elite rice hybrid. Theoretical andApplied Genetics,2005,112:85-96
117. Liang Y S, Zhan X D, Gao Z Q, et al. Mapping of QTLs associated with important agronomictraits using three populations derived from a super hybrid rice Xieyou9308. Euphytica,2012,184:1-13
118. Lu C F, Shen L S, He P, et al. Comparative mapping of QTLs for agronomic traits of rice acrossenvironments by using a doubled-haploid population. Theoretcal and Applied Genetics,1997,94:145-150
119. Luo L J, Li Z K, Mei H W, et al. Overdominant epistatic loci are the primary genetic basis ofinbreeding depression and heterosis in rice.Ⅱ.Grain yield components. Genetics,2001,158:1755-1771
120. Luo X J, Fu Y C, Zhang P J, et al. Additive and over-dominant effects resulting from epistatic lociare the primary genetic basis of heterosis in rice. Journal of Integrative Plant Biology,2009,51:393-408
121. Lynch M, Walsh B. Genetics analysis of quantitative traits. Sunderland: Sinauer Associates Press,1998
122. Margulies M, Egholm M, Altman W E, et al. Genome sequencing in microfabricated high-densitypicolitre reactors. Nature,2005,437:376-380
123. Mason M G. Multiple type-B response regulators mediate cytokinin signal transduction inArabidopsis. The Plant Cell,2005,17:3007-3018
124. McCouch S R, Cho Y G, Yano M, et al. Report on QTL nomenclature. Rice Genetics Newsletter,1997,14:11-13
125. Menegus F, Cattaruzza L, Chersi A, et al. Differences in the anaerobic lactate-succinate productionand in the changes of cell sap pH for plants with high and low resistance to anoxia. PlantPhysiology,1989,90:29-32
126. Messmer R, Fracheboud Y, Banziger M, et al. Drought stress and tropical maize:QTL-by-environment interactions and stability of QTLs across environments for yield componentsand secondary traits. Theoretical and Applied Genetics,2009,119:913-930
127. Meyer R C. Heterosis of biomass production in Arabidopsis. Establishment during earlydevelopment. Plant Physiology,2004,134:1813-1823
128. Ming F, Zheng X W, Mi G H, et al. Identification of quantitative trait loci affecting tolerance to lowphosphorus in rice (Oryza sativa L.). Chinese Science Bulletin,2000,45:520-525
129. Mir G N. Development of commercial hybrids for hills-problems, present status and future scope,In: Recent advances in rice production technology in hills, SKUAST-K.2002,107-111
130. Mizuno H, Kawahara Y, Sakai H, et al. Massive parallel sequencing of mRNA in identification ofunannotated salinity stress-inducible transcripts in rice (Oryza sativa L.). BMC Genomics,2010,11:683
131. Morgan H D, Dean W, Coker H A, et al. Activation-induced cytidine deaminase deaminates5-methylcytosine in DNA and is expressed in pluripotent tissues: implications for epigeneticreprogramming. The Journal of Biological Chemistry,2004,279:52353-52360
132. Mortazavi A, Williams B A, McCue K, et al. Mapping and quantifying mammalian transcriptomesby RNA-Seq. Nature Methods,2008,5:621-628
133. Moudal S K, Kour K. Genetic variability and correlation coefficients of some root characteristicsand yield components in bread wheat (Triticum aestivum L.) under rainfed condition. Environmentand Ecology,2004,22:646-648
134. Nguyen H T, Babu R C, Blum A. Breeding for drought resistance in rice: physiology and moleculargenetics considerations. Crop Science,1997,37:1426-1434
135. Ni J J, Wu P, Senadhira D, et al. Mapping QTLs for phosphorus deficiency tolerance in rice (Oryzasativa L.). Theoretical and Applied Genetics,1998,97:1361-1369
136. O'Carra P, Mulcahy P: Lactate dehydrogenase in plants: distribution and function. Phytochemistry1996,42:581-587
137. Ogawa A, Ando F, Toyofuku K, et al. Sucrose metabolism for the development of seminal root inmaize seedlings. Plant Production Science,2009,12:9-16
138. Ogawa A, Yamauchi A. Root osmotic adjustment under osmotic stress in maize seedlings.2. Modeof accumulation of several solutes for osmotic adjustment in the root. Plant Production Science,2006,9:39-46
139. Oono Y, Kawahara Y, Kanamori H, et al. mRNA-Seq reveals a comprehensive transcriptomeprofile of rice under phosphate stress. Rice,2011,4:50-65
140. Pandey A, Mann M. Proteomics to study genes and genomes. Nature,2000,405:837-846
141. Paschold A, Marcon C, Hoecker N, et al. Molecular dissection of heterosis manifestation duringearly maize root development. Theoretical and Applied Genetics,2009,120:383-388
142. Pastinen T. Genome-wide allele-specific analysis: insights into regulatory variation. NatureReviews Genetics,2010,11:533-538
143. Price A H, Steele K A, Moore B J, et al. Upland rice grown in soil-filled chambers and exposed tocontrasting water-deficit regimes: II. Mapping quantitative trait loci for root morphology anddistribution. Field Crop Research,2002,76:25-43
144. Rabin R S, Stewart V. Dual response regulators (NarL and NarP) interact with dual sensors (NarXand NarQ) to control nitrate-and nitrite-regulated gene expression in Escherichia coli K-12. Journalof Bacteriology,1993,175:3259-3268
145. Rebouillat J, Dievart A, Verdeil J L, et al. Molecular genetics of rice root development. Rice,2009,2:15-34
146. Rieseberg L H, Raymond O, Rosenthal D M, et al. Major ecological transitions in wild sunflowersfacilitated by hybridization. Science,2003,301:1211-1216
147. Rieseberg L H. Hybrid origins of plant species. Annual Review Ecology, Evolution, andSystematics,1997,28:359-389
148. Robin S, Pathan M S, Courtois B, et al. Mapping osmotic adjustment in an advanced back-crossinbred population of rice. Theoretical and Applied Genetics,2003,107:1288-1296
149. Robinson M D, McCarthy D J, Smyth G K. edgeR: a Bioconductor package for differentialexpression analysis of digital gene expression data. Bioinformatics,2010,26:139-140
150. Rodriguez H G, Roberts J K M, Jordan W R, et al. Growth, water relations, and accumulation oforganic and inorganic solutes in roots of maize seedlings during salt stress. Plant Physiology,1997,113:881-893
151. Sakthivel K, Girishkumar K, Ramkumar G, et al. Alterations in inheritance pattern and level ofcytosine DNA methylation, and their relationship with heterosis in rice. Euphytica,2010,175:303-314
152. Sanger F, Nicklen S, Chase A R. DNA sequencing with chain termiating inhibitors. Proceedings ofthe National Academy of Sciences,1977,74:5463-5468
153. Santiago J, Dupeux F, Round A, et al. The abscisic acid receptor PYR1in complex with abscisicacid. Nature,2009a,462:665-668
154. Santiago J, Rodrigues A, Saez A, et al. Modulation of drought resistance by the abscisic acidreceptor PYL5through inhibition of clade A PP2Cs. The Plant Journal,2009b,60:575-588
155. Schena M, Shalon D, Davis R W, et al. Quantitative monitoring of gene expression patterns with acomplementary DNA microarray. Science,1995,270:467-470
156. Sharp R E, Silk W K, Hsiao T C. Growth of the maize primary root at low water potentials: I.Spatial distribution of expansive growth. Plant Physiology,1988,87:50-57
157. Shen L, Courtois B, McNally K L, et al. Evaluation of near-isogenic lines of rice introgressed withQTLs for root depth through marker-aided selection. Theoretical and Applied Genetics,2001,103:75-83
158. Shen Y, Catchen J, Garcia T, et al. Identification of transcriptome SNPs between Xiphophorus linesand species for assessing allele specific gene expression within F1interspecies hybrids.Comparative Biochemistry and Physiology Part C: Pharmacology, Toxicology and Endocrinology,2012,155:102-108
159. Shimizu A, Kato K, Komatsu A, et al. Genetic analysis of root elongation induced by phosphorusdeficiency in rice (Oryza sativa L.): fine QTL mapping and multivariate analysis of related traits.Theoretical and Applied Genetics,2008,117:987-996
160. Shimizu A, Yanagihara S, Kawasaki S, et al. Phosphorus deficiency-induced root elongation and itsQTL in rice (Oryza sativa L.). Theoretical and Applied Genetics,2004,109:1361-1368
161. Shull G H. The composition of a field of maize. American Breeders Association Report,1908,4:296-301
162. Singh N, Murata Y, Oda S, et al. Allelic expression changes in Medaka (Oryzias latipes) hybridsbetween inbred strains derived from genetically distant populations. PLoS One,2012,7: e36875
163. Somerville C, Bauer S, Brininstool G, et al. Toward a systems approach to understanding plant cellwalls. Science,2004,306:2206-2211
164. Song G S, Zhai H L, Peng Y G, et al. Comparative transcriptional profiling and preliminary studyon heterosis mechanism of super-hybrid rice. Molecular Plant,2010,3:1012-1025
165. Sourjik V, Schmitt R. Phosphotransfer between CheA, CheY1, and CheY2in the chemotaxis signaltransduction chain of Rhizobium meliloti. Biochemistry,1998,37:2327-2335
166. Springer N M, Stupar R M. Allelic variation and heterosis in maize: How do two halves makemore than a whole? Genome Research,2007a,17:264-275
167. Springer N M, Stupar R M. Allelic-specific expression patterns reveal biases and embryo-specificparent-of-origin effects in hybrid maize. The Plant Cell,2007b,19:2391-2402
168. Stupar R M, Spirnger N M. Cis-transcriptional variation in maize inbred lines B73and Mo17leadsto additive expression patterns in the F1hybrid. Genetics,2006,173:2199-2210
169. Suzuki M M, Bird A. DNA methylation landscapes: provocative insights from epigenomics. NatureReviews Genetics,2008,9:465-476
170. Tirosh I, Reikhav S, Levy A A, et al. A yeast hybrid provides insight into the evolution of geneexpression. Science,2009,324:659-662
171. To J P C, Deruère J, Maxwell B B, et al. Cytokinin regulates type-A Arabidopsis response regulatoractivity and protein stability via two-component phosphorelay. The Plant Cell,2007,19:3901-3914
172. Tsai Y C, Weir N R, Hill K, et al. Characterization of genes involved in cytokinin signaling andmetabolism from rice. Plant Physiology,2012,158:1666-1684
173. Tuberosa R, Sanguineti M C, Landi P, et al. Identification of QTL for root characteristics in maizegrown in hydroponics and analysis of their overlap with QTL for grain yield in the field at twowater regimes. Plant Molecular Biology,2002,48:697-712
174. Tuong T P, Bouman B, Mortimer M. More rice less water-integrated approaches for increasingwater productivity in irrigated rice based systems in Asia. Plant Production Science,2005,8:231-241
175. Velculescu V E, Zhang L, Vogelstein B, et al. Serial analysis of gene expression. Science,1995,270:484-487
176. Vuylsteke M, Van Eeuwijk F, Van Hummelen P, et al. Genetic analysis of variation in geneexpression in Arabidopsis thaliana. Genetics,2005,171:1267-1275
177. Wang D, Pan Y J, Zhao X Q, et al. Genome-wide temporal-spatial gene expression profiling ofdrought responsiveness in rice. BMC Genomics,2011,12:149
178. Wang W W, Meng B, Ge X M, et al. Proteomic profiling of rice embryos from a hybrid ricecultivar and its parental lines. Proteomics,2008,8:4808-4821
179. Wang X, Cnops G, Vanderhaeghen R, et al. AtCSLD3, a cellulose synthase-like gene important forroot hair growth in Arabidopsis. Plant Physiology,2001,126:575-586
180. Wang Y H, Li J Y. Branching in rice. Current Opinion in Plant Biology,2010,14:94-99
181. Wang Z K, Ni Z F, Wu H L, et al. Heterosis in root development and differential gene expressionbetween hybrids and their parental inbreds in wheat (Triticum aestivum L.). Theoretical andApplied Genetics,2006,113:1283-1294
182. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptome. Nature ReviewGenetics,2009,10:57-63
183. Wasaki J, Yonetani R, Kuroda S, et al. Transcriptional analysis of metabolic changes byphosphorus stress in rice plant roots. Plant, Cell and Environment,2003,26:1515-1523
184. Wasinger V C, Cordwell S J, Cerpa-Poljak A, et al. Progress with gene-product mapping of theMollicutes: Mycoplasma genitalium. Electrophoresis,1995,16:1090-1094
185. Wei G, Tao Y, Liu G Z, et al. A transcriptomic analysis of superhybrid rice LYP9and its parents.Proceedings of the National Academy of Sciences,2009,106:7695-7701
186. Wittkopp P J, Haerum B K, Clark A G. Evolutionary changes in cis and trans gene regulation.Nature,2004,430:85-88
187. Wu P, Ni J, Luo A. QTL underlying rice tolerance to low-potassium stress in rice seedlings. Cropscience,1998,38:1458-1462
188. Xiao J, Li J, Yuan L, et al. Dominance is the major genetic basis of heterosis in rice as revealed byQTL analysis using molecular markers. Genetics,1995,140:745-754
189. Xie Z S, Wang J Q, Cao M L, et al. Pedigree analysis of an elite rice hybrid using proteomicapproach. Proteomics,2006,6:474-486
190. Xiong L Z, Xu C G, Saghai-Maroof M A, et al. Patterns of cytosine methylation in an elite ricehybrid and its parental lines detected by a methylation-sensitive amplification polymorphismtechnique. Molecular and General Genetics,1999,261:439-446
191. Xu J C, Li X B, Zhu L H. Comparative mapping of rice root traits in seedlings grown in nutrient ornon-nutrient solution. Process in Natural Science,2004,14:327-331
192. Xu M L, Li X Q, Korban S S. AFLP-based detection of DNA methylation. Plant MolecularBiology Report,2000,18:361-368
193. Yamamoto M, Wakatsuki T, Hada A, et al. Use of serial analysis of gene expression (SAGE)technology. Journal of Immunological Methods,2001,250:45-66
194. Yan H, Yuan W S, Velculescu V E, et al. Allelic variation in human gene expression. Science,2002,297:1143-1143
195. Yao Y Y, Ni Z F, Zhang Y H, et al. Identification of differentially expressed genes in leaf and rootbetween wheat hybrid and its parental inbreds using PCR-based cDNA subtraction. PlantMolecular Biology,2005,58:367-384
196. Ye J, Fang L, Zheng H K, et al. WEGO: a web tool for plotting GO annotations. Nucleic AcidsResearch,2006,34:293-297
197. Yebra M J, Bhagwat A S. A cytosine methyltransferase converts5-methylcytosine in DNA tothymine. Biochemistry,1995,34:14752-14757
198. Yu S B, Li J X, Xu C G, et al. Importance of epistasis as the genetic basis of heterosis in an eliterice hybrid. Proceedings of the National Academy of Sciences,1997,94:9226-9231
199. Yue B, Xue W Y, Xiong L Z, et al. Genetic basis of drought resistance at reproductive stage in rice:separation of drought tolerance from drought avoidance. Genetics,2006,172:1213-1228
200. Zeng Z B. Precision mapping of quantitative trait loci. Genetics,1994,136:1457-468
201. Zhang C, Yin Y, Zhang A, et al. Comparative proteomic study reveals dynamic proteome changesbetween superhybrid rice LYP9and its parents at different developmental stages. Journal of PlantPhysiology,2012a,169:387-398
202. Zhang H Y, He H, Chen L B, et al. A genome-wide transcriptome analysis reveals a closecorrelation of promoter INDEL polymorphism and heterotic gene expression in rice hybrids.Molecular Plant,2008,1:720-731
203. Zhang J W, Xu L, Wu Y R, et al. OsGLU3, a putative membrane-bound endo-1,4-beta-glucanase,is required for root cell elongation and division in rice (Oryza sativa L.). Molecular Plant,2012b,5:176-186
204. Zhang W P, ShenX Y, Wu P, et al. QTLs and epistasis for seminal root length under a differentwater supply in rice (Oryza sativa L.). Theoretical and Applied Genetics,2001,103:118-123
205. Zhang X, Borevitz J O. Global analysis of allele-specific expression in Arabidopsis thaliana.Genetics,2009,182:943-954
206. Zhang Y, Xiao W K, Luo L J, et al. Downregulation of OsPK1, a cytosolic pyruvate kinase, byT-DNA insertion causes dwarfism and panicle enclosure in rice. Planta,2011,235:25-38
207. Zheng B S, Yang L, Zhang W P, et al. Mapping QTLs and candidate genes for rice root traits underdifferent water-supply conditions and comparative analysis across three population. Theoreticaland Applied Genetics,2003,107:1505-1515
208. Zhu J, Weir B S. Mixed model approaches for genetic analysis of quantitative traits. In AdvancedTopics in Biomathematics: Proceedings of International Conference on Mathematical Biology.1998,1:321-330
209. Zhuang Y, Adams K L. Extensive allelic variation in gene expression in populus F1hybrids. NatureGenetics,2007,177:1987-1996
© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号 地址：北京市海淀区学院路29号 邮编：100083 电话：办公室：(+86 10)66554848；文献借阅、咨询服务、科技查新：66554700 |