玉米苗期耐渍相关性状的QTL定位和功能标记的开发
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摘要
渍害是影响作物生长、生物学产量以及籽粒产量的重要的非生物逆境胁迫因子之一。世界范围内农业生产因受其影响每年造成大量的减产；随着全球气候的不断变化,渍水胁迫日渐频发,因此培育具有高产潜力的耐渍玉米新品种也成为玉米主要育种目标之一。本研究在使用耐渍性自交系(HZ32)和敏感性自交系(K12)构建含有266个单株的高代回交作图群体(AB-QTL)的基础上,利用混合线性模型和完备区间作图的方法,重定位玉米苗期耐渍性相关的数量性状位点(QTLs),相关性状主要包括株高(PH)、根长(RL)、茎鲜重(SFW)、根鲜重(RFW)、根干重(RDW)、茎干重(SDW)、总干重(TDW)以及各性状相应的耐渍系数。另一方面,在前人鉴定的玉米苗期耐渍性相关的候选基因的基础上,应用SSR标记锚定的区域开发与耐渍性主效QTL共定位的功能标记。主要结果总结如下：
1.七个耐渍性相关性状的正态性检验表明,在两个环境下,除渍害胁迫条件下SDW和RDW两性状外,BC2F2：3家系各性状频率分布均呈现正态分布。各性状偏度和峰度均小于1.0,表明各性状均表现为数量遗传效应。
2.在两个试验环境下,大多数性状的广义遗传力(矿)较高,茎干重和总干重耐渍系数遗传力最低为0.62,渍害胁迫下根鲜重遗传力最高为0.83。较高的遗传力意味着各性状大部分的表型变异都是受遗传控制,并且能够通过选择育种程序得以有效地改良。
3.在两个实验环境下,分别计算七个苗期性状在渍害胁迫、正常条件和耐渍系数的成对相关系数表明：在各实验环境下,根干重、根鲜重和茎干重以及它们的耐渍系数之间具有显著的相关性,而根长和根干重之间具有较弱的相关性。
4.利用12个功能性分子标记(3个来源于EST标记和9个来源于miRNA标记)和155对多态性的SSR标记,构建了一张新的连锁图,连锁图谱总长1797.6cM,标记间平均间距为10.8cM。各标记在连锁图谱上的线性顺序与IBM2008参考图谱基本一致。
5.EXP.1和EXP.2各定位到53和68个QTLs。其中,水分胁迫和正常条件下分别定位到56和34个QTLs,耐渍系数定位到31个QTLs。这些QTL分布在玉米的10条染色体上,LOD值变幅为从2.58到14.74,单个QTL位点可解释的表型变异为3.77到31.44%。其中30个主效QTL分别被定位到第1,2,3,4,6,7和9染色体上,单个QTL解释表型变异至少为15%,这些QTLs主要与根长(RL),株高(PH),茎干重(SDW),根干重(RDW),总干重(TDW)和根鲜重(RFW)等性状相关
6.定位EST和miRNA标记表明,10个候选基因与已经鉴定的QTLs分别共定位于染色体1、2、4、6、7和9上,它们很可能是玉米耐渍性重要的候选基因。
本研究结果表明前人定位到的主效QTL能够被AB-QTL重定位,并且能够在回交群体中选择用于精细定位。主效QTL与功能性标记的共定位也表明一些miRNA可能调控与耐渍性相关的代谢通路和直接相应耐渍胁迫。虽然这些基因的功能需要进一步通过转基因和关联分析确认,但是本研究为发掘和定位渍害响应基因提供了新的策略。这些结果为玉米苗期渍害响应的分子机理提供了新的视角,并为分子标记辅助选择提供了有用的分子标记。
Waterlogging stress, negatively affect plant growth, biomass production, and potential yield. This stress affects agriculture in many countries, causing multi-million dollar losses for farmers and the agriculture industry and contributing to poverty worldwide. Incidence of waterlogging stress is increasing due to the effects of climate change. The development of waterlogging-tolerant varieties with high yield potential should be one of the main goals of the maize breeding program. Our study aimed to remap the quantitative trait loci (QTLs) associated with waterlogging tolerance related traits, including plant height (PH), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), root dry weight (RDW), shoot dry weight (SDW), total dry weight (TDW) and their waterlogging tolerance coefficient (WTC) during maize seedling stage by using advanced backcross QTL (AB-QTL) analysis approach in a mixed linear model and inclusive composite interval mapping method under waterlogging and control conditions. On the other hand, based on earlier studies results of candidate genes detected associated with waterlogging tolerance at the seeding stage, functional markers co-localized with major waterlogging tolerant QTLs were developed using the simple sequence repeat markers flanking target regions. A266BC2F2population derived from a cross between a waterlogging-tolerant'HZ32'and a susceptible 'K12' was used. Results summary are as follows:
1. Normality tests performed on the seven waterlogging-related traits, showed that the frequency distributions of the BC2F2:3families were normal over two seasons except of SDW and RDW under waterlogging stress. Both skew and kurtosis values of each trait were<1.0, suggesting that these traits were quantitative genetic effects.
2. The broad sense heritability's (h2) of the various phenotypic traits were relatively high across the two pot experiments, ranging from0.62for the WTC of shoot dry weight and total dry weight to0.83for root fresh weight under waterlogging stress. The high h2implied that most of the phenotypic variance for each trait was genetic and could be effectively improved by selective breeding programs.
3. Correlation coefficients between pairs of all seven seedling traits were calculated under waterlogged, normal conditions and their WTC in the two seasons separately. Highly significant correlations were observed in both Experiments, for root dry weight, root fresh weight, shoot dry weight and their WTC. While, a weak relationship was observed between root length and root dry weight.
4. A new linkage map constructed for the BC2F2population, consisting of three ESTs, nine miRNA and155polymorphic SSR markers, spanned1797.6cM in length across a maize genome, with an average distance of10.8cM between adjacent markers. The linear order of markers on the linkage map was a good agreement with IBM2008Neighbors.
5. A total of fifty-three and sixty-eight QTLs were detected in EXP.1and EXP.2, separately. Of these,56and34putative QTLs were detected under waterlogging treatment and control conditions, respectively.31putative QTLs were detected for waterlogging treatment coefficient. These QTLs were distributed over all10chromosomes, and had LOD scores ranging from2.58to14.74, explaining3.77to31.44%phenotypic variation in the individual traits. Out of which, thirty major QTLs individually accounted for more than15%of the phenotypic variation; they were governed traits associated with RL, PH, SDW, RDW, TDW and RFW were mapped in the different genomic region on chromosomes1,2,3,4,6,7and9.
6. In order to provide additional evidence regarding the role of corresponding genes in waterlogging tolerance, mapping of Expressed Sequence Tags (EST) markers and micro RNAs were conducted. Ten candidate genes were observed to co-localize with the identified QTLs on chromosomes1,2,4,6,7and9, and may important candidate genes for waterlogging tolerance.
The study results reveal that the former major QTL remapped by AB-QTL, could be selected in backcross population for fine mapping of waterlogging tolerance. The co-localization of major QTL and developmental markers indicated that some miRNA may be contributed to waterlogging tolerance pathways and directly response for waterlogging related traits. Although the functions of these genes need to be confirmed deeply through transgenic and association analysis, the strategy used in the current study is a good starting point for the discovery and mapping of waterlogging-responsive genes. The results may provide new insight into the molecular basis of the waterlogging response of seedlings stage and useful markers for MAS.
1.七个耐渍性相关性状的正态性检验表明,在两个环境下,除渍害胁迫条件下SDW和RDW两性状外,BC2F2：3家系各性状频率分布均呈现正态分布。各性状偏度和峰度均小于1.0,表明各性状均表现为数量遗传效应。
2.在两个试验环境下,大多数性状的广义遗传力(矿)较高,茎干重和总干重耐渍系数遗传力最低为0.62,渍害胁迫下根鲜重遗传力最高为0.83。较高的遗传力意味着各性状大部分的表型变异都是受遗传控制,并且能够通过选择育种程序得以有效地改良。
3.在两个实验环境下,分别计算七个苗期性状在渍害胁迫、正常条件和耐渍系数的成对相关系数表明：在各实验环境下,根干重、根鲜重和茎干重以及它们的耐渍系数之间具有显著的相关性,而根长和根干重之间具有较弱的相关性。
4.利用12个功能性分子标记(3个来源于EST标记和9个来源于miRNA标记)和155对多态性的SSR标记,构建了一张新的连锁图,连锁图谱总长1797.6cM,标记间平均间距为10.8cM。各标记在连锁图谱上的线性顺序与IBM2008参考图谱基本一致。
5.EXP.1和EXP.2各定位到53和68个QTLs。其中,水分胁迫和正常条件下分别定位到56和34个QTLs,耐渍系数定位到31个QTLs。这些QTL分布在玉米的10条染色体上,LOD值变幅为从2.58到14.74,单个QTL位点可解释的表型变异为3.77到31.44%。其中30个主效QTL分别被定位到第1,2,3,4,6,7和9染色体上,单个QTL解释表型变异至少为15%,这些QTLs主要与根长(RL),株高(PH),茎干重(SDW),根干重(RDW),总干重(TDW)和根鲜重(RFW)等性状相关
6.定位EST和miRNA标记表明,10个候选基因与已经鉴定的QTLs分别共定位于染色体1、2、4、6、7和9上,它们很可能是玉米耐渍性重要的候选基因。
本研究结果表明前人定位到的主效QTL能够被AB-QTL重定位,并且能够在回交群体中选择用于精细定位。主效QTL与功能性标记的共定位也表明一些miRNA可能调控与耐渍性相关的代谢通路和直接相应耐渍胁迫。虽然这些基因的功能需要进一步通过转基因和关联分析确认,但是本研究为发掘和定位渍害响应基因提供了新的策略。这些结果为玉米苗期渍害响应的分子机理提供了新的视角,并为分子标记辅助选择提供了有用的分子标记。
Waterlogging stress, negatively affect plant growth, biomass production, and potential yield. This stress affects agriculture in many countries, causing multi-million dollar losses for farmers and the agriculture industry and contributing to poverty worldwide. Incidence of waterlogging stress is increasing due to the effects of climate change. The development of waterlogging-tolerant varieties with high yield potential should be one of the main goals of the maize breeding program. Our study aimed to remap the quantitative trait loci (QTLs) associated with waterlogging tolerance related traits, including plant height (PH), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), root dry weight (RDW), shoot dry weight (SDW), total dry weight (TDW) and their waterlogging tolerance coefficient (WTC) during maize seedling stage by using advanced backcross QTL (AB-QTL) analysis approach in a mixed linear model and inclusive composite interval mapping method under waterlogging and control conditions. On the other hand, based on earlier studies results of candidate genes detected associated with waterlogging tolerance at the seeding stage, functional markers co-localized with major waterlogging tolerant QTLs were developed using the simple sequence repeat markers flanking target regions. A266BC2F2population derived from a cross between a waterlogging-tolerant'HZ32'and a susceptible 'K12' was used. Results summary are as follows:
1. Normality tests performed on the seven waterlogging-related traits, showed that the frequency distributions of the BC2F2:3families were normal over two seasons except of SDW and RDW under waterlogging stress. Both skew and kurtosis values of each trait were<1.0, suggesting that these traits were quantitative genetic effects.
2. The broad sense heritability's (h2) of the various phenotypic traits were relatively high across the two pot experiments, ranging from0.62for the WTC of shoot dry weight and total dry weight to0.83for root fresh weight under waterlogging stress. The high h2implied that most of the phenotypic variance for each trait was genetic and could be effectively improved by selective breeding programs.
3. Correlation coefficients between pairs of all seven seedling traits were calculated under waterlogged, normal conditions and their WTC in the two seasons separately. Highly significant correlations were observed in both Experiments, for root dry weight, root fresh weight, shoot dry weight and their WTC. While, a weak relationship was observed between root length and root dry weight.
4. A new linkage map constructed for the BC2F2population, consisting of three ESTs, nine miRNA and155polymorphic SSR markers, spanned1797.6cM in length across a maize genome, with an average distance of10.8cM between adjacent markers. The linear order of markers on the linkage map was a good agreement with IBM2008Neighbors.
5. A total of fifty-three and sixty-eight QTLs were detected in EXP.1and EXP.2, separately. Of these,56and34putative QTLs were detected under waterlogging treatment and control conditions, respectively.31putative QTLs were detected for waterlogging treatment coefficient. These QTLs were distributed over all10chromosomes, and had LOD scores ranging from2.58to14.74, explaining3.77to31.44%phenotypic variation in the individual traits. Out of which, thirty major QTLs individually accounted for more than15%of the phenotypic variation; they were governed traits associated with RL, PH, SDW, RDW, TDW and RFW were mapped in the different genomic region on chromosomes1,2,3,4,6,7and9.
6. In order to provide additional evidence regarding the role of corresponding genes in waterlogging tolerance, mapping of Expressed Sequence Tags (EST) markers and micro RNAs were conducted. Ten candidate genes were observed to co-localize with the identified QTLs on chromosomes1,2,4,6,7and9, and may important candidate genes for waterlogging tolerance.
The study results reveal that the former major QTL remapped by AB-QTL, could be selected in backcross population for fine mapping of waterlogging tolerance. The co-localization of major QTL and developmental markers indicated that some miRNA may be contributed to waterlogging tolerance pathways and directly response for waterlogging related traits. Although the functions of these genes need to be confirmed deeply through transgenic and association analysis, the strategy used in the current study is a good starting point for the discovery and mapping of waterlogging-responsive genes. The results may provide new insight into the molecular basis of the waterlogging response of seedlings stage and useful markers for MAS.
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