水稻抗纹枯病QTL qSB-9~（Tq）的遗传分析和精细定位研究
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摘要
纹枯病是世界性的水稻3大病害之一。水稻对纹枯病的抗性属于典型的数量性状。迄今,在水稻的多个研究群体上一共检测到30个左右的抗纹枯病QTL,涉及全部的水稻12条染色体。水稻第9染色体是发现抗纹枯病QTL次数最多的染色体。其中来自相对抗病品种特青(Teqing)第9染色体的抗纹枯病QTL qSB-9~(Tq)被不同研究者多次定位到,具有较高的重演性,并受到较多的关注。因此,本研究围绕qSB-9~(Tq)开展了一系列的遗传研究,并对其进行了精细定位。主要研究结果如下。
采用标记辅助选择结合性状鉴定的回交验证策略,构建了Teqing与相对感病亲本Lemont(轮回亲本)的回交群体,每个回交世代均以RM201和RM6971作为qSB-9~(Tq)的双侧标记对其进行选择。于回交BC_5F_1世代证实qSB-9~(Tq)是一个真实的抗性QTL(QRL,quantitative resistance locous),而且利用分子标记RM201和RM6971对其选择是有效的。在此基础上,为了更精确地评价qSB-9~(Tq)的抗病效应,我们适当扩大目标区间的选择范围,利用覆盖该QRL置信区间的7个多态性分子标记进行前景选择,于BC_6_1世代用114个均匀覆盖水稻12条染色体的分子标记对前景选择的中选单株进行背景选择,从中筛选出前景标记基因型均为杂合型,且在所有背景标记位点上均与轮回亲本Lemont完全一致的1个单株。连续两年对该单株的扩繁后代(BC_6F_2)及随后获得的近等基因系(BC_6F_3)采取完全随机试验和随机区组试验2种不同的试验设计,对qSB-9~(TqTq)纯合型、qSB-9~(LeLe)纯合型和qSB-9~(TqLe)杂合型等3种基因型个体(BC_6F_2)和近等基因系(BC_6F_3)间的病级差异分别进行统计分析。结果表明:两种实验设计结果表现出一致的趋势,即qSB-9~(Tq)存在于分子标记RM242-Y92.5之间,可减轻病级0.7-1级(0-9级病情分级系统)左右,且其抗性表现为几乎完全的显性特征。
之前在水稻品种Jasmine85和明恢63(Minghui63)的第9染色体上也分别定位到抗纹枯病QTL,根据其有利等位基因的来源分别被命名为qSB-9~(J85)和qSB-9~(MH63)。通过分子标记与水稻物理图谱间的整合分析,发现qSB-9~(J85)、qSB-9~(MH63)和qSB-9~(Tq)等3个QTL的置信区间相近或局部重叠。采用标记辅助选择结合性状鉴定的回交验证策略,以感病亲本Lemont为轮回亲本构建Jasmine85/Lemont和Minghui63/Lemont两个回交组合的拟染色体片段代换系群体。在两个不同的回交世代对这2个QTL进行了验证,证实qSB-9~(J85)和qSB-9~(MH63)真实位于第9染色体上的分子标记RM6971-RM201区间内,而根据上述分析,qSB-9~(Tq)也很可能位于该区间内。这3个QRL在杂合状态下平均可减轻病级1.0级左右,初步推测它们可能是同一个QRL。
本课题组之前已经利用Teqing/Lemont(轮回亲本)组合的回交群体证实了水稻品种Lemont第11染色体上的抗纹枯病QTL qSB-11~(Le)。本研究利用相同组合,也证实了来自Teqing第7染色体的抗水稻纹枯病QTLqSB-7~(Tq)。在此基础上,为了研究qSB-9~(Tq)与这两个QRL之间的聚合效应及相互之间的互作关系,我们利用3个QRL的双侧分子标记辅助连续回交结合性状鉴定,通过将Teqing与Lemont(轮回亲本)杂交并连续回交,构建了这3个QRL的一套近等基因系。在一致的遗传背景下,对各QRL的主效应、聚合效应及其互作关系进行了研究。结果显示,3个QRL单独存在或在聚合状态下均能显著提高水稻品种对纹枯病的抗性水平,而且,不同QRL之间普遍存在互作关系。
为了更有效地开展qSB-9~(Tq)的标记辅助育种以及对其进行克隆和抗性机理的研究,我们采用构建目标区间染色体单片段叠代系的策略,对qSB-9~(Tq)进行了精细定位研究。首先在其选择区间RM242-Y92.5(第三章)以及外侧一定距离内,发展和筛选到在两个亲本间具有多态的PCR分子标记共22个,其平均物理间距为319.753kb,可较高密度地覆盖整个大区间。利用这些分子标记,对本论文第三章近等基因系构建过程中获得的1个BC_6F_1中选单株(背景为轮回亲本Lemont基因型,仅在目标大区间为杂合基因型)进行标记检测,结果显示该单株的22个标记位点均为杂合型。随后我们对其自交后代进行标记检测,并根据不同的标记基因型,构建了在不同标记间发生交换重组的44类共894个染色体单片段代换系(染色体单片段叠代系)。于2007年正季选择其中的240个叠代系,进行2个区组重复的田间接种试验,于抽穗期后30天调查各叠代系的病级和病指。随后对各叠代系的几个主要农艺性状进行调查,并发现在大区间内存在一个控制分蘖角的主效QTL(大分蘖角基因来自供体亲本Teqing)。为了排除该分蘖角QTL对病情的干扰,我们选择不携带该大分蘖角基因的叠代系对qSB-9~(Tq)进行精细定位。对叠代系两个重复的病级和病指进行联合聚类分析。采用的聚类方法分别为系统聚类的离差平方和法,以及动态聚类的最小组内平方和法。以动态聚类结果为基础,系统聚类方法结果为参考,对各叠代系进行抗感分型并确定目标QTL的左右边界,从而实现qSB-9~(Tq)的精细定位。结果表明,在整个目标大区间内存在2个抗纹枯病QTL,分别位于分蘖角QTL的左侧和右侧,分别命名这2个QTL为L-qSB-9~(Tq)和R-qSB-9~(Tq)。这两个QRL的物理区间分别为Z77.2-Y77.7和Y86-Y90.2,区间大小分别为180.875Kb和207.724 kb。
综上所述,本研究首次在近等基因系的水平下,研究了一个水稻抗纹枯病QTL qSB-9~(Tq)的效应和作用方式。该QRL的抗性表现为几乎完全的显性,预示着其在水稻杂种优势利用方面具有较大的应用潜力。同时,该QRL与qSB-11~(Le)和qSB-7~(Tq)之间存在的互作关系,也暗示着其在分子标记辅助聚合育种中具有潜在的利用价值。进一步对其进行精细定位研究,不仅可以更高效地进行qSB-9~(Tq)的分子标记辅助育种,而且还将为该QRL的克隆和数量抗性机理研究打下坚实的基础。
Sheath blight(SB) disease is one of the three most serious diseases in rice worldwide.The resistance to rice sheath blight is a typical quantitative trait.Until now,approximately 30 QTLs contributing to rice SB resistance had been detected in different populations.Each of the 12 rice chromosomes had been shown to possess one or more of the 30 QTLs.Several SB resistance QTLs(qSB) had been detected on chromosome 9.However,separate research endeavors had generated rice QTL data using different parental individuals and populations.Several researchers had detected a resistance QTL qSB-9~(Tq) on Teqing chromosome 9.In this study,a set of genetic analyses and fine mapping for qSB-9~(Tq) were conducted.
The strategy of marker-assisted selection(MAS) combined with backcross identification was adopted to construct a backcross combination of Teqing/Lemont(recurrent parent) and two molecular markers RM201 and RM6971 were used for selecting qSB-9~(Tq) in each generation.In BC_5F_1 generation,qSB-9~(Tq) was validated and proved that it could be selected by two molecular markers RM201 and RM6971 efficiently.In order to accurately evaluate the resistant effect of qSB-9~(Tq) in BC_6 generation,seven molecular markers flanking qSB-9~(Tq) were used for foreground selection and other 114 molecular markers evenly distributed on other regions of rice genome were adopted for background selection.One single BC_6F_1 plant with heterozygous genotype of qSB-9~(Tq) and the same background as Lemont were gained and harvested.Three genotypic individuals of qSB-9~(TqTq),qSB-9~(LeLe) and qSB-9~(TqLe), distinguished by detecting marker genotypes flanking the QTL,were gained in BC_6F_2 generation and then formed the NILs in BC_6F_3 generation in two consecutive years.Two different experiment designs were adopted and both the results suggested that qSB-9~(Tq) located between two molecular markers RM242 and Y92.5 on chromosome 9,and it was a dominant quantitative resistance QTL(QRL,quantitative resistance locous) which could reduce disease rating about 0.7-1.0 score under Rush's '0-9' disease rating system.
Two rice sheath blight(SB) resistance QTLs had been previously detected on chromosome 9 of Jasmine85 and Minghui63,respectively.According to the origin of these resistance alleles,their corresponding QTLs were named qSB-9~(J85) and qSB-9~(MH63),respectively.An integrated analysis between molecular markers and a rice physical map revealed that the intervals of the two QTLs and qSB-9~(Tq) were adjacent or partially overlapping.Marker genotype detection combined with backcross identification was applied to construct two backcross populations of Jasmine85/Lemont(recurrent parent) and Minghui63/Lemont(recurrent parent) and then 10 HCSSLs(heterozygous chromosome substitution segment lines) of each backcross combination were gained.Sequentially the two QTL intervals were validated in two different generations.The results suggested that qSB-9~(J85) and qSB-9~(MH63) were truly located in the interval of RM201 and RM6971 on chromosome 9 and the qSB-9~(Tq) on chromosome 9 of Teqing might be also in this interval.These three QRLs could reduce a disease rating score by a value of 1.0 for heterozygous genotypes and were speculated to be identical.
Moreover,The QTL of resistance to rice sheath blight,mapped on chromosome 11 of Lemont had been validated and named qSB-11~(Le).In this study,another QRL on chromosome 7 of Teqing was also confirmed using the same backcross combination of Teqing/Lemont(recurrent parent) and named qSB-7~(Tq).Together with qSB-9~(Tq),the effects and pyramiding effects of the three QRLs were studied by using a set of near-isogenic lines(NILs) under the background of Lemont.The results indicated that the three QRLs could improve the ability of resistance to rice sheath blight significantly in their single or pyramiding status.Furthermore,there were certain interactions existed among these three QRLs in this study.
In order to clone and study the QRL furthermore,and conduct MAS for qSB-9~(Tq) more efficiently,the strategy of constructing chromosome single substitution segment lines(CSSSLs) was adopted to carried out fine mapping of the QRL.Twenty two polymorphic molecular markers were developed and screened,which could cover the interval with high density that the average physical distance was 319.753kb.These markers were used for detecting the single plant gained from the backcross combination of Teqing/Lemont in Chapter3,and the genotypes of the 22 markers were all heterozygous.Then 894 CSSSLs of 44 classes were gained according to different genotypes of the 22 markers.Two hundred and forty CSSSLs were selected for field experiment with two repeats in 2007.Disease rating and disease index were investigated 30 days after late tillering stage.Then 6 agronomic traits were also investigated and a major QTL conferring tiller angle from Teqing was discovered.In order to eliminate the disturbance of the existence of the QTL, CSSSLs without carrying the QTL were selected to conduct fine mapping for qSB-9~(Tq).Two clustering approaches were used for clustering the CSSSLs by analyzing disease rating and disease index in two field repeats together. according to the clustering results the borders of the target QTLs were analyzed.The results indicated that there existed two QRLs in the interval of RM242 and Y93.5,which were L-qSB-9~(Tq) in the interval Z77.2-Y77.7 and R-qSB-9~(Tq) in the interval Y86-Y90.2 with their interval distances were 180.875kb and 207.724kb respectively.
To sum up,the paper first reported and studied the effect and functional mode of the QTL conferring resistance to rice sheath blight in a relatively resistant cultivar Teqing under the condition of NILs.The QRL exhibited almost complete dominance,which would accelerate the utilization of qSB-9~(Tq) into the practice of hybrid rice breeding.Furthermore,there existed certain interactions between qSB-7~(Tq),qSB-11~(Le) and qSB-9~(Tq) suggested the utilization of qSB-9~(Tq) in QRL pyramiding breeding.So,it is urgent to carry out fine mapping and cloning the QRL,which would benefit the efficiency of MAS breeding and lay a foundation for the theoretical study of the qSB-9~(Tq).
采用标记辅助选择结合性状鉴定的回交验证策略,构建了Teqing与相对感病亲本Lemont(轮回亲本)的回交群体,每个回交世代均以RM201和RM6971作为qSB-9~(Tq)的双侧标记对其进行选择。于回交BC_5F_1世代证实qSB-9~(Tq)是一个真实的抗性QTL(QRL,quantitative resistance locous),而且利用分子标记RM201和RM6971对其选择是有效的。在此基础上,为了更精确地评价qSB-9~(Tq)的抗病效应,我们适当扩大目标区间的选择范围,利用覆盖该QRL置信区间的7个多态性分子标记进行前景选择,于BC_6_1世代用114个均匀覆盖水稻12条染色体的分子标记对前景选择的中选单株进行背景选择,从中筛选出前景标记基因型均为杂合型,且在所有背景标记位点上均与轮回亲本Lemont完全一致的1个单株。连续两年对该单株的扩繁后代(BC_6F_2)及随后获得的近等基因系(BC_6F_3)采取完全随机试验和随机区组试验2种不同的试验设计,对qSB-9~(TqTq)纯合型、qSB-9~(LeLe)纯合型和qSB-9~(TqLe)杂合型等3种基因型个体(BC_6F_2)和近等基因系(BC_6F_3)间的病级差异分别进行统计分析。结果表明:两种实验设计结果表现出一致的趋势,即qSB-9~(Tq)存在于分子标记RM242-Y92.5之间,可减轻病级0.7-1级(0-9级病情分级系统)左右,且其抗性表现为几乎完全的显性特征。
之前在水稻品种Jasmine85和明恢63(Minghui63)的第9染色体上也分别定位到抗纹枯病QTL,根据其有利等位基因的来源分别被命名为qSB-9~(J85)和qSB-9~(MH63)。通过分子标记与水稻物理图谱间的整合分析,发现qSB-9~(J85)、qSB-9~(MH63)和qSB-9~(Tq)等3个QTL的置信区间相近或局部重叠。采用标记辅助选择结合性状鉴定的回交验证策略,以感病亲本Lemont为轮回亲本构建Jasmine85/Lemont和Minghui63/Lemont两个回交组合的拟染色体片段代换系群体。在两个不同的回交世代对这2个QTL进行了验证,证实qSB-9~(J85)和qSB-9~(MH63)真实位于第9染色体上的分子标记RM6971-RM201区间内,而根据上述分析,qSB-9~(Tq)也很可能位于该区间内。这3个QRL在杂合状态下平均可减轻病级1.0级左右,初步推测它们可能是同一个QRL。
本课题组之前已经利用Teqing/Lemont(轮回亲本)组合的回交群体证实了水稻品种Lemont第11染色体上的抗纹枯病QTL qSB-11~(Le)。本研究利用相同组合,也证实了来自Teqing第7染色体的抗水稻纹枯病QTLqSB-7~(Tq)。在此基础上,为了研究qSB-9~(Tq)与这两个QRL之间的聚合效应及相互之间的互作关系,我们利用3个QRL的双侧分子标记辅助连续回交结合性状鉴定,通过将Teqing与Lemont(轮回亲本)杂交并连续回交,构建了这3个QRL的一套近等基因系。在一致的遗传背景下,对各QRL的主效应、聚合效应及其互作关系进行了研究。结果显示,3个QRL单独存在或在聚合状态下均能显著提高水稻品种对纹枯病的抗性水平,而且,不同QRL之间普遍存在互作关系。
为了更有效地开展qSB-9~(Tq)的标记辅助育种以及对其进行克隆和抗性机理的研究,我们采用构建目标区间染色体单片段叠代系的策略,对qSB-9~(Tq)进行了精细定位研究。首先在其选择区间RM242-Y92.5(第三章)以及外侧一定距离内,发展和筛选到在两个亲本间具有多态的PCR分子标记共22个,其平均物理间距为319.753kb,可较高密度地覆盖整个大区间。利用这些分子标记,对本论文第三章近等基因系构建过程中获得的1个BC_6F_1中选单株(背景为轮回亲本Lemont基因型,仅在目标大区间为杂合基因型)进行标记检测,结果显示该单株的22个标记位点均为杂合型。随后我们对其自交后代进行标记检测,并根据不同的标记基因型,构建了在不同标记间发生交换重组的44类共894个染色体单片段代换系(染色体单片段叠代系)。于2007年正季选择其中的240个叠代系,进行2个区组重复的田间接种试验,于抽穗期后30天调查各叠代系的病级和病指。随后对各叠代系的几个主要农艺性状进行调查,并发现在大区间内存在一个控制分蘖角的主效QTL(大分蘖角基因来自供体亲本Teqing)。为了排除该分蘖角QTL对病情的干扰,我们选择不携带该大分蘖角基因的叠代系对qSB-9~(Tq)进行精细定位。对叠代系两个重复的病级和病指进行联合聚类分析。采用的聚类方法分别为系统聚类的离差平方和法,以及动态聚类的最小组内平方和法。以动态聚类结果为基础,系统聚类方法结果为参考,对各叠代系进行抗感分型并确定目标QTL的左右边界,从而实现qSB-9~(Tq)的精细定位。结果表明,在整个目标大区间内存在2个抗纹枯病QTL,分别位于分蘖角QTL的左侧和右侧,分别命名这2个QTL为L-qSB-9~(Tq)和R-qSB-9~(Tq)。这两个QRL的物理区间分别为Z77.2-Y77.7和Y86-Y90.2,区间大小分别为180.875Kb和207.724 kb。
综上所述,本研究首次在近等基因系的水平下,研究了一个水稻抗纹枯病QTL qSB-9~(Tq)的效应和作用方式。该QRL的抗性表现为几乎完全的显性,预示着其在水稻杂种优势利用方面具有较大的应用潜力。同时,该QRL与qSB-11~(Le)和qSB-7~(Tq)之间存在的互作关系,也暗示着其在分子标记辅助聚合育种中具有潜在的利用价值。进一步对其进行精细定位研究,不仅可以更高效地进行qSB-9~(Tq)的分子标记辅助育种,而且还将为该QRL的克隆和数量抗性机理研究打下坚实的基础。
Sheath blight(SB) disease is one of the three most serious diseases in rice worldwide.The resistance to rice sheath blight is a typical quantitative trait.Until now,approximately 30 QTLs contributing to rice SB resistance had been detected in different populations.Each of the 12 rice chromosomes had been shown to possess one or more of the 30 QTLs.Several SB resistance QTLs(qSB) had been detected on chromosome 9.However,separate research endeavors had generated rice QTL data using different parental individuals and populations.Several researchers had detected a resistance QTL qSB-9~(Tq) on Teqing chromosome 9.In this study,a set of genetic analyses and fine mapping for qSB-9~(Tq) were conducted.
The strategy of marker-assisted selection(MAS) combined with backcross identification was adopted to construct a backcross combination of Teqing/Lemont(recurrent parent) and two molecular markers RM201 and RM6971 were used for selecting qSB-9~(Tq) in each generation.In BC_5F_1 generation,qSB-9~(Tq) was validated and proved that it could be selected by two molecular markers RM201 and RM6971 efficiently.In order to accurately evaluate the resistant effect of qSB-9~(Tq) in BC_6 generation,seven molecular markers flanking qSB-9~(Tq) were used for foreground selection and other 114 molecular markers evenly distributed on other regions of rice genome were adopted for background selection.One single BC_6F_1 plant with heterozygous genotype of qSB-9~(Tq) and the same background as Lemont were gained and harvested.Three genotypic individuals of qSB-9~(TqTq),qSB-9~(LeLe) and qSB-9~(TqLe), distinguished by detecting marker genotypes flanking the QTL,were gained in BC_6F_2 generation and then formed the NILs in BC_6F_3 generation in two consecutive years.Two different experiment designs were adopted and both the results suggested that qSB-9~(Tq) located between two molecular markers RM242 and Y92.5 on chromosome 9,and it was a dominant quantitative resistance QTL(QRL,quantitative resistance locous) which could reduce disease rating about 0.7-1.0 score under Rush's '0-9' disease rating system.
Two rice sheath blight(SB) resistance QTLs had been previously detected on chromosome 9 of Jasmine85 and Minghui63,respectively.According to the origin of these resistance alleles,their corresponding QTLs were named qSB-9~(J85) and qSB-9~(MH63),respectively.An integrated analysis between molecular markers and a rice physical map revealed that the intervals of the two QTLs and qSB-9~(Tq) were adjacent or partially overlapping.Marker genotype detection combined with backcross identification was applied to construct two backcross populations of Jasmine85/Lemont(recurrent parent) and Minghui63/Lemont(recurrent parent) and then 10 HCSSLs(heterozygous chromosome substitution segment lines) of each backcross combination were gained.Sequentially the two QTL intervals were validated in two different generations.The results suggested that qSB-9~(J85) and qSB-9~(MH63) were truly located in the interval of RM201 and RM6971 on chromosome 9 and the qSB-9~(Tq) on chromosome 9 of Teqing might be also in this interval.These three QRLs could reduce a disease rating score by a value of 1.0 for heterozygous genotypes and were speculated to be identical.
Moreover,The QTL of resistance to rice sheath blight,mapped on chromosome 11 of Lemont had been validated and named qSB-11~(Le).In this study,another QRL on chromosome 7 of Teqing was also confirmed using the same backcross combination of Teqing/Lemont(recurrent parent) and named qSB-7~(Tq).Together with qSB-9~(Tq),the effects and pyramiding effects of the three QRLs were studied by using a set of near-isogenic lines(NILs) under the background of Lemont.The results indicated that the three QRLs could improve the ability of resistance to rice sheath blight significantly in their single or pyramiding status.Furthermore,there were certain interactions existed among these three QRLs in this study.
In order to clone and study the QRL furthermore,and conduct MAS for qSB-9~(Tq) more efficiently,the strategy of constructing chromosome single substitution segment lines(CSSSLs) was adopted to carried out fine mapping of the QRL.Twenty two polymorphic molecular markers were developed and screened,which could cover the interval with high density that the average physical distance was 319.753kb.These markers were used for detecting the single plant gained from the backcross combination of Teqing/Lemont in Chapter3,and the genotypes of the 22 markers were all heterozygous.Then 894 CSSSLs of 44 classes were gained according to different genotypes of the 22 markers.Two hundred and forty CSSSLs were selected for field experiment with two repeats in 2007.Disease rating and disease index were investigated 30 days after late tillering stage.Then 6 agronomic traits were also investigated and a major QTL conferring tiller angle from Teqing was discovered.In order to eliminate the disturbance of the existence of the QTL, CSSSLs without carrying the QTL were selected to conduct fine mapping for qSB-9~(Tq).Two clustering approaches were used for clustering the CSSSLs by analyzing disease rating and disease index in two field repeats together. according to the clustering results the borders of the target QTLs were analyzed.The results indicated that there existed two QRLs in the interval of RM242 and Y93.5,which were L-qSB-9~(Tq) in the interval Z77.2-Y77.7 and R-qSB-9~(Tq) in the interval Y86-Y90.2 with their interval distances were 180.875kb and 207.724kb respectively.
To sum up,the paper first reported and studied the effect and functional mode of the QTL conferring resistance to rice sheath blight in a relatively resistant cultivar Teqing under the condition of NILs.The QRL exhibited almost complete dominance,which would accelerate the utilization of qSB-9~(Tq) into the practice of hybrid rice breeding.Furthermore,there existed certain interactions between qSB-7~(Tq),qSB-11~(Le) and qSB-9~(Tq) suggested the utilization of qSB-9~(Tq) in QRL pyramiding breeding.So,it is urgent to carry out fine mapping and cloning the QRL,which would benefit the efficiency of MAS breeding and lay a foundation for the theoretical study of the qSB-9~(Tq).
引文
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[5]Sriram S,Babu S,Nandakumar R,et al.Differential expression of defense-related proteins and sheath blight symptoms of rice in response to active and inactive Rhizoctonia solani toxin.Archiv Phytopathol Plant Protec,2002,34(5):293-306.
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