利用染色体片段替换系定位水稻重要农艺性状QTLs
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摘要
水稻(Oryza sativa L.)是最重要的粮食作物之一,要培育出理想的水稻品种,就必须寻找有利的基因。水稻很多性状如产量等都是受多基因控制的数量性状,利用传统的研究材料和方法很难对这些数量性状位点(Quantitative trait loci,QTL)进行准确定位和克隆。由于受遗传背景影响较小,染色体片段替换系(Chromosome segment substitution lines,CSSLs)是用于对QTL进行定位的理想材料。利用已构建好的覆盖全基因组的CSSLs,不仅能定位水稻重要QTLs,为寻找籼粳亚种间优良基因提供方便,还能作为永久材料用于相关功能基因组学的研究。本研究利用已测序的两个籼粳代表水稻品种(9311和日本晴)为亲本,构建染色体片段替换系,并对控制水稻抽穗期、株高和产量等相关农艺性状的QTLs进行了初步的定位分析,研究获得的主要结果如下:
1.以籼稻品种9311为供体亲本,粳稻品种日本晴为受体亲本构建了一套CSSLs。利用已测序的水稻基因组信息和网上资源,筛选了238个多态性标记,结合杂交、回交、自交和分子标记辅助选择(MAS),选育了57个替换系。其中32个替换系仅含一个来源于供体亲本的染色体片段,11个系含有两个导入片段,其余14个系含有三个或三个以上的导入片段。此套替换系材料中共包含104个导入片段,平均每个替换系中含有约1.8个导入片段;导入染色体片段大小从0.075Mb--24.07Mb不等,平均每个导入片段大小约为3.95Mb。剔除导入染色体片段间的重叠部分,导入供体染色体片段对全基因组的覆盖率约为76.5%,导入片段总大小约为供体9311基因组大小的1.2倍。
2.利用这些构建的含纯合导入片段的CSSLs材料及其衍生出来的杂合替换系(CSSLs/NIP)群体,在不同年份和地点种植并对抽穗期、株高和产量等三个数量性状的相关农艺性状进行详细的调查分析。调查的农艺性状主要包括抽穗期、株高及其构成因素(株高、倒一节间长、主穗长)以及产量相关因素(千粒重、结实率、每穗总粒数、一次枝梗数和二次枝梗数)。根据染色体代换重叠作图原理和QTL定位原则,一共定位了12个控制抽穗期的QTLs,分布于除了第1至9等九条染色体上。对于株高及其构成因素,在所研究的替换系中总共定位了14个相关QTLs,分布于除了第4、5和12号染色体以外的其余9条染色体上。此外,还定位了32个控制产量相关构成因素的QTLs,分布于除了第9号染色体以外的其他11条染色体上。上述初步定位的58个控制三类数量性状的染色体位点分布于水稻所有12条染色体上,其中qHd-4、qPh-1、qLfi-2、qGw-4-2、qSs-3、qPbn-2-1和qSbn-10等是一批新的QTLs。这些定位结果为籼粳亚种间优良基因的精细定位和克隆提供了基础。
3.在利用替换系定位QTLs过程中,发现部分替换系,例如CS-40、CS-41、CS-10和CS-14等,所含导入供体染色体片段同时含有控制多个性状的QTLs。推测这些QTLs具有一因多效,或者同一导入片段含有影响不同性状的多个QTLs。利用分子标记辅助选择技术可对这些QTLs进行聚合,从而可为水稻分子设计育种服务。
Rice is one of the most important crops. It is important for both breeding and biological study to look for useful genes. But, in rice, many traits are controlled by quantitative trait loci (QTLs). It is very difficult to analyze and map these QTLs by using traditional genetic materials and methods. Due to the little background noise, the chromosome segmen substitution lines (CSSLs) are very useful to map and clone QTLs. Using the CSSLs covering the whole genome in sequenced rice varieties, we can not only detect new genes or alleles between indica and japonica subspecies, but also can study the function of detected genes/QTLs. In this study, the indica rice cultivar 93-11 and japonica rice cultivar Nipponbare are used as the donor and the recipient varieties respectively to develop the CSSLs. Besides, by using these CSSLs, we attemp to map the QTLs controlling important agronomic traits. The main results were as followings.
1. By using the indica variety 9311 as donor and japonica variety Nipponbare as recipient paren, we developed a set of novel population with 57 candidate CSSLs through backcross and marker-assisted selection (MAS). Each of the CSSLs contains a single or few indica introgresed chromosomal segments within the uniform japonica genetic background. Among these CSSLs, 32 lines may have only one introgresed segment from the donor, 11 CSSLs may contain two segments and the other 14 CSSLs have three or more segments. Each CSSL contains 1.8 segments. The length of these 104 introgressed segments ranged from 0.075 Mb to 24.07 Mb, with an average of 3.95 Mb. Their total length could cover 76.5% of the rice genome and was equal to 1.2 folds of the genome of 9311.
2. These CSSLs containing homologous segment(s), as well as their heterologous lines (homozygous CSSLs crossed with Nipponbare), were used to analyze and map the QTLs controlling important agronomic traits, such as heading date, plant height and related traits, yield and related traits. Based on mapping theory with CSSL, totally 58 related QTLs were mapped on all 12 chromosomes. Among these mapped QTLs, 12 QTLs were for the heading date (qHd), which located on 9 rice chromosomes (except chromosome 10,11 and 12). 14 QTLs were for the plant height and related traits (qPh, qLfi) on 9 chromosomes (except chromosome 4,5 and 12). Besides, 32 QTLs were for yeild and related traits (qGw, qSs, qPbn and qSbn) which mapped on 11 chromosomes (except chromosome 9). Several QTLs, such as qHd-4、qPh-1、qLfi-2、qGw-4-2、qSs-3、qPbn-2-1 and qSbn-10, were identified as new loci in rice. These results were very helpful to fine map and further clone useful genes/QTLs between the indica and japonica subspecies.
3. Among these analyzed CSSLs, several CSSLs, such as CS-40, CS-41, CS-10 and CS-14, were detected to contain several QTLs cotrolled different agronomic traits located on the same introgressed segment. It was presumed that the QTL in such individual CSSL would have the multiple effects on agronomic traits, or there were several genes/QTLs on the same segments. Thus, we wish to pyramid these useful QTLs together though marker-assisted selection (MAS) in the same genetic background, which would be very helpful to molecular breeding by design in rice.
1.以籼稻品种9311为供体亲本,粳稻品种日本晴为受体亲本构建了一套CSSLs。利用已测序的水稻基因组信息和网上资源,筛选了238个多态性标记,结合杂交、回交、自交和分子标记辅助选择(MAS),选育了57个替换系。其中32个替换系仅含一个来源于供体亲本的染色体片段,11个系含有两个导入片段,其余14个系含有三个或三个以上的导入片段。此套替换系材料中共包含104个导入片段,平均每个替换系中含有约1.8个导入片段;导入染色体片段大小从0.075Mb--24.07Mb不等,平均每个导入片段大小约为3.95Mb。剔除导入染色体片段间的重叠部分,导入供体染色体片段对全基因组的覆盖率约为76.5%,导入片段总大小约为供体9311基因组大小的1.2倍。
2.利用这些构建的含纯合导入片段的CSSLs材料及其衍生出来的杂合替换系(CSSLs/NIP)群体,在不同年份和地点种植并对抽穗期、株高和产量等三个数量性状的相关农艺性状进行详细的调查分析。调查的农艺性状主要包括抽穗期、株高及其构成因素(株高、倒一节间长、主穗长)以及产量相关因素(千粒重、结实率、每穗总粒数、一次枝梗数和二次枝梗数)。根据染色体代换重叠作图原理和QTL定位原则,一共定位了12个控制抽穗期的QTLs,分布于除了第1至9等九条染色体上。对于株高及其构成因素,在所研究的替换系中总共定位了14个相关QTLs,分布于除了第4、5和12号染色体以外的其余9条染色体上。此外,还定位了32个控制产量相关构成因素的QTLs,分布于除了第9号染色体以外的其他11条染色体上。上述初步定位的58个控制三类数量性状的染色体位点分布于水稻所有12条染色体上,其中qHd-4、qPh-1、qLfi-2、qGw-4-2、qSs-3、qPbn-2-1和qSbn-10等是一批新的QTLs。这些定位结果为籼粳亚种间优良基因的精细定位和克隆提供了基础。
3.在利用替换系定位QTLs过程中,发现部分替换系,例如CS-40、CS-41、CS-10和CS-14等,所含导入供体染色体片段同时含有控制多个性状的QTLs。推测这些QTLs具有一因多效,或者同一导入片段含有影响不同性状的多个QTLs。利用分子标记辅助选择技术可对这些QTLs进行聚合,从而可为水稻分子设计育种服务。
Rice is one of the most important crops. It is important for both breeding and biological study to look for useful genes. But, in rice, many traits are controlled by quantitative trait loci (QTLs). It is very difficult to analyze and map these QTLs by using traditional genetic materials and methods. Due to the little background noise, the chromosome segmen substitution lines (CSSLs) are very useful to map and clone QTLs. Using the CSSLs covering the whole genome in sequenced rice varieties, we can not only detect new genes or alleles between indica and japonica subspecies, but also can study the function of detected genes/QTLs. In this study, the indica rice cultivar 93-11 and japonica rice cultivar Nipponbare are used as the donor and the recipient varieties respectively to develop the CSSLs. Besides, by using these CSSLs, we attemp to map the QTLs controlling important agronomic traits. The main results were as followings.
1. By using the indica variety 9311 as donor and japonica variety Nipponbare as recipient paren, we developed a set of novel population with 57 candidate CSSLs through backcross and marker-assisted selection (MAS). Each of the CSSLs contains a single or few indica introgresed chromosomal segments within the uniform japonica genetic background. Among these CSSLs, 32 lines may have only one introgresed segment from the donor, 11 CSSLs may contain two segments and the other 14 CSSLs have three or more segments. Each CSSL contains 1.8 segments. The length of these 104 introgressed segments ranged from 0.075 Mb to 24.07 Mb, with an average of 3.95 Mb. Their total length could cover 76.5% of the rice genome and was equal to 1.2 folds of the genome of 9311.
2. These CSSLs containing homologous segment(s), as well as their heterologous lines (homozygous CSSLs crossed with Nipponbare), were used to analyze and map the QTLs controlling important agronomic traits, such as heading date, plant height and related traits, yield and related traits. Based on mapping theory with CSSL, totally 58 related QTLs were mapped on all 12 chromosomes. Among these mapped QTLs, 12 QTLs were for the heading date (qHd), which located on 9 rice chromosomes (except chromosome 10,11 and 12). 14 QTLs were for the plant height and related traits (qPh, qLfi) on 9 chromosomes (except chromosome 4,5 and 12). Besides, 32 QTLs were for yeild and related traits (qGw, qSs, qPbn and qSbn) which mapped on 11 chromosomes (except chromosome 9). Several QTLs, such as qHd-4、qPh-1、qLfi-2、qGw-4-2、qSs-3、qPbn-2-1 and qSbn-10, were identified as new loci in rice. These results were very helpful to fine map and further clone useful genes/QTLs between the indica and japonica subspecies.
3. Among these analyzed CSSLs, several CSSLs, such as CS-40, CS-41, CS-10 and CS-14, were detected to contain several QTLs cotrolled different agronomic traits located on the same introgressed segment. It was presumed that the QTL in such individual CSSL would have the multiple effects on agronomic traits, or there were several genes/QTLs on the same segments. Thus, we wish to pyramid these useful QTLs together though marker-assisted selection (MAS) in the same genetic background, which would be very helpful to molecular breeding by design in rice.
引文
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