普通×爆裂玉米群体单性状及多性状联合QTL分析
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摘要
爆裂玉米是一种专门用来制作玉米花系列休闲食品的特用玉米类型。由于爆裂玉米种质资源较少，严重着制约育种水平和效率的进一步提高。随着分子标记技术的发展，高密度遗传图谱的构建，在玉米数量性状基因定位方面已经取得了一定的进展。本研究以优良爆裂玉米自交系N04与普通玉米丹232杂交构建259个F_2群体及F_(2：3)家系，利用SSR分子标记构建高密度遗传图谱，采用复合区间作图法，以排列测验1000次所得LOD值作为阈值，对爆裂玉米的3个膨爆特性指标、9个穗粒性状、9个植株性状和4个籽粒营养品质进行了两个环境的合并QTL定位和效应分析，采用多区间作图法分析QTL间的上位效应，并采用多性状联合分析的复合区间作图法对膨爆特性指标间、穗粒性状间、籽粒营养品质性状间、主要植株性状间以及膨爆特性与主要穗粒性状间进行了多性状QTL联合分析，探讨各性状的分子遗传机制及其间的遗传关系，判断控制相关性状QTL存在的一因多效性或基因紧密连锁，同时验证以往相关研究结果。为进一步开展分子标记辅助选择、QTL精细定位及其克隆提供更为可靠的理论依据。
本研究主要得到以下结论：
1．用613对SSR引物对两个亲本N04和丹232进行多态性检测，获得193个共显性标记位点，占31.48％。利用Mapmaker3.0作图软件和183个共显性SSR分子标记构建了一张爆裂玉米分子标记连锁图，图谱总长度为1762.2cM，相邻两标记间的平均距离为9.63cM。
2．3个膨爆特性指标单独分析共检测到16个QTL，单个QTL贡献率为4.85％～15.39％，控制不同膨爆特性指标的QTL具有相同的标记或置信区间，部分显性、超显性、加性对膨爆特性的遗传均起着主要的作用；部分定位QTL间存在较大的互作效应；控制不同膨爆特性指标的QTL多数表现为一因多效。
3．9个穗粒性状单独分析共检测到26个QTL，单个QTL贡献率为4.66％～22.96％，部分穗粒性状QTL具有相同的标记或置信区间，表现为热点分布，部分显性效应对穗粒性状的遗传起着主要作用；定位QTL间互作较少，而且效应较小；在第2、5、10染色体上控制穗粒重和百粒重的QTL，在第10染色体上控制穗粒重和穗行数的QTL以及在第2、7、8染色体上控制穗粒重和行粒数的QTL存在为一因多效性或紧密连锁。
4．穗粒重和百粒重与膨化倍数呈极显著负相关，其QTL联合分析表明百粒重与膨化倍数在第1染色体上、穗粒重与膨化倍数在第2、8染色体上LOD曲线的峰点表现同向变化，存在QTL紧密连锁或一因多效。
5．4个籽粒营养品质性状单独分析共检测到15个QTL，单个QTL贡献率为4.95％～10.57％，加性和部分显性效应均对籽粒营养品质的遗传起着主要作用；定位QTL间互作较少，而且效应较小；大多数控制淀粉含量和蛋白含量的QTL存在一因多效或紧密连锁。
6．9个植株性状单独分析共检测到39个QTL，单个QTL贡献率为4.25％～31.44％，加性和部分显性效应对植株性状遗传起着主要的作用；定位QTL间互作较少，而且效应较小；
Popcorn is a special kind of corn type being used to make popcorn flake for a series pastime foodstuff. Breeding level and efficiency in popcorn is seriously restricted due to its quite few germplasm resource. With the development of molecular marker technology, high density gentetic linkage maps were constructed, quantitative trait loci (QTL) in maize have already been identified. In this research, two hundred and fifty-nine F_2 population and F_(2:3) family lines, developed from a cross between a dent corn indred, Dan232, and a elite popcorn indred, N04, were developed. A high-density genetic map was constructed using SSR markers. Three popping characteristics, 9 ear-kernel traits, 4 nutritional quality of krnel, and 9 plant characters for F_(2:3) population were evaluated. Data in two environments(in spring and in summer) were combined to map QTL of these traits and evaluate their effect, using composite interval mapping(CIM). The LOD threshold values were determined by 1000 times permutation test. The interactions of detected QTL were identified using multiple interval mapping (MIM) method according to the result of CIM method. The joint QTL analysis of two or three different traits were done using composite interval mapping(CIM) of multiple traits analysis, including between different popping characteristics, between different ear-kernel characters, between different nutritional quality of ear-kernel characters, and between main plant characters, and between popping characteristics and main ear-kernel traits. This was to analyze their molecular genetic mechanism and genetic correlations between different characters, and to test for linked or pleiotropic QTL controlling correlated traits. Meanwhile, previous research results in single environment were verified. The main purpose was to provide more reliable theory basis to utilize molecular marker-assisted selection, and fine map QTL and even clone them in future.
The main results in this study were as follows:
1. Totally, 613 SSR primers were employed to screen polymorphism between two parents, N04 and Dan232, only 193 markers(31.48%) were in co-dominant segregation. One hundred eighty-three pairs SSR markers were selected to construct a genetic linkage map of popcorn with the genetic distance of 1762.2 cM (centimorgan) and on an average of 9.63 cM using Mapmaker 3.0.
2. Sixteen QTL were mapped for 3 popping characteristics by single trait analysis. Contribution of single QTL to phenotypic variation varied from 4.85% to 15.39%. Most QTL controlled different popping characteristics located at the same marker loci or in the same marker confidence intervals. Partially dominant, over-dominant and additive effects all played main funcations in the heredity of popping characteristics. A little bigger interactions existed between some detected QTL. Most QTL controlling different popping characteristics showed pleiotropy.
3. Twenty-six QTL were detected for 9 ear-kernel traits using single trait
本研究主要得到以下结论：
1．用613对SSR引物对两个亲本N04和丹232进行多态性检测，获得193个共显性标记位点，占31.48％。利用Mapmaker3.0作图软件和183个共显性SSR分子标记构建了一张爆裂玉米分子标记连锁图，图谱总长度为1762.2cM，相邻两标记间的平均距离为9.63cM。
2．3个膨爆特性指标单独分析共检测到16个QTL，单个QTL贡献率为4.85％～15.39％，控制不同膨爆特性指标的QTL具有相同的标记或置信区间，部分显性、超显性、加性对膨爆特性的遗传均起着主要的作用；部分定位QTL间存在较大的互作效应；控制不同膨爆特性指标的QTL多数表现为一因多效。
3．9个穗粒性状单独分析共检测到26个QTL，单个QTL贡献率为4.66％～22.96％，部分穗粒性状QTL具有相同的标记或置信区间，表现为热点分布，部分显性效应对穗粒性状的遗传起着主要作用；定位QTL间互作较少，而且效应较小；在第2、5、10染色体上控制穗粒重和百粒重的QTL，在第10染色体上控制穗粒重和穗行数的QTL以及在第2、7、8染色体上控制穗粒重和行粒数的QTL存在为一因多效性或紧密连锁。
4．穗粒重和百粒重与膨化倍数呈极显著负相关，其QTL联合分析表明百粒重与膨化倍数在第1染色体上、穗粒重与膨化倍数在第2、8染色体上LOD曲线的峰点表现同向变化，存在QTL紧密连锁或一因多效。
5．4个籽粒营养品质性状单独分析共检测到15个QTL，单个QTL贡献率为4.95％～10.57％，加性和部分显性效应均对籽粒营养品质的遗传起着主要作用；定位QTL间互作较少，而且效应较小；大多数控制淀粉含量和蛋白含量的QTL存在一因多效或紧密连锁。
6．9个植株性状单独分析共检测到39个QTL，单个QTL贡献率为4.25％～31.44％，加性和部分显性效应对植株性状遗传起着主要的作用；定位QTL间互作较少，而且效应较小；
Popcorn is a special kind of corn type being used to make popcorn flake for a series pastime foodstuff. Breeding level and efficiency in popcorn is seriously restricted due to its quite few germplasm resource. With the development of molecular marker technology, high density gentetic linkage maps were constructed, quantitative trait loci (QTL) in maize have already been identified. In this research, two hundred and fifty-nine F_2 population and F_(2:3) family lines, developed from a cross between a dent corn indred, Dan232, and a elite popcorn indred, N04, were developed. A high-density genetic map was constructed using SSR markers. Three popping characteristics, 9 ear-kernel traits, 4 nutritional quality of krnel, and 9 plant characters for F_(2:3) population were evaluated. Data in two environments(in spring and in summer) were combined to map QTL of these traits and evaluate their effect, using composite interval mapping(CIM). The LOD threshold values were determined by 1000 times permutation test. The interactions of detected QTL were identified using multiple interval mapping (MIM) method according to the result of CIM method. The joint QTL analysis of two or three different traits were done using composite interval mapping(CIM) of multiple traits analysis, including between different popping characteristics, between different ear-kernel characters, between different nutritional quality of ear-kernel characters, and between main plant characters, and between popping characteristics and main ear-kernel traits. This was to analyze their molecular genetic mechanism and genetic correlations between different characters, and to test for linked or pleiotropic QTL controlling correlated traits. Meanwhile, previous research results in single environment were verified. The main purpose was to provide more reliable theory basis to utilize molecular marker-assisted selection, and fine map QTL and even clone them in future.
The main results in this study were as follows:
1. Totally, 613 SSR primers were employed to screen polymorphism between two parents, N04 and Dan232, only 193 markers(31.48%) were in co-dominant segregation. One hundred eighty-three pairs SSR markers were selected to construct a genetic linkage map of popcorn with the genetic distance of 1762.2 cM (centimorgan) and on an average of 9.63 cM using Mapmaker 3.0.
2. Sixteen QTL were mapped for 3 popping characteristics by single trait analysis. Contribution of single QTL to phenotypic variation varied from 4.85% to 15.39%. Most QTL controlled different popping characteristics located at the same marker loci or in the same marker confidence intervals. Partially dominant, over-dominant and additive effects all played main funcations in the heredity of popping characteristics. A little bigger interactions existed between some detected QTL. Most QTL controlling different popping characteristics showed pleiotropy.
3. Twenty-six QTL were detected for 9 ear-kernel traits using single trait
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