水稻（Oryza sativa L.）若干重要性状的QTL主效应、上位性效应及GE互作效应分析
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摘要
本研究利用珍汕97B／密阳46和协青早B／密阳46所构建的两个RIL群体(简称ZM-RIL和XM-RIL)及其相应分子遗传图谱，通过设置多环境或多处理的遗传试验，应用可以同时检测QTL主效应、上位性效应和G×E互作效应的遗传分析方法，对涉及水稻农艺、品质、抗逆等11个重要性状进行QTL定位和GE分析，并对结果进行了分析和讨论，旨在从分子水平上更深入地了解其遗传本质。主要研究内容和结果如下：
1、分蘖松散度：用XM-RIL及其遗传图谱，进行海南和杭州两地试验，以分蘖夹角为松散度(弧度)指标，对该性状的两个环境下表现数据进行联合分析。共检测到2个主效应QTL和3对显著的加性×加性双基因互作。在主效应QTL中，qTA8-2的LOD值为21.7，贡献率为23.2％；qTA9-2的LOD值为22.0，贡献率为19.5％；增加松散度基因前者来自母本、后者则来自父本；这2个QTL不存在显著的GE互作。而所检测到的3对显著双基因互作，对该性状表型变异的总贡献率仅为7.69％，显得较为次要。
2、落粒性：用ZM-RIL群体及其遗传图谱，在海南和杭州两地试验，以稻穗下落法测到的落粒率(％)为指标，进行两地数据QTL联合分析。结果表明，ZM-RIL群体的不同株系在两地间落粒率变化很大。在海南，该性状呈近似正态分布；在杭州，则呈明显偏态分布。试验共检测到8个主效应QTL，位于第1、2、3(2个)、6(2个)、7和11等6条染色体上，每个QTL影响落粒率的加性效应均不太大，其幅度为1.7％-3.9％，共解释群体落粒性性状变异的9.05％。其中，有3个主效应QTL(qSH3-1、qSH3-2和qSH6-1)存在显著的GE互作，它们均使海南增加落粒率和杭降低落粒率，且GE总贡献率几乎接近加性效应总贡献率，表明GE互作对落粒率具有重要影响。此外，试验还检测到5对上位性互作QTL，这些互作共解释群体落粒性性状变异的3.39％，单个互作的贡献率为0.47％-0.85％，未检测到上位性与环境的显著互作。
3、柱头外露率:用XM一RIL及其遗传图谱，在海南和杭州两地试验，以柱头外
露率(%)的考察指标，进行有关QTL联合分析。该性状明显表现出海南较高(21 .83%)
而杭州较低(S .35%)的趋势。试验检测到1个主效应QTL(qSE6一1)，其LOD值高达
28.16，对性状表型的贡献率为14.14%，增效等位基因来自于母本，加性效应为5.10%，
不存在显著的GE互作。试验还检测到3对显著的加性x加性双基因互作，上位性互
作性效应和贡献率相对较小，且与环境不存在显著的互作。
4、稻米透明度:用Z旅RIL及其遗传图谱，在海南和杭州两地试验，以精米透
光率(%)作为考察稻米透明度指标，进行有关QTL联合分析。共检测到5个控制该
性状的主效应QTL，分别位于第2、6(2个)、8、10染色体上，总的遗传贡献率19.15%。
其中，qTRZ一2的增加透明度有效基因来源于母本;其余4个(qTR6一z、qTR6一2、qTRS一2、
qTR10)则来自于父本。qTR6吐还与环境存在显著的GE互作效应。此外，还检测到
2对控制稻米透明度的加性上位性互作基因，但它们均未与环境存在显著互作。
5、稻米延伸性:用XM--RIL及其遗传图谱，在海南和杭州两地试验，以延伸率
(%)作为米粒延伸性考察指标，进行有关QTL联合分析。结果表明，该性状两地间的
平均表现和群体分布特征较为相似，但两地间各系表型值相关系数却较小。试验检
测到1个控制该性状的QTL基因qCRE6，其增效基因来自于父本，可提高3.99%的米
粒延伸率，它不存在与环境间显著互作。还检测到2对上位性互作基因，即qcREZ
与qCRES一1、qCRES一2与qCRE7间互作，前者与环境间存在有显著有GE互作，其
作用使在杭州有增加米粒延性效果。
6、稻米淀粉粘滞性:用Z卜RIL及其遗传图谱，经海南和杭州两地试验，以精
米粉的RVA谱中5个参数特征值PKV、HPV、CPV、BDV和SBV作为研究稻米淀粉粘滞
性的指标，进行有关QTL联合分析。结果表现:1)在所检测到涉及5个性状的9个
主效应QTL中，除PKV存在有第5染色体qPKVS外，其余8个QTL均位于第6染色
体上;2)每个性状均检测到1个位于第6染色体RM197~RZ516区间的主效应QTL，
并认为该基因即是Wx基因，表明所有性状均与Wx基因有关;3)检测到的与PKV、
HPV、BDV、CPv等4个性状有关的wx基因均表现有GE互作，且方向一致，表现为在
海南有增效作用。试验还检测到涉及5个性状的10对上位性互作效应，但均未检测
到显著的上位性x环境互作效应。
7、耐辐射损伤:用ZM一RIL及其遗传图谱，经2个丫射线剂量(35OGy和55OGy)
辐射处理，以处理后RIL群体的相对发芽率(%)和相对成苗率(%)作为考察该材
料耐辐射损伤指标，进行QTL定位和上位性分析。结果表明，RIL群体受不同剂量照
射后，表现出株系间耐辐射损伤的差异。以相对发芽率为指标，共检测到3个耐辐
射主效应QTL，其中，qRR(g)8一1在350Gy处理时检测到，有效基因来自于父本，其
遗传贡献率为6.53%;qRR(g)1一2和qRR(g)8一2则是在550Gy辐照时检测到，有效基
因分别存在于母本和父本中，共可解释14.38%变异。以相对成苗率为指标，也检测
到3个主效应QTL，它们是qRR(s)2一2(350Gy剂量)、qRR(s)5一6和qRR(s)10(550Gy
剂量)，共解释19.65%变异。
Two recombinant inbred line (RIL) populations derived from Zhenshan 97B/Miyang 46 and Xieqingzao B/Miyang 46 (hereafter referred to ZM-RIL and XM-RIL, respectively) and their genetic linkage maps were employed to map the quantitative trait loci (QTL) with main effects, epistasis, and G X E (GE) interaction effects of some important agronomic, grain quality, and anti-abiotic stress traits in different environments or with different treatments. The objective of this study was to understand the genetic basis of these traits more clearly at the molecular level. The main results were as follows.
1.Tillering angle: The XM-RIL population and its genetic linkage map were used to map QTLs controlling the tillering angle in two environments,Hangzhou and Hainan. A total of two QTLs with main effects and three pairs of additive X additive double QTL interaction effects were identified. For the main effect QTL, qTA8-2 was detected with LOD of 21.7 and could explain 23.2% of the total phenotypic variations; qTA9-2 was detected with LOD of 22.0 and could explain 19.5% of the total phenotypic variations. The additive effects of the former QTL came from female parent, but latter one came from the male parent. No GE interaction effect was detected for the main effect QTLs. The three pairs of double QTLs interactions only explained 7.69% of the total phenotypic variation, suggesting their minor importance.
2. Shattering: The ZM-RIL population and its genetic linkage map were used to map the QTLs controlling the shattering trait in two environments, Hainan and Hangzhou. The results indicated that the shattering of different lines ZM-RIL population varied dramatically in different environments. In Hainan, this triat nearly showed the normal distribution, while in Hangzhou, it showed distorted distribution. A total of eight QTLs with main effects were detected on the chromosome of 1, 2, 3(two QTLs), 6 (two QTLs), 7 and11. Each QTL only contributed little (from 1.7% to 3.9%) to the total phenotypic variations, even in total they only explained 9.05% of the variations. Of them, three QTLs (qSH3-l, qSH3-2 and qSH6-l)had significant GE interaction effects, and their effects increased shattering in Hainan and decreased it in Hangzhou. The total contribution of
these GE interaction QTLs were as large as those QTLs with main effects, suggesting that GE effects were important for shattering. In addition, five pairs of epistasis QTLs were detected with each contributing to 0.47%-0.85% of the total variation, even in whole, they only explained 3.39% of the total variation. No epistasis by environment interaction effect was detected in this experiement.
3. Stigma extruding: The XM-RIL population and its genetic linkage map were used to map QTLs controlling the stigma extruding trait in two environments, Hainan and Hangzhou. The stigma extruding rate was higher in Hainan (21.83%) than that in Hangzhou (8.35%) . Only one QTL with main effect was detected with LOD as high as 28.16, which explained 14.14% of the total phenotypic variations. The positive additive effect of this QTL was 5.10% which came from the female parent. No GE interaction effect was detected. Three additive X additive double QTL epistasis effects were detected with little contributions, and no epistasis by environment effects was detected.
4. Rice grain transparency. The ZM-RIL population and its genetic linkage map were used to map QTLs controlling rice grain transparency which was indexed as ratio of light permeating the milled rice grains in two environments. A total of five QTLs with main effects were detected on chromosomes 2, 6 (two QTLs), 8 and 10, which in total contributed to 19.15% of the total phenotypic variations. Among them, the additive effects of qTR2-2 came from the female parents while the others four (qTR6-1 qTR6-2 qTR8-2>qTR10) came from the male parent. The QTL qTR6-l was also detected significant GE interaction effects. In addition, two pairs of additive X additive epistasis QTLs were detected, but they did not show GE interaction effect.
1、分蘖松散度：用XM-RIL及其遗传图谱，进行海南和杭州两地试验，以分蘖夹角为松散度(弧度)指标，对该性状的两个环境下表现数据进行联合分析。共检测到2个主效应QTL和3对显著的加性×加性双基因互作。在主效应QTL中，qTA8-2的LOD值为21.7，贡献率为23.2％；qTA9-2的LOD值为22.0，贡献率为19.5％；增加松散度基因前者来自母本、后者则来自父本；这2个QTL不存在显著的GE互作。而所检测到的3对显著双基因互作，对该性状表型变异的总贡献率仅为7.69％，显得较为次要。
2、落粒性：用ZM-RIL群体及其遗传图谱，在海南和杭州两地试验，以稻穗下落法测到的落粒率(％)为指标，进行两地数据QTL联合分析。结果表明，ZM-RIL群体的不同株系在两地间落粒率变化很大。在海南，该性状呈近似正态分布；在杭州，则呈明显偏态分布。试验共检测到8个主效应QTL，位于第1、2、3(2个)、6(2个)、7和11等6条染色体上，每个QTL影响落粒率的加性效应均不太大，其幅度为1.7％-3.9％，共解释群体落粒性性状变异的9.05％。其中，有3个主效应QTL(qSH3-1、qSH3-2和qSH6-1)存在显著的GE互作，它们均使海南增加落粒率和杭降低落粒率，且GE总贡献率几乎接近加性效应总贡献率，表明GE互作对落粒率具有重要影响。此外，试验还检测到5对上位性互作QTL，这些互作共解释群体落粒性性状变异的3.39％，单个互作的贡献率为0.47％-0.85％，未检测到上位性与环境的显著互作。
3、柱头外露率:用XM一RIL及其遗传图谱，在海南和杭州两地试验，以柱头外
露率(%)的考察指标，进行有关QTL联合分析。该性状明显表现出海南较高(21 .83%)
而杭州较低(S .35%)的趋势。试验检测到1个主效应QTL(qSE6一1)，其LOD值高达
28.16，对性状表型的贡献率为14.14%，增效等位基因来自于母本，加性效应为5.10%，
不存在显著的GE互作。试验还检测到3对显著的加性x加性双基因互作，上位性互
作性效应和贡献率相对较小，且与环境不存在显著的互作。
4、稻米透明度:用Z旅RIL及其遗传图谱，在海南和杭州两地试验，以精米透
光率(%)作为考察稻米透明度指标，进行有关QTL联合分析。共检测到5个控制该
性状的主效应QTL，分别位于第2、6(2个)、8、10染色体上，总的遗传贡献率19.15%。
其中，qTRZ一2的增加透明度有效基因来源于母本;其余4个(qTR6一z、qTR6一2、qTRS一2、
qTR10)则来自于父本。qTR6吐还与环境存在显著的GE互作效应。此外，还检测到
2对控制稻米透明度的加性上位性互作基因，但它们均未与环境存在显著互作。
5、稻米延伸性:用XM--RIL及其遗传图谱，在海南和杭州两地试验，以延伸率
(%)作为米粒延伸性考察指标，进行有关QTL联合分析。结果表明，该性状两地间的
平均表现和群体分布特征较为相似，但两地间各系表型值相关系数却较小。试验检
测到1个控制该性状的QTL基因qCRE6，其增效基因来自于父本，可提高3.99%的米
粒延伸率，它不存在与环境间显著互作。还检测到2对上位性互作基因，即qcREZ
与qCRES一1、qCRES一2与qCRE7间互作，前者与环境间存在有显著有GE互作，其
作用使在杭州有增加米粒延性效果。
6、稻米淀粉粘滞性:用Z卜RIL及其遗传图谱，经海南和杭州两地试验，以精
米粉的RVA谱中5个参数特征值PKV、HPV、CPV、BDV和SBV作为研究稻米淀粉粘滞
性的指标，进行有关QTL联合分析。结果表现:1)在所检测到涉及5个性状的9个
主效应QTL中，除PKV存在有第5染色体qPKVS外，其余8个QTL均位于第6染色
体上;2)每个性状均检测到1个位于第6染色体RM197~RZ516区间的主效应QTL，
并认为该基因即是Wx基因，表明所有性状均与Wx基因有关;3)检测到的与PKV、
HPV、BDV、CPv等4个性状有关的wx基因均表现有GE互作，且方向一致，表现为在
海南有增效作用。试验还检测到涉及5个性状的10对上位性互作效应，但均未检测
到显著的上位性x环境互作效应。
7、耐辐射损伤:用ZM一RIL及其遗传图谱，经2个丫射线剂量(35OGy和55OGy)
辐射处理，以处理后RIL群体的相对发芽率(%)和相对成苗率(%)作为考察该材
料耐辐射损伤指标，进行QTL定位和上位性分析。结果表明，RIL群体受不同剂量照
射后，表现出株系间耐辐射损伤的差异。以相对发芽率为指标，共检测到3个耐辐
射主效应QTL，其中，qRR(g)8一1在350Gy处理时检测到，有效基因来自于父本，其
遗传贡献率为6.53%;qRR(g)1一2和qRR(g)8一2则是在550Gy辐照时检测到，有效基
因分别存在于母本和父本中，共可解释14.38%变异。以相对成苗率为指标，也检测
到3个主效应QTL，它们是qRR(s)2一2(350Gy剂量)、qRR(s)5一6和qRR(s)10(550Gy
剂量)，共解释19.65%变异。
Two recombinant inbred line (RIL) populations derived from Zhenshan 97B/Miyang 46 and Xieqingzao B/Miyang 46 (hereafter referred to ZM-RIL and XM-RIL, respectively) and their genetic linkage maps were employed to map the quantitative trait loci (QTL) with main effects, epistasis, and G X E (GE) interaction effects of some important agronomic, grain quality, and anti-abiotic stress traits in different environments or with different treatments. The objective of this study was to understand the genetic basis of these traits more clearly at the molecular level. The main results were as follows.
1.Tillering angle: The XM-RIL population and its genetic linkage map were used to map QTLs controlling the tillering angle in two environments,Hangzhou and Hainan. A total of two QTLs with main effects and three pairs of additive X additive double QTL interaction effects were identified. For the main effect QTL, qTA8-2 was detected with LOD of 21.7 and could explain 23.2% of the total phenotypic variations; qTA9-2 was detected with LOD of 22.0 and could explain 19.5% of the total phenotypic variations. The additive effects of the former QTL came from female parent, but latter one came from the male parent. No GE interaction effect was detected for the main effect QTLs. The three pairs of double QTLs interactions only explained 7.69% of the total phenotypic variation, suggesting their minor importance.
2. Shattering: The ZM-RIL population and its genetic linkage map were used to map the QTLs controlling the shattering trait in two environments, Hainan and Hangzhou. The results indicated that the shattering of different lines ZM-RIL population varied dramatically in different environments. In Hainan, this triat nearly showed the normal distribution, while in Hangzhou, it showed distorted distribution. A total of eight QTLs with main effects were detected on the chromosome of 1, 2, 3(two QTLs), 6 (two QTLs), 7 and11. Each QTL only contributed little (from 1.7% to 3.9%) to the total phenotypic variations, even in total they only explained 9.05% of the variations. Of them, three QTLs (qSH3-l, qSH3-2 and qSH6-l)had significant GE interaction effects, and their effects increased shattering in Hainan and decreased it in Hangzhou. The total contribution of
these GE interaction QTLs were as large as those QTLs with main effects, suggesting that GE effects were important for shattering. In addition, five pairs of epistasis QTLs were detected with each contributing to 0.47%-0.85% of the total variation, even in whole, they only explained 3.39% of the total variation. No epistasis by environment interaction effect was detected in this experiement.
3. Stigma extruding: The XM-RIL population and its genetic linkage map were used to map QTLs controlling the stigma extruding trait in two environments, Hainan and Hangzhou. The stigma extruding rate was higher in Hainan (21.83%) than that in Hangzhou (8.35%) . Only one QTL with main effect was detected with LOD as high as 28.16, which explained 14.14% of the total phenotypic variations. The positive additive effect of this QTL was 5.10% which came from the female parent. No GE interaction effect was detected. Three additive X additive double QTL epistasis effects were detected with little contributions, and no epistasis by environment effects was detected.
4. Rice grain transparency. The ZM-RIL population and its genetic linkage map were used to map QTLs controlling rice grain transparency which was indexed as ratio of light permeating the milled rice grains in two environments. A total of five QTLs with main effects were detected on chromosomes 2, 6 (two QTLs), 8 and 10, which in total contributed to 19.15% of the total phenotypic variations. Among them, the additive effects of qTR2-2 came from the female parents while the others four (qTR6-1 qTR6-2 qTR8-2>qTR10) came from the male parent. The QTL qTR6-l was also detected significant GE interaction effects. In addition, two pairs of additive X additive epistasis QTLs were detected, but they did not show GE interaction effect.
引文
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