基于水稻SSSLs的主要农艺性状QTL分析及杂种优势研究
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摘要
水稻是最重要的粮食作物,也是禾本科植物进行分子生物学研究的重要模式生物之一,对水稻功能基因的研究可以为水稻育种提供有力的理论指导。农作物的大多数农艺性状是由多个基因控制的数量性状,对数量性状基因座(quantitative trait loci, QTL)进行鉴定和定位在遗传研究和育种利用中具有十分重要的意义。单片段代换系(single segment substitution lines,SSSLs)可消除遗传背景的干扰,是用于QTL鉴定和精细定位的重要遗传研究材料。本实验利用已经完成基因组测序的籼稻品种93-11为受体,粳稻测序品种日本晴和三系杂交稻骨干恢复系蜀恢527为供体,结合分子标记辅助选择,建立了一套单片段代换系群体,并在此基础上进行了QTL分析和杂种优势研究。主要结果如下：
1、本实验选用均匀分布于水稻12条染色体上的447对微卫星(SSR)标记在受体亲本93-11和供体亲本日本晴与蜀恢527间进行多态性标记筛选,.结果显示共有247个SSR在亲本间具有多态性,其中有221个SSR标记在93-11与日本晴之间表现出多态性,多态率为50.78%；有55个SSR标记在93-11与蜀恢527间具有多态性,多态率为12.30%。同时,利用序列比对工具,对筛选出的多态性标记在测序品种93-11基因组上进行物理定位,构建了一张含有247个SSR多态性标记的分子图谱,标记间的平均距离为1.85Mb。
2、在BC3F2、BC4F2和BC5F2三个世代中总共获得80个含有不同片段的单片段代换系株系。这些单片段代换系在水稻12条染色体上呈不均匀分布,其中第1、5、8染色体上分布最多,共有37个；第4、7、10染色体上分布较少,各有2个。代换片段长度分布在0.52Mb-26.13Mb之间,代换片段的平均长度为6.83Mb。全部代换片段对基因组的覆盖长度为194.89Mb,覆盖率为47.56%。
3、通过T检验,以P≤0.001作为判断QTL存在的标准,对获得的80个SSSLs进行表型QTL鉴定,在55个SSSLs上检测出55个QTL,45个为不同的QTL,其中分别有6个千粒重相关的QTL,10个抽穗期相关的QTL,13个株高相关的QTL,10个着粒密度相关的QTL,3个穗长相关的QTL和3个有效穗相关的QTL。不同性状的QTL的加性效应不同,株高QTL的加性效应值最大,达到26.93；着粒密度的加性效应最小为-19.53。除了株高相关的QTL,检测到的多数QTL为负效应。本研究中检测到的qHd-6-1、qEpn-8-5、qHd-9-5、qSsd-11-2-5、qSsd-12-5所在区段没有报道过的相关QTL,属于首次定位的新QTL
4、利用重叠群代换作图分析法,将5个含有重叠区域且都表现出株型紧凑的代换系进行QTL定位,将控制分蘖角度的QTL定位于第9染色体长臂末端,标记距离为2.95Mb的RM278与CS0920区段之间。
5、利用获得的迟熟SSSLs才料V370与受体亲本93-11构建的F2分离群体进行抽穗期基因鉴定,发现早抽穗、中熟抽穗和迟抽穗单株的分离比经卡方检验符合1：2：1,说明该迟抽穗位基因表现为不完全显性。与93-11建立回交分离群体,将控制水稻生育期的QTL定位于水稻第6染色体长臂上,RM20176与RM20196之间长度为181.5Kb的区段,经检索为新基因,暂定名为qHd-6-1。
6、以蜀恢527为供体构建的SSSLs,经背景分析后筛选出12个背景相似率高的SSSLs作父本,以四川隐性核不育水稻H2S和两系不育系Y58S、广占63S做母本,进行产量及相关主要农艺性状的杂种优势和配合力分析。产量和产量构成性状的杂种优势在染色体片段上存在显著差异,单株产量有极显著杂种优势的SSSLs分别位于Chr.6和Chr.5上的RM528-RM103、RM592-RM39、RM274-RM26的微卫星标记区段,其中组合广占63S/V261和Y58S/V296的HOCH分别为28.0%、24.4%,均达极显著水平；Chr.5上RM592-RM39区段的株系号V266的SSSLs的单株粒重相对HOCH分为-7.10%,表现为显著的杂种劣势。配合力分析发现,Chr.3RM203～RM55～RM8209～RM448～RM227具有很高的单株产量一般配合力,区段Chr.8RM25～RM310～RM342A的单株产量的一般配合力很低。
Rice is one of the most important crops which is also one of the model organisms for plant molecular biology. So it is useful for plant breeding to understand the genes'function in rice. Most traits of crop are quantitative, which are controlled by polygenes. Fine mapping of quantitative trait loci (QTL) is very important for crop genetic and breeding improvement. Single segment substitution lines (SSSLs) containing only one chromosome segment of donor in the recipient genetic background are useful for the analysis of genes or QTLs. In this research, as the indica rice cultivar93-11receptor, Japonica Rice Varieties Nipponbare and three line hybrid rice restorer line Shuhui527backbone for the donor, by using microsatellite market-assisted selection (MAS), a set of single segment substitution lines (SSSLs) population has been established..And on this basis, the research have been carried out abou analysis of important traits and heterosis. The main results are as follows:
1.447microsatellite markers which uniform distribution on rice12chromosomes were used to indentify polymorphism ammong recipient parent93-11,donor parent Nipponbare and Shuhui527.247molecular markers were showed polymorphism among these parents,221molecular markers,50.78%of totals, showed polymorphism between93-11and Nipponbare,55molecular markers,12.30%of totals, showed polymorphism between93-11and Shuhui527. Finally, a molecular map that based on93-11was developed and247markers more or less distributed in12chromosomes on this map. The average distance between two adjacent markers on this map was1.85Mb.
2.80different SSSLs with the93-11genetic background have been developed in BC3F2^BC4F2and BC5F2generations. Substituted segments of these SSSLs uneven distribute on12chromosomes of rice. The largest proportion of single segments24of80in Chrl,Chr2, Chr4.The smallest proportion of single segments hold9of80in Chr9. The length of the80SSSLs is from0.52Mb to26.13Mb and the average length was6.83Mb.194.89Mb of rice genome is covered by80SSSLs and the coverage is31.03%.
3. Student t-test (p≤0.001) showed55QTLs have significant difference between55of80SSSLs. There are46different QTLs in55QTLs. Among these6,10,13,10,3QTLs are respectively involved in grain weight (Gw), heading date (Hd), plant height (Ph), spikelet setting density (Ssd) and spike length. The additive effect of different Trait's QTL,the additive effect of,the Ph QTL,was the most, it was26.93; grain density additive effect of minimum-19.53. Except of Ph QTL most of the value of additive effect were negative effect. qHd-6-1, qEpn-8--5, qHd-9--5, qSsd-11-2--5, qSsd-12--5have not been reported they were the new QTL located in This study.
4.Using overlapping substitution mapping of5SSSLs, we mapped compact plant architecture with extremely erect tillers QTL. The QTL which controlled the tiller angle was mapped to a2.97Mb region of the long arm in Chr9, the upstream and downstream nearest markers are RM278and CS0920.
5.Using the developed SSSLs, a QTL of the heading date was located on a181.5Kb region of the long arm in Chr6, the upstream and downstream nearest markers are RM20176and RM20196. The F2segregating population from backcrosses to recipient parent93-11. In the segregating population, the segregation ratio of early, middle and late heading plants matched1:2:1, indicating this allele is incomplete dominance genes.It's a new gene about HD.
6. We screened the SSSLs(Shuhui527as the donor) and got12SSSLs which background are similar.Using the12SSSLs as male,H2S(a nucleic male sterility rice line in Sichuan),Y58s and Guanzhan63s(two elite amphibious sterile lines used widely in China)as female,we studied the yield and its relatived agronomic traits.Also, we analysed the heterosis and combining ability. We got those results:
Yield and its related agronomic traits' heterosis is significantly variation among the chromosome segments.The SSSLs which contain the heterosis of grain weight per plant(GWPP) are on Chr.5and Chr.6,the segments are RM528-RM103, RM592-RM39and RM274-RM26.The HOCH of the combinations Guangzhan63S/V261and Y58S/V296are28%and24.4%respectily,all get significantly variation. We discovered a hybrid weakness segments on Chr.5defined by marker RM592and RM39.The line is V266and its relative HOCH of GWPP is -7.10%.We alse discovered that the segment RM203-RM55-RM8209-RM448-RM227on Chr.3possesses a high general combining ability(GCA) of GWPP. Oppositely,the GCA of the segment RM25～RM310～RM342A on Chr.8is minimum.
1、本实验选用均匀分布于水稻12条染色体上的447对微卫星(SSR)标记在受体亲本93-11和供体亲本日本晴与蜀恢527间进行多态性标记筛选,.结果显示共有247个SSR在亲本间具有多态性,其中有221个SSR标记在93-11与日本晴之间表现出多态性,多态率为50.78%；有55个SSR标记在93-11与蜀恢527间具有多态性,多态率为12.30%。同时,利用序列比对工具,对筛选出的多态性标记在测序品种93-11基因组上进行物理定位,构建了一张含有247个SSR多态性标记的分子图谱,标记间的平均距离为1.85Mb。
2、在BC3F2、BC4F2和BC5F2三个世代中总共获得80个含有不同片段的单片段代换系株系。这些单片段代换系在水稻12条染色体上呈不均匀分布,其中第1、5、8染色体上分布最多,共有37个；第4、7、10染色体上分布较少,各有2个。代换片段长度分布在0.52Mb-26.13Mb之间,代换片段的平均长度为6.83Mb。全部代换片段对基因组的覆盖长度为194.89Mb,覆盖率为47.56%。
3、通过T检验,以P≤0.001作为判断QTL存在的标准,对获得的80个SSSLs进行表型QTL鉴定,在55个SSSLs上检测出55个QTL,45个为不同的QTL,其中分别有6个千粒重相关的QTL,10个抽穗期相关的QTL,13个株高相关的QTL,10个着粒密度相关的QTL,3个穗长相关的QTL和3个有效穗相关的QTL。不同性状的QTL的加性效应不同,株高QTL的加性效应值最大,达到26.93；着粒密度的加性效应最小为-19.53。除了株高相关的QTL,检测到的多数QTL为负效应。本研究中检测到的qHd-6-1、qEpn-8-5、qHd-9-5、qSsd-11-2-5、qSsd-12-5所在区段没有报道过的相关QTL,属于首次定位的新QTL
4、利用重叠群代换作图分析法,将5个含有重叠区域且都表现出株型紧凑的代换系进行QTL定位,将控制分蘖角度的QTL定位于第9染色体长臂末端,标记距离为2.95Mb的RM278与CS0920区段之间。
5、利用获得的迟熟SSSLs才料V370与受体亲本93-11构建的F2分离群体进行抽穗期基因鉴定,发现早抽穗、中熟抽穗和迟抽穗单株的分离比经卡方检验符合1：2：1,说明该迟抽穗位基因表现为不完全显性。与93-11建立回交分离群体,将控制水稻生育期的QTL定位于水稻第6染色体长臂上,RM20176与RM20196之间长度为181.5Kb的区段,经检索为新基因,暂定名为qHd-6-1。
6、以蜀恢527为供体构建的SSSLs,经背景分析后筛选出12个背景相似率高的SSSLs作父本,以四川隐性核不育水稻H2S和两系不育系Y58S、广占63S做母本,进行产量及相关主要农艺性状的杂种优势和配合力分析。产量和产量构成性状的杂种优势在染色体片段上存在显著差异,单株产量有极显著杂种优势的SSSLs分别位于Chr.6和Chr.5上的RM528-RM103、RM592-RM39、RM274-RM26的微卫星标记区段,其中组合广占63S/V261和Y58S/V296的HOCH分别为28.0%、24.4%,均达极显著水平；Chr.5上RM592-RM39区段的株系号V266的SSSLs的单株粒重相对HOCH分为-7.10%,表现为显著的杂种劣势。配合力分析发现,Chr.3RM203～RM55～RM8209～RM448～RM227具有很高的单株产量一般配合力,区段Chr.8RM25～RM310～RM342A的单株产量的一般配合力很低。
Rice is one of the most important crops which is also one of the model organisms for plant molecular biology. So it is useful for plant breeding to understand the genes'function in rice. Most traits of crop are quantitative, which are controlled by polygenes. Fine mapping of quantitative trait loci (QTL) is very important for crop genetic and breeding improvement. Single segment substitution lines (SSSLs) containing only one chromosome segment of donor in the recipient genetic background are useful for the analysis of genes or QTLs. In this research, as the indica rice cultivar93-11receptor, Japonica Rice Varieties Nipponbare and three line hybrid rice restorer line Shuhui527backbone for the donor, by using microsatellite market-assisted selection (MAS), a set of single segment substitution lines (SSSLs) population has been established..And on this basis, the research have been carried out abou analysis of important traits and heterosis. The main results are as follows:
1.447microsatellite markers which uniform distribution on rice12chromosomes were used to indentify polymorphism ammong recipient parent93-11,donor parent Nipponbare and Shuhui527.247molecular markers were showed polymorphism among these parents,221molecular markers,50.78%of totals, showed polymorphism between93-11and Nipponbare,55molecular markers,12.30%of totals, showed polymorphism between93-11and Shuhui527. Finally, a molecular map that based on93-11was developed and247markers more or less distributed in12chromosomes on this map. The average distance between two adjacent markers on this map was1.85Mb.
2.80different SSSLs with the93-11genetic background have been developed in BC3F2^BC4F2and BC5F2generations. Substituted segments of these SSSLs uneven distribute on12chromosomes of rice. The largest proportion of single segments24of80in Chrl,Chr2, Chr4.The smallest proportion of single segments hold9of80in Chr9. The length of the80SSSLs is from0.52Mb to26.13Mb and the average length was6.83Mb.194.89Mb of rice genome is covered by80SSSLs and the coverage is31.03%.
3. Student t-test (p≤0.001) showed55QTLs have significant difference between55of80SSSLs. There are46different QTLs in55QTLs. Among these6,10,13,10,3QTLs are respectively involved in grain weight (Gw), heading date (Hd), plant height (Ph), spikelet setting density (Ssd) and spike length. The additive effect of different Trait's QTL,the additive effect of,the Ph QTL,was the most, it was26.93; grain density additive effect of minimum-19.53. Except of Ph QTL most of the value of additive effect were negative effect. qHd-6-1, qEpn-8--5, qHd-9--5, qSsd-11-2--5, qSsd-12--5have not been reported they were the new QTL located in This study.
4.Using overlapping substitution mapping of5SSSLs, we mapped compact plant architecture with extremely erect tillers QTL. The QTL which controlled the tiller angle was mapped to a2.97Mb region of the long arm in Chr9, the upstream and downstream nearest markers are RM278and CS0920.
5.Using the developed SSSLs, a QTL of the heading date was located on a181.5Kb region of the long arm in Chr6, the upstream and downstream nearest markers are RM20176and RM20196. The F2segregating population from backcrosses to recipient parent93-11. In the segregating population, the segregation ratio of early, middle and late heading plants matched1:2:1, indicating this allele is incomplete dominance genes.It's a new gene about HD.
6. We screened the SSSLs(Shuhui527as the donor) and got12SSSLs which background are similar.Using the12SSSLs as male,H2S(a nucleic male sterility rice line in Sichuan),Y58s and Guanzhan63s(two elite amphibious sterile lines used widely in China)as female,we studied the yield and its relatived agronomic traits.Also, we analysed the heterosis and combining ability. We got those results:
Yield and its related agronomic traits' heterosis is significantly variation among the chromosome segments.The SSSLs which contain the heterosis of grain weight per plant(GWPP) are on Chr.5and Chr.6,the segments are RM528-RM103, RM592-RM39and RM274-RM26.The HOCH of the combinations Guangzhan63S/V261and Y58S/V296are28%and24.4%respectily,all get significantly variation. We discovered a hybrid weakness segments on Chr.5defined by marker RM592and RM39.The line is V266and its relative HOCH of GWPP is -7.10%.We alse discovered that the segment RM203-RM55-RM8209-RM448-RM227on Chr.3possesses a high general combining ability(GCA) of GWPP. Oppositely,the GCA of the segment RM25～RM310～RM342A on Chr.8is minimum.
引文
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