粳稻穗部性状遗传分析和QTL定位及关联作图
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摘要
中国的粳稻种植面积701.1万hm2占全世界粳稻种植面积(1254.2万hm2)的一半以上。杂交粳稻年种植面积仅占粳稻种植总面积的3%,与取得巨大成就的杂交籼稻相比,杂交粳稻还有很大的发展空间。杂交粳稻在抗病虫等方面具有一定的优势,但产量竞争优势并不明显。改良穗部性状是提高产量的有效途径。发掘穗部性状有利等位变异是改良穗部性状的基础。本研究首先利用栽培粳稻品种秀水79和粳稻恢复系C堡及其衍生的含有370个家系的重组自交系群体对一次枝梗数和二次枝梗数进行了遗传分离分析。然后以其中254个家系为作图群体构建了粳稻SSR标记连锁图谱,并在此图谱基础上对粳稻的穗部性状和剑叶性状进行了QTL定位。最后利用SSR分子标记对太湖流域粳稻地方品种和现今生产上大面积推广应用的育成品种组成的粳稻自然群体进行穗部性状和标记的关联分析。主要研究结果如下：
1.运用主基因+多基因混合遗传模型,对2005年和2006年粳稻品种秀水79与C堡及其杂交后代通过一粒传衍生的重组自交系群体(F7:8和F8:9,简称“秀堡RIL群体”)370个家系的主茎穗一次枝梗数和二次枝梗数进行遗传分析的结果显示,一次枝梗数性状受两对连锁主基因控制,同时存在多基因,主基因遗传率分别为66%和40%,多基因遗传率分别为11%和41%;二次枝梗数性状受2对独立的主基因控制,同时存在多基因,主基因遗传率分别为80%和65%,多基因遗传率分别为10%和12%。
2.以915对SSR引物扩增粳稻品种秀水79和粳稻恢复系C堡的总DNA,发现105对引物在双亲之间存在多态性。第1染色体多态率最小,为7.8%。第7染色体多态率最大,为16.4%。以秀堡RIL群体中的254个家系(F10:11)为作图群体,用这105对引物进行基因型鉴定,构建了粳稻SSR分子标记连锁图谱。由91个信息位点构成的连锁图谱全长969cM,位点间平均图距10.6 cM。秀水79总等位基因频率为0.537,C堡为0.463,符合1:1的分离比例。
3.在2个生长环境下种植秀堡RIL群体254个家系(F10:11)及其亲本,调查穗部6个性状和剑叶4个性状。利用上述SSR分子标记连锁图谱,进行加性效应位点,加性与加性互作位点对,以及QTL与环境互作效应的检测,结果(1)10个性状共检测到53个加性位点。一次枝梗数检测到5个加性位点,解释表型变异的4%-11%。二次枝梗数检测到4个加性位点,解释表型变异的2%-16%。穗长检测到6个加性位点,解释表型变异的1%-34%。每穗颖花数检测到6个加性位点,解释表型变异的2%-11%。每穗实粒数检测到6个加性位点,解释表型变异的3%-6%。着粒密度检测到4个加性位点,解释表型变异的2%-21%。剑叶长检测到3个加性位点,解释表型变异的8%-40%。剑叶宽检测到5个加性位点,解释表型变异的4%-16%。剑叶叶面积指数检测到5个加性位点,解释表型变异的0.6%-14%。剑叶卷曲度检测到9个加性位点,解释表型变异的2%-9%。(2)在检测到的所有加性位点中,发现3个多效性位点同时作用于剑叶性状和穗部性状,其中第9染色体分别位于RM6570-RM5652和RM5652-RM410区段内的2个位点均同时控制剑叶长和穗长,分别解释剑叶长表型变异的41%和40%和穗长表型变异的34%和34%。这种多效性现象与剑叶长和穗长的相关性(r=0.86,P<0.01)一致。(3)除二次枝梗数没有检测到互作位点外,其它9个性状共检测到29对加性×加性互作位点,解释单个性状表型变异的1.0%-17.5%。所有检测到的主效位点和上位性互作位点均不存在基因型与环境的互作。
4.利用91个SSR标记对太湖流域粳稻地方品种核心种质(58份代表性材料)及目前生产上大面积推广的粳稻育成品种(36份代表性材料)的基因组变异进行扫描。分别分析两个群体的连锁不平衡位点和其组成自然群体后的群体结构。采用TASSEL软件的GLM (general linear model)方法对粳稻穗部7个性状进行标记与性状的关联分析,并对与性状关联的等位变异作解析。结果(1)地方品种和推广品种在相同和不同染色体间均存在较高程度的连锁不平衡,且LD衰减较慢。(2)对这两个群体组成的自然群体进行结构分析发现,此群体由8个亚群组成,且亚群的划分与抽穗期生态类型划分相关,表明抽穗期的分化具有一定的遗传基础。(3)共有28个等位变异位点与7个穗部性状关联,其中17个位点同时与多个性状关联,这与多个性状间显著相关相互印证。(4)鉴定出50个优异等位变异和28个携带这些优异等位变异的载体材料。
Japonica rice growing area in China is 7,011,000 hm2 each year and accounts for more than 50 percent of world's japonica area (12,542,000 hm2). The area planted with japonica hybrid rice only occupied 3% of the total area of japonica rice in China. Therefore, great space exists for developing japonica hybrid rice, compared with indica hybrid rice, in which great achievement had been made. Japonica hybrid rice has advantage in resistant to disease and pests, but competition heterosis in yield is not obvious. Improving panicle traits is an efficiency method for yield enhancement. Discovering favorable alleles for panicle traits is the foundation for panicle trait improvement. In this study, genetic segregation analysis of primary branch number and secondary branch number per panicle were performed firstly by using 370 recombinant inbred lines (RILs) and their parents, Xiushui 79 and C Bao, which are both japonica rice cultivars. Secondly, a SSR linkage map in japonica rice was constructed by using 254 RILs selected from above 370 RILs. Thirdly, QTLs of panicle traits and flag leaf traits were detected based on the map. Finally, association analysis between panicle traits and SSR markers was conducted in natural population composed of 58 core collections of landrace and 36 cultivars currently used widely in japonica rice in Taihu Lake valley. The main results are as follows:
1. Primary branch number per panicle was controlled by two linkage major genes plus polygenes. Major gene heritability was 66% in 2005 and 40% in 2006, and polygene heritability was 11% in 2005 and 41% in 2006. Secondary branch number per panicle was controlled by two major genes plus polygenes. Major gene heritability was 80% in 2005 and 65% in 2006, and polygene heritability was 10% in 2005 and 12% in 2006. The results above were obtained by analyzing 2 years of segregation data of primary branch number and secondary branch number in RIL population (370 lines, F7:8 in 2005 and F8:9 in 2006, Xiubao RIL population for short)) made from Xiushui 79 and C Bao with the mixed major-gene plus polygenes inheritance model.
2. Among 915 pairs of SSR primers used for screening polymorphism between Xiushui 79 and C Bao,105 pairs of primers amplified polymorphic products using total DNA of the two parents as template. Chromosome 1 showed the smallest polymorphism rate (7.8%). Chromosome 7 showed the largest polymorphism rate (16.4%). A SSR linkage map was constructed by genotyping 254 family lines (F10:11) from Xiubao RIL population by using above 105 SSR markers. The map containing 91 information loci has a total distance of 969 cM, averaging 10.6 cM between two loci. The total allele frequency for the RIL population was calculated at 0.537 and 0.463 for Xiushui 79 and C Bao, respectively, fitting to the expected allelic frequency of 1:1.
3. Phenotypes values of six panicle traits and four flag leaf traits in two growing environments were investigated in 254 Xiubao RILs and their parents. QTLs of additive effects and additive×additive effects for these ten traits were detected and their interaction with environments was analyzed based on above SSR linkage map. The results showed that:(1) 53 additive effects QTLs for all ten traits were identified. Five additive QTLs were detected for primary branch number per panicle, explained 4%～11% of the phenotypic variation; Four additive QTLs were detected for secondary branch number per panicle explained 2%～16% of the phenotypic variation; Six additive QTLs were detected for panicle length, explained 1%～34% of the phenotypic variation; Six additive QTLs were detected for spikelet number per panicle, explained 2%～11% of the phenotypic variation; Six additive QTLs were detected for filled grain number per panicle, explained 3%～6% of the phenotypic variation; Four additive QTLs were detected for spikelet density, explained 2%～21% of the phenotypic variation; Three additive QTLs were detected for flag leaf length, explained 8%～40% of the phenotypic variation; Five additive QTLs were detected for flag leaf width, explained 4%～16% of the phenotypic variation; Five additive QTLs were detected for flag leaf area, explained 0.6%～14% of the phenotypic variation; Nine additive QTLs were detected for leaf rolled index, explained 2%～9% of the phenotypic variation. (2) Three pleiotropic effects loci were found which have simultaneous effects on flag leaf traits and panicle traits, two large effect loci in RM6570-RM5652 and RM5652-RM410 on chromosome 9, respectively, have simultaneous positive effects on FLL and PL. They explained 41% and 40% of the phenotypic variation in FLL, respectively,34% and 34% of the phenotypic variation in PL, respectively. The pleiotropic was confirmed by correlation analysis that FLL and PL have the largest contributions to each other (r=0.86, P< 0.01). (3) Twenty nine epistatic interaction QTL pairs detected for all traits except SBN, explained 1.0%～17.5% of the phenotypic variation for single trait.
4. The genotyping data of 91 SSR markers on representative sample of 58 core collections of Japonica rice landrace in Taihu Lake valley and 36 accessions currently used widely in japonica rice production were used in the present study. Linkage disequilibriums of pairwise loci were analyzed for the two populations and population structure was analyzed for the natural population which was composed of the two above populations. Then the association analysis between SSR loci and 7 panicle traits was performed by using TASSEL GLM (general linear model) program. Alleles of loci significantly associated with the traits in two environments were analysised. The results showed that:(1) Various degrees of LD were detected not only among markers on the same chromosomes but also among markers on the different chromosomes, and the LD attenuation was slow. (2) Genetic structure analysis showed that the natural population was composed of eight subpopulations, which associated with their heading date eco-types, indicating the classification of heading date eco-types was of found genetic bases. (3) Twenty eight loci associated with the panicle traits were screened out from the natural population. Seventeen (60%) loci were found to associate with two or more traits simultaneously, which was confirmed by correlation analysis that most traits were significant correlated to each other. (4) Fifty favorable alleles and 28 their carrier materials were screened out.
1.运用主基因+多基因混合遗传模型,对2005年和2006年粳稻品种秀水79与C堡及其杂交后代通过一粒传衍生的重组自交系群体(F7:8和F8:9,简称“秀堡RIL群体”)370个家系的主茎穗一次枝梗数和二次枝梗数进行遗传分析的结果显示,一次枝梗数性状受两对连锁主基因控制,同时存在多基因,主基因遗传率分别为66%和40%,多基因遗传率分别为11%和41%;二次枝梗数性状受2对独立的主基因控制,同时存在多基因,主基因遗传率分别为80%和65%,多基因遗传率分别为10%和12%。
2.以915对SSR引物扩增粳稻品种秀水79和粳稻恢复系C堡的总DNA,发现105对引物在双亲之间存在多态性。第1染色体多态率最小,为7.8%。第7染色体多态率最大,为16.4%。以秀堡RIL群体中的254个家系(F10:11)为作图群体,用这105对引物进行基因型鉴定,构建了粳稻SSR分子标记连锁图谱。由91个信息位点构成的连锁图谱全长969cM,位点间平均图距10.6 cM。秀水79总等位基因频率为0.537,C堡为0.463,符合1:1的分离比例。
3.在2个生长环境下种植秀堡RIL群体254个家系(F10:11)及其亲本,调查穗部6个性状和剑叶4个性状。利用上述SSR分子标记连锁图谱,进行加性效应位点,加性与加性互作位点对,以及QTL与环境互作效应的检测,结果(1)10个性状共检测到53个加性位点。一次枝梗数检测到5个加性位点,解释表型变异的4%-11%。二次枝梗数检测到4个加性位点,解释表型变异的2%-16%。穗长检测到6个加性位点,解释表型变异的1%-34%。每穗颖花数检测到6个加性位点,解释表型变异的2%-11%。每穗实粒数检测到6个加性位点,解释表型变异的3%-6%。着粒密度检测到4个加性位点,解释表型变异的2%-21%。剑叶长检测到3个加性位点,解释表型变异的8%-40%。剑叶宽检测到5个加性位点,解释表型变异的4%-16%。剑叶叶面积指数检测到5个加性位点,解释表型变异的0.6%-14%。剑叶卷曲度检测到9个加性位点,解释表型变异的2%-9%。(2)在检测到的所有加性位点中,发现3个多效性位点同时作用于剑叶性状和穗部性状,其中第9染色体分别位于RM6570-RM5652和RM5652-RM410区段内的2个位点均同时控制剑叶长和穗长,分别解释剑叶长表型变异的41%和40%和穗长表型变异的34%和34%。这种多效性现象与剑叶长和穗长的相关性(r=0.86,P<0.01)一致。(3)除二次枝梗数没有检测到互作位点外,其它9个性状共检测到29对加性×加性互作位点,解释单个性状表型变异的1.0%-17.5%。所有检测到的主效位点和上位性互作位点均不存在基因型与环境的互作。
4.利用91个SSR标记对太湖流域粳稻地方品种核心种质(58份代表性材料)及目前生产上大面积推广的粳稻育成品种(36份代表性材料)的基因组变异进行扫描。分别分析两个群体的连锁不平衡位点和其组成自然群体后的群体结构。采用TASSEL软件的GLM (general linear model)方法对粳稻穗部7个性状进行标记与性状的关联分析,并对与性状关联的等位变异作解析。结果(1)地方品种和推广品种在相同和不同染色体间均存在较高程度的连锁不平衡,且LD衰减较慢。(2)对这两个群体组成的自然群体进行结构分析发现,此群体由8个亚群组成,且亚群的划分与抽穗期生态类型划分相关,表明抽穗期的分化具有一定的遗传基础。(3)共有28个等位变异位点与7个穗部性状关联,其中17个位点同时与多个性状关联,这与多个性状间显著相关相互印证。(4)鉴定出50个优异等位变异和28个携带这些优异等位变异的载体材料。
Japonica rice growing area in China is 7,011,000 hm2 each year and accounts for more than 50 percent of world's japonica area (12,542,000 hm2). The area planted with japonica hybrid rice only occupied 3% of the total area of japonica rice in China. Therefore, great space exists for developing japonica hybrid rice, compared with indica hybrid rice, in which great achievement had been made. Japonica hybrid rice has advantage in resistant to disease and pests, but competition heterosis in yield is not obvious. Improving panicle traits is an efficiency method for yield enhancement. Discovering favorable alleles for panicle traits is the foundation for panicle trait improvement. In this study, genetic segregation analysis of primary branch number and secondary branch number per panicle were performed firstly by using 370 recombinant inbred lines (RILs) and their parents, Xiushui 79 and C Bao, which are both japonica rice cultivars. Secondly, a SSR linkage map in japonica rice was constructed by using 254 RILs selected from above 370 RILs. Thirdly, QTLs of panicle traits and flag leaf traits were detected based on the map. Finally, association analysis between panicle traits and SSR markers was conducted in natural population composed of 58 core collections of landrace and 36 cultivars currently used widely in japonica rice in Taihu Lake valley. The main results are as follows:
1. Primary branch number per panicle was controlled by two linkage major genes plus polygenes. Major gene heritability was 66% in 2005 and 40% in 2006, and polygene heritability was 11% in 2005 and 41% in 2006. Secondary branch number per panicle was controlled by two major genes plus polygenes. Major gene heritability was 80% in 2005 and 65% in 2006, and polygene heritability was 10% in 2005 and 12% in 2006. The results above were obtained by analyzing 2 years of segregation data of primary branch number and secondary branch number in RIL population (370 lines, F7:8 in 2005 and F8:9 in 2006, Xiubao RIL population for short)) made from Xiushui 79 and C Bao with the mixed major-gene plus polygenes inheritance model.
2. Among 915 pairs of SSR primers used for screening polymorphism between Xiushui 79 and C Bao,105 pairs of primers amplified polymorphic products using total DNA of the two parents as template. Chromosome 1 showed the smallest polymorphism rate (7.8%). Chromosome 7 showed the largest polymorphism rate (16.4%). A SSR linkage map was constructed by genotyping 254 family lines (F10:11) from Xiubao RIL population by using above 105 SSR markers. The map containing 91 information loci has a total distance of 969 cM, averaging 10.6 cM between two loci. The total allele frequency for the RIL population was calculated at 0.537 and 0.463 for Xiushui 79 and C Bao, respectively, fitting to the expected allelic frequency of 1:1.
3. Phenotypes values of six panicle traits and four flag leaf traits in two growing environments were investigated in 254 Xiubao RILs and their parents. QTLs of additive effects and additive×additive effects for these ten traits were detected and their interaction with environments was analyzed based on above SSR linkage map. The results showed that:(1) 53 additive effects QTLs for all ten traits were identified. Five additive QTLs were detected for primary branch number per panicle, explained 4%～11% of the phenotypic variation; Four additive QTLs were detected for secondary branch number per panicle explained 2%～16% of the phenotypic variation; Six additive QTLs were detected for panicle length, explained 1%～34% of the phenotypic variation; Six additive QTLs were detected for spikelet number per panicle, explained 2%～11% of the phenotypic variation; Six additive QTLs were detected for filled grain number per panicle, explained 3%～6% of the phenotypic variation; Four additive QTLs were detected for spikelet density, explained 2%～21% of the phenotypic variation; Three additive QTLs were detected for flag leaf length, explained 8%～40% of the phenotypic variation; Five additive QTLs were detected for flag leaf width, explained 4%～16% of the phenotypic variation; Five additive QTLs were detected for flag leaf area, explained 0.6%～14% of the phenotypic variation; Nine additive QTLs were detected for leaf rolled index, explained 2%～9% of the phenotypic variation. (2) Three pleiotropic effects loci were found which have simultaneous effects on flag leaf traits and panicle traits, two large effect loci in RM6570-RM5652 and RM5652-RM410 on chromosome 9, respectively, have simultaneous positive effects on FLL and PL. They explained 41% and 40% of the phenotypic variation in FLL, respectively,34% and 34% of the phenotypic variation in PL, respectively. The pleiotropic was confirmed by correlation analysis that FLL and PL have the largest contributions to each other (r=0.86, P< 0.01). (3) Twenty nine epistatic interaction QTL pairs detected for all traits except SBN, explained 1.0%～17.5% of the phenotypic variation for single trait.
4. The genotyping data of 91 SSR markers on representative sample of 58 core collections of Japonica rice landrace in Taihu Lake valley and 36 accessions currently used widely in japonica rice production were used in the present study. Linkage disequilibriums of pairwise loci were analyzed for the two populations and population structure was analyzed for the natural population which was composed of the two above populations. Then the association analysis between SSR loci and 7 panicle traits was performed by using TASSEL GLM (general linear model) program. Alleles of loci significantly associated with the traits in two environments were analysised. The results showed that:(1) Various degrees of LD were detected not only among markers on the same chromosomes but also among markers on the different chromosomes, and the LD attenuation was slow. (2) Genetic structure analysis showed that the natural population was composed of eight subpopulations, which associated with their heading date eco-types, indicating the classification of heading date eco-types was of found genetic bases. (3) Twenty eight loci associated with the panicle traits were screened out from the natural population. Seventeen (60%) loci were found to associate with two or more traits simultaneously, which was confirmed by correlation analysis that most traits were significant correlated to each other. (4) Fifty favorable alleles and 28 their carrier materials were screened out.
引文
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