用分子标记剖析油菜重要农艺性状的遗传基础
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摘要
许多重要农艺性状是数量性状,遗传育种的相当大部分的工作就是改良这些数量性状。尽管油菜育种工作者选育了很多的优良品种,并且杂种优势在生产上得以利用,但是总的说来,选育新品种的效率还不高,这与数量性状的遗传基础及其杂种优势机理研究得不够透彻有关。分子标记的兴起,QTL定位理论的不断完善,以及不断创新的试验群体设计给数量性状的研究提供了有效手段。
本研究利用强杂种优势的甘蓝型油菜杂交组合Quantum×No.2717-17的两个永久群体。一个为F_1小孢子培养得到的258个DH系:另一个为以DH群体为基础群体,通过系间杂交得到的258个组合的“永久F_2群体”(Immortalized F_2,IF_2)。通过三个环境下的田间试验,考察包括产量及其构成因子在内的11个性状,结合分子标记分析,对性状及其杂种优势进行QTL定位和上位性检测。主要结果如下:
1.以207个SSR标记和190个SRAP标记构建了全长为1747.4cM的遗传连锁图谱,标记间的平均距离为4.4cM。采用共同的SSR标记,将本图谱与甘蓝型油菜通用图谱进行了初步对应。
2.卡方测验表明,在DH群体中,129个标记(32.5%)表现显著偏分离(P＜0.01),且大部分偏向母本。永久F_2群体的的位点偏分离比DH群体更严重,除在DH群体中偏分离的标记外,新增加偏分离标记36个。
3.所有定位的397个位点的等位基因在DH群体中的分布为Quantum等位基因占52.1%.No.2717-17等位基因占47.9%,近似为1:1,略微偏向Quantum。在永久F_2群体中的分布为Quantum等位基因占28.1%,No.2717-17等位基因占23.5%,杂合型占52.3%,所以“永久F_2群体”的基因型组成与一般F_2群体组成相似。
4.DH群体和“永久F_2”群体变异丰富,大部分性状表现出明显的超亲分离,同时表现为正态分布。两群体的性状环境间均表现出显著差异,基因型与环境显著互作。“永久F_2”群体中性状杂种优势均表现出变幅极大的分离,而且大部分性状杂种优势值表现为正态分布。
5.应用复合区间作图法对DH群体和“永久F_2”群体进行QTL定位。QTL数目因性状而异,从13-29个不等;产量及其构成因子共定位了88个QTL,其中至少检测到两次的QTL18个:单株产量5个,单株总角果数为3个,每穗实粒数为3个,千粒重7个。其余7个农艺性状共检测到116个QTL,其中至少检测到两次的QTL有58个。
6.无论是高值亲本,还是低值亲本,都包含有对性状表现型起增效或者起减效作用的等位基因。大部分QTL都分布在“QTL簇”中,一些连锁群包含多个QTL簇。一些QTL仅在一个群体中检测到,表现出群体特异性。
7.定义杂种优势效应显著的位点为杂种优势位点(HL)。产量及其构成因子共定位了44个HL,重复检测的HL共5个。其他性状共检测到67个HL,重复检测的HL仅2个。与QTL定位比较,HL的检测更易受环境影响。
8.单个HL的贡献率一般较小。有20个HL也在IF_2群体的QTL分析中检测到。与QTL类似,部分HL也成簇分布于连锁群,表明了HL的多效性。
9.对DH群体采用混合模型的复合区间作图法,产量及其构成因子三环境下共定位到118个上位性QTL(Epistatic QTL,E-QTL);环境间仅检测到3个相同的E-QTL。其他性状定位到的E-QTLs数量为O—21个,环境间相同的E-QTLs共6个。对比单位点QTL,环境间和性状间检测到较少的相同的E-QTL,表明E-QTL更易受环境影响。部分单位点QTL也参与了位点间互作。
10.对IF_2群体,采用双因素方差分析,检测了基因组所有可能的两位点上位性互作。所有性状都检测到大量的上位性互作位点对;部分上位性互作存在2种或者2种以上的互作类型。互作类型以加性×加性居多,显性×显性最少。对显著的互作位点,两位点基因型组合中,常常以双位点纯合类型表现最好,但同时表现最差的也常常是双位点纯合基因型;而双位点杂合基因型则很少表现为最优基因型,但同时也不表现为最差基因型。上位性互作涉及到的位点,包括性状的QTL与非QTL,其形式以非QTL位点间互作最多;互作影响参与互作的QTL的效应表达。上位性互作和QTL一样有一因多效,可能同时影响多个性状
11.DH群体和IF_2的上位性位点较少重叠,说明上位性效应同样受遗传背景的影响
Most of the important agronomic traits in crops are quantitative,and variations in these traits are usually controlled by many minor genes.Improvement of these quantitative traits is one of the major objectives in rapeseed genetic breeding program. Many elite varieties and hybrids in Brassica napus have been developed using traditional breeding methods,but the efficiency to breed them is still low because the genetic basis for most of the quantitative traits is still unclear.The advent of molecular markers,improved QTL mapping theory and novel experimental designs accelerated the dissection of quantitative traits in the last decade in B.napus.
In this study,we employed two permanent populations of a highly heterotic B.napus cross,Quantum×No.2717-17.One population is 258 doubled haploid (DH) lines derived from the microspore culture of F_1,and the other one is the "immortalized F_2"(IF_2) population comprising 258 crosses resulted from randomly intermating of DH lines.Field experiments with 2 replicates following a randomized complete block design were implemented in three environments.Molecular markers were used to analyze the genetic model associated with 11 traits' performance and heterosis.The main results are summarized as follow:
1.A genetic linkage map,spanning 1747.4 cM with an average interval of 4.4 cM,was constructed using 207 simple sequence repeat(SSR) markers and 190 sequence-related amplified polymorphism(SRAP) markers.Based on the public information of microsatellites(SSR markers),our map was aligned with reference maps.
2.In the DH population,129 markers(32.5%) skewed from the expected 1:1 genotypic segregation by Chi-square test,and most of them skewed towards the Quantum(female parent).Compared to the DH population,36 more markers in the IF_2 population showed segregation distortion.
3.In the DH population,the allele frequencies of Quantum and No.2717-17 in all 397 informative loci were 52.1%and 47.9%respectively.The allele ratio approximated to the expected 1:1.The genome and their proportions in the IF_2 population are similar to those in an F_2 population.The proportions of the genotypes for Quantum,No.2717-17 and heterzygousity are 27.08%,24.03%and 52.3%,respectively.
4.Most traits in both populations showed transgressive segregation and demonstrated the normal distribution.There existed significant difference in all traits among three environments.The interactions between genotype and environment were observed for all traits.Transgressive segregation was observed for all traits' heterosis in the crosses of the IF_2 population,and the heterosis values of most traits displayed the normal distribution.
5.The entire genome was searched for QTL conferring significant effects on all scored traits by composite interval mapping in two populations.The number of QTL varied according to the different traits.A total of 88 QTL were detected for yield and its component traits in three environments and of these 18 QTL were detected for more than once.There were 116 QTL identified related to other traits, of which 58 ones were repeatedly detected.
6.QTL positive and negative additive effects were dispersed in both parents for all the traits.Most of QTL were located in QTL clusters.Some QTL were specifically detected only in one population.
7.By composite interval mapping,44 heterosis loci were detected for yield and its component traits in the IF2 population,and five HL were repeatedly detected.For other traits,67 HL were detected,and only two were repeatedly detected. Compared to QTL mapping,the detection of HL was more sensitive to environmental influence.
8.The proportion of variation explained by single HL was relatively small.Twenty HL were also detected in QTL analysis.Like QTL,some HL for different traits formed clusters on linkage groups.
9.A total of 118 epistatic QTL(E-QTL) were detected for yield and its component traits in the three environments using composite interval mapping with mixed model,and 3 of them were repeatedly detected over environments.For other traits, 0 to 21 E-QTL were resolved for each one,and 6 common E-QTL were repeatedly detected over environments.The detection of E-QTL was more sensitive to environmental effect than that of main QTL.Some main QTL were invovled in interaction.
10.All possible two-way ANOVAs between the markers on whole linkage groups were analyzed for 11 traits in the IF_2 population.A large number of significant digenic interactions were detected for all traits.In a part of loci,two or more interaction types were detected in one pair of loci.All 4 possible digenic significant interaction types(AA,AD,DA,DD) were detected,and of them AA type occurred at predominantly high frequencies with DD type being the least frequent.For two-locus combinations of significant digenic interactions, two-locus homozygotes were the best genotypes in many cases,at the same time, another two-locus homologues combinations was also the worst genotype;On the other hand,double heterozygote were rarely the best genotype and never the worst genotype.Most interactions occurred between two loci both showing non-significant effects to traits.The effects of some QTL were influenced by epistasis.Pleiotropic effects of digenic interactions were detected between or among the related traits.
11.The digenic interactions detected in the DH and IF_2 populations showed little overlapping,which suggested that effects of epistasis were influenced by the genetic background.
本研究利用强杂种优势的甘蓝型油菜杂交组合Quantum×No.2717-17的两个永久群体。一个为F_1小孢子培养得到的258个DH系:另一个为以DH群体为基础群体,通过系间杂交得到的258个组合的“永久F_2群体”(Immortalized F_2,IF_2)。通过三个环境下的田间试验,考察包括产量及其构成因子在内的11个性状,结合分子标记分析,对性状及其杂种优势进行QTL定位和上位性检测。主要结果如下:
1.以207个SSR标记和190个SRAP标记构建了全长为1747.4cM的遗传连锁图谱,标记间的平均距离为4.4cM。采用共同的SSR标记,将本图谱与甘蓝型油菜通用图谱进行了初步对应。
2.卡方测验表明,在DH群体中,129个标记(32.5%)表现显著偏分离(P＜0.01),且大部分偏向母本。永久F_2群体的的位点偏分离比DH群体更严重,除在DH群体中偏分离的标记外,新增加偏分离标记36个。
3.所有定位的397个位点的等位基因在DH群体中的分布为Quantum等位基因占52.1%.No.2717-17等位基因占47.9%,近似为1:1,略微偏向Quantum。在永久F_2群体中的分布为Quantum等位基因占28.1%,No.2717-17等位基因占23.5%,杂合型占52.3%,所以“永久F_2群体”的基因型组成与一般F_2群体组成相似。
4.DH群体和“永久F_2”群体变异丰富,大部分性状表现出明显的超亲分离,同时表现为正态分布。两群体的性状环境间均表现出显著差异,基因型与环境显著互作。“永久F_2”群体中性状杂种优势均表现出变幅极大的分离,而且大部分性状杂种优势值表现为正态分布。
5.应用复合区间作图法对DH群体和“永久F_2”群体进行QTL定位。QTL数目因性状而异,从13-29个不等;产量及其构成因子共定位了88个QTL,其中至少检测到两次的QTL18个:单株产量5个,单株总角果数为3个,每穗实粒数为3个,千粒重7个。其余7个农艺性状共检测到116个QTL,其中至少检测到两次的QTL有58个。
6.无论是高值亲本,还是低值亲本,都包含有对性状表现型起增效或者起减效作用的等位基因。大部分QTL都分布在“QTL簇”中,一些连锁群包含多个QTL簇。一些QTL仅在一个群体中检测到,表现出群体特异性。
7.定义杂种优势效应显著的位点为杂种优势位点(HL)。产量及其构成因子共定位了44个HL,重复检测的HL共5个。其他性状共检测到67个HL,重复检测的HL仅2个。与QTL定位比较,HL的检测更易受环境影响。
8.单个HL的贡献率一般较小。有20个HL也在IF_2群体的QTL分析中检测到。与QTL类似,部分HL也成簇分布于连锁群,表明了HL的多效性。
9.对DH群体采用混合模型的复合区间作图法,产量及其构成因子三环境下共定位到118个上位性QTL(Epistatic QTL,E-QTL);环境间仅检测到3个相同的E-QTL。其他性状定位到的E-QTLs数量为O—21个,环境间相同的E-QTLs共6个。对比单位点QTL,环境间和性状间检测到较少的相同的E-QTL,表明E-QTL更易受环境影响。部分单位点QTL也参与了位点间互作。
10.对IF_2群体,采用双因素方差分析,检测了基因组所有可能的两位点上位性互作。所有性状都检测到大量的上位性互作位点对;部分上位性互作存在2种或者2种以上的互作类型。互作类型以加性×加性居多,显性×显性最少。对显著的互作位点,两位点基因型组合中,常常以双位点纯合类型表现最好,但同时表现最差的也常常是双位点纯合基因型;而双位点杂合基因型则很少表现为最优基因型,但同时也不表现为最差基因型。上位性互作涉及到的位点,包括性状的QTL与非QTL,其形式以非QTL位点间互作最多;互作影响参与互作的QTL的效应表达。上位性互作和QTL一样有一因多效,可能同时影响多个性状
11.DH群体和IF_2的上位性位点较少重叠,说明上位性效应同样受遗传背景的影响
Most of the important agronomic traits in crops are quantitative,and variations in these traits are usually controlled by many minor genes.Improvement of these quantitative traits is one of the major objectives in rapeseed genetic breeding program. Many elite varieties and hybrids in Brassica napus have been developed using traditional breeding methods,but the efficiency to breed them is still low because the genetic basis for most of the quantitative traits is still unclear.The advent of molecular markers,improved QTL mapping theory and novel experimental designs accelerated the dissection of quantitative traits in the last decade in B.napus.
In this study,we employed two permanent populations of a highly heterotic B.napus cross,Quantum×No.2717-17.One population is 258 doubled haploid (DH) lines derived from the microspore culture of F_1,and the other one is the "immortalized F_2"(IF_2) population comprising 258 crosses resulted from randomly intermating of DH lines.Field experiments with 2 replicates following a randomized complete block design were implemented in three environments.Molecular markers were used to analyze the genetic model associated with 11 traits' performance and heterosis.The main results are summarized as follow:
1.A genetic linkage map,spanning 1747.4 cM with an average interval of 4.4 cM,was constructed using 207 simple sequence repeat(SSR) markers and 190 sequence-related amplified polymorphism(SRAP) markers.Based on the public information of microsatellites(SSR markers),our map was aligned with reference maps.
2.In the DH population,129 markers(32.5%) skewed from the expected 1:1 genotypic segregation by Chi-square test,and most of them skewed towards the Quantum(female parent).Compared to the DH population,36 more markers in the IF_2 population showed segregation distortion.
3.In the DH population,the allele frequencies of Quantum and No.2717-17 in all 397 informative loci were 52.1%and 47.9%respectively.The allele ratio approximated to the expected 1:1.The genome and their proportions in the IF_2 population are similar to those in an F_2 population.The proportions of the genotypes for Quantum,No.2717-17 and heterzygousity are 27.08%,24.03%and 52.3%,respectively.
4.Most traits in both populations showed transgressive segregation and demonstrated the normal distribution.There existed significant difference in all traits among three environments.The interactions between genotype and environment were observed for all traits.Transgressive segregation was observed for all traits' heterosis in the crosses of the IF_2 population,and the heterosis values of most traits displayed the normal distribution.
5.The entire genome was searched for QTL conferring significant effects on all scored traits by composite interval mapping in two populations.The number of QTL varied according to the different traits.A total of 88 QTL were detected for yield and its component traits in three environments and of these 18 QTL were detected for more than once.There were 116 QTL identified related to other traits, of which 58 ones were repeatedly detected.
6.QTL positive and negative additive effects were dispersed in both parents for all the traits.Most of QTL were located in QTL clusters.Some QTL were specifically detected only in one population.
7.By composite interval mapping,44 heterosis loci were detected for yield and its component traits in the IF2 population,and five HL were repeatedly detected.For other traits,67 HL were detected,and only two were repeatedly detected. Compared to QTL mapping,the detection of HL was more sensitive to environmental influence.
8.The proportion of variation explained by single HL was relatively small.Twenty HL were also detected in QTL analysis.Like QTL,some HL for different traits formed clusters on linkage groups.
9.A total of 118 epistatic QTL(E-QTL) were detected for yield and its component traits in the three environments using composite interval mapping with mixed model,and 3 of them were repeatedly detected over environments.For other traits, 0 to 21 E-QTL were resolved for each one,and 6 common E-QTL were repeatedly detected over environments.The detection of E-QTL was more sensitive to environmental effect than that of main QTL.Some main QTL were invovled in interaction.
10.All possible two-way ANOVAs between the markers on whole linkage groups were analyzed for 11 traits in the IF_2 population.A large number of significant digenic interactions were detected for all traits.In a part of loci,two or more interaction types were detected in one pair of loci.All 4 possible digenic significant interaction types(AA,AD,DA,DD) were detected,and of them AA type occurred at predominantly high frequencies with DD type being the least frequent.For two-locus combinations of significant digenic interactions, two-locus homozygotes were the best genotypes in many cases,at the same time, another two-locus homologues combinations was also the worst genotype;On the other hand,double heterozygote were rarely the best genotype and never the worst genotype.Most interactions occurred between two loci both showing non-significant effects to traits.The effects of some QTL were influenced by epistasis.Pleiotropic effects of digenic interactions were detected between or among the related traits.
11.The digenic interactions detected in the DH and IF_2 populations showed little overlapping,which suggested that effects of epistasis were influenced by the genetic background.
引文
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