大豆品种绥农14遗传基础分析及优异基因鉴定
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摘要
绥农14是目前中国推广面积最大的大豆品种之一,该品种经过5轮杂交涉及17个亲本,这些亲本中包含有对全国大豆育种贡献最大的5个祖先亲本和2个国外种质。本研究以绥农14及其血缘亲本为实验材料,在表型、生理和基因组水平方面进行比较,建立绥农14系谱的遗传组成数据库,将表型及分子数据库相结合,通过系谱群体进行in silico mapping QTL定位,检测绥农14及其亲本优良性状在不同年间、不同地点稳定相关的QTL;追踪基因在系谱中的传递来明确绥农14的优良特征及亲本来源。采用连锁不平衡鉴定方法对在分子水平上呈现复杂遗传方式的经济性状进行分析以揭示其遗传规律,为选育高产、优质、广适的大豆品种提供理论依据。
研究结果如下:
1构建绥农14系谱亲本的分子数据库。选取均匀分布于大豆公共图谱20个连锁群的550个SSR(simple sequence repeats)位点在绥农14系谱亲本中进行检测,其中多态性位点占全部位点的86.72%,期望杂合度(PIC)大于70%位点占10.18%。
2构建绥农14系谱包括生长发育性状、产量性状、品质性状、抗病虫性状、根瘤性状、耐盐性状等50个性状在内的表型数据库。随着世代的递增,生长发育性状中株高、底荚高及倒伏度呈明显降低的趋势,产量性状中百粒重和产量呈增加的趋势,绥农14和合丰25的产量与祖先品种相比有显著的提高;品质性状、抗病性状绥农14和合丰25与其祖先品种相比没有显著的改变。
3用SSR分子标记解析绥农14系谱亲本的遗传关系。根据Neighbour-jioning构建的树状图与实际系谱图相符,表明绥农14系谱材料的选育过程可分为3个阶段,品种聚为不同类别的原因与育种时期和组合方式的变化有关。比较相似系数法(S法)、遗传贡献率法(G法)和共祖先系数法(CP法)对阐明绥农14系谱亲本的遗传关系的特点,结果表明在系谱信息完整的情况下应以亲本贡献率(G法)作为研究亲本遗传关系的指标,在未知系谱或系谱信息缺失的情况下建议以遗传相似系数(S法)作为衡量亲本遗传关系的指标。
4国外种质对拓宽中国大豆优良品种遗传基础的贡献。利用系谱追踪与SSR标记分析了大豆品种绥农14和合丰25的遗传组成,结果表明,利用日本种质Tokachi nagaha和美国种质Amsoy作亲本育成的、包括绥农14和合丰25在内的中国大豆品种与其系谱中其他品种存在明显差异。两个国外种质特有SSR变异位点中,Tokachi nagaha有14个与产量、抗病性及油分等相关的QTL传递给合丰25和绥农14;Amsoy有12个与百粒重、油分等有关的QTL由绥农8号传递给绥农14,表明国外种质中的优良基因在我国大豆品种改良中发挥了重要作用。
5连锁不平衡分析表明,在绥农14系谱中存在着连锁不平衡现象,在P＜0.01的水平上有0.149‰的位点对存在完全连锁不平衡。其中紧密连锁位点(＜1.5cM)1对、松散连锁位点(＞1.5cM)3对和非连锁位点13对。合丰25和绥农14共有的116个多态性标记的6728对位点中,7对检测到LD,其中一些SSR连锁位点与农艺性状的呈显著相关。
6单一环境下in silico mapping-QTL及基因在系谱中的传递。32个农艺性状中除四粒荚、褐斑、盐害指数外的其余29性状均检测到了QTL,共检测到QTL位点141个,平均每个性状4.86个。美国品种Amsoy和日本品种Tokachi nagaha分别有12个和3个QTL传递给了后代。
7多环境下in silico mapping-QTL及基因在系谱中的传递。在三个生态区内的六个不同环境下对绥农14系谱亲本的8个农艺性状进行了测定,用in silicomapping-QTL进行单性状定位,除节数外检测到与其余7个性状相关QTL位点49个,这些QTL分布在14个连锁群,对这些单性状位点进行分析发现有些位点与多个性状相关,为了验证这些单个性状检测到的QTL,更精确地定位一因多效QTL,剔出环境对性状的影响,提出了用in silico mapping来分析多性状的方法,通过该方法共检测到了10个一因多效位点,研究结果表明单性状定位和多性状定位有较高的吻合度。进一步分析国外种质对拓宽中国大豆遗传基础的QTL贡献,发现连锁群D1a的Sat_036、连锁群L的Satt182及连锁群B2的Satt726等QTL位点能够证明国外种质中的优良基因在我国大豆品种改良中的遗传贡献。
8超性状in silico mapping-QTL及基因在系谱中的传递。在北方春大豆生态区测定了绥农14系谱亲本的26个表型农艺性状,对这26个农艺性状进行主成分分析,确定了6个主成分,接着计算出了多性状的特征值和特征向量。根据特征值的累积贡献率计算主成分,用特征向量对原始的性状进行加权相加,构成6个超性状。通过In silico mqpping方法在13个连锁群上分别定位了24个与6个超性状相关的QTL,其中14个QTL表现出一因多效。在绥农14系谱中对这些功能基因进行追踪,结果表明一些基因能够解释在品种形成和品质改良过程中国外种质对国内品种的遗传贡献及国内祖先亲本对后代的遗传机制。
Suinong14 was one of the largest-scale grown soybean (Glycine max L.) variety and the typical elite cultivar in China. Tracing its breeding pedigree, it had been found that Suinong14 was derived from five generations of recombination between 17 genotypes which included 5 well-known domestic cultivars and 2 oversea ones. Molecular database and phenotype database on Suinong14 pedigree obtained from different planting areas have been constructed. With in silico mapping method, the QTLs related to agronomic traits were detected in the pedigree of Suinong 14. Trancing of gene transmission in the pedigree elucidates the heredity pattern of exotic genes in typical elite cultivars and explores the utilization of exotic germplasm in soybean breeding program. Some economic traits used to present in a complex inheritance pattern. Association study of these complex traits based on linkage disequilibrium (LD) originally used in human genetics would help to reveal their genetic pattern and offer useful information in soybean breeding.
1 Construction of soybean Molecular datebase. Based on the public integreted map, a total of 550 SSR markers distributed on 20 linkage groups were chosen and analyzed, of which 477 markers performed polymorphic among 14 inbreeding lines in the pedigree of Suinong14. The Percentage of polymorphic locus was 86.72% and the percent of the locus whose PIC was over 70% was 10.18%.
2 Construction of soybean agronomic traits datebase. 50 agronomic traits were chosen and analyzed. According to nature of every trait, the 50 agricultural traits were adivided into 6 groups, Growth traits, Yield traits, Quality traits, Resistance traits, Nodule traits and salt tolerance traits. PH, PHB and L of Growth traits decreased with the generation, Y and SW of Suinong14 and Hefeng25 were significantly improved compared with cultivars developed earlier. There were no significant difference in Resistance traits and Quality traits between different generations.
3 Analysis of Genetic Relationship among Parents of Elite Soybean Cultivars Suinong14 Pedigree Revealed by SSR Markers. 550 SSR loci, distributed on 20 linkage groups were analyzed to explain evolvement and genetic relationship of Suinong 14 and its pedigree. Three methods, including similarity coefficient (SC), genetic contribution (GC) and coefficient (Neighbour-jioning method), were used to reveale genetic relationship in Suinong14 pedigree parents. The accessions clustered result were different because of the different of parental original and mating types. The characteristics of the times and mating types leaded to diversity of genetic structure of Suinong 14 pedigree. GC should be the index in a study of the genetic relationship with known pedigree information, SC should be the index in a study of the genetic relationship with unknown pedigree information.
4. Genetic contribution of foreign germplasm to elite Chinese soybean cultivars revealed by SSR markers. SSR analysis, combined with pedigree analysis, was used to trace the genetic constitutes of Suinong 14 and Hefeng 25, so as to clarify the contribution of foreign germplasm to those elite cultivars, and to provide instruction for further utilization of foreign germplasm effectively in Chinese soybean breeding. SSR clustering results indicated that the genetic base of elite Chinese soybean cultivars, including Suinong 14 and Hefeng 25, was broaden due to the introduction of Amsoy from America and Shishengchangye from Japan during soybean genetic improvment. Among the special alleles of foreign parents, 12 special loci in Amsoy were transferred to Suinong 14, and 14 loci from Shishengchangye to Suinong 14. Some SSR loci had been proved to be correlated with phenotypes, indicating that the two foreign parents might have important contribution in developing Suinong14 and Hefeng 25.
5. A total of 477 SSR polymorphic loci consisted of 113764bps had been identified, LD was significant at a comparison-wise 0.01 level in nearly 0.149%o of SSR marker pairs when all cultivars were included. According to linkage distance of SSR loci, all tested loci could be evaluated as tightly linked (<1.5cM), loosely linked(<1.5cM within one LG) and unlinked loci. The number of SSR loci of each LD type was one, three and 13, respectively. Seven of 116 specific SSR loci shared by Suinong14 and Hefeng25 showed LD. Association analysis of 6 SSR loci with LD and agronomic traits showed that significant correlation could be observed between two pair of LD loci and agronomic traits (p<0.01). which indicated the existence of LD in genes related to agronomic traits.
6 We extended in silico mapping for single trait to mapping peiotropic QTL for multiple traits by defining new statistic to measure the correlation between multiple traits and the markers. Data included phenotypes of 32 agronomic traits extracted from Northern Spring soybean ecotypes area and genotyped 477 polymorphic markers on public integrated genetic map, on 14 inbreeding lines in the pedigree of Suinong14. With in silico mapping, a total of 141 markers distributing on 18 linkage groups were identified as QTL, no QTL are found for SII, N3SP, K. The mean of QTL was 4.86. Tracing the transmission of functional genes in the pedigree, it was found that 15 genes were capable to explain the genetic mechanism for the contribution of exotic germplasm to soybean cultivars in the improvement of the performance and quality.
7 Gene discovery and transmission of functional genes in the pedigree of an elite soybean cultivar Suinong 14. In this study, we performed in silico mapping for single trait to analyze data from multiple environments by calculating inter-correlations and to mapping peiotropic QTL for multiple traits by defining new statistic to measure the correlation between multiple traits and the marker. Data include phenotypes of 8 agronomic traits obtained from 6 different ecological environments and years, and genotyped 477 polymorphic markers on public integrated genetic map, on 14 inbreeding lines in the pedigree of Suinong14. With in silico mapping, a total of 49 markers distributing on 14 linkage groups were detected separately as QTL responsible for 8 agronomic traits and 10 QTL were precisely identified as pleiotrpic ones. Tracing the transmission of functional genes in the pedigree found that some genes explain the genetic mechanism for the contribution of exotic germplasm and domestic founders in the improvement of the performance and quality of soybean cultivars.
8 In silico mapping QTL for multiple traits in the pedigree of soybean cultivars. In silico mapping for single trait is performed to analyze many agronomic traits in the pedigree of soybean. Twenty six agronomic traits are measured and 477 polymorphic markers chosen on public genetic map are genotyped on 14 inbreeding lines in the pedigree of Suinong14. We determined 6 principal components from 26 agronomic traits using the principal component analysis and constructed 6 "super traits" by the multiplication of the vector of the standardized original traits by the eigenvectors corresponding to the principle components. With in silico mapping, a total of 24 markers distributing on 13 linkage groups are detected separately as quantitative trait loci (QTL) responsible for 6 "super traits", of which 14 QTL performed pleiotropy. Tracing the transmission of functional genes in the pedigree found that some genes are capable to explain the genetic mechanism for the contribution of exotic germplasm and domestic founders in the improvement of the performance and quality of soybean cultivars.
研究结果如下:
1构建绥农14系谱亲本的分子数据库。选取均匀分布于大豆公共图谱20个连锁群的550个SSR(simple sequence repeats)位点在绥农14系谱亲本中进行检测,其中多态性位点占全部位点的86.72%,期望杂合度(PIC)大于70%位点占10.18%。
2构建绥农14系谱包括生长发育性状、产量性状、品质性状、抗病虫性状、根瘤性状、耐盐性状等50个性状在内的表型数据库。随着世代的递增,生长发育性状中株高、底荚高及倒伏度呈明显降低的趋势,产量性状中百粒重和产量呈增加的趋势,绥农14和合丰25的产量与祖先品种相比有显著的提高;品质性状、抗病性状绥农14和合丰25与其祖先品种相比没有显著的改变。
3用SSR分子标记解析绥农14系谱亲本的遗传关系。根据Neighbour-jioning构建的树状图与实际系谱图相符,表明绥农14系谱材料的选育过程可分为3个阶段,品种聚为不同类别的原因与育种时期和组合方式的变化有关。比较相似系数法(S法)、遗传贡献率法(G法)和共祖先系数法(CP法)对阐明绥农14系谱亲本的遗传关系的特点,结果表明在系谱信息完整的情况下应以亲本贡献率(G法)作为研究亲本遗传关系的指标,在未知系谱或系谱信息缺失的情况下建议以遗传相似系数(S法)作为衡量亲本遗传关系的指标。
4国外种质对拓宽中国大豆优良品种遗传基础的贡献。利用系谱追踪与SSR标记分析了大豆品种绥农14和合丰25的遗传组成,结果表明,利用日本种质Tokachi nagaha和美国种质Amsoy作亲本育成的、包括绥农14和合丰25在内的中国大豆品种与其系谱中其他品种存在明显差异。两个国外种质特有SSR变异位点中,Tokachi nagaha有14个与产量、抗病性及油分等相关的QTL传递给合丰25和绥农14;Amsoy有12个与百粒重、油分等有关的QTL由绥农8号传递给绥农14,表明国外种质中的优良基因在我国大豆品种改良中发挥了重要作用。
5连锁不平衡分析表明,在绥农14系谱中存在着连锁不平衡现象,在P＜0.01的水平上有0.149‰的位点对存在完全连锁不平衡。其中紧密连锁位点(＜1.5cM)1对、松散连锁位点(＞1.5cM)3对和非连锁位点13对。合丰25和绥农14共有的116个多态性标记的6728对位点中,7对检测到LD,其中一些SSR连锁位点与农艺性状的呈显著相关。
6单一环境下in silico mapping-QTL及基因在系谱中的传递。32个农艺性状中除四粒荚、褐斑、盐害指数外的其余29性状均检测到了QTL,共检测到QTL位点141个,平均每个性状4.86个。美国品种Amsoy和日本品种Tokachi nagaha分别有12个和3个QTL传递给了后代。
7多环境下in silico mapping-QTL及基因在系谱中的传递。在三个生态区内的六个不同环境下对绥农14系谱亲本的8个农艺性状进行了测定,用in silicomapping-QTL进行单性状定位,除节数外检测到与其余7个性状相关QTL位点49个,这些QTL分布在14个连锁群,对这些单性状位点进行分析发现有些位点与多个性状相关,为了验证这些单个性状检测到的QTL,更精确地定位一因多效QTL,剔出环境对性状的影响,提出了用in silico mapping来分析多性状的方法,通过该方法共检测到了10个一因多效位点,研究结果表明单性状定位和多性状定位有较高的吻合度。进一步分析国外种质对拓宽中国大豆遗传基础的QTL贡献,发现连锁群D1a的Sat_036、连锁群L的Satt182及连锁群B2的Satt726等QTL位点能够证明国外种质中的优良基因在我国大豆品种改良中的遗传贡献。
8超性状in silico mapping-QTL及基因在系谱中的传递。在北方春大豆生态区测定了绥农14系谱亲本的26个表型农艺性状,对这26个农艺性状进行主成分分析,确定了6个主成分,接着计算出了多性状的特征值和特征向量。根据特征值的累积贡献率计算主成分,用特征向量对原始的性状进行加权相加,构成6个超性状。通过In silico mqpping方法在13个连锁群上分别定位了24个与6个超性状相关的QTL,其中14个QTL表现出一因多效。在绥农14系谱中对这些功能基因进行追踪,结果表明一些基因能够解释在品种形成和品质改良过程中国外种质对国内品种的遗传贡献及国内祖先亲本对后代的遗传机制。
Suinong14 was one of the largest-scale grown soybean (Glycine max L.) variety and the typical elite cultivar in China. Tracing its breeding pedigree, it had been found that Suinong14 was derived from five generations of recombination between 17 genotypes which included 5 well-known domestic cultivars and 2 oversea ones. Molecular database and phenotype database on Suinong14 pedigree obtained from different planting areas have been constructed. With in silico mapping method, the QTLs related to agronomic traits were detected in the pedigree of Suinong 14. Trancing of gene transmission in the pedigree elucidates the heredity pattern of exotic genes in typical elite cultivars and explores the utilization of exotic germplasm in soybean breeding program. Some economic traits used to present in a complex inheritance pattern. Association study of these complex traits based on linkage disequilibrium (LD) originally used in human genetics would help to reveal their genetic pattern and offer useful information in soybean breeding.
1 Construction of soybean Molecular datebase. Based on the public integreted map, a total of 550 SSR markers distributed on 20 linkage groups were chosen and analyzed, of which 477 markers performed polymorphic among 14 inbreeding lines in the pedigree of Suinong14. The Percentage of polymorphic locus was 86.72% and the percent of the locus whose PIC was over 70% was 10.18%.
2 Construction of soybean agronomic traits datebase. 50 agronomic traits were chosen and analyzed. According to nature of every trait, the 50 agricultural traits were adivided into 6 groups, Growth traits, Yield traits, Quality traits, Resistance traits, Nodule traits and salt tolerance traits. PH, PHB and L of Growth traits decreased with the generation, Y and SW of Suinong14 and Hefeng25 were significantly improved compared with cultivars developed earlier. There were no significant difference in Resistance traits and Quality traits between different generations.
3 Analysis of Genetic Relationship among Parents of Elite Soybean Cultivars Suinong14 Pedigree Revealed by SSR Markers. 550 SSR loci, distributed on 20 linkage groups were analyzed to explain evolvement and genetic relationship of Suinong 14 and its pedigree. Three methods, including similarity coefficient (SC), genetic contribution (GC) and coefficient (Neighbour-jioning method), were used to reveale genetic relationship in Suinong14 pedigree parents. The accessions clustered result were different because of the different of parental original and mating types. The characteristics of the times and mating types leaded to diversity of genetic structure of Suinong 14 pedigree. GC should be the index in a study of the genetic relationship with known pedigree information, SC should be the index in a study of the genetic relationship with unknown pedigree information.
4. Genetic contribution of foreign germplasm to elite Chinese soybean cultivars revealed by SSR markers. SSR analysis, combined with pedigree analysis, was used to trace the genetic constitutes of Suinong 14 and Hefeng 25, so as to clarify the contribution of foreign germplasm to those elite cultivars, and to provide instruction for further utilization of foreign germplasm effectively in Chinese soybean breeding. SSR clustering results indicated that the genetic base of elite Chinese soybean cultivars, including Suinong 14 and Hefeng 25, was broaden due to the introduction of Amsoy from America and Shishengchangye from Japan during soybean genetic improvment. Among the special alleles of foreign parents, 12 special loci in Amsoy were transferred to Suinong 14, and 14 loci from Shishengchangye to Suinong 14. Some SSR loci had been proved to be correlated with phenotypes, indicating that the two foreign parents might have important contribution in developing Suinong14 and Hefeng 25.
5. A total of 477 SSR polymorphic loci consisted of 113764bps had been identified, LD was significant at a comparison-wise 0.01 level in nearly 0.149%o of SSR marker pairs when all cultivars were included. According to linkage distance of SSR loci, all tested loci could be evaluated as tightly linked (<1.5cM), loosely linked(<1.5cM within one LG) and unlinked loci. The number of SSR loci of each LD type was one, three and 13, respectively. Seven of 116 specific SSR loci shared by Suinong14 and Hefeng25 showed LD. Association analysis of 6 SSR loci with LD and agronomic traits showed that significant correlation could be observed between two pair of LD loci and agronomic traits (p<0.01). which indicated the existence of LD in genes related to agronomic traits.
6 We extended in silico mapping for single trait to mapping peiotropic QTL for multiple traits by defining new statistic to measure the correlation between multiple traits and the markers. Data included phenotypes of 32 agronomic traits extracted from Northern Spring soybean ecotypes area and genotyped 477 polymorphic markers on public integrated genetic map, on 14 inbreeding lines in the pedigree of Suinong14. With in silico mapping, a total of 141 markers distributing on 18 linkage groups were identified as QTL, no QTL are found for SII, N3SP, K. The mean of QTL was 4.86. Tracing the transmission of functional genes in the pedigree, it was found that 15 genes were capable to explain the genetic mechanism for the contribution of exotic germplasm to soybean cultivars in the improvement of the performance and quality.
7 Gene discovery and transmission of functional genes in the pedigree of an elite soybean cultivar Suinong 14. In this study, we performed in silico mapping for single trait to analyze data from multiple environments by calculating inter-correlations and to mapping peiotropic QTL for multiple traits by defining new statistic to measure the correlation between multiple traits and the marker. Data include phenotypes of 8 agronomic traits obtained from 6 different ecological environments and years, and genotyped 477 polymorphic markers on public integrated genetic map, on 14 inbreeding lines in the pedigree of Suinong14. With in silico mapping, a total of 49 markers distributing on 14 linkage groups were detected separately as QTL responsible for 8 agronomic traits and 10 QTL were precisely identified as pleiotrpic ones. Tracing the transmission of functional genes in the pedigree found that some genes explain the genetic mechanism for the contribution of exotic germplasm and domestic founders in the improvement of the performance and quality of soybean cultivars.
8 In silico mapping QTL for multiple traits in the pedigree of soybean cultivars. In silico mapping for single trait is performed to analyze many agronomic traits in the pedigree of soybean. Twenty six agronomic traits are measured and 477 polymorphic markers chosen on public genetic map are genotyped on 14 inbreeding lines in the pedigree of Suinong14. We determined 6 principal components from 26 agronomic traits using the principal component analysis and constructed 6 "super traits" by the multiplication of the vector of the standardized original traits by the eigenvectors corresponding to the principle components. With in silico mapping, a total of 24 markers distributing on 13 linkage groups are detected separately as quantitative trait loci (QTL) responsible for 6 "super traits", of which 14 QTL performed pleiotropy. Tracing the transmission of functional genes in the pedigree found that some genes are capable to explain the genetic mechanism for the contribution of exotic germplasm and domestic founders in the improvement of the performance and quality of soybean cultivars.
引文
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