我国大豆育成品种的遗传多样性，农艺性状QTL关联定位及优异变异在育种系谱内的追踪
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摘要
1923—-2005年我国共育成大豆品种1300个,这是我国大豆育种最重要核心的种质资源,揭示其遗传多样性、特异性和群体间遗传关系,可为拓宽我国大豆的遗传基础提供理论依据。本研究选取由378份我国大豆育成品种所组成的代表性样本,加上朝鲜半岛、东南亚和南亚的110份栽培大豆为参照,利用大豆核基因组均匀分布的64个SSR标记分析我国大豆育成品种及亚洲引入大豆品种的遗传多样性,探讨我国大豆育成品种不同群体的遗传特异性与互补性,以及亚洲引入品种对拓宽我国大豆遗传基础的潜在可能性。在此基础上,增加与农艺性状相关的21个SSR标记合计85个标记对378份中的我国黄淮和南方190份有代表性的大豆育成品种基因组进行扫描,检测群体结构、搜索连锁不平衡位点,并采用TASSEL软件的GLM方法对2年有重复田间试验的11个农艺性状QTL进行关联分析,进一步追查产量和品质优异等位变异在黄淮和南方主要大豆育成品种家族系谱中的踪迹。获得主要结果如下。
1.我国大豆育成品种群体遗传丰富度为572个等位变异,平均每个位点等位变异数为8.94个,多态性信息量PIC为0.752。文自翔(2008)利用基本同样标记研究我国大豆地方品种群体、野生大豆群体平均每个位点等位变异数(Simpson指数)分别为16.3个(0.74)、17.6个(0.86)。我国大豆育成品种群体相对于大豆地方品种群体、野生大豆群体,局限在所用的祖先亲本,其遗传基础趋于狭窄,宜拓宽其遗传基础保障未来大豆育种可持续发展。
2.在遗传丰富度和多样性指数基础上提出用群体间特有、特缺、互补等位变异评价我国大豆育成品种亚群间遗传多样性,分省亚群(黑龙江、吉林、辽宁、河南、山东、安徽、北京和江苏)间都存在较多互补等位变异,最多的在辽宁与河南亚群间。分时期亚群随着时间推移旧的等位变异在消失,而新的等位变异不断增加,绝大部分亚群新增加的等位变异多于旧消失的。分省亚群、分时期亚群分类与SSR标记遗传距离聚类间有显著相关,省份分群、时期分群都有其相应的遗传基础。研究结果启示分省亚群间存在的互补等位变异较多,在新品种选育中应加强各省间大豆育成品种种质交流、增加优异基因相互渗透,找到拓宽分省亚群遗传多样性恰当的对象亚群；各分时期亚群有着明显遗传差异,保存过去的大豆育成品种为培育新品种贮备材料。
3.亚洲大豆育成品种群体遗传丰富度为585个等位变异,平均每个位点等位变异数为9.14个,多态性信息量PIC为0.733。SSR标记无根树状遗传关系聚类群体分类将亚洲大豆育成品种归为我国国内与国外2大类群,群体结构研究亚洲全群由2类血缘组成,分别占我国国内和国外2大类群的绝大部分；地理群体间2类血缘组成的差异明显。国外大豆是由中国传播出去的,但是各国特殊的地理生态条件和人工选择,使其与我国国内大豆产生分化。
4.亚洲大豆育成品种地理群体间,即我国东北、我国黄淮、我国南方、朝鲜半岛、东南亚、南亚群体间,存在较多互补等位变异,最多的在我国黄淮与南亚群体间；各地理群体拥有各自特有、特缺的等位变异。国内与国外各群体间以我国南方与东南亚育成品种群体间分化最小；国外群体以东南亚与朝鲜半岛育成品种群体间分化最小；国内群体以我国黄淮与我国南方的育成品种群体分化最小。亚洲大豆育成品种地理群体间具有位点和等位变异的特异性,各群体间可以相互补充的位点及其等位变异甚丰富,利用亚洲引入品种有可能拓宽我国大豆的遗传基础。
5.大豆育成品种群体在公共图谱上不论共线性或非共线性的SSR位点组合广泛存在连锁不平衡(LD),但不平衡程度D’>0.5的位点组合数只占总位点组合的1.71%,共线位点D'值随遗传距离的衰减较快。SSR数据遗传结构的分析结果,大豆育成品种群体由7个亚群体组成,矫正后全群体中共有45个位点累计有136个位点(次)与11个大豆农艺性状QTL关联,其中有22个位点(次)与家系连锁定位的QTL区间相重,43个位点(次)2年重复出现。与文自翔(2008)利用大体相同的标记对大豆地方品种群体和野生群体进行关联分析结果只有少数关联位点相同,而大多数关联位点不同。大豆育成品种群体与大豆地方品种群体、野生大豆群体在百粒重、株高等6个性状相同关联位点总数占总位点数的分别为3.3%、3.4%。表明大豆育成品种群体遗传结构的确与大豆地方品种群体、野生大豆群体存在明显差异。
6.我国黄淮和南方的主要大豆育成品种家族58-161、徐豆1号、齐黄1号、南农493-1、南农1138-2的产量优异等位变异追踪结果,系谱祖先具有各自的优异等位变异,在系谱祖先基础上新品种衍生过程中逐步累积了更多的优异等位变异；随着育种轮次的推移,系谱祖先具有的优异等位变异在后育成品种中有较多丢失的表现；大豆高产与低产、各高产品种之间优异等位变异结构差异非常明显；高产品种没有吸纳全部产量优异等位变异,启示大豆产量有进一步改良潜力。
There were 1300 soybean released cultivars (SRC) in China between 1923 and 2005, this was most importance core germplasm, the marked purport of the present study was to reveal the genetic diversity, population specificity and genetic relation of SRC in China, and the practical guidance to broaden improving on present SRC. This study selected 378 SRC to be composed of representative sample, and to select reference 110 soybean cultivars from Korean Peninsula, Southern Asia and South Asia. A total of 64 simple sequence repeat (SSR) markers scattered on the genome were used to analyze the genetic diversity of SRC sampled in China and Asia introduction cultivars (AIC), and the study to reveal the population specificity and complementary in each population of China, and AIC on the application to broad genetic base of SRC in China. The genotyping data of 85 SSR markers (based on 64 SSR markers increased 21 SSR to be relation with agronomic trait) on 190 representative released cultivar population (RCP) (190 cultivars was the component part of 378 SRC in China) were obtained and analyzed for LD of pairwise loci and population structure, and then for association between SSR loci and 11 soybean agronomic traits of two-year-experimentation in the field under TASSEL GLM (General linear model) program, and the study on trace of elite alleles (EA) of yield and quality traits in the pedigree of major cultivar families released in Huanghuai Valleys and Southern China. The main results were obtained as follows.
There were 572 alleles of genetic richness,8.94 alleles per locus,0.752 of PIC in RCP of China. There were 16.3 (0.74) and 17.6 (0.86) of alleles per locus (Simpson index) respectively in landrace and wild population of China, using basic same marker by study of Wen Zixiang in 2008. There existed to tend narrow genetic base of RCP in China, to broad its genetic base for soybean future last breeding.
Based on genetic richness and genetic diversity indexes as well as specifically existent, specifically deficient and complementary alleles, there existed a plenty of genetic diversity in RCP of China as well as a plenty of complementary alleles among provincial subpopulations (Heilongjiang, Jilin, Liaoning, Henan, Shandong, Anhui, Beijing and Jiangsu), especially most between Liaoning and Henan subpopulation. Along with the period advance, some of the old alleles in earlier subpopulation disappeared and some new alleles came out in later subpopulation with the new ones mostly more than the old ones. Specifically existent and specifically deficient alleles in each subpopulation were detected. Significant relationship was found between SSR clusters and provincial subpopulations as well as period subpopulations, indicating the sound genetic bases of the classification of provincial subpopulations as well as period subpopulations. There existed plenty of complementary alleles between pairs of populations for broadening the genetic bases of the respective geographic cultivar populations, along with there markedly existed genetic different from each period subpopulation for cultivating new breed to store material in earlier SRC.
There were 585 alleles of genetic richness,9.14 alleles per locus,0.733 of PIC in RCP of Asia. According to the model-based clustering method for using multilocus data to infer population structure and assign cultivars to populations (structure analysis), two ancestry sources in Asia were detected, one composing the most part of Chinese cultivar group, another composing the most part of exotic cultivar group. The composition of the two ancestry sources in the geographic populations was different markedly. The soybean of foreign was spread from China, there was differentiation in soybean between China and foreign, because of each country specific condition of geographic and manual work selection.
There existed a plenty of alleles and genetic diversity of RCP in Asia as well as a plenty of complementary alleles among geographic populations (Northeast China, Huanghuai China, Southern China, Korean Peninsula, Southeast Asia and South Asia), especially most between Huanghuai China population and South Asia population. Specifically existent and specifically deficient alleles in each geographic population were detected. Significant differentiation among geographic populations was found, while the least differentiation between the Chinese group and exotic group was in the pair of Southern China population vs. Southeast Asia population, that within exotic group was in the pair of Southeast Asia population vs. Korean Peninsula population, and that within Chinese group was in the pair of Huanghuai China population and Southern China population. There existed plenty of specifically existent and deficient loci and alleles in each geographic population, and therefore, plenty of complementary alleles between pairs of populations for broadening the genetic bases of RCP in China by AIC.
LD was detected extensively not only among syntenic markers but also among nonsyntenic ones in RCP, while the loci pairs with D'>0.5 accounted for only 1.71% of the total ones. The syntenic D value attenuated fastly along with the increase of genetic distance. Genetic structure analysis showed that RCP was composed of seven subpopulations. The 45 SSR loci with a total of 136 loci (time) was found to be associated with 11 agronomic traits in the RCP. Among those,22 loci (time) were consistent with mapped QTLs from family-based linkage mapping procedure and 43 loci (time) were consistently detected in two experiment years. There were only a few same association loci and most different loci among SRC and landrace, wild population of China, with landrace and wild population of China using most same marker by study of Wen Zixiang in 2008. There was 3.3% or 3.4% same association loci ratio total loci about 100-seed, plant height, etc.6 traits between SRC and landrace or wild of population. There existed to be found markedly different genetic structure among SRC and landrace or wild population.
The yield EA were emphasis on analysis in mainly family (58-161, Xudou 1, Qihuang 1, Nannong 493-1 and Nannong 1138-2) of SRC Huanghuai Valleys and Southern in China, there were EA each other in pedigree ancestor, based on pedigree ancestor new cultivar cumulative more EA in course of derivation. EA of pedigree ancestor were more lost in new cultivars along with breeding cycle change. There was markedly different EA structure between high yield and low yield cultivars, and there was different EA structure in each high yield cultivar.5 families' cultivars were furthered improve yield potential.
1.我国大豆育成品种群体遗传丰富度为572个等位变异,平均每个位点等位变异数为8.94个,多态性信息量PIC为0.752。文自翔(2008)利用基本同样标记研究我国大豆地方品种群体、野生大豆群体平均每个位点等位变异数(Simpson指数)分别为16.3个(0.74)、17.6个(0.86)。我国大豆育成品种群体相对于大豆地方品种群体、野生大豆群体,局限在所用的祖先亲本,其遗传基础趋于狭窄,宜拓宽其遗传基础保障未来大豆育种可持续发展。
2.在遗传丰富度和多样性指数基础上提出用群体间特有、特缺、互补等位变异评价我国大豆育成品种亚群间遗传多样性,分省亚群(黑龙江、吉林、辽宁、河南、山东、安徽、北京和江苏)间都存在较多互补等位变异,最多的在辽宁与河南亚群间。分时期亚群随着时间推移旧的等位变异在消失,而新的等位变异不断增加,绝大部分亚群新增加的等位变异多于旧消失的。分省亚群、分时期亚群分类与SSR标记遗传距离聚类间有显著相关,省份分群、时期分群都有其相应的遗传基础。研究结果启示分省亚群间存在的互补等位变异较多,在新品种选育中应加强各省间大豆育成品种种质交流、增加优异基因相互渗透,找到拓宽分省亚群遗传多样性恰当的对象亚群；各分时期亚群有着明显遗传差异,保存过去的大豆育成品种为培育新品种贮备材料。
3.亚洲大豆育成品种群体遗传丰富度为585个等位变异,平均每个位点等位变异数为9.14个,多态性信息量PIC为0.733。SSR标记无根树状遗传关系聚类群体分类将亚洲大豆育成品种归为我国国内与国外2大类群,群体结构研究亚洲全群由2类血缘组成,分别占我国国内和国外2大类群的绝大部分；地理群体间2类血缘组成的差异明显。国外大豆是由中国传播出去的,但是各国特殊的地理生态条件和人工选择,使其与我国国内大豆产生分化。
4.亚洲大豆育成品种地理群体间,即我国东北、我国黄淮、我国南方、朝鲜半岛、东南亚、南亚群体间,存在较多互补等位变异,最多的在我国黄淮与南亚群体间；各地理群体拥有各自特有、特缺的等位变异。国内与国外各群体间以我国南方与东南亚育成品种群体间分化最小；国外群体以东南亚与朝鲜半岛育成品种群体间分化最小；国内群体以我国黄淮与我国南方的育成品种群体分化最小。亚洲大豆育成品种地理群体间具有位点和等位变异的特异性,各群体间可以相互补充的位点及其等位变异甚丰富,利用亚洲引入品种有可能拓宽我国大豆的遗传基础。
5.大豆育成品种群体在公共图谱上不论共线性或非共线性的SSR位点组合广泛存在连锁不平衡(LD),但不平衡程度D’>0.5的位点组合数只占总位点组合的1.71%,共线位点D'值随遗传距离的衰减较快。SSR数据遗传结构的分析结果,大豆育成品种群体由7个亚群体组成,矫正后全群体中共有45个位点累计有136个位点(次)与11个大豆农艺性状QTL关联,其中有22个位点(次)与家系连锁定位的QTL区间相重,43个位点(次)2年重复出现。与文自翔(2008)利用大体相同的标记对大豆地方品种群体和野生群体进行关联分析结果只有少数关联位点相同,而大多数关联位点不同。大豆育成品种群体与大豆地方品种群体、野生大豆群体在百粒重、株高等6个性状相同关联位点总数占总位点数的分别为3.3%、3.4%。表明大豆育成品种群体遗传结构的确与大豆地方品种群体、野生大豆群体存在明显差异。
6.我国黄淮和南方的主要大豆育成品种家族58-161、徐豆1号、齐黄1号、南农493-1、南农1138-2的产量优异等位变异追踪结果,系谱祖先具有各自的优异等位变异,在系谱祖先基础上新品种衍生过程中逐步累积了更多的优异等位变异；随着育种轮次的推移,系谱祖先具有的优异等位变异在后育成品种中有较多丢失的表现；大豆高产与低产、各高产品种之间优异等位变异结构差异非常明显；高产品种没有吸纳全部产量优异等位变异,启示大豆产量有进一步改良潜力。
There were 1300 soybean released cultivars (SRC) in China between 1923 and 2005, this was most importance core germplasm, the marked purport of the present study was to reveal the genetic diversity, population specificity and genetic relation of SRC in China, and the practical guidance to broaden improving on present SRC. This study selected 378 SRC to be composed of representative sample, and to select reference 110 soybean cultivars from Korean Peninsula, Southern Asia and South Asia. A total of 64 simple sequence repeat (SSR) markers scattered on the genome were used to analyze the genetic diversity of SRC sampled in China and Asia introduction cultivars (AIC), and the study to reveal the population specificity and complementary in each population of China, and AIC on the application to broad genetic base of SRC in China. The genotyping data of 85 SSR markers (based on 64 SSR markers increased 21 SSR to be relation with agronomic trait) on 190 representative released cultivar population (RCP) (190 cultivars was the component part of 378 SRC in China) were obtained and analyzed for LD of pairwise loci and population structure, and then for association between SSR loci and 11 soybean agronomic traits of two-year-experimentation in the field under TASSEL GLM (General linear model) program, and the study on trace of elite alleles (EA) of yield and quality traits in the pedigree of major cultivar families released in Huanghuai Valleys and Southern China. The main results were obtained as follows.
There were 572 alleles of genetic richness,8.94 alleles per locus,0.752 of PIC in RCP of China. There were 16.3 (0.74) and 17.6 (0.86) of alleles per locus (Simpson index) respectively in landrace and wild population of China, using basic same marker by study of Wen Zixiang in 2008. There existed to tend narrow genetic base of RCP in China, to broad its genetic base for soybean future last breeding.
Based on genetic richness and genetic diversity indexes as well as specifically existent, specifically deficient and complementary alleles, there existed a plenty of genetic diversity in RCP of China as well as a plenty of complementary alleles among provincial subpopulations (Heilongjiang, Jilin, Liaoning, Henan, Shandong, Anhui, Beijing and Jiangsu), especially most between Liaoning and Henan subpopulation. Along with the period advance, some of the old alleles in earlier subpopulation disappeared and some new alleles came out in later subpopulation with the new ones mostly more than the old ones. Specifically existent and specifically deficient alleles in each subpopulation were detected. Significant relationship was found between SSR clusters and provincial subpopulations as well as period subpopulations, indicating the sound genetic bases of the classification of provincial subpopulations as well as period subpopulations. There existed plenty of complementary alleles between pairs of populations for broadening the genetic bases of the respective geographic cultivar populations, along with there markedly existed genetic different from each period subpopulation for cultivating new breed to store material in earlier SRC.
There were 585 alleles of genetic richness,9.14 alleles per locus,0.733 of PIC in RCP of Asia. According to the model-based clustering method for using multilocus data to infer population structure and assign cultivars to populations (structure analysis), two ancestry sources in Asia were detected, one composing the most part of Chinese cultivar group, another composing the most part of exotic cultivar group. The composition of the two ancestry sources in the geographic populations was different markedly. The soybean of foreign was spread from China, there was differentiation in soybean between China and foreign, because of each country specific condition of geographic and manual work selection.
There existed a plenty of alleles and genetic diversity of RCP in Asia as well as a plenty of complementary alleles among geographic populations (Northeast China, Huanghuai China, Southern China, Korean Peninsula, Southeast Asia and South Asia), especially most between Huanghuai China population and South Asia population. Specifically existent and specifically deficient alleles in each geographic population were detected. Significant differentiation among geographic populations was found, while the least differentiation between the Chinese group and exotic group was in the pair of Southern China population vs. Southeast Asia population, that within exotic group was in the pair of Southeast Asia population vs. Korean Peninsula population, and that within Chinese group was in the pair of Huanghuai China population and Southern China population. There existed plenty of specifically existent and deficient loci and alleles in each geographic population, and therefore, plenty of complementary alleles between pairs of populations for broadening the genetic bases of RCP in China by AIC.
LD was detected extensively not only among syntenic markers but also among nonsyntenic ones in RCP, while the loci pairs with D'>0.5 accounted for only 1.71% of the total ones. The syntenic D value attenuated fastly along with the increase of genetic distance. Genetic structure analysis showed that RCP was composed of seven subpopulations. The 45 SSR loci with a total of 136 loci (time) was found to be associated with 11 agronomic traits in the RCP. Among those,22 loci (time) were consistent with mapped QTLs from family-based linkage mapping procedure and 43 loci (time) were consistently detected in two experiment years. There were only a few same association loci and most different loci among SRC and landrace, wild population of China, with landrace and wild population of China using most same marker by study of Wen Zixiang in 2008. There was 3.3% or 3.4% same association loci ratio total loci about 100-seed, plant height, etc.6 traits between SRC and landrace or wild of population. There existed to be found markedly different genetic structure among SRC and landrace or wild population.
The yield EA were emphasis on analysis in mainly family (58-161, Xudou 1, Qihuang 1, Nannong 493-1 and Nannong 1138-2) of SRC Huanghuai Valleys and Southern in China, there were EA each other in pedigree ancestor, based on pedigree ancestor new cultivar cumulative more EA in course of derivation. EA of pedigree ancestor were more lost in new cultivars along with breeding cycle change. There was markedly different EA structure between high yield and low yield cultivars, and there was different EA structure in each high yield cultivar.5 families' cultivars were furthered improve yield potential.
引文
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