中国玉米地方品种的多样性研究与种族划分
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摘要
玉米是我国重要的粮、经、饲兼用作物之一,在我国农业生产中占有重要地位。自传入我国后,经过近500年的种植与栽培,在对我国复杂多样的生态环境的适应过程中,形成了大量的地方品种,并在这些品种中积累了广泛的遗传变异。作为一种重要的基础资源,地方品种为我国早期的玉米生产作出了重要贡献,并对后续的品种选育与改良具有重要的意义。因此,对这部分资源进行全面、精细的评价则是高效管理与深入利用这些资源的基础与关键。从20世纪50年代至90年代末,我国共收集与保存玉米品种16779份,其中包括地方品种13521份。尽管我国玉米品种资源的收集工作开展较早,并取得了显著成效,但对这些资源的全面评价与相关研究则严重滞后,尤其是地方品种资源。并且有关我国玉米品种的种族划分的正式研究,至今仍未开展。
基于品种的地理来源与表型多样性评价数据,中国农业科学院构建了我国玉米地方品种的核心种质。本研究以这些核心种质为材料,对我国玉米地方品种进行了系统的多样性研究与种族划分,目的在于:1)全面分析我国玉米地方品种的表型多样性,并比较来自不同生态区的地方品种在表型多样性上的差异;2)评价我国玉米地方品种在DNA水平上的遗传多样性,并分析这些品种的遗传多样性在不同生态区之间的分布;3)了解我国玉米地方品种的群体结构以及各亚群的遗传多样性水平;4)明确我国玉米地方品种的种族结构;5)构建我国玉米地方品种的微核心种质,为我国玉米地方品种资源的有效管理、深入利用以及后续的相关研究建立一个高效的可行性平台。
本研究广泛选取了30个表型性状以及覆盖玉米全基因组的55个SSR标记展开了我国玉米地方品种的全面分析,主要研究结论如下:
1.基于27个数量性状与3个质量性状的Shannon-Weaver多样性指数分析结果显示,我国玉米地方品种存在较高水平的表型多样性。其中,表型多样性最高的是百粒重与株高,其Shannon-Weaver多样性指数依次为2.10与2.09,而多样性水平最低的是轴色与抽雄-散粉间隔期,其Shannon-Weaver多样性指数仅0.64与0.84。来自9个生态区的品种存在较大表型多样性差异,其中,西南区玉米地方品种的表型多样性水平最高,而西北区与高原区则相对较低。表型多样性的分析结果表明,西南生态区玉米种质资源的表型变异明显高于另8个区,具有较高的保护价值和利用潜力。
2.利用覆盖玉米全基因组的55个SSR标记,采用TP-M13-SSR检测技术研究了846份玉米核心地方品种的遗传多样性,并比较了不同类型的SSR标记在揭示研究材料遗传多样性上的差异。结果显示我国玉米核心地方品种的平均遗传多样性为0.65,总等位变异805个,平均14.64个/位点,特异等位变异114个,平均2.07个/位点,稀有等位变异597个,平均10.85个/位点。来自9个生态区的品种的遗传多样性水平比较一致,但在等位变异上存在明显差异,其中等位变异数、特异等位变异数与稀有等位变异数最高的均是西南区,依次为621个、40个和433个,明显高于另8个生态区,说明该区的玉米地方品种存在最丰富的等位变异。
在55个SSRs中,重复序列为2bp的SSRs在等位变异的检测效率上明显高于重复序列＞2bp的SSRs(P＝0.0144),在遗传多样性的检测效率上也明显高于后者(P＜＜0.001)。基因内SSRs在等位变异的检测效率上与基因间SSRs差异不显著(P=0.3563),但在遗传多样性的检测效率上则显著高于后者(P=0.0125)
3.基于模型(Model-based)的群体结构分析将我国玉米核心地方品种划分为5个亚群,其中来自3个玉米主产区西南区、黄淮海区与北方区的品种依次构成了亚群2、亚群3与亚群4,而来自南方区的品种则构成了其余的2个亚群,其中来自广东、海南以及部分来自江西品种构成了亚群5,而来自该区其它省市的品种则构成了亚群1846份核心地方品种的群体结构分析结果显示了我国玉米地方品种在群体结构上存在极明显的地理来源特征。
4.基于30个表型性状的主成分分析所确定的12个主要候选性状,开展了我国玉米地方品种的种族划分研究。结果将我国760份核心玉米地方品种划分为9个种族,综合各种族所包含品种的地理来源以及在4个花期相关性状与主茎叶片数所构建的综合生育期上的具体表现,将这9个种族依次定名为西南马齿种族、西南糯玉米种族、北方硬粒种族、西南白色硬粒种族、黄色硬粒种族、西南黄色硬粒种族、衍生种族、北方马齿种族与爆裂种族。
5.以最多等位变异捕获量为选择依据,基于核心种质构建了我国玉米地方品种的微核心种质。285份微核心种质中有233份分别来自我国的29个省、市与地区,有52份则引自美洲、欧洲与其它国家,具有广泛的地理来源。基于55个覆盖玉米全基因组的SSR标记的遗传多样性分析显示,285份微核心种质在等位变异与稀有等位变异上分别捕获了核心种质的91.05%与83.32%,且与核心种质差异不显著(P值分别为0.4119和0.2126),其遗传多样性则为0.65,与核心种质的差异也不显著(P=0.6019)。此外基于55个SSRs的聚类结果显示285份微核心种质中来自北方区、黄淮海区、西南区以及南方区的品种均被划分为2个不同的亚组,表明这些微核心种质之间存在较大的遗传差异。
品种的地理来源以及遗传多样性分析结果均表明,本研究所构建的微核心种质具有广泛的地缘差异与遗传差异,可代表我国玉米地方品种的核心种质,全面应用于玉米的品种选育、改良以及优异等位基因资源的发掘等后续的相关研究。
Maize is one of the most important cereals and forage crops in China,and plays a key role in Chinese agriculture.During the long term adaptation to the complicated eco-environments in the nearly 500 years since its first importing into China,a vast number of landraces have formed,in which abundant genetic diversity has accumulated.Being important basic germplasm resources,these landraces have heavily improved the development of maize production in the early stage in China,and will still be of great importance to the current and future improvement of maize cultivars.So it is of full necessary to carry out a systematic and fine evaluation on the phenotypie and DNA level before the thorough use of these landraees germpalsm.On the other hand,from 1950s to the end of 1990s,a total of 16779 accessions of maize was gathered and preserved in China National Genebank(CNG),including 13521 landraces accessions.Though great accomplishments have gained in the maize germplasm collection,systematic evaluation and related analysis of these germplasm, especially of the maize landraees,are extremely feeble.What's more,there are still no normal reports on the racial classification of maize landraees preserved in CNG.
Based on the geographical distribution and phenotypie analysis of all the landrace accessions conserved in CNG,a core collection of all the maize landrace accessions was established.We fingerprinted the core aeeessions with 30 phenotypic traits and 55 simple sequenee repeat(SSR)markers,and the goals were to:(1)study the phenotypic diversity of Chinese maize landraces thoroughly,and compare the differences of phenotypic diversity among 9 maize regions;(2)evaluate the genetic diversity of maize landraces preserved in CNG on DNA level,and analyze the distribution of genetic diversity among different maize regions;(3)reveal the population structure of Chinese maize landraces and the genetic diversity of each subpopulations;(4)examine the races of maize germplasm in China;and(5)establish a mini core set of the core collections,so as to construct a feasible and easily attainable platform of maize landraces for the efficient management,thoroughly utility and succeeding related researches.
A total of 760 landrace accessions were used for the phenotypic analysis and racial classification while 846 landrace accessions were used for the evaluation of genetic diversity.The main results were as follows:
1.Based on the analysis of 27 quantitative traits and 3 qualitative traits,the whole set of 760 core maize landrace accessions preserved in CNG showed a relatively high level of phenotypic diversity.Among all of the 30 traits,100-kernel weight and plant height represented the highest level of phenotypic diversity,with the value of Shannon-Weaver diversity indices of 2.10 and 2.09 separately,while the traits of cob color and tassel-pollenshedding interval showed the lowest phenotypic diversity,with Shannon-Weaver diversity indices only of 0.64 and 0.84 respectively.At the same time, there existed distinct discrepancy among the accessions from 9 maize regions in China, among which Southwest Region possessed the highest phenotypic diversity,while Northwest Region and Plateau Region possessed the lowest.The results of phenotypic diversity analysis suggested that maize landraces from Southwest Region contained broader phenotypic variation,existing relatively high protection value and utility potential.
2.Fingerprinted with a set of 55 TP-M13-SSRs(simple sequence repeat with tailed primer M13)covered the entire maize genome,all of 846 maize core landrace accessions existed a high level of genetic/gene diversity.Totally,we observed 805 alleles,114 specific alleles and 597 rare alleles across 55 SSRs,with an average of 14.64,2.07 and 10.85 alleles per locus respectively,and the total genetic diversity was 0.65,conforming the broad genetic base of maize landraces in China.Comparisons among landraces with different geographical origins showed slightly difference of genetic diversity among the accessions from 9 maize regions,while distinct discrepancy existed in total alleles,specific alleles,and rare alleles among these regions,and Southwest Region held higher number of these three types of allelcs than the other 8 regions,implied the most abundant genetic diversity.
Among the whole set of 55 simple scqucnce repeats,dinuclcotide SSRs could capture more alleles and genetic diversity than other repeat SSRs(P=0.0144 and p＜＜0.001 respectively),while gene-based SSRs could capture higher genetic diversity than genomic SSRs(P=0.0125),but almost the same alleles as the latter(P=0.3563).
3.Model-based population structure analysis showed that 846 core accessions could be grouped into 5 subpopulations,which were Group1,Group2,Group3,Group4,and Groups in turn.Among these 5 subpopulations,Group2,Group3,and Group4 were formed by the accessions from Southwest Region,Huang Huaihai Region,and North Region respectively,and Groups was formed by the accessions from provinces of Guangdong and Hainan and part of Jiangxi province in South Region,while Groupl was formed by the accessions form the other provinces and regions in South Region. The result of population structure of 846 landrace accessions showed a strong geographical trend.
4.Principle component analysis(PCoA)of 30 phenotypic traits determined 12 candidates for the racial classification of all the 760 landrace accessions,and the results of PCoA indicated that the maize landraces preserved in CNG included 9 races. Based on the geographical origin and performance of each race on the integrated trait of maturity constructed by four flowering related traits and leaves per plant,these 9 races were named by southwestern dents,waxy race,northern flints,southwestern white flints,yellow flints,southwestern yellow flints,derived race,northern dents,and popcom race.
5.To efficiently assist in the use of maize landrace germplasm,we define mini core set of these accessions that capture the maximum number of SSR alleles using the Line Selection function in PowerMarker V3.25.A mini core set contained 285 accessions was established,of which 233 mini corc accessions were from 29 provinces,cities,or regions throughout China,and the other 52 mini core acccssions wcrc imported from America,Europe,and other countries and regions around the world,which indicated a roughly broad geographical distribution of all the 285 mini core accessions.
All of these 285 mini core accessions were fingerprinted with the same set of 55 SSR markers that covered the entire maize genome,the results showed that the mini core set captured 91.05%alleles and 83.32%rare alleles of the original core accessions,and there existed no significant diffcrcnccs between the mini core set and the core set on both of alleles and rare alleles(P=0.4119 and 0.2126 respectively),as well as genetic diversity(P=0.6019).Phylogenetic analysis of all the 285 mini core accessions based on 55 SSRs indicated that the accessions from North Region,Huang Huaihai Region, Southwest Region,and South Regin could be separated into two different subclusters, which implied a rather broad genetic variation among these mini core accessions. The geographical distribution and genetic diversity of the whole set of 285 mini core accessions confirmed that the mini core set established in this research existed an extensive wide geographical origin,and a broad genetic variation,which suggested that this mini core set well represented the core accessions.All the results confirmed that in stead of the maize landrace accessions conserved in core set and CNG full scaly, the mini core set could be thoroughly used in the improvement of maize breeding in China,as well as mining of the favorable alleles contained in these germplasm and other related succeeding researches on maize landraces
基于品种的地理来源与表型多样性评价数据,中国农业科学院构建了我国玉米地方品种的核心种质。本研究以这些核心种质为材料,对我国玉米地方品种进行了系统的多样性研究与种族划分,目的在于:1)全面分析我国玉米地方品种的表型多样性,并比较来自不同生态区的地方品种在表型多样性上的差异;2)评价我国玉米地方品种在DNA水平上的遗传多样性,并分析这些品种的遗传多样性在不同生态区之间的分布;3)了解我国玉米地方品种的群体结构以及各亚群的遗传多样性水平;4)明确我国玉米地方品种的种族结构;5)构建我国玉米地方品种的微核心种质,为我国玉米地方品种资源的有效管理、深入利用以及后续的相关研究建立一个高效的可行性平台。
本研究广泛选取了30个表型性状以及覆盖玉米全基因组的55个SSR标记展开了我国玉米地方品种的全面分析,主要研究结论如下:
1.基于27个数量性状与3个质量性状的Shannon-Weaver多样性指数分析结果显示,我国玉米地方品种存在较高水平的表型多样性。其中,表型多样性最高的是百粒重与株高,其Shannon-Weaver多样性指数依次为2.10与2.09,而多样性水平最低的是轴色与抽雄-散粉间隔期,其Shannon-Weaver多样性指数仅0.64与0.84。来自9个生态区的品种存在较大表型多样性差异,其中,西南区玉米地方品种的表型多样性水平最高,而西北区与高原区则相对较低。表型多样性的分析结果表明,西南生态区玉米种质资源的表型变异明显高于另8个区,具有较高的保护价值和利用潜力。
2.利用覆盖玉米全基因组的55个SSR标记,采用TP-M13-SSR检测技术研究了846份玉米核心地方品种的遗传多样性,并比较了不同类型的SSR标记在揭示研究材料遗传多样性上的差异。结果显示我国玉米核心地方品种的平均遗传多样性为0.65,总等位变异805个,平均14.64个/位点,特异等位变异114个,平均2.07个/位点,稀有等位变异597个,平均10.85个/位点。来自9个生态区的品种的遗传多样性水平比较一致,但在等位变异上存在明显差异,其中等位变异数、特异等位变异数与稀有等位变异数最高的均是西南区,依次为621个、40个和433个,明显高于另8个生态区,说明该区的玉米地方品种存在最丰富的等位变异。
在55个SSRs中,重复序列为2bp的SSRs在等位变异的检测效率上明显高于重复序列＞2bp的SSRs(P＝0.0144),在遗传多样性的检测效率上也明显高于后者(P＜＜0.001)。基因内SSRs在等位变异的检测效率上与基因间SSRs差异不显著(P=0.3563),但在遗传多样性的检测效率上则显著高于后者(P=0.0125)
3.基于模型(Model-based)的群体结构分析将我国玉米核心地方品种划分为5个亚群,其中来自3个玉米主产区西南区、黄淮海区与北方区的品种依次构成了亚群2、亚群3与亚群4,而来自南方区的品种则构成了其余的2个亚群,其中来自广东、海南以及部分来自江西品种构成了亚群5,而来自该区其它省市的品种则构成了亚群1846份核心地方品种的群体结构分析结果显示了我国玉米地方品种在群体结构上存在极明显的地理来源特征。
4.基于30个表型性状的主成分分析所确定的12个主要候选性状,开展了我国玉米地方品种的种族划分研究。结果将我国760份核心玉米地方品种划分为9个种族,综合各种族所包含品种的地理来源以及在4个花期相关性状与主茎叶片数所构建的综合生育期上的具体表现,将这9个种族依次定名为西南马齿种族、西南糯玉米种族、北方硬粒种族、西南白色硬粒种族、黄色硬粒种族、西南黄色硬粒种族、衍生种族、北方马齿种族与爆裂种族。
5.以最多等位变异捕获量为选择依据,基于核心种质构建了我国玉米地方品种的微核心种质。285份微核心种质中有233份分别来自我国的29个省、市与地区,有52份则引自美洲、欧洲与其它国家,具有广泛的地理来源。基于55个覆盖玉米全基因组的SSR标记的遗传多样性分析显示,285份微核心种质在等位变异与稀有等位变异上分别捕获了核心种质的91.05%与83.32%,且与核心种质差异不显著(P值分别为0.4119和0.2126),其遗传多样性则为0.65,与核心种质的差异也不显著(P=0.6019)。此外基于55个SSRs的聚类结果显示285份微核心种质中来自北方区、黄淮海区、西南区以及南方区的品种均被划分为2个不同的亚组,表明这些微核心种质之间存在较大的遗传差异。
品种的地理来源以及遗传多样性分析结果均表明,本研究所构建的微核心种质具有广泛的地缘差异与遗传差异,可代表我国玉米地方品种的核心种质,全面应用于玉米的品种选育、改良以及优异等位基因资源的发掘等后续的相关研究。
Maize is one of the most important cereals and forage crops in China,and plays a key role in Chinese agriculture.During the long term adaptation to the complicated eco-environments in the nearly 500 years since its first importing into China,a vast number of landraces have formed,in which abundant genetic diversity has accumulated.Being important basic germplasm resources,these landraces have heavily improved the development of maize production in the early stage in China,and will still be of great importance to the current and future improvement of maize cultivars.So it is of full necessary to carry out a systematic and fine evaluation on the phenotypie and DNA level before the thorough use of these landraees germpalsm.On the other hand,from 1950s to the end of 1990s,a total of 16779 accessions of maize was gathered and preserved in China National Genebank(CNG),including 13521 landraces accessions.Though great accomplishments have gained in the maize germplasm collection,systematic evaluation and related analysis of these germplasm, especially of the maize landraees,are extremely feeble.What's more,there are still no normal reports on the racial classification of maize landraees preserved in CNG.
Based on the geographical distribution and phenotypie analysis of all the landrace accessions conserved in CNG,a core collection of all the maize landrace accessions was established.We fingerprinted the core aeeessions with 30 phenotypic traits and 55 simple sequenee repeat(SSR)markers,and the goals were to:(1)study the phenotypic diversity of Chinese maize landraces thoroughly,and compare the differences of phenotypic diversity among 9 maize regions;(2)evaluate the genetic diversity of maize landraces preserved in CNG on DNA level,and analyze the distribution of genetic diversity among different maize regions;(3)reveal the population structure of Chinese maize landraces and the genetic diversity of each subpopulations;(4)examine the races of maize germplasm in China;and(5)establish a mini core set of the core collections,so as to construct a feasible and easily attainable platform of maize landraces for the efficient management,thoroughly utility and succeeding related researches.
A total of 760 landrace accessions were used for the phenotypic analysis and racial classification while 846 landrace accessions were used for the evaluation of genetic diversity.The main results were as follows:
1.Based on the analysis of 27 quantitative traits and 3 qualitative traits,the whole set of 760 core maize landrace accessions preserved in CNG showed a relatively high level of phenotypic diversity.Among all of the 30 traits,100-kernel weight and plant height represented the highest level of phenotypic diversity,with the value of Shannon-Weaver diversity indices of 2.10 and 2.09 separately,while the traits of cob color and tassel-pollenshedding interval showed the lowest phenotypic diversity,with Shannon-Weaver diversity indices only of 0.64 and 0.84 respectively.At the same time, there existed distinct discrepancy among the accessions from 9 maize regions in China, among which Southwest Region possessed the highest phenotypic diversity,while Northwest Region and Plateau Region possessed the lowest.The results of phenotypic diversity analysis suggested that maize landraces from Southwest Region contained broader phenotypic variation,existing relatively high protection value and utility potential.
2.Fingerprinted with a set of 55 TP-M13-SSRs(simple sequence repeat with tailed primer M13)covered the entire maize genome,all of 846 maize core landrace accessions existed a high level of genetic/gene diversity.Totally,we observed 805 alleles,114 specific alleles and 597 rare alleles across 55 SSRs,with an average of 14.64,2.07 and 10.85 alleles per locus respectively,and the total genetic diversity was 0.65,conforming the broad genetic base of maize landraces in China.Comparisons among landraces with different geographical origins showed slightly difference of genetic diversity among the accessions from 9 maize regions,while distinct discrepancy existed in total alleles,specific alleles,and rare alleles among these regions,and Southwest Region held higher number of these three types of allelcs than the other 8 regions,implied the most abundant genetic diversity.
Among the whole set of 55 simple scqucnce repeats,dinuclcotide SSRs could capture more alleles and genetic diversity than other repeat SSRs(P=0.0144 and p＜＜0.001 respectively),while gene-based SSRs could capture higher genetic diversity than genomic SSRs(P=0.0125),but almost the same alleles as the latter(P=0.3563).
3.Model-based population structure analysis showed that 846 core accessions could be grouped into 5 subpopulations,which were Group1,Group2,Group3,Group4,and Groups in turn.Among these 5 subpopulations,Group2,Group3,and Group4 were formed by the accessions from Southwest Region,Huang Huaihai Region,and North Region respectively,and Groups was formed by the accessions from provinces of Guangdong and Hainan and part of Jiangxi province in South Region,while Groupl was formed by the accessions form the other provinces and regions in South Region. The result of population structure of 846 landrace accessions showed a strong geographical trend.
4.Principle component analysis(PCoA)of 30 phenotypic traits determined 12 candidates for the racial classification of all the 760 landrace accessions,and the results of PCoA indicated that the maize landraces preserved in CNG included 9 races. Based on the geographical origin and performance of each race on the integrated trait of maturity constructed by four flowering related traits and leaves per plant,these 9 races were named by southwestern dents,waxy race,northern flints,southwestern white flints,yellow flints,southwestern yellow flints,derived race,northern dents,and popcom race.
5.To efficiently assist in the use of maize landrace germplasm,we define mini core set of these accessions that capture the maximum number of SSR alleles using the Line Selection function in PowerMarker V3.25.A mini core set contained 285 accessions was established,of which 233 mini corc accessions were from 29 provinces,cities,or regions throughout China,and the other 52 mini core acccssions wcrc imported from America,Europe,and other countries and regions around the world,which indicated a roughly broad geographical distribution of all the 285 mini core accessions.
All of these 285 mini core accessions were fingerprinted with the same set of 55 SSR markers that covered the entire maize genome,the results showed that the mini core set captured 91.05%alleles and 83.32%rare alleles of the original core accessions,and there existed no significant diffcrcnccs between the mini core set and the core set on both of alleles and rare alleles(P=0.4119 and 0.2126 respectively),as well as genetic diversity(P=0.6019).Phylogenetic analysis of all the 285 mini core accessions based on 55 SSRs indicated that the accessions from North Region,Huang Huaihai Region, Southwest Region,and South Regin could be separated into two different subclusters, which implied a rather broad genetic variation among these mini core accessions. The geographical distribution and genetic diversity of the whole set of 285 mini core accessions confirmed that the mini core set established in this research existed an extensive wide geographical origin,and a broad genetic variation,which suggested that this mini core set well represented the core accessions.All the results confirmed that in stead of the maize landrace accessions conserved in core set and CNG full scaly, the mini core set could be thoroughly used in the improvement of maize breeding in China,as well as mining of the favorable alleles contained in these germplasm and other related succeeding researches on maize landraces
引文
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