中国水稻微核心种质遗传多样性分析与新基因发掘
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摘要
水稻是世界重要粮食作物之一,人类为了自身的生存和发展,对亚洲栽培稻的“驯化”自远古以来一直未曾停过。突破性品种的培育成功往往与种质资源中有利基因的发现和利用相关。在种质资源中发掘新的重要性状基因,对水稻的分子育种具有重要意义。本研究主要利用一套来自中国水稻种质资源的微核心种质、非洲栽培稻和AA组野生稻,通过田间农艺性状的考察和功能基因标记的基因型鉴定,初步建立微核心种质数据库；分析重要农艺性状在微核心种质中、水稻亚种间以及它们与野生近缘种间的变异；通过基因多样性分析和关联分析,发掘重要基因及其单倍型的变异和分布。主要结果如下：
1.参照《水稻种质资源描述规范和数据标准》考察213份微核心种质的田间农艺性状,将农艺性状数据标准化,初步建立微核心种质数据库,该数据库收录了包括213份微核心种质在内的441份种质资源从2005年至2008年4个年度的155项描述性和特性数据共7,029条记录。
2.对微核心种质的15项重要农艺性状的统计分析结果显示,该套微核心种质的农艺性状具有丰富的多样性,平均变异系数在0.14-0.48之间；4个与产量相关的性状的变异较大：单株实粒重平均变异系数0.45,二次枝梗数平均变异系数0.44,每穗颖花数平均变异系数0.43,有效穗数平均变异系数0.36。微核心种质多个年度试验中各农艺性状间普遍存在着紧密的相关性。决定水稻植株形态构成的几个性状,如株高、剑叶长以及产量相关性状如有效穗数、每穗颖花数与单株实粒重等表现出显著或极显著相关。剑叶SPAD值(叶绿素荧光吸收率)与10个农艺性状呈显著相关。
3.利用24个分布于12条染色体的SSR标记对微核心种质的群体结构进行分析,显示k=2时该群体结构稳定,即微核心种质分成两个亚群对应籼粳亚群。
4.利用生物信息学方法鉴定7个淀粉合成代谢途径的重要基因(RSs3、Waxy、SSS1、ALK、SBEI、SDE-Iso和SDE-pu)的多态性位点并开发RSs3、SDE-Iso和SDE-pu的基因标记。结合已报道的Waxy、SSSI、ALK和SBEI基因标记,对213份微核心种质、6份非洲栽培稻、29份野生稻进行多样性分析。7个淀粉合成代谢途径重要基因中除了ALK和SDE-pu其它5个基因的多态性位点在籼粳亚群间表现明显的分化,而野生稻的所有7个位点都没有明显的分化。野生稻在7个淀粉合成代谢途径重要基因中存在亚洲栽培稻以前未报道的等位基因,特别是发现RSs3、SSSI、ALK、SBEI、SDE-Iso和SDE-pu等在野生稻中存在亚洲栽培稻中没有的等位变异。非洲栽培稻在这7个淀粉合成代谢途径重要基因中也存在与亚洲栽培稻完全不同的等位基因组合。
5.品质基因GS3在最后一个内含子和最后一个外显子存在变异位点,该位点可能对GS3基因TM和TNFR功能结构域有影响。针对这些位点开发了标记RGS1和RGS2；结合另两个基因标记SF28和SF17对213份微核心种质、49份非洲栽培稻和28份野生稻进行多样性分析,结果显示SF28、RGS1和RGS2位点和粒长高度关联,能够解释微核心种质中粒型的较大遗传变异。非洲栽培稻在RGS1位点具有特异的等位变异,利用非洲栽培稻ACC9/ZS97B回交重组自交系和近等基因系验证了ACC9在RGS1位点的等位变异能够导致谷粒的长度由短粒变为中长粒。
As a major food of the world, rice has been domesticated more than 10000 years by human being. Germplasm resources play an important role in crop breeding as innovative cultivars were always bred successfully by using favorable alleles that discovered in the germplasm. Several cloned genes have revealed important roles in building rice plant structure and/or increasing yield productivity. Genetic diversity and new allele mining of favorable genes in rice germplasm are of very significance for rice molecular breeding. Two hundred eighty-seven accessions, including the mini-core collection of 213 landraces, varieties and elite parents of hybrid rice,46 African cultivated rice (O. glaberrima), and 28 AA-genome wild rice accessions(O. rufipogon, O. nivara, O. barthii and O. meridionalis), were used for allelic diversity analysis and allele mining. The objectives of this study are:to investigate the agronomic characters, of the collection and construct a database of the germplasm collection; analyze gene diversity in the rice mini core collection, subspecies, and wild ancestor; discovery favorable alleles by association mapping. The main results are as follows:
1. Fifteen important agronomic characters of the collection were investigated in 4 environments according to the "rice germplasm describe criterion and data standard". A database was constructed base on the phenotypic dataand can be searched in intra-network.
2. The mini-core collection holds abundant diversity of agronomic characters with average CV range from 0.14 to 0.48. There are significant correlation coefficients between different agronomic characters. Notably, the SPAD value has close relationship with 10 agronomic characters.
3. A set of 24 unlinked SSR markers from 12 chromosomes were used to analysis population structure. Based on model-based estimation of the 24 SSR markers, the germplasm population showed a predominant structure with two subpopulations in correspondence with indica and japonica subspecies.
4. We discovered three polymorphic loci in starch biosynthesis genes RSs3、SDE-Iso and SDE-pu. The three markers together with 4 markers targeted to the other starch biosynthesis genes were used to assess diversities in a panel of rice germplasm which included the 213 Chinese mini core collections,6 African cultivated rice (O. glaberrima), and 29 AA-genome wild rice accessions (O. rufipogon, O. nivara, O. barthii and O. meridionalis). Genealogy treesshowed that there is a distinct divergence between indica and japonica. Furthermore, wild rice has new alleles in the 6 starch biosynthesis related genes, and the O. glaberrima has a set of unique alleles in the starch biosynthesis pathway distinct from that in O. sativa.
5. Two novel polymorphic loci, RGS1 and RGS2, were discovered in the last intron and the final exon of GS3, respectively. Together with other two polymorphic loci SF28 and SR17, a number of alleles at these four polymorphic loci were observed in a total of 287 accessions including the mini core collection, African rice and AA-genome wild relatives. Association mapping showed that polymorphic loci SF28, RGS1 and RGS2 were all highly associated with rice grain, and explained a large propotion of the variation. The genic marker RGS1 based on the motifs (AT)n was further validated as a functional marker using two sets of backcross recombinant inbred lines.
1.参照《水稻种质资源描述规范和数据标准》考察213份微核心种质的田间农艺性状,将农艺性状数据标准化,初步建立微核心种质数据库,该数据库收录了包括213份微核心种质在内的441份种质资源从2005年至2008年4个年度的155项描述性和特性数据共7,029条记录。
2.对微核心种质的15项重要农艺性状的统计分析结果显示,该套微核心种质的农艺性状具有丰富的多样性,平均变异系数在0.14-0.48之间；4个与产量相关的性状的变异较大：单株实粒重平均变异系数0.45,二次枝梗数平均变异系数0.44,每穗颖花数平均变异系数0.43,有效穗数平均变异系数0.36。微核心种质多个年度试验中各农艺性状间普遍存在着紧密的相关性。决定水稻植株形态构成的几个性状,如株高、剑叶长以及产量相关性状如有效穗数、每穗颖花数与单株实粒重等表现出显著或极显著相关。剑叶SPAD值(叶绿素荧光吸收率)与10个农艺性状呈显著相关。
3.利用24个分布于12条染色体的SSR标记对微核心种质的群体结构进行分析,显示k=2时该群体结构稳定,即微核心种质分成两个亚群对应籼粳亚群。
4.利用生物信息学方法鉴定7个淀粉合成代谢途径的重要基因(RSs3、Waxy、SSS1、ALK、SBEI、SDE-Iso和SDE-pu)的多态性位点并开发RSs3、SDE-Iso和SDE-pu的基因标记。结合已报道的Waxy、SSSI、ALK和SBEI基因标记,对213份微核心种质、6份非洲栽培稻、29份野生稻进行多样性分析。7个淀粉合成代谢途径重要基因中除了ALK和SDE-pu其它5个基因的多态性位点在籼粳亚群间表现明显的分化,而野生稻的所有7个位点都没有明显的分化。野生稻在7个淀粉合成代谢途径重要基因中存在亚洲栽培稻以前未报道的等位基因,特别是发现RSs3、SSSI、ALK、SBEI、SDE-Iso和SDE-pu等在野生稻中存在亚洲栽培稻中没有的等位变异。非洲栽培稻在这7个淀粉合成代谢途径重要基因中也存在与亚洲栽培稻完全不同的等位基因组合。
5.品质基因GS3在最后一个内含子和最后一个外显子存在变异位点,该位点可能对GS3基因TM和TNFR功能结构域有影响。针对这些位点开发了标记RGS1和RGS2；结合另两个基因标记SF28和SF17对213份微核心种质、49份非洲栽培稻和28份野生稻进行多样性分析,结果显示SF28、RGS1和RGS2位点和粒长高度关联,能够解释微核心种质中粒型的较大遗传变异。非洲栽培稻在RGS1位点具有特异的等位变异,利用非洲栽培稻ACC9/ZS97B回交重组自交系和近等基因系验证了ACC9在RGS1位点的等位变异能够导致谷粒的长度由短粒变为中长粒。
As a major food of the world, rice has been domesticated more than 10000 years by human being. Germplasm resources play an important role in crop breeding as innovative cultivars were always bred successfully by using favorable alleles that discovered in the germplasm. Several cloned genes have revealed important roles in building rice plant structure and/or increasing yield productivity. Genetic diversity and new allele mining of favorable genes in rice germplasm are of very significance for rice molecular breeding. Two hundred eighty-seven accessions, including the mini-core collection of 213 landraces, varieties and elite parents of hybrid rice,46 African cultivated rice (O. glaberrima), and 28 AA-genome wild rice accessions(O. rufipogon, O. nivara, O. barthii and O. meridionalis), were used for allelic diversity analysis and allele mining. The objectives of this study are:to investigate the agronomic characters, of the collection and construct a database of the germplasm collection; analyze gene diversity in the rice mini core collection, subspecies, and wild ancestor; discovery favorable alleles by association mapping. The main results are as follows:
1. Fifteen important agronomic characters of the collection were investigated in 4 environments according to the "rice germplasm describe criterion and data standard". A database was constructed base on the phenotypic dataand can be searched in intra-network.
2. The mini-core collection holds abundant diversity of agronomic characters with average CV range from 0.14 to 0.48. There are significant correlation coefficients between different agronomic characters. Notably, the SPAD value has close relationship with 10 agronomic characters.
3. A set of 24 unlinked SSR markers from 12 chromosomes were used to analysis population structure. Based on model-based estimation of the 24 SSR markers, the germplasm population showed a predominant structure with two subpopulations in correspondence with indica and japonica subspecies.
4. We discovered three polymorphic loci in starch biosynthesis genes RSs3、SDE-Iso and SDE-pu. The three markers together with 4 markers targeted to the other starch biosynthesis genes were used to assess diversities in a panel of rice germplasm which included the 213 Chinese mini core collections,6 African cultivated rice (O. glaberrima), and 29 AA-genome wild rice accessions (O. rufipogon, O. nivara, O. barthii and O. meridionalis). Genealogy treesshowed that there is a distinct divergence between indica and japonica. Furthermore, wild rice has new alleles in the 6 starch biosynthesis related genes, and the O. glaberrima has a set of unique alleles in the starch biosynthesis pathway distinct from that in O. sativa.
5. Two novel polymorphic loci, RGS1 and RGS2, were discovered in the last intron and the final exon of GS3, respectively. Together with other two polymorphic loci SF28 and SR17, a number of alleles at these four polymorphic loci were observed in a total of 287 accessions including the mini core collection, African rice and AA-genome wild relatives. Association mapping showed that polymorphic loci SF28, RGS1 and RGS2 were all highly associated with rice grain, and explained a large propotion of the variation. The genic marker RGS1 based on the motifs (AT)n was further validated as a functional marker using two sets of backcross recombinant inbred lines.
引文
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