Genetic diversity provides the foundation for plant breeding and genetic research.Over 3000 rice genomes were recently sequenced as part of the 3K Rice Genome(3KRG)Project.We added four additional Indian rice accessio...Genetic diversity provides the foundation for plant breeding and genetic research.Over 3000 rice genomes were recently sequenced as part of the 3K Rice Genome(3KRG)Project.We added four additional Indian rice accessions to create a panel of 3004 accessions.However,such a large collection of germplasm is difficult to preserve and evaluate.The construction of core and mini-core collections is an efficient method for the management of genetic resources.In this study,we developed a mini-core comprising 520 accessions that captured most of the SNPs and represented all of the phenotypes and geographic regions from the original panel.The mini-core was validated using different statistical analyses and contained representatives from all major rice groups,including japonica,indica,aus/boro,and aromatic/basmati.Genomewide association analyses of the mini-core panel efficiently reproduced the marker–trait associations identified in the original panel.Haplotype analysis validated the utility of the mini-core panel.In the current era with many ongoing large-scale sequencing projects,such a strategy for mini-core design should be useful in many crops.The rice mini-core collection developed in this study would be valuable for agronomic trait evaluation and useful for rice improvement via marker-assisted molecular breeding.展开更多
【目的】评价中国栽培大豆微核心种质的群体结构和遗传多样性水平,为拓宽大豆遗传基础、发掘优异基因、改良大豆品种提供理论依据。【方法】利用大豆20个连锁群上的100个SSR位点,对来自全国28个省补充完善的248份栽培大豆微核心种质进行...【目的】评价中国栽培大豆微核心种质的群体结构和遗传多样性水平,为拓宽大豆遗传基础、发掘优异基因、改良大豆品种提供理论依据。【方法】利用大豆20个连锁群上的100个SSR位点,对来自全国28个省补充完善的248份栽培大豆微核心种质进行SSR遗传多样性及群体结构分析;采用PowerMarker Version 3.25软件统计等位变异数、平均等位变异数、多态性信息量(PIC值)及亚群特有等位变异数等参数;基于遗传距离建立了栽培大豆微核心种质的无根Neighbor-Joining树;用Structure2.2软件对微核心种质的群体结构进行评价。【结果】100个SSR位点在248份材料中共检测出等位变异1460个,每个位点变异范围为2—33个,平均为14.6个,每个位点PIC值变异范围为0.158—0.932,平均为0.743。基于模型的群体结构分析显示,依据LnP(D)无法判断最佳K值(群组数),但通过计算系数ΔK发现,K=3为微核心种质的最佳群体结构。结合种质的生态类型及品种类型分析发现,地理来源相同的种质具有聚在一起的倾向,但来源相同的种质也有分在不同组的情况。不同生态类型及品种类型间均存在较多的互补等位变异和特有等位变异。【结论】中国栽培大豆微核心种质具有丰富的遗传多样性,可以用来拓宽大豆品种遗传基础;不同生态类型及品种类型间存在较多的互补及特有等位变异,是种质创新及品种改良的物质基础;栽培大豆微核心种质存在明显的群体结构,为微核心种质在育种中的直接或间接利用提供了理论依据。展开更多
基金supported by the grants BT/AB/NIPGR/SEED BIOLOGY/2012 and BT/BI/04/069/2006 for the establishment of Distrib-uted Information Sub-Centre from the Department of Biotechnology,Gov-ernment of India.
文摘Genetic diversity provides the foundation for plant breeding and genetic research.Over 3000 rice genomes were recently sequenced as part of the 3K Rice Genome(3KRG)Project.We added four additional Indian rice accessions to create a panel of 3004 accessions.However,such a large collection of germplasm is difficult to preserve and evaluate.The construction of core and mini-core collections is an efficient method for the management of genetic resources.In this study,we developed a mini-core comprising 520 accessions that captured most of the SNPs and represented all of the phenotypes and geographic regions from the original panel.The mini-core was validated using different statistical analyses and contained representatives from all major rice groups,including japonica,indica,aus/boro,and aromatic/basmati.Genomewide association analyses of the mini-core panel efficiently reproduced the marker–trait associations identified in the original panel.Haplotype analysis validated the utility of the mini-core panel.In the current era with many ongoing large-scale sequencing projects,such a strategy for mini-core design should be useful in many crops.The rice mini-core collection developed in this study would be valuable for agronomic trait evaluation and useful for rice improvement via marker-assisted molecular breeding.
文摘【目的】评价中国栽培大豆微核心种质的群体结构和遗传多样性水平,为拓宽大豆遗传基础、发掘优异基因、改良大豆品种提供理论依据。【方法】利用大豆20个连锁群上的100个SSR位点,对来自全国28个省补充完善的248份栽培大豆微核心种质进行SSR遗传多样性及群体结构分析;采用PowerMarker Version 3.25软件统计等位变异数、平均等位变异数、多态性信息量(PIC值)及亚群特有等位变异数等参数;基于遗传距离建立了栽培大豆微核心种质的无根Neighbor-Joining树;用Structure2.2软件对微核心种质的群体结构进行评价。【结果】100个SSR位点在248份材料中共检测出等位变异1460个,每个位点变异范围为2—33个,平均为14.6个,每个位点PIC值变异范围为0.158—0.932,平均为0.743。基于模型的群体结构分析显示,依据LnP(D)无法判断最佳K值(群组数),但通过计算系数ΔK发现,K=3为微核心种质的最佳群体结构。结合种质的生态类型及品种类型分析发现,地理来源相同的种质具有聚在一起的倾向,但来源相同的种质也有分在不同组的情况。不同生态类型及品种类型间均存在较多的互补等位变异和特有等位变异。【结论】中国栽培大豆微核心种质具有丰富的遗传多样性,可以用来拓宽大豆品种遗传基础;不同生态类型及品种类型间存在较多的互补及特有等位变异,是种质创新及品种改良的物质基础;栽培大豆微核心种质存在明显的群体结构,为微核心种质在育种中的直接或间接利用提供了理论依据。
