Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers.
Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers.
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DOI：
10.1007/s00122-009-1256-2
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发表时间：
2010-05
影响因子：
5.4
通讯作者：
Stich, Benjamin
中科院分区：
文献类型：
--
作者：
Van Inghelandt, Delphine;Melchinger, Albrecht E.;Lebreton, Claude;Stich, Benjamin
关于优良育种材料的遗传多样性和群体结构的信息对于作物的改良具有根本重要性。本研究的目的是（a）基于简单重复序列（SSR）标记检测玉米优良种质的群体结构和遗传多样性;（B）将这些结果与单核苷酸多态性（SNP）标记的结果进行比较;（c）将系谱记录计算的共祖系数与SSR和SNP标记计算的遗传距离估计值进行比较。我们的研究是基于1，537个玉米自交系的359个SSR和8，244个SNP标记的基因型。每个位点的平均等位基因数、群体特异性等位基因数和基因多样性（D）SSR均高于SNP。修改罗杰距离（MRD）估计和成员的概率的结构矩阵SSR比SNP标记，但种质组织在4个杂种优势池是一致的结构结果的基础上SSR和SNP。两个标记系统计算的MRD估计值高度相关（0.87）。结果表明，两种标记类型在杂种优势库的结构和多样性方面具有相同的结论。此外，虽然我们的研究结果表明，获得MRD或D估计具有类似的精度所需的SSR和SNPs的数量的比例在不同的精度水平是不恒定的，我们建议，7至11倍的SNPs比SSR应用于分析人口结构和遗传多样性。本文的在线版本（doi：10.1007/s 00122 -009-1256-2）包含补充材料，可供授权用户使用。
Information about the genetic diversity and population structure in elite breeding material is of fundamental importance for the improvement of crops. The objectives of our study were to (a) examine the population structure and the genetic diversity in elite maize germplasm based on simple sequence repeat (SSR) markers, (b) compare these results with those obtained from single nucleotide polymorphism (SNP) markers, and (c) compare the coancestry coefficient calculated from pedigree records with genetic distance estimates calculated from SSR and SNP markers. Our study was based on 1,537 elite maize inbred lines genotyped with 359 SSR and 8,244 SNP markers. The average number of alleles per locus, of group specific alleles, and the gene diversity (D) were higher for SSRs than for SNPs. Modified Roger’s distance (MRD) estimates and membership probabilities of the STRUCTURE matrices were higher for SSR than for SNP markers but the germplasm organization in four heterotic pools was consistent with STRUCTURE results based on SSRs and SNPs. MRD estimates calculated for the two marker systems were highly correlated (0.87). Our results suggested that the same conclusions regarding the structure and the diversity of heterotic pools could be drawn from both markers types. Furthermore, although our results suggested that the ratio of the number of SSRs and SNPs required to obtain MRD or D estimates with similar precision is not constant across the various precision levels, we propose that between 7 and 11 times more SNPs than SSRs should be used for analyzing population structure and genetic diversity. The online version of this article (doi:10.1007/s00122-009-1256-2) contains supplementary material, which is available to authorized users.
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影响因子：
2.3
作者：
Lübberstedt, T;Melchinger, AE;Kuiper, M
通讯作者：
Kuiper, M
在评估玉米多样性和相关性评估中简单序列重复和单核苷酸多态性的经验比较。
影响因子：
3.7
作者：
Hamblin, Martha T.;Warburton, Marilyn L.;Buckler, Edward S.
通讯作者：
Buckler, Edward S.
影响因子：
2.3
作者：
MESSMER, MM;MELCHINGER, AE;BOPPENMAIER, J
通讯作者：
BOPPENMAIER, J
影响因子：
5.4
作者：
Pejic, I;Ajmone-Marsan, P;Motto, M
通讯作者：
Motto, M
影响因子：
2.3
作者：
MELCHINGER, AE;MESSMER, MM;LAMKEY, KR
通讯作者：
LAMKEY, KR