Comparative Performance of Single Nucleotide Polymorphism and Microsatellite Markers for Population Genetic Analysis
Comparative Performance of Single Nucleotide Polymorphism and Microsatellite Markers for Population Genetic Analysis
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DOI：
10.1093/jhered/esp028
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发表时间：
2009-09-01
影响因子：
3.1
通讯作者：
Lewis, Leslie C.
中科院分区：
文献类型：
--
作者：
Coates, Brad S.;Sumerford, Douglas V.;Lewis, Leslie C.
微卫星基因座是群体遗传学分析的标准遗传标记，而单核苷酸多态性（SNPs）是最近的工具，需要在群体遗传学中评估中性和适当的使用。12个SNP标记被用来描述在美国的玉米根萤叶甲（LeConte;鞘翅目：萤叶甲科）的遗传结构，并揭示了一个高的平均观察杂合性（0.40 +/- 0.059）和低的全球F-ST（0.029）。F-ST值在0.007 ~ 0.045之间，除2个群体外，其余群体均表现出显著的遗传分化（P < 0.008）。基于SNP标记的群体参数和结论类似于通过使用微卫星标记从相同的群体样品中获得的。基于SNP的F-ST估计值比来自微卫星的相应估计值高3倍，其中较低的微卫星F-ST估计值可能是由于等位基因大小的收敛（同质性）而高估了亚群之间的迁移率。在群体内非中性的SNP或微卫星标记位点的比例没有显着差异。SNP标记提供的群体遗传参数的估计与微卫星数据一致，其低回复突变率可能会导致在估计群体参数的错误倾向降低。
Microsatellite loci are standard genetic markers for population genetic analysis, whereas single nucleotide polymorphisms (SNPs) are more recent tools that require assessment of neutrality and appropriate use in population genetics. Twelve SNP markers were used to describe the genetic structure of Diabrotica virgifera virgifera (LeConte; Coleoptera: Chrysomelidae) in the United States of America and revealed a high mean observed heterozygosity (0.40 +/- 0.059) and low global F-ST (0.029). Pairwise F-ST estimates ranged from 0.007 to 0.045, and all but 2 populations showed significant levels of genetic differentiation (P < 0.008). Population parameters and conclusions based on SNP markers were analogous to that obtained by use of microsatellite markers from the identical population samples. SNP-based F-ST estimates were 3-fold higher than corresponding estimates from microsatellites, wherein lower microsatellite F-ST estimates likely resulted from an overestimate of migration rates between subpopulations due to convergence of allele size (homoplasy). No significant difference was observed in the proportion of SNP or microsatellite markers loci that were nonneutral within populations. SNP markers provided estimates of population genetic parameters consistent with those from microsatellite data, and their low back mutation rates may result in reduced propensity for error in estimation of population parameters.