Kim Kyung Seok, Ratcliffe Susan T, French B Wade, Liu Lei, Sappington Thomas W
The USDA-ARS, Corn Insects and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50011, USA.
J Hered. 2008 Mar-Apr;99(2):112-24. doi: 10.1093/jhered/esm104. Epub 2008 Jan 24.
Microsatellite, or simple sequence repeat (SSR), loci can be identified by mining expressed sequence tag (EST) databases, and where these are available, marker development time and expense can be decreased considerably over conventional strategies of probing the entire genome. However, it is unclear whether they provide information on population structure similar to that generated by anonymous genomic SSRs. We performed comparative population genetic analyses between EST-derived SSRs (EST-SSRs) and anonymous SSRs developed from genomic DNA for the same set of populations of the insect Diabrotica virgifera, a beetle in the family Chrysomelidae. Compared with noncoding, nontranscribed regions, EST-SSRs were generally less polymorphic but had reduced occurrence of null alleles and greater cross-species amplification. Neutrality tests suggested the loci were not under positive selection. Across all populations and all loci, the genomic and EST-SSRs performed similarly in estimating genetic diversity, F(IS), F(ST), population assignment and exclusion tests, and detection of distinct populations. These findings, therefore, indicate that the EST-SSRs examined can be used with confidence in future genetic studies of Diabrotica populations and suggest that EST libraries can be added as a valuable source of markers for population genetics studies in insects and other animals.
微卫星，即简单序列重复（SSR）位点，可以通过挖掘表达序列标签（EST）数据库来识别。如果有这些数据库，与探测整个基因组的传统策略相比，标记开发时间和成本可以大幅降低。然而，尚不清楚它们提供的群体结构信息是否与由匿名基因组SSR产生的信息相似。我们对来自EST的SSR（EST-SSR）和从基因组DNA开发的匿名SSR进行了比较群体遗传分析，分析对象是同一组群体的昆虫——叶甲科的一种甲虫，即马铃薯甲虫。与非编码、非转录区域相比，EST-SSR通常多态性较低，但无效等位基因的出现频率降低，且跨物种扩增能力更强。中性检验表明这些位点没有受到正选择。在所有群体和所有位点中，基因组SSR和EST-SSR在估计遗传多样性、F(IS)、F(ST)、群体归属和排除检验以及检测不同群体方面表现相似。因此，这些发现表明，所检测的EST-SSR可在未来马铃薯甲虫群体的遗传研究中放心使用，并表明EST文库可作为昆虫和其他动物群体遗传学研究的有价值的标记来源。
