利用基因组数据对长爪沙鼠微卫星位点的筛选与优化

Screening and optimization of microsatellite loci in Mongolian gerbils using genomic data

目的利用基因组数据筛选更多有效的长爪沙鼠微卫星位点用于近交系和封闭群遗传质量分析,丰富长爪沙鼠遗传数据。方法通过对长爪沙鼠全基因组测序结果分析,选出符合微卫星标准的重复序列357个,根据每个位点的侧翼序列设计并合成相应引物。提取长爪沙鼠基因组DNA进行PCR扩增,经引物序列和PCR条件优化以及凝胶电泳实验分析,对成功扩增的位点通过不同近交系和封闭群长爪沙鼠进行验证和优化,筛选出适于遗传质量分析的位点。结果在357个微卫星位点引物中,135个位点引物成功扩增PCR产物。分析结果显示,其中10个位点可以将长爪沙鼠脑缺血和糖尿病模型近交系区分开。在12只封闭群长爪沙鼠中,23个位点呈现出多态性。结论成功筛选出了135个长爪沙鼠微卫星位点,部分位点可用于近交系和封闭群长爪沙鼠遗传质量分析。

Objective To screen for,and identify more-effective microsatellite loci for genetic quality analysis and enrichment of the genetic data in Mongolian gerbils using genomics.Methods Altogether,357 repetitive sequences in accordance with the microsatellite criteria were selected from whole-genome sequencing data of Mongolian gerbils.The corresponding primers were designed and synthesized based on the flanking sequences of each locus.The genomic DNA of the Mongolian gerbils was extracted and polymerase chain reaction(PCR)-amplified with their corresponding primers.After optimizing the primer sequences,the PCR condition,and the gel electrophoresis experiments,the most efficient loci for successful amplification were verified and optimized in various inbred lines and an outbred group of Mongolian gerbils.The loci were also screened to identify those suitable for genetic quality analysis.Results Among the 357 microsatellite sequences,135 loci primers were successfully amplified with the PCR product.Ten of them could be used to distinguish two inbred strains of Mongolian gerbils,including the cerebral ischemia model and the diabetes model.Also,12 gerbils from the outbred group had 23 loci that exhibited polymorphism.Conclusions In all,135 microsatellite loci of gerbils are successfully screened,some of which can be used for genetic quality analysis in both inbred and outbred groups of Mongolian gerbils.