Effectiveness of microsatellite and SNP markers for parentage and identity analysis in species with low genetic diversity: the case of European bison
Effectiveness of microsatellite and SNP markers for parentage and identity analysis in species with low genetic diversity: the case of European bison
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DOI：
10.1038/hdy.2009.73
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发表时间：
2009-10-01
期刊：
影响因子：
3.8
通讯作者：
Bendixen, C.
中科院分区：
文献类型：
--
作者：
Tokarska, M.;Marshall, T.;Bendixen, C.
欧洲野牛（Bison bonasus）在经历了大约 90 年前的严重瓶颈后已成功恢复，但遗传变异性较低，可能会严重阻碍亲子关系和身份分析。根据谱系分析，当代种群中80%以上的基因仅源自两种始祖动物，近交系数平均接近0.5，而微卫星杂合度不超过0.3。我们比较了 17 个微卫星标记和 960 个单核苷酸多态性 (SNP) 标记在欧洲野牛亲子鉴定和身份分析中的有效性。基于微卫星的亲子关系和身份分析由于标记杂合性低而不成功，并且在该物种中不是一种实用的方法。使用 SNP 标记进行的模拟表明，80-90 个随机选择的基因座，或仅 50-60 个最杂合的基因座，就足以确保该物种成功进行亲子鉴定和身份分析。为了标准化未来的分析，可以选择一组具有高杂合性和基因组均匀分布特征的 50-60 个牛 SNP。这组标记可以使用 VeraCode (Illumina) 或类似的 SNP 基因分型系统进行分型。与 16 个位点微卫星调查相比，这些 SNP 基因分型方法的成本较低，这意味着为家养物种开发的现成 SNP 基因分型系统代表了相关物种遗传分析的强大工具，甚至在其他标记（如微卫星）杂合性可能非常低的瓶颈物种中也有效。遗传 (2009) 103, 326-332; doi：10.1038/hdy.2009.73； 2009 年 7 月 22 日在线发布
The European bison (Bison bonasus) has recovered successfully after a severe bottleneck about 90 years ago but has been left with low genetic variability that may substantially hinder parentage and identity analysis. According to pedigree analysis, over 80% of the genes in the contemporary population descend from just two founder animals and inbreeding coefficients averaged almost 0.5, whereas microsatellite heterozygosity does not exceed 0.3. We present a comparison of the effectiveness of 17 microsatellite and 960 single nucleotide polymorphism (SNP) markers for paternity and identity analysis in the European bison. Microsatellite-based paternity and identity analysis was unsuccessful because of low marker heterozygosity and is not a practical approach in this species. Simulations using SNP markers suggest that 80-90 randomly selected loci, or just 50-60 of the most heterozygous loci, would be sufficient to ensure successful paternity and identity analysis in this species. For the purpose of standardizing future analysis, a panel of 50-60 bovine SNPs characterized by high heterozygosity and an even distribution in the genome could be selected. This panel of markers could be typed using VeraCode (Illumina) or similar SNP genotyping systems. The low cost of these SNP genotyping methods compared with a 16 locus microsatellite survey means that off-the-shelf SNP genotyping systems developed for domestic species represent powerful tools for genetic analysis in related species, and can be effective even in bottlenecked species in which heterozygosity of other markers such as microsatellites may be very low. Heredity (2009) 103, 326-332; doi: 10.1038/hdy.2009.73; published online 22 July 2009