CSIRO Livestock Industries, St Lucia, Australia.
Anim Genet. 2010 Apr;41(2):199-202. doi: 10.1111/j.1365-2052.2009.01972.x. Epub 2009 Sep 26.
Large collections of single nucleotide polymorphisms (SNPs) have recently been identified from a number of livestock genomes. This raises the possibility that SNP arrays might be useful for analysis in related species for which few genetic markers are currently available. To address the likely success of such an approach, the aim of this study was to examine the threshold number and position of flanking mutations which act to prevent genotype calls being produced. Sequence diversity was measured across 16 loci containing SNPs known either to work successfully between species or fail between species. In pairwise comparisons between domestic and wild sheep, sequence divergence surrounding working SNP assays was significantly lower than that surrounding non-functional assays. In addition, the location of flanking mismatches tended to be closer to the target SNP in loci that failed to generate genotype calls across species. The magnitude of sequence divergence observed for both working and non-functional assays was compared with the divergence separating domestic sheep from European Mouflon, African Barbary, goat and cattle. The results suggest that the utility of SNP arrays for analysis of shared polymorphism will be restricted to closely related pairs of species. Analysis across more divergent species will, however, be successful for other objectives, such as the identification of the ancestral state of SNPs.
最近从许多家畜基因组中鉴定出了大量的单核苷酸多态性(SNPs)。这就提出了一种可能性，即 SNP 芯片可能对那些目前可用的遗传标记很少的相关物种的分析有用。为了探讨这种方法的可能成功性，本研究的目的是研究阻止产生基因型的侧翼突变的数量和位置的阈值。在包含已知在物种间成功或在物种间失败的 SNP 的 16 个基因座上测量了序列多样性。在绵羊的家养和野生种间的成对比较中，在成功的 SNP 检测周围的序列分化明显低于非功能检测周围的序列分化。此外，在不能在物种间产生基因型的基因座中，侧翼错配的位置往往更接近目标 SNP。与将家养绵羊与欧洲盘羊、非洲巴巴里绵羊、山羊和牛区分开来的分歧相比，观察到的工作和非功能检测的序列分歧的幅度。结果表明，SNP 芯片用于分析共享多态性的效用将仅限于亲缘关系密切的物种对。然而，对于其他目标，如 SNP 的祖先状态的鉴定，跨越更具分歧的物种的分析将是成功的。
