Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
Department of Biology, University of Western Ontario, London, Ontario, Canada.
PeerJ. 2024 Feb 26;12:e16946. doi: 10.7717/peerj.16946. eCollection 2024.
Due to their abundance and relative ease of genotyping, single nucleotide polymorphisms (SNPs) are a commonly used molecular marker for contemporary population genetic and genomic studies. A high-density and cost-effective way to type SNP loci is Allegro targeted genotyping (ATG), which is a form of targeted genotyping by sequencing developed and offered by Tecan genomics. One major drawback of this technology is the need for a reference genome and information on SNP loci when designing a SNP assay. However, for some non-model species genomic information from other closely related species can be used. Here we describe our process of developing an ATG assay to target 50,000 SNPs in Rocky Mountain bighorn sheep, using a reference genome from domestic sheep and SNP resources from prior bighorn sheep studies. We successfully developed a high accuracy, high-density, and relatively low-cost SNP assay for genotyping Rocky Mountain bighorn sheep that genotyped ~45,000 SNP loci. These loci were relatively evenly distributed throughout the genome. Furthermore, the assay produced genotypes at tens of thousands of SNP loci when tested on other mountain sheep species and subspecies.
由于单核苷酸多态性（SNPs）数量丰富且易于基因分型，因此它们是当代群体遗传和基因组学研究中常用的分子标记。一种高通量且具有成本效益的 SNP 基因分型方法是 Allegro 靶向基因分型（ATG），这是一种由 Tecan 基因组学公司开发并提供的测序靶向基因分型形式。该技术的一个主要缺点是在设计 SNP 检测时需要参考基因组和 SNP 基因座的信息。然而，对于一些非模式物种，可以使用来自其他密切相关物种的基因组信息。在这里，我们描述了使用来自家养绵羊的参考基因组和先前大角羊研究中的 SNP 资源，为落基山大角羊开发靶向 50,000 个 SNP 的 ATG 检测的过程。我们成功开发了一种高精度、高密度且相对低成本的 SNP 检测方法，用于对落基山大角羊进行基因分型，可对约 45,000 个 SNP 基因座进行基因分型。这些基因座在基因组中分布相对均匀。此外，该检测方法在对其他山地绵羊物种和亚种进行测试时，可产生数万个 SNP 基因座的基因型。
