Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA.
Sci Rep. 2019 Apr 23;9(1):6407. doi: 10.1038/s41598-019-42885-5.
The use of single nucleotide polymorphism (SNP) arrays to generate large SNP datasets for comparison purposes have recently become an attractive alternative to other genotyping methods. Although most SNP arrays were originally developed for domestic organisms, they can be effectively applied to wild relatives to obtain large panels of SNPs. In this study, we tested the cross-species application of the Affymetrix 600K Chicken SNP array in five species of North American prairie grouse (Centrocercus and Tympanuchus genera). Two individuals were genotyped per species for a total of ten samples. A high proportion (91%) of the total 580 961 SNPs were genotyped in at least one individual (73-76% SNPs genotyped per species). Principal component analysis with autosomal SNPs separated the two genera, but failed to clearly distinguish species within genera. Gene ontology analysis identified a set of genes related to morphogenesis and development (including genes involved in feather development), which may be primarily responsible for large phenotypic differences between Centrocercus and Tympanuchus grouse. Our study provided evidence for successful cross-species application of the chicken SNP array in grouse which diverged ca. 37 mya from the chicken lineage. As far as we are aware, this is the first reported application of a SNP array in non-passerine birds, and it demonstrates the feasibility of using commercial SNP arrays in research on non-model bird species.
利用单核苷酸多态性（SNP）阵列生成用于比较目的的大型 SNP 数据集，最近已成为其他基因分型方法的一种有吸引力的替代方法。尽管大多数 SNP 阵列最初是为国内生物开发的，但它们可以有效地应用于野生亲属，以获得大量的 SNP 面板。在这项研究中，我们测试了 Affymetrix 600K 鸡 SNP 阵列在北美草原松鸡的五个物种（Centrocercus 和 Tympanuchus 属）中的跨物种应用。每个物种有两个个体进行基因分型，总共十个样本。共有 580961 个 SNP 中的高比例（91%）至少在一个个体中进行了基因分型（每个物种中 73-76%的 SNP 进行了基因分型）。常染色体 SNP 的主成分分析将两个属分开，但未能清楚地区分属内的物种。基因本体论分析确定了一组与形态发生和发育相关的基因（包括参与羽毛发育的基因），这些基因可能是 Centrocercus 和 Tympanuchus 松鸡之间表型差异的主要原因。我们的研究为在与鸡谱系分化约 3700 万年的松鸡中成功应用鸡 SNP 阵列提供了证据。据我们所知，这是首次在非雀形目鸟类中报道 SNP 阵列的应用，它证明了在非模式鸟类物种研究中使用商业 SNP 阵列的可行性。
