Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1C, 30-248, Kraków, Poland.
Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
J Appl Genet. 2024 Sep;65(3):575-589. doi: 10.1007/s13353-024-00857-0. Epub 2024 Apr 3.
A potential application of single nucleotide polymorphisms (SNPs) in animal husbandry and production is identification of the animal breed. In this study, using chosen marker selection methods and genotypic data obtained with the use of Illumina Bovine SNP50 BeadChip for individuals belonging to ten cattle breeds, the reduced panels containing the most informative SNP markers were developed. The suitability of selected SNP panels for the effective and reliable assignment of the studied individuals to the breed of origin was checked by three allocation algorithms implemented in GeneClass 2. The studied breeds set included both Polish-native breeds under the genetic resources conservation programs and highly productive breeds with a global range. For all of the tested marker selection methods ("delta" and two F-based variants), two separate methodological approaches of marker assortment were used and three marker panels were created with 96, 192, and 288 SNPs respectively, to determine the minimum number of markers required for effective differentiation of the studied breeds. Moreover, the usefulness of the most effective panels of markers to assess the population structure and genetic diversity of the analyzed breeds was examined. The conducted analyses showed the possibility of using SNP subsets from medium-density genotypic microarrays to distinguish breeds of cattle kept in Poland and to analyze their genetic structure.
单核苷酸多态性（SNPs）在畜牧业和生产中的一个潜在应用是鉴定动物品种。在这项研究中，我们使用选择的标记选择方法和使用 Illumina Bovine SNP50 BeadChip 获得的个体基因型数据，开发了包含最具信息量 SNP 标记的简化面板。通过在 GeneClass 2 中实现的三种分配算法，检查了所选 SNP 面板对将研究个体有效且可靠地分配到起源品种的适用性。研究的品种集包括在遗传资源保护计划下的波兰本土品种和具有全球范围的高生产性品种。对于所有测试的标记选择方法（"delta"和两种基于 F 的变体），使用了两种单独的标记组合方法，并创建了分别包含 96、192 和 288 个 SNP 的三个标记面板，以确定有效区分研究品种所需的最小标记数量。此外，还检查了最有效的标记面板来评估分析品种的群体结构和遗传多样性的有用性。进行的分析表明，从中密度基因芯片中使用 SNP 子集来区分在波兰饲养的牛品种并分析它们的遗传结构是可能的。
