Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India.
Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Bareilly, India.
Anim Biotechnol. 2021 Feb;32(1):130-136. doi: 10.1080/10495398.2019.1646266. Epub 2019 Jul 31.
Single nucleotide polymorphisms (SNPs) have now replaced microsatellite markers in several species for various genetic investigations like parentage assignment, genetic breed composition, assessment for individuality and, most popularly, as a useful tool in genomic selection. However, such a resource, which can offer to assist breed identification in a cost-effective manner is still not explored in cattle breeding programs. In our study, we have tried to describe methods for reducing the number of SNPs to develop a breed-specific panel. We have used SNP data from Dryad open public access repository. Starting from a global dataset of 178 animals belonging to 10 different breeds, we selected five panels each comprising of similar number of SNPs using different methods i.e., Delta, Pairwise Wright's F, informativeness for assignment, frequent item feature selection (FIFS) and minor allele frequency-linkage disequilibrium (MAF-LD) based method. MAF-LD based method has been recently developed by us for construction of breed-specific SNP panels. The STRUCTURE software analysis of MAF-LD based method showed appropriate clustering in comparison to other panels. Later, the panel of 591 breed-specific SNPs was called to their respective breeds using Venny 2.1.0 and UGent web tools software. Breed-specific SNPs were later annotated by using various Bioinformatics softwares.
单核苷酸多态性（SNPs）现在已经在许多物种中取代了微卫星标记，用于各种遗传研究，如亲子关系鉴定、遗传品种组成、个体评估，以及最流行的基因组选择中的有用工具。然而，在牛的育种计划中，仍然没有探索出这样一种可以提供低成本、高效率的品种鉴定的资源。在我们的研究中，我们试图描述减少 SNP 数量的方法，以开发特定品种的面板。我们使用了来自 Dryad 开放公共访问存储库的 SNP 数据。从属于 10 个不同品种的 178 只动物的全球数据集开始，我们使用不同的方法选择了五个包含相似 SNP 数量的面板，即 Delta、Pairwise Wright's F、赋值信息量、频繁项特征选择（FIFS）和基于最小等位基因频率-连锁不平衡（MAF-LD）的方法。MAF-LD 基于方法是我们最近为构建特定品种的 SNP 面板而开发的。与其他面板相比，MAF-LD 基于方法的 STRUCTURE 软件分析显示出适当的聚类。然后，使用 Venny 2.1.0 和 UGent web tools 软件将 591 个特定品种的 SNP 面板调用到各自的品种中。然后使用各种生物信息学软件对特定品种的 SNPs 进行注释。
