Тhe population-genetic structure of native Tagil cattle by STR- and SNP-markers

Rearing specialized cattle breeds or several intra-breed lines reduces the breed and genetic diversity and creates a real threat of extinction of native livestock. Microsatellite analysis and genome-wide SNP (single nucleotide polymorphism) genotyping are common methods to study the population genetic structure of local breeds with unique adaptive traits and diseases resistance. The history of the Tagil breed is more than 200 years old. Currently, in Russia and the world, there is the only herd of Tagil cattle of about 600 animals molecular genetic characteristics of which remain insufficiently poor studied. Here we present the first results of identification of STR and SNP genotypes of the unique local Tagil breed. The work aimed to assess genetic diversity and survey the population structure of the modern population of indigenous Tagil cattle by microsatellite analysis (STR) and genome-wide analysis of single nucleotide polymorphism (SNPs). Genotypes of the Tagil animals (TAGIL, n = 98; SPK Shorokhov, Perm Territory, 2021) were studied by multiplex analysis using 11 microsatellites (TGLA227, BM2113, TGLA53, ETH10, SPS115, TGLA122, INRA0623, TGL1812 ETH225, BM1824). For interbreed differentiation by STR markers in PCA, we used a set of breeds that could be potentially involved in the formation of the modern population of Tagil cattle (TAGIL) - Holstein (HLST), Kholmogory Holsteinized (Tatarstan type) (TAT), Kholmogorsk purebred (Pechora type) (PECH), black-and-white (old type) (Ch_P_OLD), Tagil (TAG) (samples from the ONIS BioTechZh database, 2020, https://www.vij.ru/2-obshchaya/226-infrastruktura-test). To cover maximum genetic diversity in genotyping of TAGIL by SNP markers, the most unrelated animals ( n = 48) were selected based on the results of analysis of STR genotypes. Genome-wide genotyping for SNP markers was performed using a high density GGP Bovine HD 150K BeadChip DNA chip (150,000 SNPs, Illumina, Inc., USA) (10,8432 SNPs before and 62,809 SNPs after LD filtration). A database of genome-wide SNP genotypes of Tagil cattle (TAGIL) was formed to analyze the results of SNP genotyping (population genetic and phylogenetic studies). Holstein animals (HLST) ( n = 45) were the reference group. We clearly differentiated the Tagil (TAGIL) and Holstein animals by PCA method. Cluster analysis based on genetic distances FST divided the Tagil and Holstein animals into two separate groups. Genome-wide SNP genotyping revealed genomic regions in which allelic variants are specific for the Tagil cattle (TAGIL). The hapFLK analysis showed five regions (p function show_eabstract() { $('#eabstract1').hide(); $('#eabstract2').show(); $('#eabstract_expand').hide(); }