Whole genome study of single nucleotide polymorphisms’ associations with withers height in local and transboundary breeds in Russia

The stature of an animal is a classic quantitative trait that affects the predisposition to certain diseases and is associated with the productivity of farm animals. Currently, many quantitative trait loci (QTL) have been mapped that affect the cattle’s growth constituents, which confirms its polygenic determinism. An assessment of the frequencies of SNPs alleles associated with withers height in cattle populations bred in Russia has been carried out firstly in this work. The prevalence of alleles associated with high stature of animals in three out of four identified single nucleotide polymorphisms in Russian local breeds was revealed. The aim of the work was to identify loci that are under selection pressure and associated with body size in populations of Russian local breeds and transboundary breeds bred in the territory of the Russian Federation, belonging to different types of productivity, as well as with an unequal degree of pressure of artificial selection and distribution in the world. Thirteen cattle breeds ( n = 670) subjected to our study including Angus ( n = 39), Ayrshire ( n = 144), Black-and-White ( n = 50), Holstein ( n = 184), Istoben ( n = 22), Jersey ( n = 32), Kalmyk ( n = 27), Kholmogor ( n = 26), Kyrgyz ( n = 24), Mongolian ( n = 26), Tagil ( n = 26), Yakut ( n = 29) and Yaroslavl ( n = 41). Samples of blood, tissue and sperm stored in UNU “Genetic material bank of domestic and wild animal species and birds” of the Ernst Federal Research Center for Animal Husbandry were used as a source of DNA for this study. The samples were genotyped using DNA arrays GGP Bovine 150K and BovineHD BeadChip (Illumina Inc., USA) with the different density. In the course of data processing, SNPs common for the two arrays were determined and were used for further analysis. The genome-wide study of the associations of genotyping data with measurements of physical development of animals was carried out by the PLINK 1.9 program using filters (--geno 0.1), (--mind 0.2), (--maf 0.05). Height at withers for the studied breeds was obtained from the FAO database. All studied breeds were divided into groups according to the following criteria: growth (tall, short), type of productivity (dairy, meat), the degree of pressure of artificial selection (primitive, commercial) and distribution in the world (local, transboundary). Four SNPs were identified in total. Three of them were localized on chromosome 4 (ARS-BFGL-NGS-116590, Hapmap53144-ss46525999, BovineHD0400021479), and one on chromosome 14 (BovineHD1400007259). The alternative alleles in the detected SNPs significantly differ in their frequency in different groups of breeds, and also have significant positive or negative correlations with the height at the withers. The diversity and heterogeneity of the breeds presented in the study allows us to consider the identified traces of selection not as characteristic of one breed, region or type of productivity, but as for a group of breeds of the species Bos taurus taurus , the distribution of which from the center of domestication proceeded along the Danube Route. Thus, the identified SNPs can be used as genetic markers in breeding programs in order to increase the stature of animals and their productivity.