Genetic diversity and genomic signatures of selection among cattle breeds from Siberia, eastern and northern Europe

Abstract

Domestication in the near eastern region had a major impact on the gene pool of humpless taurine cattle (Bos taurus). As a result of subsequent natural and artificial selection, hundreds of different breeds have evolved, displaying a broad range of phenotypic traits. Here, 10 Eurasian B. taurus breeds from different biogeographic and production conditions, which exhibit different demographic histories and have been under artificial selection at various intensities, were investigated using the Illumina BovineSNP50 panel to understand their genetic diversity and population structure. In addition, we scanned genomes from eight breeds for signatures of diversifying selection. Our population structure analysis indicated six distinct breed groups, the most divergent being the Yakutian cattle from Siberia. Selection signals were shared (experimental P-value < 0.01) with more than four breeds on chromosomes 6, 7, 13, 16 and 22. The strongest selection signals in the Yakutian cattle were found on chromosomes 7 and 21, where a miRNA gene and genes related to immune system processes are respectively located. In general, genomic regions indicating selection overlapped with known QTL associated with milk production (e.g. on chromosome 19), reproduction (e.g. on chromosome 24) and meat quality (e.g. on chromosome 7). The selection map created in this study shows that native cattle breeds and their genetic resources represent unique material for future breeding.

Domestication of cattle: Two or three events?

“…Illumina's BovineSNP50 v.1, v.2 and Bovine High Density BeadChip 770k SNP array data were merged from several previously published studies ( Supporting Information Table S1; Bovine Hapmap et al 2009;Decker et al, 2009;Gautier, Laloë, & Moazami-Goudarzi, 2010;McTavish, Decker, Schnabel, Taylor, & Hillis, 2013;Decker et al, 2014;Mbole-Kariuki et al, 2014;Orozco-terWengel et al, 2015;Park et al, 2015;Iso-Touru et al, 2016;Upadhyay et al, 2017;Pitt et al, 2018). After removing duplicated copies of individuals, the final data set comprised ~54,000 SNPs in most samples and corresponded to 3,196 individuals representing 180 breeds/populations of both taurine (n = 2,041) and indicine (n = 408) cattle, including hybrids of the two subspecies (Supporting Information Table S1).…”

Molecular-Genetic Analysis of Cows Genetic Structure and Determination of Genealogical Relatedness Level of Bulls of Modern Dairy Breeds

“…Only those PCR products were analyzed, which were clearly reproduced on the gels in the range of molecular weights relative to the marker: from 200 bp up to 3000 bp in the course of 3 repetitive amplification reactions. The received profiles were processed in the standard computer program GenAlex6 (Buys, 1990;Peakall and Smouse, 2006). The construction of the cluster was carried out according to the values of genetic distances in the MEGA 4 program (Tamura et al, 2004).…”

“…One of the directions of the use of these immunogenetic studies in breeding is the study of the genetic structure of the breeding populations, herds, lines by marker genes. Studies of many scientists proved the reliability of using the blood genetic markers for the cattle genotype evaluation (Iso-Touru et al, 2016).…”

Whole genome studies of origin, selection and adaptation of the Russian cattle breeds

“…Недавние исследования по полногеномному генотипированию коренных европейских пород скота включали несколько коренных российских пород (Зиновьева и др., 2016;Iso-Touru et al, 2016;Upadhyay et al, 2017). Однако при этом авторы, как правило, не проводили исчерпывающего сравнения между российским скотом и мировыми породами.…”