Estimation of genetic relationships of black-and-white cattle breeds with ancestral populations based of genome-wide SNP-genotyping of modern and museum samples

Kholmogor and Yaroslavl cattle are the most widespread among Russian local breeds. However, the history of their origin and development is still a matter of debate and requires clarification. The large-scale use of Holstein bulls for improvement could lead to a significant alterations in the allele pool of local breeds. The inclusion of museum samples in the analyses allows shed the light on the history of creation and development of the breeds and to assess whether ancestral components are preserved in the modern Kholmogor and Yaroslavl breeds. For the first time in this work describes the results of analyses of genetic diversity and structure of modern Black-and-White cattle in comparison with ancestral populations using high-density DNA microarray, and assesses the influence of imported breeds on the formation of the gene pool of Kholmogor and Yaroslavl cattle in the end XIX-early XX century. The aim of our work was to analyze the genetic relationships between ancestral and modern populations of Black-and-White cattle, to estimate the proportion of ancestral components in modern breeds, to clarify the history of origin and development of the Kholmogor and Yaroslavl breeds of cattle based on genotyping data using a high-density DNA microarray. DNA extraction from museum samples was carried out using the COrDIS Extract Decalcine kit (GORDIZ LLC, Russia) with some modifications (increased lysis time and volume of reagents per sample) of the DNA extraction protocol recommended by the manufacturer. Whole-genome analysis of 68 museum samples using a high-density DNA microarray (Bovine GGP HD BeadChip, Illumina, Inc., USA) containing about 150,000 SNPs was carried out using the iScan system (Illumina, Inc., USA). The obtained SNP-genotypes were used to generate a combined dataset including SNP-genotypes of 31 museum (Kholmogor breed, H_KHLM, n = 17; Yaroslavl breed, H_YRSL, n = 12; Great Russian cattle, H_GRUS, n = 1; East Friesian cattle, H_OFRZ, n = 1) and 132 modern samples (Yaroslavl, YRSL, n = 53; Kholmogor, KHLM, n = 26; Holstein, HLST, n = 54). To estimate genetic diversity in each breed, observed (HO) and unbiased expected (UHE) heterozygosity, inbreeding coefficient (UFIS) and allelic diversity adjusted for sample size (AR) were calculated using the R package ‘diveRsity’. Genetic differences between breeds were estimated in PLINK v1.90 by principal component analysis (PCA) visualised using the R package ‘ggplot2’. Pairwise distances for identical-by-state (identical-by-state, IBS) fragments were used to construct a ‘neighbourhood network’ dendrogram in SplitsTree 4.14.5 software. Pairwise F ST values were calculated in the R-package ‘diveRsity’ and used to construct ‘neighbourhood network’ dendrograms in SplitsTree 4.14.5 software. The cluster structure of populations was investigated in ADMIXTURE v1.23 software. Visualisation of the analysis results was performed using the R package ‘BITE’. To assess the presence and degree of introgression between breeds, D-statistics and F4-statistics were calculated using the R package ‘admixr’. To assess the degree of population divergence and extent of gene exchange between breeds, TreeMix 1.12 software was used. Yakut breed was used as an outgroup in the construction of TreeMix maximum likelihood (ML) tree. The results of our studies indicate more significant changes in the gene pool of the Yaroslavl breed over the XX century compared to the Kholmogor breed, both due to the breeding process and using limited number of bull sires because of a decrease in the population. It was found that allelic diversity (AR) in ancestral populations of Kholmogor and Yaroslavl cattle was significantly (p ST = 0.040; D = 0.257) compared to their counterparts for H_YRSL and YRSL (F ST = 0.099; D = 0.353). The results of introgression analysis using D- and F-statistics and TreeMix analysis confirmed the genetic relationships between H_GRUS and H_YRSL. The presence of some proportion of East Friesian cattle genomic components in historical samples of Kholmogor and Yaroslavl breeds was shown which confirms the use of imported foreign breeds in breeding of Russian local cattle at the turn of the XIX-XX centuries. The modern populations of Kholmogor and Yaroslavl breeds almost have no introgression of Holstein breed, but they retain genomic components of ancestral populations.