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Mixed linear models have been applied for predicting breeding values of dairy cattle in most of the developed countries since the 1980s. However, the Russian Federation is still using the old contemporary comparison method. The objective of our study was to develop a best linear unbiased prediction (BLUP) for an animal model of breeding values for the Leningrad region. We tested both a first-lactation model (FLM) and a multi-lactation repeatability model (MLM). The data included milk records of 206 114 cows from 49 herds. Estimated heritabilities from FLM were 0.24, 0.20, and 0.20 for milk, protein, and fat yields, respectively, and 0.18, 0.19, and 0.20 from MLM. Repeatabilities were 0.34 for milk yield and 0.31 for both fat and protein yields. Genetic trends were similar for both models (FLM vs MLM): 59 vs 56 kg year-1 for milk, 1.90 vs 1.84 kg year-1 for fat, and 1.67 vs 1.62 kg year-1 for protein yield during 2000–2016. Based on the difference between the genetic trends in FLM and MLM, the applied BLUP method passed the validation method I by Interbull.

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Holstein bulls and semen have been imported to Russia from Western countries since the 1970s. The objective of our study was to examine the effect of this introgression on genetic diversity between various commercial Holstein herds in the Leningrad region. A total of 803 Holstein cows from 13 herds were genotyped using the Illumina BovineSNP50 v.2 array. The pairwise Hudson’s estimator of Fst values between 13 herds varied from 0.002 to 0.015, which is less than values usually obtained between dairy cattle breeds (> 0.1). The mean of these pairwise Fst values revealed differences between herds depending, mainly, on the proportion of common sires shared between the herds. In addition, we investigated the cause of negative Fst values. Based on our results, these negative values could be interpreted as an excess of within-herd genetic diversity over the between-herds genetic diversity. Our results show that introgressions of Holstein genes into Russian Black and White cattle of the Leningrad region have created genetic separation between herds similar with those for Jersey cows in USA, Australia and New Zealand.