One of the most economically important areas within the Russian agricultural sector is dairy and beef cattle farming contributing about $11 billion to the Russian economy annually. Trade connections, selection and breeding have resulted in the establishment of a number of breeds that are presumably adapted to local climatic conditions. Little however is known about the ancestry and history of Russian native cattle. To address this question, we genotyped 274 individuals from 18 breeds bred in Russia and compared them to 135 additional breeds from around the world that had been genotyped previously. Our results suggest a shared ancestry between most of the Russian cattle and European taurine breeds, apart from a few breeds that shared ancestry with the Asian taurines. The Yakut cattle, belonging to the latter group, was found to be the most diverged breed in the whole combined dataset according to structure results. Haplotype sharing further suggests that the Russian cattle can be divided into four major clusters reflecting ancestral relations with other breeds. Herein, we therefore shed light on to the history of Russian cattle and identified closely related breeds to those from Russia. Our results will facilitate future research on detecting signatures of selection in cattle genomes and eventually inform future genetics-assisted livestock breeding programs in Russia and in other countries.

BackgroundThe origin of native and locally developed Russian cattle breeds is linked to the historical, social, cultural, and climatic features of the diverse geographical regions of Russia. In the present study, we investigated the population structure of nine Russian cattle breeds and their relations to the cattle breeds from around the world to elucidate their origin. Genotyping of single nucleotide polymorphisms (SNPs) in Bestuzhev (n = 26), Russian Black-and-White (n = 21), Kalmyk (n = 14), Kholmogor (n = 25), Kostromsky (n = 20), Red Gorbatov (n = 23), Suksun (n = 20), Yakut (n = 25), and Yaroslavl cattle breeds (n = 21) was done using the Bovine SNP50 BeadChip. SNP profiles from an additional 70 breeds were included in the analysis as references.ResultsThe observed heterozygosity levels were quite similar in eight of the nine studied breeds (HO = 0.337–0.363) except for Yakut (Ho = 0.279). The inbreeding coefficients FIS ranged from -0.028 for Kalmyk to 0.036 for Russian Black-and-White and were comparable to those of the European breeds. The nine studied Russian breeds exhibited taurine ancestry along the C1 axis of the multidimensional scaling (MDS)-plot, but Yakut was clearly separated from the European taurine breeds on the C2 axis. Neighbor-Net and admixture analyses, discriminated three groups among the studied Russian breeds. Yakut and Kalmyk were assigned to a separate group because of their Turano-Mongolian origin. Russian Black-and-White, Kostromsky and Suksun showed transboundary European ancestry, which originated from the Holstein, Brown Swiss, and Danish Red breeds, respectively. The lowest level of introgression of transboundary breeds was recorded for the Kholmogor, Yaroslavl, Red Gorbatov and Bestuzhev breeds, which can be considered as an authentic genetic resource.ConclusionsWhole-genome SNP analysis revealed that Russian native and locally developed breeds have conserved authentic genetic patterns in spite of the considerable influence of Eurasian taurine cattle. In this paper, we provide fundamental genomic information that will contribute to the development of more accurate breed conservation programs and genetic improvement strategies.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0408-8) contains supplementary material, which is available to authorized users.

Conservation of local cattle genetic resources is an important strategy for achieving Russia’s food security. During last decades, in the Russian Federation, local livestock populations were either crossbred or replaced by highly productive imported breeds, which led to a loss of the major part of original breeds identities. The objective of our study was to identify genetic differences between the populations of Kholmogor and Black-and-white cattle with varying degrees of admixture with the Holstein breed. The aforementioned breeds were studied using their whole-genome single nucleotide polymorphism (SNP) genotypes. The Kholmogor breed was subdivided into three groups: purebred (KHLM, n = 3), admixed with Holsteins (KHLM-HLST, n = 4) and representatives of old-type breed (KHLM-INTA, n = 15). Blackand-white was subdivided into four groups: purebred (BLWT, n = 9), with a low (BLWT-75, n = 8) and a high (BLWT-HLST, n = 10) level of admixture with Holstein, and represented by archival samples from the 1970s and 1980s (BLWT-OLD, n = 15). The Holsteins genetic profiles (HLST, n = 27) were taken as a comparison group. PLINK 1.07, Admixture 1.3, SplitsTree 4.14.6 and R package StAMPP were used to infer genetic relationship between the studied groups. After quality control, 29 688 SNPs were selected for analysis. Multidimensional scaling (MDS), Admixture analysis and a dendrogram constructed using the Neighbor-Net method, revealed the presence of three clusters belonging to the Kholmogor, Black-and-white and Holstein breeds. The first one included KHLM and KHLM-INTA, the second – BLWT and BLWT-OLD, and the third – HLST, KHLM-HLST and BLWT-HLST. The BLWT-75 samples were placed between HLST and BLWT. Thus, our results showed that currently the populations of native cattle breeds with valuable genotypes still exist. The populations with a high level of admixture with Holsteins could be considered neither as the Kholmogor nor as Blackand-white breeds, and would rather be referred as the Holstein breed of local breeding.

Abstract.Comparative characteristics of different methods for estimation of freshness of eggs are presented: by the air chamber size; reducing the weight of eggs; mobility yolk; protein consistency; the index of albumen and yolk; and other indicators. The advantage of assessment eggs by freshness index, actual density to the initial density (fresh eggs) is described. The initial density is determined by elastic deformation of the shell, which does not change during storage of eggs. A table has been developed to determine the initial density by elastic deformation. The notion "hydro-density" (in mg·cm -3 ) is introduced; the mass of an egg in distilled water did not change the volume during storage. "Hydro-density" is a simplified expression of density: 1085 g·cm -3 equals to 85 mg·cm -3 . The freshness index varies from 100 to 0 % (the egg floats in water). It is proposed that if eggs have the freshness index 88 % they are considered as dietary eggs, which have 64 % -as table eggs; that corresponds to daily shrinkage of eggs not more than 0.17-0.14 %. The valuation technique of eggs by the freshness index is objective, it does not require opening the eggs and can be used for quality control of food and hatching eggs.Keywords: "hydro-density", egg, freshness of eggs. IntroductionThe egg is the best source of amino acids, which the UN FAO adopted as the standard [1]. However, an egg is a highly unsustainable biological stuff, because of a huge variety of nutrients and biologically active substances enclosed in a small package. These substances are suspension systems that facilitate interaction between them and progress in inevitable reactions. Moreover, through the pores of the eggshell inside the egg aggressive oxygen and various bacteria penetrate. In this regard, the egg quickly loses its freshness, gets old and becomes unfit for food purposes or reproduction (incubation) [2]. The aging process starts immediately after laying eggs [3]. Dissolved carbon dioxide in protein (average 3.5 mg per day) exits through the pores of the shell from the egg in the first days. With loss of CO 2 the protein pH (from 7.6 to 9.2) significantly increases. This leads to rapid destruction of the gel consistency of the protein dense layer [4][5][6]. An aging egg accompanied by loosening shell of yolk is up to rupture. The old egg lost its protective reserves, exposed various kinds of bacteria and fungi leading to its final damage [4; 5; 7].For successful effort to contain aging and to preserve freshness of eggs it is necessary to assess its "age" objectively. There are several methods of estimating the age of eggs, one of them onto the intact egg, the others after its autopsies.Currently, many researches have been focused on egg quality examination. For example, different non-destructive techniques for automatically detecting cracks, dirt and blood spots have been investigated [9][10][11]. Although these criteria could be useful as exclusion criteria in an on-line system, they could not demonstrate the internal quality of eggs. The...