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.

BackgroundIt is generally accepted that domestication of pigs took place in multiple locations across Eurasia; the breeds that originated in Europe and Asia have been well studied. However, the genetic structure of pig breeds from Russia, Belorussia, Kazakhstan and Ukraine, which represent large geographical areas and diverse climatic zones in Eurasia, remains largely unknown.ResultsThis study provides the first genomic survey of 170 pigs representing 13 breeds from Russia, Belorussia, Kazakhstan and Ukraine; 288 pigs from six Chinese and seven European breeds were also included for comparison. Our findings show that the 13 novel breeds tested derived mainly from European pigs through the complex admixture of Large White, Landrace, Duroc, Hampshire and other breeds, and that they display no geographic structure based on genetic distance. We also found a considerable Asian contribution to the miniature Siberian pigs (Minisib breed) from Russia. Apart from the Minisib, Urzhum, Ukrainian Spotted Steppe and Ukrainian White Steppe breeds, which may have undergone intensive inbreeding, the breeds included in this study showed relatively high genetic diversity and low levels of homozygosity compared to the Chinese indigenous pig breeds.ConclusionsThis study provides the first genomic overview of the population structure and genetic diversity of 13 representative pig breeds from Russia, Belorussia, Kazakhstan and Ukraine; this information will be useful for the preservation and management of these breeds.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0196-y) contains supplementary material, which is available to authorized users.

Reproductive productivity depend on a complex set of characteristics. The number of piglets at birth (Total number born, Litter size, TNB) and the number of alive piglets at birth (Total number born alive, NBA) are the main indicators of the reproductive productivity of sows in pig breeding. Great hopes are pinned on GWAS (Genome-Wide Association Studies) to solve the problems associated with studying the genetic architecture of reproductive traits of pigs. This paper provides an overview of international studies on SNP (Single nucleotide polymorphism) associated with TNB and NBA in pigs presented in PigQTLdb as “Genome map association”. Currently on the base of Genome map association results 306 SNPs associated with TNB (218 SNPs) and NBA (88 SNPs) have been identified and presented in the Pig QTLdb database. The results are based on research of pigs such as Large White, Yorkshire, Landrace, Berkshire, Duroc and Erhualian. The presented review shows that most SNPs found in chromosome areas where candidate genes or QTLs (Quantitative trait locus) have been identified. Further research in the given direction will allow to obtain new data that will become an impulse for creating breakthrough breeding technologies and increase the production efficiency in pig farming.

Industrial pig farming is associated with negative technological pressure on the bodies of pigs. Leg weakness and lameness are the sources of significant economic loss in raising pigs. Therefore, it is important to identify the predictors of limb condition. This work presents assessments of the state of limbs using indicators of growth and meat characteristics of pigs based on machine learning algorithms. We have evaluated and compared the accuracy of prediction for nine ML classification algorithms (Random Forest, K-Nearest Neighbors, Artificial Neural Networks, C50Tree, Support Vector Machines, Naive Bayes, Generalized Linear Models, Boost, and Linear Discriminant Analysis) and have identified the Random Forest and K-Nearest Neighbors as the best-performing algorithms for predicting pig leg weakness using a small set of simple measurements that can be taken at an early stage of animal development. Measurements of Muscle Thickness, Back Fat amount, and Average Daily Gain were found to be significant predictors of the conformation of pig limbs. Our work demonstrates the utility and relative ease of using machine learning algorithms to assess the state of limbs in pigs based on growth rate and meat characteristics.

A b s t r a c tAt the current stage of biological development is impossible to establish conservation programs and to monitor genetic resources of sheep without a preliminary study by DNA markers. The Russian sheep breeding is represented by wide variety of breeds, including all productivity and wool types. However, until recently only some sheep breeds, which belong to the same breeding zone or productivity type, were investigated by DNA markers including microsatellites. We studied 25 Russian sheep breeds (n = 751), including fine-fleeced -Dagestan Mountain (DAG), Grozny (GRZ), Kulunda (KUL), Manych Merino (MNM), Salskaya (SAL), Stavropol (STA), Soviet Merino (SVM), Volgograd (VOL), Baikal's fine-fleeced (ZBL); semi fine-fleeced -Altay Mountain (ALT), Kuibyshev (KUI), North Caucasian (NC), Russian long-haired (RLH), Tsigai (TSIG); coarsewooled -Andean (AND), Buubey (BUB), Edilbai (EDL), Karachaev (KAR), Kuchugur (KCH), Kalmyk (KLM), Karakul (KRK), Lezgin (LEZ), Romanov (ROM), Tushin (TSH), Tuvan short fat-tailed (TUV). The research was conducted using 11 microsatellite loci (OarCP49, INRA063, HSC, OarAE129, MAF214, OarFCB11, INRA005, SPS113, INRA23, MAF65 и McM527). The data were processed using GenAIEx 6.5 and PAST software. In general, the studied breeds were characterized by moderately high allelic diversity. The average number of alleles per locus is varied from 7.20±0.98 in KUL and 10.30±0.99 in TSIG. The values of Na≥10.0 were found in TSIG, TUV, BUB and KRK, values of Na≤8.0 were identified in KUL, RLH and SVM. The effective allele number was the highest in the KRK and TUV (Ne≥5.7) and the minimum was detected in KCH, ALT, RLH and NC (Ne≤4.3). The level of the observed heterozygosity in 21 of the 25 studied breeds ranged from 0.489±0.095 in TUV to 0.651±0.050 in ROM and 0.651±0.060 in SVM, and four other breeds (BUB, TSIG, ZBL and TUV) it varied from 0.798±0.023 in BUB up 0.977±0.017 in TUV. There was a substantial deficit of heterozygotes in 21 of the 25 studied breeds (F IS values ranged from 0.13 in ROM to 0.36 in KAR and SAL), in the other four (BUB, TSIG, ZBL and TUV) an excess of heterozygotes (F IS values ranged from 0.04 to 0.22) was detected. The analysis of molecular variance (AMOVA) showed that 5.02 % of genetic variation is composed of differences among breeds and 94.98 % is explained by within breeds' component. Analysis of the structure of the UMPGA phylogenetic tree, based on the matrix of pairwise genetic distances by M. Nei (1972), showed that the nature of the identified relationships is mainly related with the wool type, productivity type and breeding region. Thus, the identified polymorphism of eleven microsatellite loci is quite powerful for differentiating sheep of various breeds. For a better understanding population structure and obtaining new information on the genetic diversity at the genomic level the application of DNA microarrays, based on the multiple SNPs-markers, is required.