Evaluation of current gene pool of Kholmogor and Black-and-white cattle breeds based on whole genome SNP analysis

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.

cattle, SNP, markers, whole-genome analysis, genetic resources conservation

1. Alexander D.H., Novembre J., Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19:1655-1664. DOI 10.1101/gr.094052.109.

2. Baranov A.V. Problems of biodiversity conservation in animal husbandry. Dostizheniya Nauki i Tekhniki APK = Achievements of Science and Technology of AIC. 2011;9:21-22. (in Russian)

3. Decker J.E., Pires J.C., Contant G.C., McKay S.D., Heaton M.P., Chen K., Cooper A., Vilkki J., Seabury C.M., Caetano A.R., Johnson G.S., Brenneman R.A., Hanotte O., Eggert L.S., Wiener P., Kim J.-J., Kim K.S., Sonstegard T.S., VanTassell C.P., Neibergs H.L., McEwan J.C., Brauning R., Coutinho L.L., Babar M.E., Wilson G.A., McClure M.C., Rolf M.M., Kim J.W., Schnabel R.D., Taylor J.F. Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proc. Natl. Acad. Sci. USA. 2009;106(44):18644-18649. DOI 10.1073/pnas.0904691106.

4. Dmitriev N.G. Cattle Breeds in the World. Leningrad: Spra vochnaya Kniga Publ., 1978. (in Russian) Dmitriev N.G., Paronyan I.A. Genetic Resources of Farm Animals in Russia and Neighboring Countries. St. Petersburg, 1994. (in Russian)

5. Elsik C.G., Bovine Genome Sequencing and Analysis Consortium. The genome sequence of taurine cattle: A window to ruminant biology and evolution. Science. 2009;324(5926):522-528. DOI 10.1126/science.1169588.

6. Ernst L.K., Beguchev A.P., Levantin D.L. Livestock Husbandry. Moscow: Kolos Publ., 1977. (in Russian)

7. Francis R.M. POPHELPER: an R package and web app to analyse and visualize population structure. Mol. Ecol. Resour. 2017;17:27-32. DOI 10.1111/1755-0998.12509.

8. Huson D.H., Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2006;23:254-267. DOI 10.1093/molbev/msj030.

9. Kalantar A.A. The fate of the “Russian” cattle. Puti Sel’skogo Hozyajstva = Paths of Farming. 1927a;10:181-190. (in Russian)

10. Kalantar A.A. The fate of the “Russian” cattle. Puti Sel’skogo Hozyajstva = Paths of Farming. 1927b;11:100-108. (in Russian)

11. Kuehn L.A., Keele J.W., Bennett G.L., McDaneld T.G., Smith T.P., Snelling W.M., Sonstegard T.S., Thallman R.M. Predicting breed composition using breed frequencies of 50,000 markers from the US Meat Animal Research Center 2,000 Bull Project. J. Anim. Sci. 2011;89(6):1742-1750. DOI 10.2527/jas.2010-3530.

12. Kuznetsov A.F. (Ed.) Cattle: Maintenance, Feeding, Diseases: Diagnosis and Treatment. St. Petersburg: Lan’ Publ., 2016. (in Russian)

13. Matyukov V.S., Tyrina Yu.O., Kantanen Yu., Stolpovskiy Yu.A. On features and the selective value of the gene pool in local cattle by the example of the Kholmogory breed. Selskokhozyaystvennaya Biologiya = Agricultural Biology. 2013;2:19-30. DOI 10.15389/agrobiology.2013.2.19eng (in Russian)

14. Matyukov V.S., Zharikov Ya.A. Methods of Modern Breeding and Preservation of the Gene Pool of Dairy Cattle in the Komi Republic (Recommendations for optimizing the use and conservation of the gene pool of Kholmogor cattle). Syktyvkar, 2012. (in Russian)

15. Matyukov V.S., Zharikov Ya.A., Zinovieva N.A. The genetic history and value of the gene pool of the endangered Kholmogory breed. Molochnoe i Myasnoe Skotovodstvo = Dairy and Beef Cattle Farming. 2018;2:2-8. DOI 10.25632/MMS.2018.2.13747. (in Russian)

16. McTavish E.J., Decker J.E., Schnabel R.D., Taylor J.F., Hillis D.M. New World cattle show ancestry from multiple independent domestication events. Proc. Natl. Acad. Sci. USA. 2013;110(15):E1398-E1406. DOI 10.1073/pnas.1303367110.

17. Pembleton L.W., Cogan N.O., Forster J.W. StAMPP: an R package for calculation of genetic differentiation and structure of mixedploidy level populations. Mol. Ecol. Resour. 2013;13:946-952. DOI 10.1111/1755-0998.12129.

18. Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M.A., Ben der D., Maller J., Sklar P., de Bakker P.I.W., Daly M.J., Sham P.C. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 2007;81:559-575. DOI 10.1086/519795.

19. R Core Team. R: a language and environment for statistical computing. R Foundation for statistical computing. Vienna, Austria, 2012. http://www.Rproject.org.

20. Rukhlova T.A., Yaluga V.L., Prozherin V.P. The “Northern” intrabreed type of Kholmogory cattle. Farm Animals. 2014;2(6):4855. (in Russian)

21. Saksa E.I., Barsukova O.E. Breeding and genetic characterization of highly productive holsteinized black-and-white cattle in the Leningrad region. Molochnoe i Myasnoe Skotovod - stvo = Dairy and Beef Cattle Farming. 2013;6:11-15. (in Russian)

22. Sermyagin A.A., Dotsev A.V., Gladyr E.A., Traspov A.A., Deniskova T.E., Kostyunina O.V., Reyer H., Wimmers K., Barbato M., Paronyan I.A., Plemyashov K.V., Sölkner J., Popov R.G., Brem G., Zi novieva N.A. Whole-genome SNP analysis elucidates the genetic structure of Russian cattle and its relationship with Eurasian taurine breeds. Genet. Sel. Evol. 2018;50:37. DOI 10.1186/s12711-018-0408-8.

23. Vereshchagin N. Reply to Mr. Polto ra tskiy’s story “On the improvement of cattle breeding in Russia”. Vestnik Russkogo Sel’skogo Khozyaystva = Herald of Russian Farming. 1889;8:657-662. (in Russian)

24. Wickham H. ggplot2: Elegant Graphics for Data Analysis. New York: Springer-Verlag, 2009. Yurchenko A., Yudin N., Aitnazarov R., Plyusnina A., Brukhin V., Soloshenko V., Lhasaranov B., Popov R., Paronyan I.A., Plemyashov K.V., Larkin D.M. Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds. Heredity. 2018; 120(2):125-137. DOI 10.1038/s41437-017-0024-3.

25. Zimin A.V., Delcher A.L., Florea L., Kelley D.R., Schatz M.C., Puiu D., Hanrahan F., Pertea G., VanTassell C.P., Sonstegard T.S., Marçais G., Roberts M., Subramanian P., Yorke J.A., Salzberg S.L. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol. 2009;10(4):R42. DOI 10.1186/gb-200910-4-r42.

26. Zinovieva N.A., Dotsev A.V., Sermyagin A.A., Wimmers K., Reyer H., Sölkner J., Deniskova T.E., Brem G. Study of the genetic diversity and population structure of five Russian cattle breeds by genome-wide SNP analysis. Selskokho zyaystvennaya Biologiya = Agricultural Biology. 2016;51(2):788-800. DOI 10.15389/agrobiology.2016.6.788eng.