Linkage disequilibrium decay in the dairy cattle population of the Sverdlovsk region
https://doi.org/10.31677/2072-6724-2025-77-4-217-225
Abstract
Over the past two decades, the dairy cattle population in the Sverdlovsk region has undergone a transition from Black Pied to Holstein breeds, raising questions about its consequences for the genome structure. Analysis of linkage disequilibrium is a key tool for evaluating genetic structure, efficiency of genomic selection, and preservation of genetic diversity. A comparison of two generations of female stock in the Sverdlovsk region revealed that younger animals have 20–35 % higher values of linkage disequilibrium compared to older ones. The average values of determination coefficient (R²) across the genome were 0.10 and 0.08, while normalized coefficients (D’) were 0.59 and 0.50 for younger and older generations, respectively. Despite differences in mean values, the overall pattern of distribution of linkage disequilibrium along chromosomes remains consistent (Spearman correlation coefficient >0.94). Linkage disequilibrium peaks are observed on chromosomes BTA14, BTA16, and BTA20, where loci associated with milk productivity and health are located. The rate of decay of linkage disequilibrium is higher in the older generation compared to young individuals. These findings indicate an increase in selection intensity and greater homogeneity of the genome in modern populations, which is important for optimizing regional programs of genomic selection.
About the Authors
G. A. Lihodeevskiy
Ural State Agrarian University
Russian Federation
Russian Federation
Junior Researcher Laboratories of molecular and biological research
Yekaterinburg
O. A. Minina
Ural State Agrarian University
Russian Federation
Russian Federation
Lab Research Assistant Laboratory of veterinary and sanitary examination
Yekaterinburg
P. S. Bogatova
Ural State Agrarian University
Russian Federation
Russian Federation
Junior Researcher Laboratories of molecular and biological research
Yekaterinburg
O. E. Lihodeevskaya
Ural State Agrarian University
Russian Federation
Russian Federation
Candidate of Biological Sciences, Associate Professor, Head of Laboratory of molecular and biological research
Yekaterinburg
References
1. Modorov M.V., Tkachenko I.V., Green A.A. [et al.], Population genetic structure of Ural Black Pied cattle, Russian Journal of Genetics, 2021, Vol. 57, No. 4, pp. 453–459, DOI: 10.1134/S1022795421040104.
2. Lihodeevskiy G.A., Bogatova P.S., Lihodeevskaya O.E. [et al.], Dynamics of the genetic structure of dairy cattle population in the Sverdlovsk region, BIO Web Conferences, 2025, Vol. 179, pp. 03002, DOI: 10.1051/bioconf/202517903002.
3. Hill W.G., Robertson A., Linkage disequilibrium in finite populations, Theor Appl Genet, 1968, Vol. 38, No. 6, pp. 226–231, DOI: 10.1007/BF01245622. PMID: 24442307.
4. Lewontin R.C., The Interaction of Selection and Linkage. I. General Considerations; Heterotic Models, Genetics, 1964, Vol. 49, No. 1, pp. 49–67, DOI: 10.1093/genetics/49.1.49.
5. Qanbari S., On the Extent of Linkage Disequilibrium in the Genome of Farm Animals, Front Genet, 2020, Vol. 10, pp. 1304, DOI: 10.3389/fgene.2019.01304.
6. Vallejo R.L., Li Y.L., Rogers G.W. [et al.], Genetic diversity and background linkage disequilibrium in the North American Holstein cattle population, Journal of Dairy Science, 2003, Vol. 86, No. 12, pp. 4137–4147, DOI: 10.3168/jds.S0022-0302(03)74028-4).
7. Sargolzaei M, Schenkel FS, Jansen GB, Schaeffer LR., Extent of linkage disequilibrium in Holstein cattle in North America, J Dairy Sci, 2008, Vol. 91, No. 5, pp. 2106–2117, DOI: 10.3168/jds.2007-0553.
8. Bohmanova J., Sargolzaei M., Schenkel F.S., Characteristics of linkage disequilibrium in North American Holsteins, BMC Genomics, 2010, Vol. 11, pp. 421, DOI: 10.1186/1471-2164-11-421.
9. Khatkar M.S., Nicholas F.W., Collins A.R. [et al.], Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel, BMC Genomics, 2008, Vol. 9, pp. 187, DOI: 10.1186/1471-2164-9-187.
10. Qanbari S., Pimentel E.C.G., Tetens J. [et al.], The pattern of linkage disequilibrium in German Holstein cattle, Anim Genet, 2010, Vol. 41, pp. 346–356, DOI: 10.1111/j.1365-2052.2009.02011.x.
11. Tenesa A., Wright A.F., Knott S.A. [et al.], Extent of linkage disequilibrium in a Sardinian sub-isolate: sampling and methodological considerations, Hum Mol Genet, 2004, Vol. 13, No. 1, pp. 25–33, DOI: 10.1093/hmg/ddh001.
12. Salem M., Thompson G., Chen S. [et al.], Linkage Disequilibrium and Haplotype Block Structure in Portuguese Holstein Cattle, Czech Journal of Animal Science, 2018, Vol. 63, pp. 61–96, DOI: 10.17221/56/2017-CJAS.
13. Šaran M., Štrbac L., Jankovic D. [et al.], Genomic characterization of Serbian Holstein-Friesian cattle population, Czech Journal of Animal Science, 2023, Vol. 68, pp 468–496, DOI: 10.17221/89/2023-CJAS.
14. Špehar M., Ivkić Z., Solić D. [et al.], The estimation of linkage disequilibrium decay in Croatian Holstein cattle: potential for genomic selection, I. Majić, ed., Z. Antunović, ed. Zbornik radova 57. hrvatskog i 17. međunarodnog simpozija agronoma. Osijek: Fakultet agrobiotehničkih znanosti Sveučilišta Josipa Jurja Strossmayera, 2022, pp. 521– 525, URL: https://urn.nsk.hr/urn:nbn:hr:204:965296.
15. Bordbar F., Jensen J., Wadood A.A. [et al.], Linkage Disequilibrium Decay in Selected Cattle Breeds, Animals (Basel), 2024, Vol. 14, No. 22, pp. 3317, DOI: 10.3390/ani14223317.
16. de Roos A.P., Hayes B.J., Spelman R.J. [et al.], Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle, Genetics, 2008, Vol. 179, No. 3, pp. 1503–1512, DOI: 10.1534/genetics.107.084301.
17. Peters S.O., Kizilkaya K., Ibeagha-Awemu E.M. [et al.], Comparative accuracies of genetic values predicted for economically important milk traits, genome-wide association, and linkage disequilibrium patterns of Canadian Holstein cows, J Dairy Sci, 2021, Vol. 104, No. 2, pp. 1900–1916, DOI: 10.3168/jds.2020-18489.
18. Zhang M., Xu L., Lu H. [et al.], Genomic prediction based on a joint reference population for the Xinjiang Brown cattle, Front Genet, 2024, No. 15, pp. 1394636, DOI: 10.3389/fgene.2024.1394636. PMID: 38737126. PMCID: PMC11082323.
19. Sermyagin AA, Belous AA, Konte AF, et al., Sel’skokhozyaistvennaya biologiya, 2017, No. 52 (6), pp. 1148–1156, DOI: 10.15389/agrobiology.2017.6.1148rus. (In Russ.)
20. Bordbar F., Jensen J., Wadood A.A. [et al.], Linkage Disequilibrium Decay in Selected Cattle Breeds, Animals (Basel), 2024, Vol. 14, No. 22, pp. 3317, DOI: 10.3390/ani14223317.
21. R Core Team. R: A language and environment for statistical computing: – Version 4.3.2. – Vienna: R Foundation for Statistical Computing, 2023, URL: https://www.r-project.org.
22. Purcell S., Neale B., Todd-Brown K. [et al.], PLINK: A tool set for whole-genome association and population-based linkage analyses, American Journal of Human Genetics, 2007, No. 81, pp. 559–575.
23. Manichaikul A., Mychaleckyj J.C., Rich S.S. [et al.], Robust relationship inference in genome-wide association studies, Bioinformatics, 2010, Vol. 15, No. 22, pp. 2867–2873, DOI: 10.1093/bioinformatics/btq559.
24. Clayton, D. snpStats: SnpMatrix and XSnpMatrix classes and methods: – Версия 1.59.2. – 2025, URL: https://bioconductor.org/packages/snpStats.
25. Muggeo V.M.R., Estimating regression models with unknown break-points, Statistics in Medicine, 2003, Vol. 22, pp. 3055–3071, DOI: doi.org/10.1002/sim.1545.
26. Wickham H., ggplot2: Elegant Graphics for Data Analysis, Cham: Springer International Publishing, 2016, 260 p.
27. Lu D., Sargolzaei M., Kelly M. [et al.], Linkage disequilibrium in Angus, Charolais, and Crossbred beef cattle, Front Genet, 2012, Vol. 3, pp. 152, DOI: 10.3389/fgene.2012.00152.
28. Wibowo T.A., Gaskins C.T., Newberry R.C. [et al.], Genome assembly anchored QTL map of bovine chromosome 14, Int J Biol Sci, 2008, Vol. 4, No. 6, pp. 406–414, DOI: 10.7150/ijbs.4.406.
29. Sun D., Jia J., Ma Y. [et al.], Effects of DGAT1 and GHR on milk yield and milk composition in the Chinese dairy population, Anim Genet, 2009, Vol. 40, No 6, pp. 997–1000, DOI: 10.1111/j.1365-2052.2009.01945.x.
30. Jiang J., Ma L., Prakapenka D. [et al.], A Large-Scale Genome-Wide Association Study in U.S. Holstein Cattle, Front Genet, 2019, Vol. 10, pp. 412, DOI: 10.3389/fgene.2019.00412.
31. Bekele R., Taye M., Abebe G. [et al.], Genomic Regions and Candidate Genes Associated with Milk Production Traits in Holstein and Its Crossbred Cattle: A Review, Int J Genomics, 2023, Vol. 2023, pp. 8497453, DOI: 10.1155/2023/8497453.
32. Kadri N.K., Guldbrandtsen B., Lund M.S. [et al.], Genetic dissection of milk yield traits and mastitis resistance quantitative trait loci on chromosome 20 in dairy cattle, J Dairy Sci, 2015, Vol. 98, No. 12, pp. 9015–9025, DOI: 10.3168/ jds.2015-9599.
33. Canive M., Badia-Bringué G., Vázquez P. [et al.], A Genome-Wide Association Study for Tolerance to Paratuberculosis Identifies Candidate Genes Involved in DNA Packaging, DNA Damage Repair, Innate Immunity, and Pathogen Persistence, Front Immunol, 2022, Vol. 13, pp. 820965, DOI: 10.3389/fimmu.2022.820965.
34. Sousa Junior L.P.B., Pinto L.F.B., Cruz V.A.R. [et al.], Genome-wide association and functional genomic analyses for body conformation traits in North American Holstein cattle, Front Genet, 2024, Vol. 15, pp. 1478788, DOI: 10.3389/fgene.2024.1478788.
Review
For citations:
Lihodeevskiy G.A., Minina O.A., Bogatova P.S., Lihodeevskaya O.E. Linkage disequilibrium decay in the dairy cattle population of the Sverdlovsk region. Bulletin of NSAU (Novosibirsk State Agrarian University). 2025;(4):217-225. (In Russ.) https://doi.org/10.31677/2072-6724-2025-77-4-217-225
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