Analysis of haplotype frequency distribution by CSN2 and CSN3 locus in the cattle population of the ukrainian black-and-white dairy breed

DOI: 10.32900/2312-8402-2022-128-94-104

Kulibaba Roman,
Doctor agricultural science, senior scientist,,
Sakhatskyi M. I.,
Doctor of Biological Sci., Professor, Academician of NAAS,,
National University of Life and Environmental Sciences of Ukraine
Liashenko Yurii,
Candidate of Agricultural Sciences, senior scientist,,
Institute of animal science of NAAS of Ukraine

Keywords: polymorphism, population, cows, allele, genotype, haplotype, linkage, marker


The study of the genetic structure of the cow population of the Ukrainian Black-and-White dairy breed were carried out in loci of beta-casein (CSN2) and kappa-casein (CSN3) loci, and the distribution of haplotype frequencies was analyzed. The polymorphism of the experimental loci was determined using AS-PCR (allele-specific PCR) in the case of CSN2 and PCR-RFLP (restriction analysis) in the case of CSN3. The frequencies of genotypes and alleles, the value of observable (Ho) and expected (He) heterozygosity, the Wright fixation index (Fis) and the effective number of alleles (ne) were determined based on the results of the studies. Haplotype frequencies were determined by calculating the EM-algorithm using the EH+ program. Calculations of the standardized measure of deviation by linkage from the equilibrium state were made using the 2LD program. According to the results of the studies, polymorphism was revealed for both experimental loci in the cattle population of the Ukrainian Black-and-White dairy breed. At the CSN2 locus, the A1 allele frequency was 0.44; A2 – 0.56. At the CSN3 locus, the A allele frequency was 0.80; allele B – 0.20. The experimental cattle population was in a state of genetic equilibrium in accordance with both polymorphic loci. Based on the analysis of the haplotype frequencies distribution, haplotype CSN2A1-CSN3A was found to have the highest frequency (0,46), haplotype CSN2A2-CSN3B had the smallest (0,085). In the experimental cattle population of the Ukrainian Black-and-White dairy breed there is no deviation from the equilibrium state by linkage (D′ = 0.33; which is significantly less than the critical value) between the identified allelic variants of the CSN2 and CSN3 loci. This indicates that the distribution of haplotype frequencies is the result of the particularities of the corresponding alleles frequency distribution.


  1. Eigel, W. N., Butler, J. E., Ernstrom, C. A., Farrell, H. M., Harwalkar, V. R., Jenness, R., & Whitney, R. M. (1984). Nomenclature of Proteins of Cow’s Milk: Fifth Revision. Journal of Dairy Science, 67(8), 1599–1631.
  2. Martin, P., Bianchi, L., Cebo, C., & Miranda, G. (2012). Genetic Polymorphism of Milk Proteins. Advanced Dairy Chemistry, 463–514.
  3. Jolles, P., Levy-Toledano, S., Fiat, A.-M., Soria, C., Gillessen, D., Thomaidis, A., & Caen, J. P. (1986). Analogy between fibrinogen and casein. Effect of an undecapeptide isolated from k-casein on platelet function. European Journal of Biochemistry, 158(2), 379–382.
  4. Alexander, L. J., Stewart, A. F., Mackinlay, A. G., Kapelinskaya, T. V., Tkach, T. M., & Gorodetsky, S. I. (1988). Isolation and characterization of the bovine k-casein gene. European Journal of Biochemistry, 178(2), 395–401.
  5. Azevedo, A. L. S., Nascimento, C. S., Steinberg, R. S., Carvalho, M. R. S., Peixoto, M. G. C. D., T’eodoro, R. L., Verneque, R. S., Guimarães, S. E. F., & Machado, M. A. (2008). Genetic polymorphism of the kappa-casein gene in Brazilian cattle. GeneticsandMolecularResearch, 7(3), 623–630.
  6. Cinar, M. U., Akyuz, B., Arslan, K., & Ilgar, E. G. (2015). Genotyping of the kappa-casein and beta-lactoglobulin genes in Anatolian water buffalo by PCR-RFLP. International Journal of Dairy Technology, 69(2), 308–311.
  7. Margawati, E. T., Volkandari, S. D., & Indriawati, C. T. (2016). Genotyping of Kappa-Casein Gene of Buffalo in Indonesian. Proceedings of International Seminar on Livestock Production and Veterinary Technology. 37–44.
  8. Miluchova, M., Trakovicka, A., & Gabor, M. (2009). Analiza polimorfismului genei β-cazeinei prin metoda PCR-RFLP pentru alelele. AI şi A2 la taurinele de rasă Pinzgau Slovacă. Lucrări ştiinţifice Zootehnie şi Biotehnologii, 42 (2).
  9. Review of the potential health impact of β-casomorphins and related peptides. (2009). EFSA Journal, 7(2), 231r. doi:10.2903/j.efsa.2009.231r.
  10. Gus’kova, S. V. (2017). A2 moloko – produkciya dlya detskogo pitaniya. Inform. Byulleten’. Nacional’nyj soyuz plemennyh organizacij. №1. Moskva.
  11. Ladyka, V. I., Skliarenko, Yu. I., & Pavlenko, Yu. M. (2020). Kharakterystyka henetychnoi struktury plidnykiv lebedynskoi porody za henamy beta- (CSN2) ta kapa-kazeinu (CSN3). Zbirnyk naukovykh prats «Tekhnolohiia vyrobnytstva i pererobky produktsii tvarynnytstva». 2, 88–96.
  12. Ladyka, V. I., Skliarenko, Yu. I., & Pavlenko, Yu. M. (2020). Analiz buhaiv-plidnykiv molochnykh porid za kompleksnymy henotypamy beta- i kappa kazeinu. Rozvedennia i henetyka tvaryn, 60, 99–109.
  13. Bonfatti, V., Di Martino, G., Cecchinato, A., Degano, L., & Carnier, P. (2010). Effects of β-κ-casein (CSN2-CSN3) haplotypes, β-lactoglobulin (BLG) genotypes, and detailed protein composition on coagulation properties of individual milk of Simmental cows. Journal of Dairy Science, 93(8), 3809–3817. .
  14. Keating, A., Smith, T., Ross, R., & Cairns, M. (2008). A note on the evaluation of a beta-casein variant in bovine breeds by allele-specific PCR and relevance to β-casomorphin. Irish Journal of Agricultural and Food Research, 47, 99–104.
  15. Denicourt, D., Sabour, M. P., & McAllister, A. J. (1990). Detection of bovine κ-casein genomic variants by the polymerase chain reaction method. Animal Genetics, 21(2), 215–216.
  16. Yeh, F. C., Yang, R., Boyle, T. J., Ye, Z., & Xiyan, J. M. (2000). PopGene32, Microsoft Windows-based freeware for population genetic analysis, version 1.32. Mol. Biol. Biotechnol. Centre, Univ. Alberta, Edmonton, Alberta, Canada.
  17. Zhao, J. H., Curtis, D., & Sham, P. C. (2000). Model-free analysis and permutation tests for allelic associations. Hum Hered. 50, 133–139.
  18. Zapata, C., Carollo, C., & Rodriguez, S. (2001). Sampling variance and distribution of the D measure of overall gametic disequilibrium between multiallelic loci. Ann Hum Genet., 65, 395–406.