Genetic diversity and bottleneck analysis of the Red Steppe cattle based on microsatellite markers

A.S. Kramarenko, E.A. Gladyr, S.S. Kramarenko, T.V. Pidpala, L.A. Strikha, N.A. Zinovieva


Thirty-nine dairy cows representing the Red Steppe (RS) cattle breed (the State Enterprise “Pedigree Reproducers “Stepove” Mykolayiv region, Ukraine) were included in the study. A set of 11 microsatellite markers recommended by International Society of Animal Genetics (ISAG) for cattle was used to study genetic diversity in the RS cattle population. All of the studied loci were highly informative and polymorphic. In total, 71 alleles were detected at 11 microsatellite loci, from which 16 (22.5%) had frequency lower than 5%. The number of detected alleles per locus (TNA) ranged from four to ten, with a mean value of 6.45±0.51. The mean effective number of alleles (Ae) was 3.77±0.37. The allele frequencies ranged from 0.013 to 0.714. The average values for observed (Ho) and expected (He) heterozygosities were 0.607±0.085 and 0.703±0.034, respectively. The within breed estimate FIS indicates heterozygosity shortage of 0.179.  The Hardy-Weinberg equilibrium test revealed that 2 out of 11 loci deviated from equilibrium. The RS cattle population is non-bottlenecked, i.e., it has not undergone any recent reduction in the effective population size and remained at mutation-drift equilibrium. The estimated mean Ne for the RS cattle population was 23.3 (95% CIs = 11-74) individuals. These low values emphasize the need of controlling the rate of increase of inbreeding in the RS cattle herds.


genetic diversity;allele pool;bottleneck-effect;microsatellites DNA;Red Steppe cattle;dairy cow

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Asbjarnardottir, M.G., Kristjansson, T., Jonsson, M.B., & Hallsson, J.H. (2010). Analysis of genetic diversity and population structure within the Icelandic cattle breed using molecular markers. Acta Agriculturae Scand. Section A, 60(4), 203−210. doi: 10.1080/09064702.2010.538714

Cornuet, J.M., & Luikart, G. (1996). Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics, 144(4), 2001−2014.

de Ponte Bouwer, P., Visser, C., & Mostert, B.E. (2013). Analysis of inbreeding of the South African Dairy Swiss breed. South African Journal of Animal Science, 43(1), 38−43. doi: 10.4314/sajas.v43i1.4

Corrales, R., Näsholm, A., Malmfors, B., & Philipsson, J. (2010). Population structure of Reyna Creole cattle in Nicaragua. Tropical Animal Health and Production, 42(7), 1427−1434. doi: 10.1007/s11250-010-9571-9

Do, C., Waples, R.S., Peel, D., Macbeth, G.M., Tillett, B.J., & Ovenden, J.R. (2014). NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources, 14(1), 209−214. doi: 10.1111/1755-0998.12157

Felius, M., Koolmees, P.A., Theunissen, B., Lenstra, J.A., & European Cattle Genetic Diversity Consortium. (2011). On the breeds of cattle − historic and current classifications. Diversity, 3(4), 660−692. doi: 10.3390/d3040660

Goddard, M.E., & Hayes, B.J. (2007). Genomic selection. Journal of Animal Breeding and Genetics, 124(6), 323−330. doi: 10.1111/j.1439-0388.2007.00702.x

Goddard, M.G., & Smith, C. (1990). Optimum number of bull sires in dairy cattle breeding. Journal of Dairy Science, 73(4), 1113−1122. doi: 10.3168/jds.S0022-0302(90)78771-1

Goudet, J. (2002). FSTAT, a program to estimate and test gene diversities and fixation indices, version 2.9.3.

Guo, S.W., & Thompson, E.A. (1992). Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics, 361−372. doi: 10.2307/2532296

Hayes, B.J., Bowman, P.J., Chamberlain, A.J., & Goddard, M.E. (2009). Invited review: Genomic selection in dairy cattle: Progress and challenges. Journal of Dairy Science, 92(2), 433−443. doi: 10.3168/jds.2008-1646

Hayes, B.J., Visscher, P.M., McPartlan, H.C., & Goddard, M.E. (2003). Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Research, 13(4), 635−643. doi: 10.1101/gr.387103

Kamiti, D., Ilatsia, E., Bett, R., & Kahi, A. (2016). Population structure and demographic trends of the registered Sahiwal cattle in Kenya. Tropical Animal Health and Production, 48(5), 1029−1036. doi: 10.1007/s11250-016-1055-0

Kramarenko, O., Hladyr, H., Naydyonova, V., Dubinsky, O. & Zinov’eva, N. (2015). Analysis of the microsatellite loci polymorphism of the Southern Meat cattle breed. Collection of Scientific Works of the Podilsky State Agricultural and Technical University: Agricultural Sciences, 23: 382−390 (In Ukrainian).

Leroy, G., Mary-Huard, T., Verrier, E., Danvy, S., Charvolin, E., & Danchin-Burge, C. (2013). Methods to estimate effective population size using pedigree data: examples in dog, sheep, cattle and horse. Genetics Selection Evolution, 45(1), 1.

Maiwashe, A., Nephawe, K.A., van der Westhuizen, R.R., Mostert, B.E., & Theron, H.E. (2006). Rate of inbreeding and effective population size in four major South African dairy cattle breeds. South African Journal of Animal Science, 36(1), 50−57.

Mason, I.L. (1996). A World Dictionary of Livestock Breeds, Types and Varieties. Fourth Edition. CAB International.

Melka, M.G., Sargolzaei, M., Miglior, F., & Schenkel, F. (2013). Genetic diversity of Guernsey population using pedigree data and gene-dropping simulations. Animal, 7(2), 192−201. doi: 10.1017/S1751731112001723

Meuwissen, T.H.E., & Woolliams, J. A. (1994). Effective sizes of livestock populations to prevent a decline in fitness. Theoretical and Applied Genetics, 89(7-8), 1019−1026. doi: 10.1007/BF00224533

Ndiaye, N.P., Sow, A., Ndiaye, S., Sawadogo, G.J., & Sembene, M. (2015). Bottleneck and molecular variance analyses in Senegalese local cattle breeds using microsatellite markers. Research Opinions in Animal and Veterinary Sciences, 5(4), 158−164.

Özşensoy, Y., & Kurar, E. (2014). Genetic diversity of native Turkish cattle breeds: Mantel, AMOVA and bottleneck analysis. Journal of Advanced Veterinary and Animal Research, 1(3), 86−93. doi: 10.5455/javar.2014.a21

Pandey, A.K., Sharma, R., Singh, Y., Prakash, B.B., & Ahlawat, S.P.S. (2006). Genetic diversity studies of Kherigarh cattle based on microsatellite markers. Journal of Genetics, 85(2), 117−122. doi: 10.1007/BF02729017

Peakall, R., & Smouse, P.E. (2012). GenAIEx 6.5: genetic analysis in Excel. Population genetic software for teaching and researchd − an update. Bioinformatics, 28(19), 2537−2539. doi: 10.1093/bioinformatics/bts460

Putman, A.I., & Carbone, I. (2014). Challenges in analysis and interpretation of microsatellite data for population genetic studies. Ecology and Evolution, 4(22), 4399−4428. doi: 10.1002/ece3.1305

Qanbari, S., Pimentel, E.C.G., Tetens, J., Thaller, G., Lichtner, P., Sharifi, A.R., & Simianer, H. (2010). The pattern of linkage disequilibrium in German Holstein cattle. Animal Genetics, 41(4), 346−356. doi: 10.1111/j.1365-2052.2009.02011.x

Rodríguez-Ramilo, S.T., Fernández, J., Toro, M.A., Hernández, D., & Villanueva, B. (2015). Genome-wide estimates of coancestry, inbreeding and effective population size in the Spanish Holstein population. PLoS One, 10(4), e0124157. doi:10.1371/journal.pone.0124157

Rousset, F. (2008). genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources, 8(1), 103−106. doi: 10.1111/j.1471-8286.2007.01931.x

Sasazaki, S., Honda, T., Fukushima, M., Oyama, K., Mannen, H., Mukai, F., & Tsuji, S. (2004). Genealogical relationship between pedigree and microsatellite information and analysis of genetic structure of a highly inbred Japanese black cattle strain. Asian Australasian Journal of Animal Sciences, 17(10), 1355−1359.

Shelyov, A.V. (2015). Polymorphism of microsatellite DNA loci in different species of farm animals. Animal Breeding and Genetics, 50, 183−189 (In Ukrainian).

Shelyov, A.V., Kopylov, K.V., Kramarenko, S.S., and Kramarenko, O.S. (2017). Analysis of population-genetic processes in different cattle breeds by microsatellite loci of DNA. Agricultural Science and Practice, 4(1), 74−78. doi: 10.15407/agrisp4.01.074

Shin, D.H., Cho, K.H., Park, K.D., Lee, H.J., & Kim, H. (2013). Accurate estimation of effective population size in the Korean dairy cattle based on linkage disequilibrium corrected by genomic relationship matrix. Asian-Australasian Journal of Animal Sciences, 26(12), 1672−1679. doi: 10.5713/ajas.2013.13320

Shkavro N.N., Radko, A., Slota, E., & Rossokha, V.I. (2010). Microsatellite DNA loci polymorphism of two cattle breeds. The Journal of V.N. Karazin Kharkiv National University. Series: biology, 11(905), 120−126 (In Ukrainian).

Stachowicz, K., Sargolzaei, M., Miglior, F., & Schenkel, F.S. (2011). Rates of inbreeding and genetic diversity in Canadian Holstein and Jersey cattle. Journal of Dairy Science, 94(10), 5160−5175. doi: 10.3168/jds.2010-3308

Weigel, K. A. (2001). Controlling inbreeding in modern breeding programs. Journal of Dairy Science, 84, E177−E184. doi: 10.3168/jds.S0022-0302(01)70213-5


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