Estimation of effective population size in Sarabi cattle based on single nucleotide polymorphism markers

Document Type : Research Paper


1 Ph. D. Student, Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, and Member of Young Researchers, Shahid Bahonar University of Kerman, Iran

2 Associate Professor, Faculty of Agriculture, Shahid Bahonar University of Kerman, Iran


The objective of this study was to estimate the effective number of breeders in Sarabi cattle population using heterozygote-excess method based on single nucleotide polymorphism markers. Data consisted of 20 Sarabi cows. SNP genotyping was performed using Illumina High-density Bovine BeadChip designed to genotype 777,962 SNPs. Average observed heterozygosity, expected heterozygosity, minor allele frequencies and percentage of deviation from Hardy-Weinberg test were estimated. Effective number of breeders was estimated per each chromosome using NEESTIMATOR (v2) software based on heterozygote-excess method. Average chromosome-wise effective number of breeders was equal to 28 and corresponding average confidence interval was between 17.3 and 40.2. Results of this study indicated that Sarabi breed is on serious risk of extinction. Design of appropriate programs is necessary to conserve remaining purebred cattles.


  1. Caballero, A. (1994). Developments in the prediction of effective population size. Heredity, 73, 657–679.
  2. 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.
  3. Edea, Z., Dadi, H., Kim, S.W., Dessie, T., Lee, T., Kim, H., Kim, J.J. & Kim, K.S. (2013). Genetic diversity, population structure and relationships in indigenous cattle populations of Ethiopia and Korean Hanwoo breeds using SNP markers. Frontiers in Genetics, 4, 35.
  4. Engelsma, K.A., Veerkamp, R.F., Calus, M.P.l., Bijma, P. & Windig, J.J. (2012). Pedigree and marker based methods in the estimation of genetic diversity in small groups of Holstein cattle. Jouranl of Animal Breeding and Genetics, 129, 195-205.
  5. Engelsma, K.A., Veerkamp, R.F., Calus, M.P.L. & Windig, J.J. (2014). Consequences for diversity when animals are prioritized for conservation of the whole genome or of one specific allele. Journal of Animal Breeding and Genetics, 131(1), 61-70.
  6. Fahlén, J. (2014). SNP-based conservation genetics of  the southern Swedish brown bear (Ursus arctos). M.Sc dissertation, Swedish University of Agricultural Sciences, Sweden.
  7. Frankham, R. (1995). Effective population size/adult population size ratios in wildlife: a review. Genetical Research, 66, 95–107.
  8. Frankham, R. (2005). Genetics and extinction. Biological Conservation, 126, 131-140.
  9. Frankham, R., Bradshaw, C.J.A. & Brook, B.W. (2014). Genetics in conservation and management: Revised recommendations for the 50/500 rules, Red List criteria and population viability analyses. Biological Conservation, 170, 56-63.
  10. Franklin, I.R. (1980). Evolutionary change in small populations. In: M.E. Soulé & B.A. Wilcox (Ed.), Conservation biology: An evolutionary-ecological perspective. (pp. 135–150). Sunderland, Massachusetts: Sinauer Associates.
  11. Gautier, M., Faraut, T., Moazami-Goudarzi, K., Navratil, V., Foglio, M., Grohs, C., Boland, A., Garnier, J.G., Boichard, D., Lathrop, G.M., Gut, I.G. & Eggen, A. (2007). Genetic and haplotypic structure in 14 European and African cattle breeds. Genetics, 177, 1059-1070.
  12. Hedgecock, D., Launey, S.,  Pudovkin, A.I., Naciri, Y., Lape`gue, S. & Bonhomme, F. (2007). Small effective number of parents (N b ) inferred for a naturally spawned cohort of juvenile European flat oysters Ostrea edulis. Molecular Biology, 150,1173–1182.
  13. Helyar, S.J., Hemmer-Hansen, J., Bekkevold, D., Taylor, M.I., Ogden, R., Limborg, M.T., Cariani, A., Maes, G.E., Diopere, E., Carvalho, G.R. & Nielsen, E.E. (2011). Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Molecular Ecology Resources, 11, 123-136.
  14. Hill, W.G. (1981). Estimation of effective population size from data on linkage disequilibrium. Genetical Research, 38, 209–216.
  15. Lachance, J. & Tishkoff, S.A. (2013). SNP ascertainment bias in population genetic analyses: why it is important, and how to correct it. Bioessays, 35, 780-786.
  16. Lin, B.Z., Sasazaki, S. & Mannen, H. (2010). Genetic diversity and structure in Bos taurus and Bos indicus populations analyzed by SNP markers. Animal Science Journal, 81, 281–289.
  17. Luikart, G. & Cornuet, J.M. (1999). Estimating the effective number of breeders from heterozygote excess in progeny. Genetics, 151, 1211–1216. 
  18. Luikart, G., Ryman, N., Tallmon, D.A., Schwartz, M.K. & Allendorf, F.W. (2010). Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches. Conservation Genetics, 11, 355–373.
  19. Matukumalli, L.K., Lawley, C.T., Schnabel, R.D., Taylor, J.F., Allan, M.F., Heaton, M.P., O'Connell, J., Moore, S.S., Smith, T.P., Sonstegard, T.S. & Van Tassell, C.P. (2009). Development and characterization of a high density SNP genotyping assay for cattle. PLoS ONE, 4, e5350.
  20. Nomura, T. (2008). Estimation of effective number of breeders from molecular coancestry of single cohort sample. Evolutionary Applications, 1(3), 462–474.
  21. Nomura, T. (2009). Interval estimation of the effective population size from heterozygote-excess in SNP markers. Biometrical Journal, 51(6), 996–1016.
  22. Pollak, E. (1983). A new method for estimating the effective population size from allele frequency changes. Genetics, 104, 531–548.
  23. Pruett, C.L. & Winker, K. (2008). The effects of sample size on population genetic diversity estimates in song sparrows Melospiza melodia. Journal of Avian Biology, 39, 252-256.
  24. Pudovkin, A.I., Zaykin, D.V. & Hedgecock, D. (1996). On the potential for estimating the effective number of breeders from heterozygote-excess in progeny. Genetics, 144, 383–387.
  25. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A., Bender, D., Maller, J., Sklar, P., de Bakker, P.I., Daly, M.J. & Sham, P.C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics, 81, 559-575.
  26. Robertson, A. (1965). The interpretation of genotypic ratios in domestic animal populations. Animal Production, 7, 319–324.
  27. Schmeller, D. &  Meril¨a, J. (2006). Demographic and genetic estimates of effective population and breeding size in the Amphibian Rana temporaria. Conservation Biology, 21(1), 142–151.
  28. Smith, O. & Wang, J. (2014). When can noninvasive samples provide sufficient information in conservation genetics studies?. Molecular Ecology Resources, 14, 1011-23.
  29. Willing, E., Dreyer, C. & van Oosterhout, C. (2012). Estimates of genetic differentiation measured by FST do not necessarily require large sample sizes when using many snp markers. PLoS ONE 7(8): e42649.