Document Type : Research Paper


1 Ph.D. Candidate in Animal Breeding and Genetics, Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran

2 Professor, Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran

3 Assistant Professor in Animal Breeding and Genetics, Department of Animal Science, Iowa State University, USA


Increased homozygosity resulted from mating of relatives is considered as one of the challenges faced in dairy farming industry which has attracted the attentions. This research has been conducted to measure homozygosity based on SNP and ROH in high- and low-producing Holstein cows. In current research, both random regression and pedigree index approaches were used to obtain candidate animals for genotyping process. The samples were obtained from 150 Holstein dairy cows (75 by high- and 75 by low-EBV for milk production). We proposed a suitable method, by integrating breeding value estimation calculated by random regression and pedigree index, to select the candidate animals for genotyping. The results showed that putting too much emphasis on production traits in high-producing dairy cows had negative impact on the traits associated with fertility (DPR = -0.55) and productive life (PL = 0.1). The calculated homozygosity based on ROH showed different amount of variation in different chromosomes in the cows with high and low production which may be related to uneven distribution of genes influencing production traits in different chromosomes.


  1. Bjelland, D., Weigel, K., Vukasinovic, N. & Nkrumah, J. (2013). Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding. Journal of Dairy Science96, 4697-4706.
  2. Boichard, D. & Brochard, M. (2012). New phenotypes for new breeding goals in dairy cattle. Animal 6, 544-550.
  3. Boichard, D., Ducrocq, V. & Fritz, S. (2015). Sustainable dairy cattle selection in the genomic era. Journal of Animal Breeding and Genetics132, 135-143.
  4. Curik, I., Ferenčaković, M. & Sölkner, J. (2014). Inbreeding and runs of homozygosity: a possible solution to an old problem. Livestock Science166, 26-34.
  5. García-Ruiz, A., Cole, J.B., VanRaden, P.M., Wiggans, G.R., Ruiz-López, F.J. & Van Tassell, C.P. (2016). Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection. Proceedings of the National Academy of Sciences, 201519061.
  6. Hayes, B.J., Lien, S., Nilsen, H., Olsen, H.G., Berg, P., Maceachern, S., Potter, S. & Meuwissen, T. (2008). The origin of selection signatures on bovine chromosome 6. Animal genetics39, 105-111.
  7. Henryon, M., Berg, P. & Sørensen, A.C. (2014). Animal-breeding schemes using genomic information need breeding plans designed to maximise long-term genetic gains. Livestock Science166, 38-47.
  8. Hill, W.G. & Kirkpatrick, M. (2010). What animal breeding has taught us about evolution. Annual Review of Ecology, Evolution, and Systematics41, 1-19.
  9. Hill, W.G. & Weir, B. (2011). Variation in actual relationship as a consequence of Mendelian sampling and linkage. Genetics Research93, 47-64.
  10. Ismael, A., Strandberg, E., Berglund, B., Kargo, M., Fogh, A. & Løvendahl, P. (2016). Genotype by environment interaction for activity-based estrus traits in relation to production level for Danish Holstein. Journal of Dairy Science99, 9834-9844.
  11. Keller, M.C., Visscher, P.M. & Goddard, M.E. (2011). Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data. Genetics189, 237-249.
  12. Kim, E.-S., Cole, J.B., Huson, H., Wiggans, G.R., Van Tassell, C.P., Crooker, B.A., Liu, G., Da, Y. & Sonstegard, T.S. (2013). Effect of artificial selection on runs of homozygosity in US Holstein cattle. PLoS One8, e80813.
  13. Lagerkvist, G., Johansson, K. & Lundeheim, N. (1994). Selection for litter size, body weight, and pelt quality in mink (Mustela vison): correlated responses. Journal of Animal Science 72, 1126-1137.
  14. 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 Evolution45, 1.
  15. MacArthur, D.G., Balasubramanian, S., Frankish, A., Huang, N., Morris, J., Walter, K., Jostins, L., Habegger, L., Pickrell, J.K. & Montgomery, S.B. (2012). A systematic survey of loss-of-function variants in human protein-coding genes. Science335, 823-828.
  16. Marras, G., Gaspa, G., Sorbolini, S., Dimauro, C., Ajmone‐Marsan, P., Valentini, A., Williams, J.L. & Macciotta, N.P. (2015). Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy. Animal Genetics46, 110-121.
  17. McQuillan, R., Leutenegger, A.-L., Abdel-Rahman, R., Franklin, C.S., Pericic, M., Barac-Lauc, L., Smolej-Narancic, N., Janicijevic, B., Polasek, O. & Tenesa, A. (2008). Runs of homozygosity in European populations. The American Journal of Human Genetics83, 359-372.
  18. Pryce, J., Hayes, B. & Goddard, M. (2012). Novel strategies to minimize progeny inbreeding while maximizing genetic gain using genomic information. Journal of Dairy Science95, 377-388.
  19. Pryce, J., Royal, M., Garnsworthy, P. & Mao, I.L. (2004). Fertility in the high-producing dairy cow. Livestock Production Science86, 125-135.
  20. 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. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics81, 559-575.
  21. Purfield, D.C., Berry, D.P., McParland, S. & Bradley, D.G. (2012). Runs of homozygosity and population history in cattle. Bmc Genetics13, 70.
  22. Rokouei, M., Torshizi, R.V., Shahrbabak, M.M., Sargolzaei, M. & Sørensen, A. (2010). Monitoring inbreeding trends and inbreeding depression for economically important traits of Holstein cattle in Iran. Journal of Dairy Science93, 3294-3302.
  23. Smith, L.A., Cassell, B. & Pearson, R. (1998). The effects of inbreeding on the lifetime performance of dairy cattle. Journal of Dairy Science81, 2729-2737.
  24. Sonesson, A. & Woolliams, J. (2010). Maximising genetic gain whilst controlling rates of genomic inbreeding using genomic optimum contribution selection. In: Proceedings of the 9th World Congr Genet Appl Livest Prod.
  25. Su, G., Madsen, P., Nielsen, U.S., Mäntysaari, E.A., Aamand, G.P., Christensen, O.F. & Lund, M.S. (2012). Genomic prediction for Nordic Red Cattle using one-step and selection index blending. Journal of Dairy Science 95, 909-917.
  26. Team, R.C. (2014). R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing. Available online at: h ttp. www R-project org.
  27. Walsh, S., Williams, E. & Evans, A. (2011). A review of the causes of poor fertility in high milk producing dairy cows. Animal Reproduction Science123, 127-138.
  28. Wiggans, G., VanRaden, P. & Zuurbier, J. (1995). Calculation and use of inbreeding coefficients for genetic evaluation of United States dairy cattle. Journal of Dairy Science78, 1584-1590.