The admixed population structure in Danish Jersey dairy cattle challenges accurate genomic predictions

Journal of Animal Science

Volumn 91, Issue 7, 2013, Pages 3105-3112

  Thomasen, J R ^a,b   Sorensen A C ^b   Su, G ^b   Madsen, P ^b   Lund, M S ^b   Guldbrandtsen, B ^b  

^a Viking Genetics International Denmark   (Denmark)

^b AARHUS UNIVERSITY   (Denmark)

Author keywords

Cattle; Genomic predictions; Population structure

Indexed keywords

EID: 84879376639     PISSN: 00218812     EISSN: 15253163     Source Type: Journal    
DOI: 10.2527/jas.2012-5490     Document Type: Article

References (34)

1. Brøndum, R. F., E. Rius-Vilarrasa, I. Strandén, G. Su, B. Guldbrandtsen, W. F. Fikse, and M. S. Lund. 2011. Reliabilities of genomic prediction using combined reference data of the Nordic Red dairy cattle populations. J. Dairy Sci. 94:4700-4707.
2. Danish Cattle Federation. 2012. Calculation of breeding values. www.landbrugsinfo.dk/kvaeg/avl/avlsanalyser/sider/startside.aspx. (Accessed December 27, 2012.)
3. de Roos, A. P. W., B. J. Hayes, and M. E. Goddard. 2009. Reliability of genomic predictions across multiple populations. Genetics 183:1545-1553.
4. de Roos, A. P. W., B. J. Hayes, R. J. Spelman, and M. E. Goddard. 2008. Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus Cattle. Genetics 179:1503-1512.
5. Falush, D., M. Stephens, and J. K. Pritchard. 2003. Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164:1567-1587.
6. Flury, C., M. Tapio, T. Sonstegard, C. Drogemuller, T. Leeb, H. Simianer, O. Hanotte, and S. Rieder. 2010. Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium. J. Anim. Breed. Genet. 127:339-347.
7. Frkonja, A., B. Gredler, U. Schnyder, I. Curik, and J. Sölkner. 2012. Prediction of breed composition in an admixed cattle population. Anim. Genet. 43:696-703.
8. Gao, H., O. Christensen, P. Madsen, U. Nielsen, Y. Zhang, M. Lund, and G. Su. 2012. Comparison on genomic predictions using three GBLUP methods and two single-step blending methods in the Nordic Holstein population. Genet. Sel. Evol. 44:8.
9. Gautier, M., T. Faraut, K. Moazami-Goudarzi, V. Navratil, M. Foglio, C. Grohs, A. Boland, J. G. Garnier, D. Boichard, G. M. Lathrop, I. G. Gut, and A. Eggen. 2007. Genetic and haplotypic structure in 14 European and African cattle breeds. Genetics 177:1059-1070.
10. Goddard, M. E., and B. J. Hayes. 2009. Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat. Rev. Genet. 10:381-391.
11. Hayes, B. J., P. J. Bowman, A. J. Chamberlain, and M. E. Goddard. 2009. Invited review: Genomic selection in dairy cattle: Progress and challenges. J. Dairy Sci. 92:433-443.
12. Hayes, B. J., P. M. Visscher, H. C. McPartlan, and M. E. Goddard. 2003. Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genet. Res. 13:635-643.
13. Heringstad, B., G. Su, T. R. Solberg, B. Guldbrandtsen, M. Svendsen, and M. S. Lund. 2011. Genomic predictions based on a joint reference population for Scandinavian red breeds. Book of Abstracts of the 62nd Annual Meeting of the European Federation of Animal Science, Stavanger, Norway. Wageningen Acedemic Publishers, Wageningen, the Netherlands.
14. Lewontin, R. C. 1964. The interaction of selection and linkage. I. General considerations: Heterotic models. Genetics 49:49-67.
15. Lund, M., A. de Roos, A. de Vries, T. Druet, V. Ducrocq, S. Fritz, F. Guillaume, B. Guldbrandtsen, Z. Liu, R. Reents, C. Schrooten, F. Seefried, and G. Su. 2011. A common reference population from four European Holstein populations increases reliability of genomic predictions. Genet. Sel. Evol. 43:43.
16. Madsen, P., and J. Jensen. 2010. A user's guide to DMU, version 6, release 5.0. http://dmu.agrsci.dk/dmuv6_guide.5.0.pdf. (Accessed December 27, 2012.)
17. Matukumalli, L. K., C. T. Lawley, R. D. Schnabel, J. F. Taylor, M. F. Allan, M. P. Heaton, J. O'Connell, S. S. Moore, T. P. L. Smith, T. S. Sonstegard, and C. P. Van Tassell. 2009. Development and characterization of a high density SNP genotyping assay for cattle. PLoS ONE 4:e5350.
18. McKay, S., R. Schnabel, B. Murdoch, L. Matukumalli, J. Aerts, W. Coppieters, D. Crews, E. Neto, C. Gill, C. Gao, H. Mannen, P. Stothard, Z. Wang, C. Van Tassell, J. Williams, J. Taylor, and S. Moore. 2007. Whole genome linkage disequilibrium maps in cattle. BMC Genet. 8:74.
19. Meuwissen, T. H. E., B. J. Hayes, and M. E. Goddard. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819-1829.
20. Negussie, E., M. Lindauer, E. A. Mäntysaari, I. Strandén, J. Pösö, U. S. Nielsen, J. Johansson, J. Å. Eriksson, and G. P. Aamand. 2010. Combining test day SCS with clinical mastitis and udder type traits: A random regression model for joint genetic evaluation of udder health in Denmark, Finland and Sweden. Interbull Bulletin No.42. Interbull Centre, Uppsala, Sweden.
21. Nomura, T. 1996. Effective size of selected populations with overlapping generations. J. Anim. Breed. Genet. 113:1-16.
22. Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
23. Pryce, J. E., S. Bolormaa, A. J. Chamberlain, P. J. Bowman, K. Savin, M. E. Goddard, and B. J. Hayes. 2010. A validated genome-wide association study in 2 dairy cattle breeds for milk production and fertility traits using variable length haplotypes. J. Dairy Sci. 93:3331-3345.
24. Qanbari, S., E. C. G. Pimentel, J. Tetens, G. Thaller, P. Lichtner, A. R. Sharif, and H. Simianer. 2010. The pattern of linkage disequilibrium in German Holstein cattle. Anim. Genet. 41:346-356.
25. Rius-Vilarrasa, E., T. Iso-Touru, I. Strandén, N. Schulman, B. Guldbrandtsen, E. Strandberg, M. S. Lund, J. Vilkki, and W. F. Fikse. 2011. Characterization of linkage disequilibrium in a Danish, Swedish and Finish Red cattle population. Book of Abstracts of the 62nd Annual Meeting of the European Federation of Animal Science, Stavanger, Norway. Wageningen Acedemic Publishers, Wageningen, the Netherlands.
26. Scheet, P., and M. Stephens. 2006. A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase. Am. J. Hum. Genet. 78:629-644.
27. Sørensen, A. C., M. K. Sørensen, and P. Berg. 2005. Inbreeding in Danish dairy cattle breeds. J. Dairy Sci. 88:1865-1872.
28. Strandén, I., and E. A. Mäntysaari. 2010. A recipe for multiple trait deregression. Interbull Bulletin No.42., Interbull Centre, Uppsala, Sweden.
29. Su, G., B. Guldbrandtsen, V. R. Gregersen, and M. S. Lund. 2010. Preliminary investigation on reliability of genomic estimated breeding values in the Danish Holstein population. J. Dairy Sci. 93:1175-1183.
30. Su, G., P. Madsen, U. S. Nielsen, E. A. Mäntysaari, G. P. Aamand, O. F. Christensen, and M. S. Lund. 2012. Genomic prediction for Nordic Red cattle using one-step and selection index blending. J. Dairy Sci. 95:909-917.
31. Sved, J. A. 1971. Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor. Popul. Biol. 2:125-141.
32. Thomasen, J. R., B. Guldbrandtsen, G. Su, R. F. Brøndum, and M. S. Lund. 2012. Reliabilities of genomic estimated breeding values in Danish Jersey. Animal 6:789-796.
33. Toosi, A., R. L. Fernando, and J. C. M. Dekkers. 2010. Genomic selection in admixed and crossbred populations. J. Anim. Sci. 88:32-46.
34. Zimin, A. V., A. L. Delcher, L. Florea, D. R. Kelley, M. C. Schatz, D. Puiu, F. Hanrahan, G. Pertea, C. P. Van Tassell, T. S. Sonstegard, G.Marcais, M. Roberts, P. Subramanian, J. A. Yorke, and S. L. Salzberg. 2009. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol. 10:R42.