Accuracies of direct genomic breeding values in Hereford beef cattle using national or international training populations

Journal of Animal Science

Volumn 91, Issue 4, 2013, Pages 1538-1551

  Saatchi, M ^a   Ward, J ^b   Garrick, D J ^a,c  

^a IOWA STATE UNIVERSITY   (United States)

^b American Hereford Association   (United States)

^c MASSEY UNIVERSITY   (New Zealand)

Author keywords

Accuracy; Genetic relationship; Genomic breeding values; Genomic selection; Hereford; K means

Indexed keywords

ANIMAL; BAYES THEOREM; BIOLOGICAL MODEL; BOVINAE; BREEDING; DNA MICROARRAY; FEMALE; GENETICS; GENOME; MALE; PEDIGREE; QUANTITATIVE TRAIT; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM; STANDARDS; UNITED STATES; VETERINARY;

ANIMALS; BAYES THEOREM; BREEDING; CATTLE; FEMALE; GENOME; MALE; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT, HERITABLE; REPRODUCIBILITY OF RESULTS; UNITED STATES;

EID: 84882651849     PISSN: 00218812     EISSN: 15253163     Source Type: Journal    
DOI: 10.2527/jas.2012-5593     Document Type: Article

References (34)

1. Bolormaa, S., B. J. Hayes, K. Savin, R. Hawken, W. Barendse, P. F. Arthur, R. M. Herd, and M. E. Goddard. 2011. Genome-wide association studies for feedlot and growth traits in cattle. J. Anim. Sci. 89:1684-1697.
2. Brøndum, R. F., E. Rius-Vilarrasa, I. Strandén, G. Su, B. Guldbrandtsen, W. F. Fikse, and M. S. Lund. 2011. Reliabilities of genomic predictions using combined reference data of the Nordic Red dairy cattle populations. J. Dairy Sci. 94:4700-4707.
3. Fernando, R. L., and D. J. Garrick. 2009. GenSel: User manual for a portfolio of genomic selection related analyses. Accessed 1 September 2010. http://taurus.ansci.iastate.edu.
4. Garrick, D. J. 2011. The nature, scope and impact of genomic prediction in beef cattle in the United States. Genet. Sel. Evol. 43:17.
5. Garrick, D. J., and B. L. Golden. 2009. Producing and genetic evaluations in the United States beef industry of today. J. Anim. Sci. 87(E. Suppl.):E11-E18.
6. Garrick, D. J., J. F. Taylor, and R. L. Fernando. 2009. Deregressing estimated breeding values and weighting information for genomic regression analyses. Genet. Sel. Evol. 41:55.
7. Gilmour, A. R., B. J. Gogel, B. R. Culls, and R. Thompson. 2009. ASReml user guide. Release 3.0. VSN International Ltd, Hernel Hempstead, UK. Accessed 1 June 2011. http://www.vsni.co.uk/downloads/asreml/release3/UserGuide.pdf.
8. 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.
9. Habier, D., R. L. Fernando, and J. C. M. Dekkers. 2007. The impact of genetic relationship information of genome-assisted breeding values. Genetics 177:2389-2397.
10. Habier, D., R. L. Fernando, K. Kizilkaya, and D. J. Garrick. 2011. Extension of the Bayesian alphabet for genomic selection. BMC Bioinformatics 12:186.
11. Habier, D., J. Tetens, F. Seefried, P. Lichtner, and G. Thaller. 2010. The impact of genetic relationship information on genomic breeding values in German Holstein cattle. Genet. Sel. Evol. 42:5.
12. Hartigan, J. A., and M. A. Wong. 1979. Algorithm AS 136: A k-means clustering algorithm. Appl. Stat. 28:100-108.
13. 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.
14. Kizilkaya, K., Fernando, R. L., and D. J. Garrick. 2010. Genomic prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes. J. Anim. Sci. 88:544-551.
15. Luan, T., J. A. Wooliams, S. Lien, M. Kent, M. Svendsen, and T. H. E. Meuwissen. 2009. The accuracy of genomic selection in Norwegian Red cattle assessed by cross-validation. Genetics 183:1119-1126.
16. MacNeil, M. D., J. D. Nkrumah, B. W. Woodward, and S. L. Northcutt. 2010.Genetic evaluation of Angus cattle for carcass marbling and ultrasound and genomic indicators. J. Anim. Sci. 88:517-522.
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. McClure, M. C., N. Morsci, R. D. Schnabel, J. W. Kim, P. Yao, M. M. Rolf, S. D. McKay, S. J. Gregg, R. H. Chapple, S. L. Northcutt, and J. F. Taylor. 2010. A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus. Anim. Genet. 41:597-607.
19. Meuwissen, T. H., B. J. Hayes, and M. E. Goddard. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819-1829.
20. Misztal, I., A. Legarra, and I. Aguilar. 2009. Computing procedures for genetic evaluation including phenotypic, full pedigree, and genomic information. J. Dairy Sci. 92:4648-4655.
21. Ostersen, T., O. F. Christensen, M. Henryon, G. Su, and P. Madsen. 2011. Deregressed EBV as the response variable yield more reliable genomic predictions than traditional EBV in pure-bred pigs. Genet. Sel. Evol. 43:38.
22. R Development Core Team. 2011. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Accessed 1 June 2011. http://www.r-project.org.
23. Rolf, M. M., J. F. Taylor, R. D. Schnabel, S. D. McKay, M. C. McClure, S. L. Northcutt, M. S. Kerley, and R. L. Weaber. 2010. Impact of reduced marker set estimation of genomic relationship matrices on genomic selection for feed efficiency in Angus cattle. BMC Genet. 11:24.
24. Saatchi, M., M. C. McClure, S. D. McKay, M. M. Rolf, J. Kim, J. E. Decker, T. M. Taxis, R. H. Chapple, H. R. Ramey, S. L. Northcutt, S. Bauck, B. Woodward, J. C. M. Dekkers, R. L. Fernando, R. D. Schnabel, D. J. Garrick, and J. F. Taylor. 2011. Accuracies of genomic breeding values in American Angus beef cattle using K-means clustering for cross-validation. Genet. Sel. Evol. 43:40.
25. Saatchi, M., S. R. Miraei-Ashtiani, A. Nejati-Javaremi, M. Moradi-Shahrebabak, and H. Mehrabani-Yeganeh. 2010. The impact of information quantity and strength of relationship between training set and validation set on accuracy of genomic estimated breeding values. Afri. J. Biot. 9:438-442.
26. Saatchi, M., R. D. Schnabel, M. M. Rolf, J. F. Taylor and D. J. Garrick. 2012. Accuracy of direct genomic breeding values for nationally evaluated traits in US Limousin and Simmental beef cattle. Genet. Sel. Evol. 44:38.
27. Sargolzaei, M., H. Iwaisaki, and J. J. Colleau. 2006. CFC: A tool for monitoring genetic diversity. Proc. 8th World Congr. Genet. Appl. Livest. Prod., Belo Horizonte, Brazil.
28. Schaeffer, L. R. 2006. Strategy for applying genome-wide selection in dairy cattle. J. Anim. Breed. Genet. 123:218-223.
29. Snelling, W. M., M. F. Allan, J. W. Keele, L. A. Keuhn, R. M. Thallman, G. L. Bennett, C. L. Ferrell, T. G. Jenkins, H. C. Freetly, M. K. Nielsen, and K. M. Rolfe. 2011. Partial-genome evaluation of postweaning feed intake and efficiency of crossbred beef cattle. J. Anim. Sci. 89:1731-1741.
30. Strandén, I., and D. J. Garrick. 2009. Technical note: Derivation of equivalent computing algorithms for genomic predictions and reliabilities of animal merit. J. Dairy Sci. 92:2971-2975.
31. Su, G., B. Guldbrandsen, 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.
32. VanRaden, P. M., C. P. Van Tassell, G. R. Wiggans, T. S. Sonstegard, R. D. Schnabel, J. F. Taylor, and F. S. Schenkel. 2009. Invited review: Reliability of genomic predictions for North American Holstein bulls. J. Dairy Sci. 92:16-24.
33. Wolc, A., C. Stricker, J. Arango, P. Settar, J. E. Fulton, N. P. O'Sullivan, R. Preisinger, D. Habier, R. L. Fernando, D. J. Garrick, S. J. Lamont, and J. C. M. Dekkers. 2011. Breeding values prediction for production traits in layer chickens using pedigree or genomic relationships in a reduced animal model. Genet. Sel. Evol. 43:5.
34. Zhang, Z., J. Liu, X. Ding, P. Bijma, D-J. de Koning, and Q. Zhang. 2010. Best linear unbiased prediction of genomic breeding values using a trait specific marker derived relationship matrix. PLOS One. 5(9):e12648.