The accuracy of genomic selection in Norwegian red cattle assessed by cross-validation

Genetics

Volumn 183, Issue 3, 2009, Pages 1119-1126

  Luan, Tu ^a   Woolliams, John A ^a,b   Lien, Sigbjørn ^a   Kent, Matthew ^a   Svendsen, Morten ^c   Meuwissen, Theo H E ^a  

^a NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c Geno Breeding and Artificial Insemination Association   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

FAT; PROTEIN;

ARTICLE; BAYES THEOREM; BREEDING; CATTLE; FEMALE; GENETIC SELECTION; GENETIC TRAIT; GENOME; GENOTYPE; HERITABILITY; LACTATION; MALE; MASTITIS; METHODOLOGY; MILK; NONHUMAN; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION PROCESS;

ALGORITHMS; ANIMAL HUSBANDRY; ANIMALS; BAYES THEOREM; BREEDING; CATTLE; FEMALE; GENOME; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; MALE; MILK; NORWAY; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; REPRODUCIBILITY OF RESULTS; SELECTION, GENETIC;

BOS; BOVINAE; HUMAN HERPESVIRUS 4;

EID: 72449137120     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.109.107391     Document Type: Article

References (26)

1. Calus, M. P. L., and R. F. Veerkamp, 2007 Accuracy of breeding values when using and ignoring the polygenic effect in genomic breeding value estimation with a marker density of one SNP per cM. J. Anim. Breed. Genet. 124: 362-368.
2. Calus, M. P. L., T. H. E. Meuwissen, A. P. W. de Roos and R. F. Veerkamp, 2008 Accuracy of genomic selection using different methods to define haplotypes. Genetics 178: 553-561.
3. Daetwyler, H. D., B. Villanueva and J. A. Woolliams, 2008 Accuracy of predicting the genetic risk of disease using a genomewide approach. PLoS ONE 3: e3395.
4. George, E. I., and R. E. McCulloch, 1996 Stochastic search variable selection, pp. 441-461 in Markov Chain Monte Carlo in Practice, edited by W. R. Gilks, S. Richardson and D. J. Spiegelhalter. Chapman & Hall/CRC, London/New York.
5. Goddard, M. E., and B. J. Hayes, 2007 Genomic selection. J. Anim. Breed. Genet. 124: 323-330.
6. 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.
7. Gonzalez-Recio, O., D. Gianola, G. J. M. Rosa, K. A. Weigel and A. Kranis, 2009 Genome-assisted prediction of a quantitative trait measured in parents and progeny: application to food conversion rate in chickens. Genet. Sel. Evol. 41: 3.
8. Grisart, B., W. Coppieters, F. Farnir, L. Karim, C. Ford et al., 2002 Positional candidate cloning of a QTL in dairy cattle: identification of amissensemutation in the bovineDGAT1 gene withmajor effect onmilk yield and composition.GenomeRes. 12: 222-231.
9. Habier, D., R. L. Fernando and J. C. M. Dekkers, 2007 The impact of genetic relationship information on genome-assisted breeding values. Genetics 177: 2389-2397.
10. Harris, B. L., D. L. Johnson and R. J. Spelman, 2008 Genomic selection in New Zealand and the implications for national genetic evaluation. Proceedings of the InterbullMeeting, Niagara Falls,NY.
11. Hayes, B. J., M. Carrick, P. Bowman and M. E. Goddard, 2003 Genotype x environment interaction for milk production of daughters of Australian dairy sires from test-day records. J. Dairy Sci. 86: 3736-3744.
12. 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.
13. Henderson, C. R., 1975 Best linear unbiased estimation and prediction under a selection model. Biometrics 31: 423-447.
14. Kolbehdari, D., L. R. Schaeffer and J. A. B. Robinson, 2007 Estimation of genome-wide haplotype effects in half-sib designs. J. Anim. Breed. Genet. 124: 356-361.
15. Lee, S. H., J. H. J. van der Werf, B. J. Hayes, M. E. Goddard and P. M. Visscher, 2008 Predicting unobserved phenotypes for complex traits from whole-genome SNP data. PLoS Genet. 4: e1000231.
16. Legarra, A., C. Robert-Granie, E. Manfredi and J. M. Elsen, 2008 Performance of genomic selection in mice. Genetics 180: 611-618.
17. 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.
18. Riquet, J., W. Coppieters, N. Cambisano, J. J. Arranz, P. Berzi et al., 1999 Fine-mapping of quantitative trait loci by identity by descent in outbred populations: application to milk production in dairy cattle. Proc. Natl. Acad. Sci. USA 96: 9252-9257.
19. Schaeffer, L. R., 2006 Strategy for applying genome-wide selection in dairy cattle. J. Anim. Breed. Genet. 123: 218-223.
20. Silverman, B. W., 1996 Smoothed functional principal, components analysis by choice of norm. Ann. Stat. 24: 1-24.
21. Solberg, T. R., A. K. Sonesson, J. A. Woolliams and T. H. E. Meuwissen, 2008 Genomic selection using different marker types and densities. J. Anim. Sci. 86: 2447-2454.
22. Sorensen, D., and D. Gianola, 2007 Likelihood, Bayesian and MCMC Methods in Quantitative Genetics. Springer-Verlag, New York.
23. VanRaden, P.M., C. P. Van Tassell, G.R.Wiggans, T. S. Sonstegard, R. D. Schnabel et al., 2009 Invited review: reliability of genomic predictions for North American Holstein bulls. J. Dairy Sci. 92: 16-24.
24. Weedon, M. N., H. Lango, C. M. Lindgren, C. Wallace, D. M. Evans et al., 2008 Genome-wide association analysis identifies 20 loci that influence adult height. Nat. Genet. 40: 575-583.
25. Wiggans, G. R., P. M. VanRaden and R. L. Powell, 1992 A method for combining United-States and Canadian bull evaluations. J. Dairy Sci. 75: 2834-2839.
26. Zhong, S., J. C. M. Dekkers, R. L. Fernando and J. L. Jannink, 2009 Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: a barley case study. Genetics 182: 355-364.