title: The accuracy of Genomic Selection in Norwegian red cattle assessed by cross-validation.
abstract: Genomic Selection (GS) is a newly developed tool for the estimation of breeding values for quantitative traits through the use of dense markers covering the whole genome. For a successful application of GS, accuracy of the prediction of genomewide breeding value (GW-EBV) is a key issue to consider. Here we investigated the accuracy and possible bias of GW-EBV prediction, using real bovine SNP genotyping (18,991 SNPs) and phenotypic data of 500 Norwegian Red bulls. The study was performed on milk yield, fat yield, protein yield, first lactation mastitis traits, and calving ease. Three methods, best linear unbiased prediction (G-BLUP), Bayesian statistics (BayesB), and a mixture model approach (MIXTURE), were used to estimate marker effects, and their accuracy and bias were estimated by using cross-validation. The accuracies of the GW-EBV prediction were found to vary widely between 0.12 and 0.62. G-BLUP gave overall the highest accuracy. We observed a strong relationship between the accuracy of the prediction and the heritability of the trait. GW-EBV prediction for production traits with high heritability achieved higher accuracy and also lower bias than health traits with low heritability. To achieve a similar accuracy for the health traits probably more records will be needed.
authors.affiliation: Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Box 5003, N-1432 As, Norway. tu.luan@umb.no
authors.forename: Tu
authors.initials: T
authors.lastname: Luan
authors.forename: John A
authors.initials: JA
authors.lastname: Woolliams
authors.forename: Sigbjørn
authors.initials: S
authors.lastname: Lien
authors.forename: Matthew
authors.initials: M
authors.lastname: Kent
authors.forename: Morten
authors.initials: M
authors.lastname: Svendsen
authors.forename: Theo H E
authors.initials: TH
authors.lastname: Meuwissen
mesh_terms: D000465:Algorithms; D000822:Animal Husbandry / Q000379:methods; D000818:Animals; D001499:Bayes Theorem; D001947:Breeding / Q000379:methods*; D002417:Cattle / Q000235:genetics* / Q000378:metabolism; D005260:Female; D016678:Genome / Q000235:genetics*; D055106:Genome-Wide Association Study; D005838:Genotype; D008297:Male; D008892:Milk / Q000378:metabolism / Q000592:standards; D009664:Norway; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics; D015203:Reproducibility of Results; D012641:Selection, Genetic
references.citation: Biometrics. 1975 Jun;31(2):423-47
references.pmid: 1174616
references.citation: Nat Genet. 2008 May;40(5):575-83
references.pmid: 18391952
references.citation: Genetics. 2007 Dec;177(4):2389-97
references.pmid: 18073436
references.citation: J Anim Breed Genet. 2007 Dec;124(6):323-30
references.pmid: 18076469
references.citation: J Dairy Sci. 2009 Feb;92(2):433-43
references.pmid: 19164653
references.citation: J Anim Breed Genet. 2007 Dec;124(6):356-61
references.pmid: 18076472
references.citation: J Anim Sci. 2008 Oct;86(10):2447-54
references.pmid: 18407980
references.citation: Genet Sel Evol. 2009 Jan 05;41:3
references.pmid: 19284693
references.citation: J Anim Breed Genet. 2006 Aug;123(4):218-23
references.pmid: 16882088
references.citation: Genome Res. 2002 Feb;12(2):222-31
references.pmid: 11827942
references.citation: Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):9252-7
references.pmid: 10430929
references.citation: J Dairy Sci. 1992 Oct;75(10):2834-9
references.pmid: 1430487
references.citation: PLoS One. 2008;3(10):e3395
references.pmid: 18852893
references.citation: Genetics. 2008 Jan;178(1):553-61
references.pmid: 18202394
references.citation: PLoS Genet. 2008 Oct;4(10):e1000231
references.pmid: 18949033
references.citation: J Dairy Sci. 2003 Nov;86(11):3736-44
references.pmid: 14672205
references.citation: Genetics. 2008 Sep;180(1):611-8
references.pmid: 18757934
references.citation: J Dairy Sci. 2009 Jan;92(1):16-24
references.pmid: 19109259
references.citation: Genetics. 2001 Apr;157(4):1819-29
references.pmid: 11290733
references.citation: Nat Rev Genet. 2009 Jun;10(6):381-91
references.pmid: 19448663
references.citation: Genetics. 2009 May;182(1):355-64
references.pmid: 19299342
references.citation: J Anim Breed Genet. 2007 Dec;124(6):362-8
references.pmid: 18076473