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Paper

Effect of Prior Distributions on Accuracy of Genomic Breeding Values for Two Dairy Traits

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Article: e91 | Received 26 Jun 2013, Accepted 07 Sep 2013, Published online: 18 Feb 2016

References

  • CattleQTLdb, 2013. Animal Quantitative Trait Locus database (Bovine), Release 13. Available from: http://www.animalgenome.org/cgi-bin/gbrowse/cattle/
  • ClevelandM. ForniS. DeebN. MalteccaC. 2010. Genomic breeding value prediction using three Bayesian methods and application to reduced density marker panels. BMC Proceedings 4(Suppl.1):S6.
  • ColeJ.B. VanRadenP.M. O’ConnellJ.R. Van TasselC.P. SonstegardT.S. SchnabelR.D. TaylorJ.F. WiggansG.R. 2009. Distribution and location of genetic effects for dairy traits. J. Dairy Sci. 92:2931-2946.
  • CrooksL. SahanaG. de KoningD. LundM.S. CarlborgÖ. 2009. Comparison of analyses of the QTL-MAS XII common dataset. II: genome-wide association and fine mapping. BMC Proceedings 3(Suppl.1):S2.
  • CrossaJ. de los CamposG. PerezP. GianolaD. BurguenoJ. ArausJ.L. MakumbiD. SinghR. DreisigackerS. YanJ. AriefV. BanzigerM. BraunH.J. 2010. Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers. Genetics 186:713-724.
  • de los CamposG. NayaH. GianolaD. CrossaJ. LegarraA. ManfrediE. WeigelK. CotesJ.M. 2009. Predicting quantitative traits with regression models for dense molecular markers and pedigree. Genetics 182:375-385.
  • GaspaG. PintusM.A. NicolazziE.L. VicarioD. ValentiniC. MacciottaN.P.P. 2013. Use of principal component approach to predict direct genomic breeding values for beef traits in Italian Simmental cattle. J. Anim. Sci. 91:29-37.
  • GoddardM.E. HayesB.J. 2007. Genomic selection. J. Anim. Breed. Genet. 124:323-330.
  • Gonzàles-RecioO. GianolaD. RosaG.J. WeigelK.A. KranisA. 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.
  • GredlerB. NireaK.G. SolbergT.R. Egger-DannerC. MeuwissenT.H.E. SölknerJ.A. 2009. Comparison of methods for genomic selection in Austrian dual purpose Simmental cattle. Proc. 18th Nat. Conf. of Ass. Advanc. Anim. Breed. Genet., Barossa Valley, South Australia, 18:568-571.
  • GrisartB. CoppietersW. FarnirF. KarimL. FordC. BerziP. CambisanoN. MniM. ReidS. SimonP. SpelmanR. GeorgesM. SnellR. 2002. Positional candidate cloning of a QTL in dairy cattle: identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield and composition. Genome Res. 12:222-231.
  • HabierD. TetensJ. SeefriedF. LichtnerP. ThallerG. 2010. The impact of genetic relationship information on genomic breeding values in German Holstein cattle. Genet. Sel. Evol. 42:5.
  • HarrisB.L. JohnsonD.L. SpelmanR.J. 2008. Genomic selection in New Zealand and the implications for national genetic evaluation. Proc. 36th ICAR Biennial Session, Niagara Falls, Canada, 38:325-330.
  • HayesB.J. GoddardM.E. 2001. The distribution of the effects of genes affecting quantitative traits in livestock. Genet. Sel. Evol. 33:209-229.
  • HayesB.J. BowmanP.J. ChamberlainA.J. GoddardM.E. 2009. Invited review: Genomic selection in dairy cattle: progress and challenges. J. Dairy Sci. 92:433-445.
  • LegarraA. Robert-GranieC. ManfrediE. ElsenJ.M. 2008. Performance of genomic selection in mice. Genetics 180:611-618.
  • LiJ. DasK. FuG. LiR. WuR. 2011. The Bayesian lasso for genome-wide association studies. Bioinformatics 27:516-523.
  • LuanT. WooliamsJ. LienS. KentM. SvendsenM. MeuwissenT. 2009. The accuracy of genomic selection in Norwegian red cattle assessed by cross-validation. Genetics 183:1119-1126.
  • MacciottaN.P.P. GaspaG. SteriR. NicolazziE.L. DimauroC. PieramatiC. Cappio-BorlinoA. 2010. Using eigenvalues as variance priors in the prediction of genomic breeding values by principal component analysis. J. Dairy Sci. 93:2765-2774.
  • MeuwissenT.H.E. HayesB.J. GoddardM.E. 2001. Prediction of total genetic values using genome-wide dense marker maps. Genetics 157:1819-1829.
  • OlsenH.G. Gomez-RayaL. VageD.I. OlsakerI. KlunglandH. SvendsenM. AdnoyT. SabryA. KlemetsdalG. SchulmanN. KramerW. ThallerG. RonningenK. LienS. 2002. A genome scan for quantitative trait loci affecting milk production in Norwegian dairy cattle. J. Dairy Sci. 85:3124-3130.
  • ParkT. CasellaG. 2008. The Bayesian Lasso. J. Am. Stat. Assoc. 103:681-686.
  • PérezP. de los CamposG. CrossaJ. GianolaD. 2010. Genomic-enabled prediction based on molecular markers and pedigree using the Bayesian linear regression package in R. Plant Gen. 2:106-116.
  • PintusM.A. NicolazziE.L. Van KaamJ.B. BiffaniS. StellaA. GaspaG. DimauroC. MacciottaN.P. 2013. Use of different statistical models to predict direct genomic values for productive and functional traits in Italian Holstein. J. Anim. Breed Genet. 130:32-40.
  • ter BraakC.J.F. BoerM.P. BinkM.C.A.M. 2005. Extending Xu’s Bayesian model for estimating polygenic effects using markers of the entire genome. Genetics 170:1435-1438.
  • ThallerG. KrämerW. WinterA. KaupeB. ErhardtG. FriesR. 2003. Effects of DGAT1 variants on milk production traits in German cattle breeds. J. Anim Sci. 81:1911-1918.
  • TibshiraniR. 1996. Regression shrinkage and selection via the Lasso. J. R. Stat. Soc. 58:267-288.
  • van der WerfJ.H.J. 2009. Potential benefit of genomic selection in sheep. Proc. 18th Nat. Conf. of Ass. Advanc. Anim. Breed. Genet., Barossa Valley, South Australia, 18:38-41.
  • VanRadenP.M. Van TassellC.P. WiggansG.R. SonstegardT.S. SchnabelR.D. TaylorJ.F. SchenkelF. 2009. Invited review: Reliability of genomic predictions for North American Holstein bulls. J. Dairy Sci. 92:16-24.
  • VazquezA.I. RosaG.J.M. WeigelK.A. de los CamposG. GianolaD. AllisonD.B. 2010. Predictive Ability of Subsets of SNP with and without Parent Average in US Holsteins. J. Dairy Sci. 93:5942-5949.
  • VerbylaK. BowmanP.J. HayesB.J. GoddardM.E. 2010. Sensitivity of genomic selection to using different prior distributions. BMC Proceedings 4(Suppl.1):S5.
  • ViitalaS. SzydaJ. BlottS. SchulmanN. LidauerM. Mäki-TanilaA. GeorgesM. VilkkiJ. 2006. The role of the bovine growth hormone receptor and prolactin receptor genes in milk, fat and protein production in Finnish Ayrshire dairy cattle. Genetics 173:2151-2164.
  • ViitalaS.M. SchulmanN.F. de KoningD.J. EloK. KinosR. VirtaA. VirtaJ. Maki-TanilaA. VilkkiJ.H. 2003. Quantitative trait loci affecting milk production traits in Finnish Ayrshire dairy cattle. J. Dairy Sci. 86:1828-1836.
  • WeigelK.A. de los CamposG. Gonzàles-RecioO. NayaH. WuX.L. LongN. RosaG.J.M. GianolaD. 2009. Predictive ability of direct genomic values for lifetime net merit of Holstein sires using selected subsets of single nucleotide polymorphism markers. J. Dairy Sci. 92:5248-5257.
  • WeigelK.A. de los CamposG. VazquezA.I. RosaG.J.M. GianolaD. Van TassellC.P. 2010. Accuracy of direct genomic values derived from imputed single nucleotide polymorphism genotypes in Jersey cattle. J. Dairy Sci. 93:5423-5435.
  • QTL-MAS, 2008. Proc. 12th Eur. Workshop, Uppsala, Sweden. Available from:http://www.computationalgenetics.se/QTLMAS 08/QTLMAS/DATA.html
  • YiN. XuS. 2008. Bayesian LASSO for quantitative trait loci mapping. Genetics 179:1045-1055.