Sensitivity of methods for estimating breeding values using genetic markers to the number of QTL and distribution of QTL variance

Genetics Selection Evolution

Volumn 42, Issue 1, 2010, Pages

  Coster, Albart ^a   Bastiaansen, John W M ^a   Calus, Mario P L ^a   Van Arendonk, Johan A M ^a   Bovenhuis, Henk ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY ASSESSMENT; ESTIMATION METHOD; GENETIC MARKER; GENOME; HERITABILITY; NUMERICAL MODEL; POPULATION STRUCTURE; REGRESSION ANALYSIS; REPRODUCTIVE BEHAVIOR; SENSITIVITY ANALYSIS;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; BREEDING; COMPARATIVE STUDY; COMPUTER SIMULATION; GENETIC MARKER; GENETIC SELECTION; QUANTITATIVE TRAIT LOCUS; REGRESSION ANALYSIS;

ANIMALS; BAYES THEOREM; BREEDING; COMPUTER SIMULATION; GENETIC MARKERS; MODELS, GENETIC; QUANTITATIVE TRAIT LOCI; REGRESSION ANALYSIS; SELECTION, GENETIC;

EID: 77952749326     PISSN: 0999193X     EISSN: 12979686     Source Type: Journal    
DOI: 10.1186/1297-9686-42-9     Document Type: Article

References (32)

1. Strategy for applying genome-wide selection in dairy cattle. Schaeffer LR, J Anim Breed Genet 2006 123 218 223 10.1111/j.1439-0388.2006.00595.x 16882088 (Pubitemid 44049951)
2. Prediction of total genetic value using genome-wide dense marker maps. Meuwissen THE, Hayes BJ, Goddard ME, Genetics 2001 157 1819 1829 11290733 (Pubitemid 32298846)
3. 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. Calus M, Veerkamp R, J Anim Breed Genet 2007 124 362 368 18076473 (Pubitemid 350231128)
4. Accuracy of genomic selection using different methods to define haplotypes. Calus MPL, Meuwissen THE, de Roos APW, Veerkamp RF, Genetics 2008 178 553 561 10.1534/genetics.107.080838 18202394 (Pubitemid 351398768)
5. Genomic selection: prediction of accuracy and maximisation of long term response. Goddard M, Genetica 2008 136 245 257 10.1007/s10709-008-9308-0 18704696
6. Reducing dimensionality for prediction of genome-wide breeding values. Solberg T, Sonesson A, Woolliams J, Meuwissen T, Genet Sel Evol 2009 41 29 10.1186/1297-9686-41-29 19296851
7. Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Sved JA, Theor Popul Biol 1971 2 125 141 10.1016/0040-5809(71) 90011-6 5170716
8. Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters. Muir W, J Anim Breed Genet 2007 124 342 355 18076471 (Pubitemid 350231126)
9. Genomic selection using different marker types and densities. Solberg TR, Sonesson AK, Woolliams JA, Meuwissen THE, J Anim Sci 2008 86 2447 2454 10.2527/jas.2007-0010 18407980
10. The distribution of the effects of genes affecting quantitative traits in livestock. Hayes B, Goddard ME, Genet Sel Evol 2001 33 209 229 10.1186/1297-9686-33-3-209 11403745 (Pubitemid 32591810)
11. Genome-Wide Evaluation of Populations. Daetwyler H, PhD thesis Wageningen University, Wageningen, The Netherlands 2009
12. Genomic selection at CRV. De Roos A, Schrooten C, Mullaart E, Beek van der S, de Jong G, Voskamp W, Interbull Bull 2009 39 47 50
13. Least angle regression. Efron B, Hastie T, Tibshirani R, Ann Stat 2004 407 499 (Pubitemid 41250302)
14. The bayesian lasso. Park T, Casella G, J Am Stat Assoc 2008 103 681 686 10.1198/016214508000000337
15. SIMPLS: An alternative approach to partial least squares regression. de Jong S, Chemom Intell Lab Syst 1993 18 251 263 10.1016/0169-7439(93)85002-X (Pubitemid 23112297)
16. Predicting patient survival from microarray data by accelerated failure time modeling using partial least squares and LASSO. Datta S, Le-Rademacher J, Datta S, Biometrics 2007 63 259 271 10.1111/j.1541-0420.2006.00660.x 17447952 (Pubitemid 46622698)
17. A comparison of five methods to predict genomic breeding values of dairy bulls from genome-wide SNP markers. Moser G, Tier B, Crump R, Khatkar M, Raadsma H, Genet Sel Evol 2009 41 56 10.1186/1297-9686-41-56 20043835
18. Coster A, Bastiaansen J, HaploSim: HaploSim 2009 [R package version 1.8]
19. R Development Core Team, R: A Language and Environment for Statistical Computing R Foundation for Statistical Computing, Vienna, Austria 2009 [ISBN 3-900051-07-0]
20. Crow JF, Kimura M, An introduction to population genetics theory Alpha Editions 1970
21. Hastie T, Efron B, lars: Least Angle Regression, Lasso and Forward Stagewise 2007 [R package version 0.9-7]
22. Wehrens R, Mevik BH, pls: Partial Least Squares Regression (PLSR) and Principal Component Regression (PCR) 2007 [R package version 2.1-0]
23. 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. Grisart B, Coppieters W, Farnir F, Karim L, Ford C, Berzi P, Cambisano N, Mni M, Reid S, Simon P, Spelman R, Georges M, Snell R, Genome Res 2002 12 222 231 10.1101/gr.224202 11827942 (Pubitemid 34162989)
24. Stearoyl-coenzyme A desaturase gene polymorphism and milk fatty acid composition in Italian Holsteins. Mele M, Conte G, Castiglioni B, Chessa S, Macciotta N, Serra A, Buccioni A, Pagnacco G, Secchiari P, J Dairy Sci 2007 90 4458 10.3168/jds.2006-617 17699067 (Pubitemid 350045225)
25. A paternally expressed QTL affecting skeletal and cardiac muscle mass in pigs maps to the IGF2 locus. Jeon J, Carlborg Törnsten A, Giuffra E, Amarger V, Chardon P, Andersson-Eklund L, Andersson K, Hansson I, Lundstrom K, Andersson L, Nature 1999 21 157 158 (Pubitemid 29070357)
26. Genome-wide association analysis identifies 20 loci that influence adult height. Weedon MN, Lango H, Lindgren CM, Wallace C, Evans DM, Mangino M, Freathy RM, Perry JRB, Stevens S, Hall AS, Samani NJ, Shields B, Prokopenko I, Farrall M, Dominiczak A, Initiative DG, Consortium TWTCC, TJ, Bergmann S, Beckmann JS, Vollenweider P, Waterworth DM, Mooser V, Palmer CNA, Morris AD, Ouwehand WH, Consortium G, Caulfield M, Munroe PB, Hattersley MI, McCarthy AT, Frayling M, Nat Genet 2008 40 575 583 10.1038/ng.121 18391952 (Pubitemid 351601210)
27. Many sequence variants affecting diversity of adult human height. Gudbjartsson DF, Walters GB, Thorleifsson G, Stefansson H, Halldorsson BV, Zusmanovich P, Sulem P, Thorlacius S, Gylfason A, Steinberg S, Helgadottir A, Ingason A, Steinthorsdottir V, Olafsdottir EJ, Olafsdottir GH, Jonsson T, Borch-Johnsen K, Hansen T, Andersen G, Jorgensen T, Pedersen O, Aben KK, Witjes JA, Swinkels DW, Heijer Md, Franke B, Verbeek ALM, Becker DM, Yanek LR, Becker LC, Tryggvadottir L, Rafnar T, Gulcher J, Kiemeney LA, Kong A, Thorsteinsdottir U, Stefansson K, Nat Genet 2008 40 609 615 10.1038/ng.122 18391951 (Pubitemid 351601211)
28. Identification of ten loci associated with height highlights new biological pathways in human growth. Lettre G, Jackson A, Gieger C, Schumacher F, Berndt S, Sanna S, Eyheramendy S, Voight B, Butler J, Guiducci C, T I, Hackett R, Heid KB, Jacobs IM, Lyssenko V, Uda M, Initiative TDG, FUSION, KORA, Colorectal TPL, Trial OCS, Study TNH, Sardi NIA, Boehnke M, Chanock SJ, Groop LC, Hu FB, Isomaa B, Kraft P, Peltonen L, Salomaa V, Schlessinger D, Hunter DJ, Hayes RB, Abecasis GR, Wichmann HE, Mohlke KL, Hirschhorn JN, Nat Genet 2008 40 584 591 10.1038/ng.125 18391950 (Pubitemid 351601214)
29. Increased accuracy of artificial selection by using the realized relationship matrix. Hayes BJ, Visscher PM, Goddard ME, Gen Res 2009 91 47 60 10.1017/S0016672308009981
30. Comparing linkage disequilibrium-based methods for fine mapping quantitative trait loci. Grapes L, Dekkers JCM, Rothschild MF, Fernando RL, Genetics 2004 166 1561 1570 10.1534/genetics.166.3.1561 15082569 (Pubitemid 38507069)
31. 2 measure of linkage disequilibrium: impact on design and interpretation of association studies. Wray N, Twin Res Hum Genet 2005 8 87 94 10.1375/twin.8.2.87 15901470 (Pubitemid 40593388)
32. Falconer DS, Mackay TFC, Quantitative Genetics England: Pearson Education Limited 1996