Comparison of single-trait and multiple-trait genomic prediction models

Meuwissen THE, Hayes BJ, Goddard ME: Prediction of total genetic value using genome-wide dense marker maps. Genetics. 2001, 157 (4): 1819-1829.

Schaeffer L: Strategy for applying genome‒wide selection in dairy cattle. J Anim Breed Genet. 2006, 123 (4): 218-223. 10.1111/j.1439-0388.2006.00595.x.

Weigel K, De Los CG, González-Recio O, Naya H, Wu X, Long N, Rosa G, Gianola D: Predictive ability of direct genomic values for lifetime net merit of Holstein sires using selected subsets of single nucleotide polymorphism markers. J Dairy Sci. 2009, 92 (10): 5248-10.3168/jds.2009-2092.

Vazquez A, Rosa G, Weigel K, De Los Campos G, Gianola D, Allison D: Predictive ability of subsets of single nucleotide polymorphisms with and without parent average in US Holsteins. J Dairy Sci. 2010, 93 (12): 5942-10.3168/jds.2010-3335.

Makowsky R, Pajewski NM, Klimentidis YC, Vazquez AI, Duarte CW, Allison DB, De Los Campos G: Beyond missing heritability: prediction of complex traits. PLoS genetics. 2011, 7 (4): e1002051-10.1371/journal.pgen.1002051.

Hayes B, Bowman P, Chamberlain A, Goddard M: Invited review: genomic selection in dairy cattle: progress and challenges. J Dairy Sci. 2009, 92 (2): 433-443. 10.3168/jds.2008-1646.

VanRaden P, Van Tassell C, Wiggans G, Sonstegard T, Schnabel R, Taylor J, Schenkel F: Invited review: reliability of genomic predictions for North American Holstein bulls. J Dairy Sci. 2009, 92 (1): 16-24. 10.3168/jds.2008-1514.

Harris B, Johnson D: Genomic predictions for New Zealand dairy bulls and integration with national genetic evaluation. J Dairy Sci. 2010, 93 (3): 1243-1252. 10.3168/jds.2009-2619.

Su G, Guldbrandtsen B, Gregersen V, Lund M: Preliminary investigation on reliability of genomic estimated breeding values in the Danish Holstein population. J Dairy Sci. 2010, 93 (3): 1175-1183. 10.3168/jds.2009-2192.

Calus MPL, Veerkamp RF: Accuracy of multi-trait genomic selection using different methods. Genet Sel Evol. 2011, 43 (1): 1-14. 10.1186/1297-9686-43-1.

Jia Y, Jannink JL: Multiple-trait genomic selection methods increase genetic value prediction accuracy. Genetics. 2012, 192 (4): 1513-1522. 10.1534/genetics.112.144246.

Hayashi T, Iwata H: A Bayesian method and its variational approximation for prediction of genomic breeding values in multiple traits. BMC bioinformatics. 2013, 14 (1): 1-14. 10.1186/1471-2105-14-1.

Aguilar I, Misztal I, Tsuruta S, Wiggans G, Lawlor T: Multiple trait genomic evaluation of conception rate in Holsteins. J Dairy Sci. 2011, 94 (5): 2621-2624. 10.3168/jds.2010-3893.

Tsuruta S, Misztal I, Aguilar I, Lawlor T: Multiple-trait genomic evaluation of linear type traits using genomic and phenotypic data in US Holsteins. J Dairy Sci. 2011, 94 (8): 4198-4204. 10.3168/jds.2011-4256.

Meuwissen T, Goddard M: Accurate prediction of genetic values for complex traits by whole-genome resequencing. Genetics. 2010, 185 (2): 623-631. 10.1534/genetics.110.116590.

Daetwyler HD, Pong-Wong R, Villanueva B, Woolliams JA: The impact of genetic architecture on genome-wide evaluation methods. Genetics. 2010, 185 (3): 1021-1031. 10.1534/genetics.110.116855.

Clark SA, Hickey JM, van der Werf JH: Different models of genetic variation and their effect on genomic evaluation. Genet Sel Evol. 2011, 43: 18-10.1186/1297-9686-43-18.

Coster A, Bastiaansen JW, Calus MP, Van Arendonk JA, Bovenhuis H: Sensitivity of methods for estimating breeding values using genetic markers to the number of QTL and distribution of QTL variance. Genet Sel Evol. 2010, 42: 9-10.1186/1297-9686-42-9.

Li Z, Sillanpää MJ: Overview of LASSO-related penalized regression methods for quantitative trait mapping and genomic selection. Theor Appl Genet. 2012, 125 (3): 419-435. 10.1007/s00122-012-1892-9.

Zhong S, Dekkers JCM, Fernando RL, Jannink JL: Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: a barley case study. Genetics. 2009, 182 (1): 355-364. 10.1534/genetics.108.098277.

Rius‒Vilarrasa E, Brøndum R, Strandén I, Guldbrandtsen B, Strandberg E, Lund M, Fikse W: Influence of model specifications on the reliabilities of genomic prediction in a Swedish–Finnish red breed cattle population. J Anim Breed Genet. 2012, 295 (5): 369-397.

De Los Campos G, Hickey JM, Pong-Wong R, Daetwyler HD, Calus MP: Whole-genome regression and prediction methods applied to plant and animal breeding. Genetics. 2013, 193 (2): 327-345. 10.1534/genetics.112.143313.

Ober U, Ayroles JF, Stone EA, Richards S, Zhu D, Gibbs RA, Stricker C, Gianola D, Schlather M, Mackay TFC: Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster. PLoS genetics. 2012, 8 (5): e1002685-10.1371/journal.pgen.1002685.

Li Z, Sillanpää MJ: Estimation of quantitative trait locus effects with epistasis by variational Bayes algorithms. Genetics. 2012, 190 (1): 231-249. 10.1534/genetics.111.134866.

Su G, Madsen P, Nielsen US, Mäntysaari EA, Aamand GP, Christensen OF, Lund MS: Genomic prediction for Nordic Red Cattle using one-step and selection index blending. J Dairy Sci. 2012, 95 (2): 909-917. 10.3168/jds.2011-4804.

Guo G, Lund M, Zhang Y, Su G: Comparison between genomic predictions using daughter yield deviation and conventional estimated breeding value as response variables. J Anim Breed Genet. 2010, 127 (6): 423-432. 10.1111/j.1439-0388.2010.00878.x.

Jairath L, Dekkers J, Schaeffer L, Liu Z, Burnside E, Kolstad B: Genetic evaluation for herd life in Canada. J Dairy Sci. 1998, 81 (2): 550-562. 10.3168/jds.S0022-0302(98)75607-3.

Hayes B, Goddard ME: The distribution of the effects of genes affecting quantitative traits in livestock. Genet Sel Evol. 2001, 33 (3): 209-230. 10.1186/1297-9686-33-3-209.

Allison DB, Fernandez JR, Heo M, Zhu S, Etzel C, Beasley TM, Amos CI: Bias in estimates of quantitative-trait–locus effect in genome scans: demonstration of the phenomenon and a method-of-moments procedure for reducing bias. Am J Hum Genet. 2002, 70 (3): 575-585. 10.1086/339273.

VanRaden P: Efficient methods to compute genomic predictions. J Dairy Sci. 2008, 91 (11): 4414-4423. 10.3168/jds.2007-0980.

Madsen P, Jensen J: DMU: A user’s guide. A package for analysing multivariate mixed models. Version 6, release 4.7. 2007, http://dmu.agrsci.dk/DMU/Doc/Current/dmuv6_guide.5.2.pdf Acessed Nov. 15, 2007

Steiger JH: Tests for comparing elements of a correlation matrix. Psychol Bull. 1980, 87 (2): 245-

Dunn OJ, Clark V: Comparison of tests of the equality of dependent correlation coefficients. J Am Stat Assoc. 1971, 66 (336): 904-908. 10.1080/01621459.1971.10482369.

Coren A, Steine T, Colleau J, Pedersen J, Pribyl J, Reinsch N: Economic values in dairy cattle breeding, with special reference to functional traits. Report of an EAAP-working group. Livest Prod Sci. 1997, 49: 1-21. 10.1016/S0301-6226(97)00041-9.