Accuracy of genomic prediction using different models and response variables in the Nordic Red cattle population

Journal of Animal Breeding and Genetics

Volumn 130, Issue 5, 2013, Pages 333-340

  Gao, H ^a,b   Lund, M S ^a   Zhang, Y ^b   Su, G ^a  

^a AARHUS UNIVERSITY   (Denmark)

^b CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

Genomic prediction; Model; Reliability; Response variable

Indexed keywords

ANIMAL; BAYES THEOREM; BOVINAE; BREEDING; DAIRYING; GENETICS; GENOMICS; REGRESSION ANALYSIS; STATISTICAL MODEL;

ANIMALS; BAYES THEOREM; BREEDING; CATTLE; DAIRYING; GENOMICS; MODELS, STATISTICAL; REGRESSION ANALYSIS;

EID: 84884710353     PISSN: 09312668     EISSN: 14390388     Source Type: Journal    
DOI: 10.1111/jbg.12039     Document Type: Article

References (25)

1. Cleveland M., Forni S., Deeb N., Maltecca C. (2010) Genomic breeding value prediction using three Bayesian methods and application to reduced density marker panels. BMC Proceedings 2012, 4(Suppl 1):S6.
2. Colombani C., Legarra A., Fritz S., Guillaume F., Croiseau P., Ducrocq V., Robert-Granié C. (2012) Application of Bayesian least absolute shrinkage and selection operator (LASSO) and BayesCπ methods for genomic selection in French Holstein and Montbéliarde breeds. J. Dairy Sci., 96, 575-591.
3. Croiseau P., Guillaume F., Fritz S. (2012) Comparison of genomic selection approaches in Brown Swiss within Intergenomics. Interbull Bulletin, 46:127-132.
4. Erbe M., Hayes B., Matukumalli L., Goswami S., Bowman P., Reich C., Mason B., Goddard M. (2012) Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels. J. Dairy Sci., 95, 4114-4129.
5. Garrick D.J., Taylor J.F., Fernando R.L. (2009) Deregressing estimated breeding values and weighting information for genomic regression analyses. Genet. Sel. Evol., 41, 55.
6. George E.I., McCulloch R.E. (1993) Variable selection via Gibbs sampling. J. Am. Stat. Assoc., 88, 881-889.
7. Guo G., Lund M.S., Zhang Y., Su G. (2010) Comparison between genomic predictions using daughter yield deviation and conventional estimated breeding value as response variables. J. Anim. Breed. Genet., 127, 423-432.
8. Hayes B.J., Visscher P.M., Goddard M.E. (2009) Increased accuracy of artificial selection by using the realized relationship matrix. Genet. Res. (Camb), 91, 47-60.
9. Hayes B.J., Pryce J., Chamberlain A.J., Bowman P.J., Goddard M.E. (2010) Genetic architecture of complex traits and accuracy of genomic prediction: coat colour, milk-fat percentage, and type in Holstein cattle as contrasting model traits. PLoS Genet., 6, e1001139.
10. Jairath L., Dekkers J.C., Schaeffer L.R., Liu Z., Burnside E.B., Kolstad B. (1998) Genetic evaluation for herd life in Canada. J. Dairy Sci., 81, 550-562.
11. Janss L. (2008) IBAY Manual Version 1.44. University of Aarhus, Faculty Agricultural Sciences (DJF), Dept of Genetics and Biotechnology, Research Centre Foulum, Tjele, Denmark.
12. Janss L. (2011) Bayz Manual Version 2.04 (available at: http://bayz.biz; last accessed 1 October 2011).
13. Madsen P., Jensen J. (2010) An User's Guide to DMU, Version 6, Release 5.0. University of Aarhus, Faculty Agricultural Sciences (DJF), Dept of Genetics and Biotechnology, Research Centre Foulum, Tjele, Denmark. (available at: http://dmu.agrsci.dk/dmuv6_guide.5.0.pdf; last accessed 1 October 2011).
14. Meuwissen T. (2009) Accuracy of breeding values of 'unrelated' individuals predicted by dense SNP genotyping. Genet. Sel. Evol., 41, 35.
15. Meuwissen T., Goddard M. (2004) Mapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data. Genet. Sel. Evol., 36, 261-279.
16. Meuwissen T.H.E., Hayes B.J., Goddard M.E. (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157, 1819-1829.
17. Olson K.M., Vanraden P.M., Tooker M.E., Cooper T.A. (2011) Differences among methods to validate genomic evaluations for dairy cattle. J. Dairy Sci., 94, 2613-2620.
18. Ostersen T., Christensen O.F., Henryon M., Nielsen B., Su G., Madsen P. (2011) Deregressed EBV as the response variable yield more reliable genomic predictions than traditional EBV in pure-bred pigs. Genet. Sel. Evol., 43, 38.
19. Park T., Casella G. (2008) The bayesian lasso. J. Am. Stat. Assoc., 103, 681-686.
20. Schaeffer L.R. (2001) Multiple trait international bull comparisons. Livest. Sci., 69, 145-153.
21. Strandén I., Mäntysaari E.A. (2010) A recipe for multiple trait deregression. Interbull Bulletin. 43:21-24.
22. Su G., Guldbrandtsen B., Gregersen V.R., Lund M.S. (2010) Preliminary investigation on reliability of genomic estimated breeding values in the Danish Holstein population. J. Dairy Sci., 93, 1175-1183.
23. Tibshirani R. (1996) Regression shrinkage and selection via the Lasso. J. R. Stat. Soc. Sereies B, 58, 267-288.
24. VanRaden P.M. (2008) Efficient methods to compute genomic predictions. J. Dairy Sci., 91, 4414-4423.
25. Yi N., Xu S. (2008) Bayesian LASSO for quantitative trait loci mapping. Genetics, 179, 1045-1055.