Efficient methods to compute genomic predictions

Journal of Dairy Science

Volumn 91, Issue 11, 2008, Pages 4414-4423

  VanRaden, P M ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

Computer program; Genomic selection; Mixed model; Relationship matrix

Indexed keywords

EID: 55849133422     PISSN: 00220302     EISSN: 15253198     Source Type: Journal    
DOI: 10.3168/jds.2007-0980     Document Type: Article

References (24)

1. Amin, N., C. M. van Duijn, and Y. S. Aulchenko. 2007. A genomic background based method for association analysis in related individuals. PLoS ONE 2:e1274.
2. Calus, M. P. L., T. H. E. Meuwissen, A. P. W. de Roos, and R. F. Veerkamp. 2008. Accuracy of genomic selection using different methods to define haplotypes. Genetics 178:553-561.
3. de Roos, A. P. W., C. Schrooten, E. Mullaart, M. P. L. Calus, and R. F. Veerkamp. 2007. Breeding value estimation for fat percentage using dense markers on Bos taurus autosome 14. J. Dairy Sci. 90:4821-4829.
4. Garrick, D. J. 2007. Equivalent mixed model equations for genomic selection. J. Dairy Scii. 90(Suppl. 1):376. (Abstr.)
5. Gengler, N., P. Mayeres, and M. Szydlowski. 2007. A simple method to approximate gene content in large pedigree populations: Application to the myostatin gene in dual-purpose Belgian Blue cattle. Animal 1:21-28.
6. Guillaume, F., S. Fritz, D. Boichard, and T. Druet. 2008. Estimation by simulation of the efficiency of the French marker-assisted selection program in dairy cattle. Genet. Sel. Evol. 40:91-102.
7. Henderson, C. R. 1963. Selection index and expected genetic advance. NAS-NRC, Natl. Acad. Sci., Washington, DC.
8. Janss, L., and G. de Jong. 1999. MCMC based estimation of variance components in a very large dairy cattle data set. Interbull Bull. 20:62-67.
9. Lee, S. H., and J. H. J. van der Werf. 2006. An efficient variance component approach implementing an average information REML suitable for combined LD and linkage mapping with a general complex pedigree. Genet. Sel. Evol. 38:25-43.
10. Legarra, A., and I. Misztal. 2008. Technical note: Computing strategies in genome-wide selection. J. Dairy Sci. 91:360-366.
11. Leutenegger, A.-L., B. Prum, E. Génin, C. Verny, A. Lemainque, F. Clerget-Darpoux, and E. A. Thompson. 2003. Estimation of the inbreeding coefficient through use of genomic data. Am. J. Hum. Genet. 73:516-523.
12. Meuwissen, T. 2007. Genomic selection: Marker-assisted selection on a genome wide scale. J. Anim. Breed. Genet. 124:321-322.
13. Meuwissen, T. H., B. J. Hayes, and M. E. Goddard. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819-1829.
14. Schaeffer, L. R. 2006. Strategy for applying genome-wide selection in dairy cattle. J. Anim. Breed. Genet. 123:218-223.
15. Schaeffer, L. R., and B. W. Kennedy. 1986. Computing strategies for solving mixed model equations. J. Dairy Sci. 69:575-579.
16. Stam, P. 1980. The distribution of the fraction of the genome identical by descent in finite random mating populations. Genet. Res. 35:131-155.
17. van der Beek, S. 2007. Effect of genomic selection on national and international genetic evaluations. Interbull Bull. 37:111-114.
18. Van Tassell, C. P., L. K. Matukumalli, C. Taylor, T. P. L. Smith, T. S. Sonstegard, R. D. Schnabel, M. V. B. De Silva, G. R. Wiggans, G. Liu, S. Moore, and J. F. Taylor. 2007. Construction and application of a bovine high-density SNP assay. J. Dairy Sci. 90(Suppl. 1):421-422. (Abstr.)
19. VanRaden, P. M. 2007. Genomic measures of relationship and inbreeding. Interbull Bull. 37:33-36.
20. VanRaden, P. M., and M. E. Tooker. 2007. Methods to explain genomic estimates of breeding value. J. Dairy Sci. 90(Suppl. 1):374. (Abstr.)
21. VanRaden, P. M., and G. R. Wiggans. 1991. Derivation, calculation, and use of national animal model information. J. Dairy Sci. 74:2737-2746.
22. VanRaden, P. M., and Multi-State Project S-1008. 2006. Net merit as a measure of lifetime profit: 2006 revision. AIPL Res. Rep. NM$3(7-06). http://aipl.arsusda.gov/reference/nmcalc-2006.htm Accessed Nov. 27, 2007.
23. Wright, S. 1922. Coefficients of inbreeding and relationship. Am. Nat. 56:330-338.
24. Zhang, Z., R. J. Todhunter, E. S. Buckler, and L. D. Van Vleck. 2007. Technical note: Use of marker-based relationships with multipletrait derivative-free restricted maximal likelihood. J. Anim. Sci. 85:881-885.