Improved accuracy of genomic prediction for dry matter intake of dairy cattle from combined European and Australian data sets

Journal of Dairy Science

Volumn 95, Issue 10, 2012, Pages 6103-6112

  de Haas, Y ^a   Calus, M P L ^a   Veerkamp, R F ^a   Wall, E ^b   Coffey, M P ^b   Daetwyler, H D ^c   Hayes, B J ^c,d,e   Pryce, J E ^c,d  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b SCOTTISH AGRICULTURAL COLLEGE   (United Kingdom)

^c DEPARTMENT OF PRIMARY INDUSTRIES   (Australia)

^d Dairy Futures Cooperative Research Centre   (Australia)

^e LA TROBE UNIVERSITY   (Australia)

Author keywords

Dry matter intake; Genomic prediction; Multi trait genomic REML; Validation

Indexed keywords

ANIMAL; ARTICLE; AUSTRALIA; BREEDING; CATTLE; EATING; FEMALE; GENETICS; GENOMICS; MALE; METHODOLOGY; NETHERLANDS; PHENOTYPE; QUANTITATIVE TRAIT; SINGLE NUCLEOTIDE POLYMORPHISM; UNITED KINGDOM;

ANIMALS; AUSTRALIA; BREEDING; CATTLE; EATING; FEMALE; GENOMICS; GREAT BRITAIN; MALE; NETHERLANDS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT, HERITABLE;

ANIMALIA; BOS; BOVINAE;

EID: 84867101935     PISSN: 00220302     EISSN: 15253198     Source Type: Journal    
DOI: 10.3168/jds.2011-5280     Document Type: Article

References (27)

1. Banos G., Coffey M.P., Veerkamp R.F., Berry D.P., Wall E. Merging and characterising phenotypic data on conventional and rare traits from dairy cattle experimental resources in three countries. Animal 2012, 6:1040-1048. http://dx.doi.org/10.1017/S1751731111002655.
2. Beerda B., Ouweltjes W., Sebek L.B.J., Windig J.J., Veerkamp R.F. Effects of genotype by environment interactions on milk yield, energy balance, and protein balance. J. Dairy Sci. 2007, 90:219-228.
3. Coffey M.P., Simm G., Hill W.G., Brotherstone S. Genetic evaluations of dairy bulls for daughter energy balance profiles using linear type scores and body condition score analyzed using random regression. J. Dairy Sci. 2003, 86:2205-2212.
4. Daetwyler H.D. Genome-wide evaluation of populations. PhD Diss 2009, Wageningen University, Wageningen, the Netherlands.
5. Daetwyler H.D., Pong-Wong R., Villanueva B., Woolliams J.A. The impact of genetic architecture on genome-wide evaluation methods. Genetics 2010, 185:1021-1031.
6. de Haas Y., Windig J.J., Calus M.P.L., Dijkstra J., de Haan M., Bannink A., Veerkamp R.F. Genetic parameters for predicted methane production and potential for reducing enteric emissions through genomic selection. J. Dairy Sci. 2011, 94:6122-6134.
7. Gilmour A.R., Cullis B.R., Welham S.J., Thompson R. ASREML: Program User Manual 2009, NSW Agriculture, Orange Agricultural Institute, Orange, NSW, Australia.
8. Hayes B.J. Technical note: Efficient parentage assignment and pedigree reconstruction with dense single nucleotide polymorphism data. J. Dairy Sci. 2011, 94:2114-2117.
9. Hegarty R.S., Goopy J.P., Herd R.M., McCorkell B. Cattle selected for lower residual feed intake have reduced daily methane production. J. Anim. Sci. 2007, 85:1479-1486.
10. Lund M.S., de Roos A.P.W., de Vries A.G., Druet T., Ducrocq V., Fritz S., Guillaume F., Guldbrandtsen B., Liu Z., Reents R., Schrooten C., Seefried F., Su G. A common reference population from four European Holstein populations increases reliability of genomic predictions. Genet. Sel. Evol. 2011, 43:43.
11. Meuwissen T.H.E., Hayes B.J., Goddard M.E. Prediction of total genetic value using genome-wide dense marker maps. Genetics 2001, 157:1819-1829.
12. Nieuwhof G.J., Van Arendonk J.A.M., Vos H., Korver S. Genetic relationships between feed intake, efficiency and production traits in growing bulls, growing heifers and lactating heifers. Livest. Prod. Sci. 1992, 32:189-202.
13. Pryce J.E., Arias J., Bowman P.J., Davis S.R., MacDonald K.A., Waghorn G.C., Wales W.J., Williams Y.J., Spelman R.J., Hayes B.J. Accuracy of genomic predictions of residual feed intake and 250 body weight in growing heifers using 625,000 SNP markers. J. Dairy Sci. 2012, 95:2108-2119.
14. Pryce J.E., Nielsen B.L., Veerkamp R.F., Simm G. Genotype and feeding system effects and interactions for health and fertility traits in dairy cattle. Livest. Prod. Sci. 1999, 57:193-201.
15. Pszczola M., Strabel T., Mulder H.A., Calus M.P.L. Reliability of direct genomic values for animals with different relationships within and to the reference population. J. Dairy Sci. 2012, 95:389-400.
16. VanRaden P.M. Efficient methods to compute genomic predictions. J. Dairy Sci. 2008, 91:4414-4423.
17. VanRaden P.M., Sullivan P.G. International genomic evaluation methods for dairy cattle. Genet. Sel. Evol. 2010, 42:7. http://dx.doi.org/10.1186/1297-9686-42-7.
18. Veerkamp, R. F., M. P. Coffey,d. P. Berry, Y. De Haas, E. Strandberg, H. Bovenhuis, M. P. L. Calus, and E. Wall. 2012. Genomewide associations for feed utilisation complex in primiparous Holstein-Friesian dairy cows from experimental research herds in four European countries. Animal http://dx.doi.org/10.1017/S1751731112001152.
19. Veerkamp R.F., Mulder H.A., Thompson R., Calus M.P.L. Genomic and pedigree-based genetic parameters for scarcely recorded traits when some animals are genotyped. J. Dairy Sci. 2011, 94:4189-4197.
20. Veerkamp R.F., Oldenbroek J.K., Van Der Gaast H.J., Van Der Werf J.H.J. Genetic correlation between days until start of luteal activity and milk yield, energy balance, and live weights. J. Dairy Sci. 2000, 83:577-583.
21. Veerkamp R.F., Simm G., Oldham J.D. Effects of interaction between genotype and feeding system on milk-production, feed-intake, efficiency and body tissue mobilization in dairy cows. Livest. Prod. Sci. 1994, 39:229-241.
22. Verbyla K.L., Calus M.P.L., Mulder H.A., de Haas Y., Veerkamp R.F. Predicting energy balance for dairy cows using high-density single nucleotide polymorphism information. J. Dairy Sci. 2010, 93:2757-2764.
23. Wall E., Simm G., Moran D. Developing breeding schemes to assist mitigation of greenhouse gas emissions. Animal 2010, 4:366-376.
24. Wilkerson V.A., Casper D.P., Mertens D.R. The prediction of methane production of Holstein cows by several equations. J. Dairy Sci. 1995, 78:2402-2414.
25. Williams Y.J., Pryce J.E., Grainger C., Wales W.J., Linden N., Porker M., Hayes B.J. Variation in residual feed intake in Holstein-Friesian dairy heifers in southern Australia. J. Dairy Sci. 2011, 94:4715-4725.
26. Wolc A., Arango J., Settar P., Fulton J.E., O'Sullivan N.P., Preisinger R., Habier D., Fernando R., Garrick D.J., Dekkers J.C.M. Persistence of accuracy of genomic estimated breeding values over generations in layer chickens. Genet. Sel. Evol. 2011, 43:23. http://dx.doi.org/10.1186/1297-9686-43-23.
27. Yang J.A., Benyamin B., McEvoy B.P., Gordon S., Henders A.K., Nyholt D.R., Madden P.A., Heath A.C., Martin N.G., Montgomery G.W., Goddard M.E., Visscher P.M. Common SNPs explain a large proportion of the heritability for human height. Nat. Genet. 2010, 42:569-571.