The genomic evaluation system in the United States: Past, present, future

Journal of Dairy Science

Volumn 94, Issue 6, 2011, Pages 3202-3211

  Wiggans, G R ^a   VanRaden, P M ^a   Cooper, T A ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

Genomic evaluation; Reliability; SNP effect

Indexed keywords

ANIMAL; ARTICLE; CATTLE; DAIRYING; FEMALE; GENETICS; GENOME; GENOTYPE; MALE; METHODOLOGY; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM; UNITED STATES;

ANIMALS; CATTLE; DAIRYING; FEMALE; GENOME; GENOTYPE; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; UNITED STATES;

ANIMALIA; BOS;

EID: 79956273022     PISSN: 00220302     EISSN: 15253198     Source Type: Journal    
DOI: 10.3168/jds.2010-3866     Document Type: Article

References (40)

1. Affymetrix. 2011. Axiom Genome-Wide BOS 1 Array Plate. Accessed January 26, 2011. http://media.affymetrix.com/support/technical/datasheets/axiom_gw_bos1_arrayplate_datasheet.pdf.
2. Aguilar I., Misztal I., Johnson D.L., Legarra A., Tsuruta S., Lawlor T.J. Hot topic: A unified approach to utilize phenotypic, full pedigree, and genomic information for genetic evaluation of Holstein final score. J. Dairy Sci. 2010, 93:743-752.
3. Andersson L. Genetic dissection of phenotypic diversity in farm animals. Nat. Rev. Genet. 2001, 2:130-138.
4. Ashwell M.S., Van Tassell C.P. The Cooperative Dairy DNA Repository-A new resource for quantitative trait loci detection and verification. J. Dairy Sci. 1999, 82(Suppl. 1):54. (Abstr.).
5. Cole J.B., VanRaden P.M. Visualization of results from genomic evaluations. J. Dairy Sci. 2010, 93:2727-2740.
6. Cole J.B., VanRaden P.M., O'Connell J.R., Van Tassell C.P., Sonstegard T.S., Schnabel R.D., Taylor J.F., Wiggans G.R. Distribution and location of genetic effects for dairy traits. J. Dairy Sci. 2009, 92:2931-2946.
7. David, X., A. de Vries, E. Feddersen, and S. Borchersen. 2010. International genomic cooperation: EuroGenomics significantly improves reliability of genomic evaluations. Interbull Bull. 41:2 pages. Accessed December 21, 2010. http://www.interbull.org/images/stories/David.pdf.
8. de Roos A.P.W., Schrooten C., Mullaart E., van der Beek S., de Jong G., Voskamp W. Genomic selection at CRV. Interbull Bull. 2009, 39:47-50.
9. Dekkers J.C.M. Commercial application of marker- and gene-assisted selection in livestock: Strategies and lessons. J. Anim. Sci. 2004, 82(E-Suppl. 1):E313-E328.
10. Druet, T., C. Schrooten, and A. P. W. de Roos. 2010. In silico genotyping of thousands of SNPs in dairy cattle for the EuroGenomics project. Commun. No. 0137 in Proc. 9th World Congr. Genet. Appl. Livest. Prod., Leipzig, Germany. Gesellschaft für Tierzuchtwissenschaften e. V., Gießen, Germany.
11. Ducrocq V., Fritz S., Guillaume F., Boichard D. French report on the use of genomic evaluation. Interbull Bull. 2009, 39:17-21.
12. EuroGenomics. 2010. Further improvement of genomic evaluation within EuroGenomics. Press release, December 15, 2010. Accessed December 22, 2010. http://www.vikinggenetics.com/dk/news/Press%20release%20Dec%202010.pdf.
13. Grisart B., Farnir F., Karim L., Cambisano N., Kim J.-J., Kvasz A., Mni M., Simon P., Frère J.-M., Coppieters W., Georges M. Genetic and functional confirmation of the causality of the DGAT1 K232A quantitative trait nucleotide in affecting milk yield and composition. Proc. Natl. Acad. Sci. USA 2004, 101:2398-2403.
14. Hayes B.J., Pryce J., Chamberlain A.J., Bowman P.J., Goddard M.E. 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 2010, 6:31001139. doi:10.1371/journal.pgen1001139.
15. Illumina. 2010a. BovineHD Genotyping BeadChip. Accessed December 14, 2010. http://www.illumina.com/Documents/products/datasheets/datasheet_bovineHD.pdf.
16. Illumina. 2010b. BovineSNP50 Genotyping BeadChip. Accessed December 14, 2010. http://www.illumina.com/Documents/products/datasheets/datasheet_bovine_snp5O.pdf.
17. Illumina. 2010c. GoldenGate Bovine3K Genotyping BeadChip. Accessed December 14, 2010. http://www.illumina.com/Documents/products/datasheets/datasheet_bovine3K.pdf.
18. Interbull. 2010. GEBV test-August 2010. Accessed December 21, 2010. http://www.interbull.org/index.php?option=com_content&view=article&id=82:gebv-test-results-august-2010&catid=4:organization&Itemid=119.
19. Inside LIC. Livestock Improvement Corporation, 2008, LIC, Hamilton, New Zealand. C. Bayly (Ed.).
20. Loberg A., Dürr J.W. Interbull survey on the use of genomic information. Interbull Bull. 2009, 39:3-13.
21. Meuwissen, T. 2010. Use of whole genome sequence data for QTL mapping and genomic selection. Commun. No. 0018 in Proc. 9th World Congr. Genet. Appl. Livest. Prod., Leipzig, Germany. Gesellschaft für Tierzuchtwissenschaften e. V., Gießen, Germany.
22. Meuwissen T.H., Hayes B.J., Goddard M.E. Prediction of total genetic value using genome-wide dense marker maps. Genetics 2001, 157:1819-1829.
23. Misztal I. Challenges of application of marker assisted selection-A review. Anim. Sci. Pap. Rep. 2006, 24:5-10.
24. Nieuwhof, G. J., K. T. Beard, K. V. Konstantinov, P. J. Bowman, and B. J. Hayes. 2010. Implementation of genomics in Australia. Preliminary proceedings of 2010 Interbull meeting, Riga, Latvia, 5 pages. Accessed December 22, 2010. http://www.interbull.org/images/stories/Nieuwhof_Implementation_of_genomics_in_Australia.pdf.
25. Reinhardt F., Liu Z., Seefried F., Thaller G. Implementation of genomic evaluation in German Holsteins. Interbull Bull. 2009, 40:219-226.
26. Soller M. Marker assisted selection-An overview. Anim. Biotechnol. 1994, 5:193-207.
27. Spelman, R. J., J. Arias, M. D. Keehan, V. Obolonkin, A. M. Winkelman, D. L. Johnson, and B. L. Harris. 2010. Application of genomic selection in the New Zealand dairy cattle industry. Commun. No. 0311 in Proc. 9th World Congr. Genet. Appl. Livest. Prod., Leipzig, Germany. Gesellschaft für Tierzuchtwissenschaften e. V., Gießen, Germany.
28. Stormont C. Contribution of blood typing to dairy science progress. J. Dairy Sci. 1967, 50:253-260.
29. Van Doormaal B.J., Kistemaker G.J., Sullivan P.G., Sargolzaei M., Schenkel F.S. Canadian implementation of genomic evaluations. Interbull Bull. 2009, 40:214-218.
30. Van Tassell C.P., Smith T.P.L., Matukumalli L.K., Taylor J.F., Schnabel R.D., Lawley C.T., Haudenschild C.D., Moore S.S., Warren W.C., Sonstegard T.S. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat. Methods 2008, 5:247-252.
31. VanRaden P.M. Efficient methods to compute genomic predictions. J. Dairy Sci. 2008, 91:4414-4423.
32. VanRaden P.M., Tooker M.E. Gains in reliability from combining subsets of 500, 5,000, 50,000 or 500,000 genetic markers. J. Dairy Sci. 2010, 93(E-Suppl. 1):534. (Abstr.).
33. VanRaden P.M., Van Tassell C.P., Wiggans G.R., Sonstegard T.S., Schnabel R.D., Taylor J.F., Schenkel F.S. Invited review: Reliability of genomic predictions for North American Holstein bulls. J. Dairy Sci. 2009, 92:16-24.
34. Vazquez A.I., Rosa G.J.M., Weigel K.A., De los Campos G., Gianola D., Allison D.B. Predictive ability of subsets of single nucleotide polymorphisms with and without parent average in US Holsteins. J. Dairy Sci. 2010, 93:5942-5949.
35. Weigel K.A., de los Campos G., Vazquez A.I., Rosa G.J.M., Gianola D., Van Tassell C.P. Accuracy of direct genomic values derived from imputed single nucleotide polymorphism genotypes in Jersey cattle. J. Dairy Sci. 2010, 93:5423-5435.
36. Wiggans G.R., Cooper T.A., VanRaden P.M. Cow adjustments for genomic predictions of Holsteins and Jersey bulls. J. Dairy Sci. 2010, 93:533-534. (Abstr.).
37. Wiggans G.R., Sonstegard T.S., VanRaden P.M., Matukumalli L.K., Schnabel R.D., Taylor J.F., Chesnais J.P., Schenkel F.S., Van Tassell C.P. Genomic evaluations in the United States and Canada: A collaboration. ICAR Tech. Ser. 2009, 13:347-353.
38. Wiggans G.R., Sonstegard T.S., VanRaden P.M., Matukumalli L.K., Schnabel R.D., Taylor J.F., Schenkel F.S., Van Tassell C.P. Selection of single-nucleotide polymorphisms and quality of genotypes used in genomic evaluation of dairy cattle in the United States and Canada. J. Dairy Sci. 2009, 92:3431-3436.
39. Wiggans G.R., VanRaden P.M. Improved reliability approximation for genomic evaluations in the United States. J. Dairy Sci. 2010, 93(E-Suppl. 1):533. (Abstr.).
40. Wiggans G.R., VanRaden P.M., Bacheller L.R., Tooker M.E., Hutchison J.L., Cooper T.A., Sonstegard T.S. Selection and management of DNA markers for use in genomic evaluation. J. Dairy Sci. 2010, 93:2287-2292.