Invited review: Genomic evaluation of cattle in a multi-breed context

Livestock Science

Volumn 166, Issue 1, 2014, Pages 101-110

  Lund, Mogens Sandø ^a   Su, Guosheng ^a   Janss, Luc ^a   Guldbrandtsen, Bernt ^a   Brøndum, Rasmus Froberg ^a  

^a AARHUS UNIVERSITY   (Denmark)

Author keywords

Genomic Prediction; Linkage disequilibrium; Multi breed

Indexed keywords

ANIMALIA; BOS;

EID: 84905571027     PISSN: 18711413     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.livsci.2014.05.008     Document Type: Article

References (52)

1. Berry D.P., McClure M.C., Mullen M.P. Within- and across-breed imputation of high-density genotypes in dairy and beef cattle from medium- and low-density genotypes. J. Anim. Breed. Genet. 2013, 131:165-172. 10.1111/jbg.12067.
2. Bolormaa S., Pryce J., Kemper K. Accuracy of prediction of genomic breeding values for residual feed intake, carcass and meat quality traits in Bos taurus, Bos indicus and composite beef cattle. J. Anim. Sci. 2013, 91:3088-3104. 10.2527/jas2012-5827.
3. Brøndum R.F., Ma P., Lund M.S., Su G. Short communication: Genotype imputation within and across Nordic cattle breeds. J. Dairy Sci. 2012, 95:6795-6800. 10.3168/jds.2012-5585.
4. Brøndum R.F., Rius-Vilarrasa E., Strandén I., Su G., Guldbrandtsen B., Fikse W.F., Lund M.S. Reliabilities of genomic prediction using combined reference data of the Nordic Red dairy cattle populations. J. Dairy Sci. 2011, 94:4700-4707. 10.3168/jds.2010-3765.
5. Brøndum R.F., Su G., Lund M.S., Bowman P.J., Goddard M.E., Hayes B.J. Genome position specific priors for genomic prediction. BMC Genomics 2012, 13:543. 10.1186/1471-2164-13-543.
6. Bulmer M. The effect of selection on genetic variability. Am. Nat. 1971, 105:201-211.
7. Calus M.P.L., Veerkamp R.F. Accuracy of multi-trait genomic selection using different methods. Genet. Select. Evol. 2011, 43:26. 10.1186/1297-9686-43-26.
8. Carlborg O., Kerje S., Schur̈tz K., Jacobsson L., Jensen P., Andersson L. A global search reveals epistatic interaction between QTL for early growth in the chicken. Genome Res. 2003, 13:413-421. 10.1101/gr.528003.
9. Chen L., Schenkel F., Vinsky M., Crews D.H., Li C. Accuracy of predicting genomic breeding values for residual feed intake in Angus and Charolais beef cattle. J. Anim. Sci. 2013, 91:4669-4678. 10.2527/jas2013-5715.
10. Daetwyler H.D., Capitan A., Pausch H., Stothard P., van Binsbergen R., Brøndum R.F., Liao X., Grohs C., Jung S., Baur A., Esquerré D., Gollnick N., Legrain S., Laurent P., Djari A., Rossignol M.-N., Klopp C., Rocha D., Fritz S., Eggen A., Bowman P., Coote D., Chamberlain A., VanTassel C.P., Hulsegge I., Goddard M., Guldbrandtsen B., Lund M.S., Veerkamp R., Boichard D., Fries R., Hayes B.J. The 1000 bull genomes project. Nat. Genet. 2014, (in press).
11. Daetwyler H.D., Kemper K.E., van der Werf J.H.J., Hayes B.J. Components of the accuracy of genomic prediction in a multi-breed sheep population. J. Anim. Sci. 2012, 90:3375-3384. 10.2527/jas.2011-4557.
12. Erbe M., Hayes B.J., Matukumalli L.K., Goswami S., Bowman P.J., Reich C.M., Mason B.a, Goddard M.E. Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels. J. Dairy Sci. 2012, 95:4114-4129. 10.3168/jds.2011-5019.
13. Felsenstein J. The effect of linkage on directional selection. Genetics 1965, 52:349-363.
14. Gao H., Su G., Janss L., Zhang Y., Lund M.S. Model comparison on genomic predictions using high-density markers for different groups of bulls in the Nordic Holstein population. J. Dairy Sci. 2013, 96:4678-4687. 10.3168/jds.2012-6406.
15. Goddard M. Genomic selection: prediction of accuracy and maximisation of long term response. Genetica 2009, 136:245-257. 10.1007/s10709-008-9308-0.
16. Grisart B., Coppieters W., Farnir F., Karim L., Ford C., Berzi P., Cambisano N., Mni M., Reid S., Simon P., Spelman R., Georges M., Snell R. Positional candidate cloning of a QTL in dairy cattle: identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield and composition. Genome Res. 2002, 12:222-231. 10.1101/gr.224202.
17. Habier D., Fernando R.L., Garrick D.J. Genomic-BLUP decoded: a look into the black box of genomic prediction. Genetics 2013, 194:597-607. 10.1534/genetics.113.152207.
18. Habier D., Fernando R.L., Kizilkaya K., Garrick D.J. Extension of the bayesian alphabet for genomic selection. BMC Bioinf. 2011, 12:186. 10.1186/1471-2105-12-186.
19. Habier D., Tetens J., Seefried F., Lichtner P., Thaller G. The impact of genetic relationship information on genomic breeding values in German Holstein cattle. Genet. Select. Evol. 2010, 42:5. 10.1186/1297-9686-42-5.
20. Hayes B.J., Bowman P.J., Chamberlain A.C., Verbyla K., Goddard M.E. Accuracy of genomic breeding values in multi-breed dairy cattle populations. Genet. Select. Evol. 2009, 41:51. 10.1186/1297-9686-41-51.
21. Hayes B.J., Visscher P.M., McPartlan H.C., Goddard M.E. Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res. 2003, 13:635-643. 10.1101/gr.387103.
22. Heringstad B., Su G., Solberg T.R., Guldbrandtsen B., Svendsen M., Lund M.S. Genomic predictions based on a joint reference population for Scandinavian red breeds. In Book of Abstracts of the 62nd Annual Meeting of the European Federation of Animal Science 2011, 29. Waageningen Academic Publishers, Stavanger, Norway.
23. Hill W.G., Robertson A. Linkage disequilibrium in finite populations. Theor. Appl. Genet. 1968, 38:226-231. 10.1007/BF01245622.
24. Hozé C., Fouilloux M.-N., Venot E., Guillaume F., Dassonneville R., Fritz S., Ducrocq V., Phocas F., Boichard D., Croiseau P. High-density marker imputation accuracy in sixteen French cattle breeds. Genet. Select. Evol. 2013, 45:33. 10.1186/1297-9686-45-33.
25. Hozé C., Fritz S., Phocas F., Boichard D., Ducrocq V., Croiseau P. Efficiency of multi-breed genomic selection for dairy cattle breeds with different sizes of reference population. J. Dairy Sci 2014, 1-12. 10.3168/jds.2013-7761.
26. Huang W., Richards S., Carbone M.A., Zhu D., Anholt R.R.H., Ayroles J.F., Duncan L., Jordan K.W., Lawrence F., Magwire M.M., Warner C.B., Blankenburg K, Han Y., Javaid M., Jayaseelan J., Jhangiani S.N., Muzny D., Ongeri F., Perales L., Wu Y.-Q., Zhang Y., Zou X., a Stone E., a Gibbs R., Mackay T.F.C. Epistasis dominates the genetic architecture of Drosophila quantitative traits. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:15553-15559. 10.1073/pnas.1213423109.
27. Kachman S.D., Spangler M.L., Bennett G.L., Hanford K.J., Kuehn L.a, Snelling W.M., Thallman R.M., Saatchi M., Garrick D.J., Schnabel R.D., Taylor J.F., Pollak E.J. Comparison of molecular breeding values based on within- and across-breed training in beef cattle. Genet. Select. Evol. 2013, 45:30. 10.1186/1297-9686-45-30.
28. Kadri N.K. Methods For Association Mapping Using Multiple Population Data, Ph.D. thesis submitted to Aarhus University 2014, ISBN: 978-87-92869-90-6.
29. Karoui S., Carabaño M.J., Díaz C., Legarra A. Joint genomic evaluation of French dairy cattle breeds using multiple-trait models. Genet. Select. Evol. 2012, 44:39. 10.1186/1297-9686-44-39.
30. Li Y., Sidore C., Kang H.M., Boehnke M., Abecasis G.R. Low-coverage sequencing: implications for design of complex trait association studies. Genome Res. 2011, 21:940-951. 10.1101/gr.117259.110.
31. De Los Campos G., Vazquez A.I., Fernando R., Klimentidis Y.C., Sorensen D. Prediction of complex human traits using the genomic best linear unbiased predictor. PLoS Genet. 2013, 9:e1003608. 10.1371/journal.pgen.1003608.
32. Lund, M.S., De Roos, A.P.W., De Vries, A.G., Druet, T., Ducrocq, V., Guillaume, F., Guldbrandtsen, B., Liu, Z., Reents, R., Schrooten, C., Seefried, M., Su, G., 2010. Improving genomic prediction by EuroGenomics collaboration. In: Proceedings of the WCGALP 2010. Leipzig. pp. 7-10.
33. Lund M.S., deRoos A.P.W., deVries A.G., Druet T., Ducrocq V., Fritz S., Guillaume F., Guldbrandtsen B., Liu Z.T., Reents R., Schrooten C., Seefried F., Su G.S. A common reference population from four European Holstein populations increases reliability of genomic predictions. Genet. Select. Evol. 2011, 43.
34. Ma P., Brøndum R.F., Zhang Q., Lund M.S., Su G. Comparison of different methods for imputing genome-wide marker genotypes in Swedish and Finnish Red Cattle. J. Dairy Sci. 2013, 96:4666-4677. 10.3168/jds.2012-6316.
35. Makgahlela M.L., Mäntysaari E.A., Strandén I., Koivula M., Nielsen U.S., Sillanpää M.J., Juga J. Across breed multi-trait random regression genomic predictions in the Nordic Red dairy cattle. J. Anim. Breed. Genet. 2012, 130:10-19. 10.1111/j.1439-0388.2012.01017.x.
36. Olson K.M., Vanraden P.M., Tooker M.E. Multibreed genomic evaluations using purebred Holsteins, Jerseys, and Brown Swiss. J. Dairy Sci. 2012, 95:5378-5383. 10.3168/jds.2011-5006.
37. Pryce J.E., Gredler B., Bolormaa S., Bowman P.J., Egger-Danner C., Fuerst C., Emmerling R., Sölkner J., Goddard M.E., Hayes B.J. Short communication: genomic selection using a multi-breed, across-country reference population. J. Dairy Sci. 2011, 94:2625-2630. 10.3168/jds.2010-3719.
38. De Roos A.P.W., Hayes B.J., Spelman R.J., Goddard M.E. Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. Genetics 2008, 179:1503-1512. 10.1534/genetics.107.084301.
39. Schenkel F., Sargolzaei M., Kistemaker G., Jansen G., Sullivan P., Van Doormaal B.J., Vanraden P.M., Wiggans G.R. Reliability of genomic evaluation of Holstein cattle in Canada. Interbull. Bull. 2009, 39:51-58.
40. Sved J. Linkage disequilibrium of chromosome segments. Theor. Popul. Biol. 1971, 2:125-141.
41. Sørensen L.P., Janss L., Madsen P., Mark T., Lund M.S. Estimation of (co)variances for genomic regions of flexible sizes: application to complex infectious udder diseases in dairy cattle. Genet. Select. Evol. 2012, 44:18. 10.1186/1297-9686-44-18.
42. Thomasen J., Sørensen A., Su G., Madsen P., Lund M., Guldbrandtsen B. The admixed population structure in Danish Jersey dairy cattle challenges accurate genomic predictions. J. Anim. Sci. 2013, 91:3105-3112. 10.2527/jas2012-5490.
43. Thomasen J.R., Guldbrandtsen B., Su G., Brøndum R.F., Lund M.S. Reliabilities of genomic estimated breeding values in Danish Jersey. Animal 2012, 6:789-796. 10.1017/S1751731111002035.
44. Thomasen J.R., Willam A., Guldbrandtsen B., Lund M.S., Sørensen A.C. Genomic selection strategies in a small dairy cattle population evaluated for genetic gain and profit. J. Dairy Sci. 2014, 97:458-470. 10.3168/jds.2013-6599.
45. VanRaden P.M. Efficient methods to compute genomic predictions. J. Dairy Sci. 2008, 91:4414-4423. 10.3168/jds.2007-0980.
46. Vanraden P.M., Null D.J., Sargolzaei M., Wiggans G.R., Tooker M.E., Cole J.B., Sonstegard T.S., Connor E.E., Winters M., van Kaam J.B.C.H.M., Valentini A, Van Doormaal B.J., Faust M.a, Doak G.a Genomic imputation and evaluation using high-density Holstein genotypes. J. Dairy Sci. 2013, 96:668-678. 10.3168/jds.2012-5702.
47. Vanraden P.M., Olson K.M., Null D.J., Sargolzaei M., Winters M., van Kaam J.B.C.H.M. Reliability increases from combining 50, 000- and 777, 000- marker genotypes from four countries. Interbull. Bull. 2012, 46:75-79.
48. Weber K., Thallman R., Keele J., Snelling W., Bennett G., Smith T., McDaneld T., Allan M., Van Eenennaam A., Kuehn L.a Accuracy of genomic breeding values in multibreed beef cattle populations derived from deregressed breeding values and phenotypes. J. Anim. Sci. 2012, 90:4177-4190. 10.2527/jas2011-4586.
49. Wientjes Y.C.J., Veerkamp R.F., Calus M.P.L. The effect of linkage disequilibrium and family relationships on the reliability of genomic prediction. Genetics 2013, 193:621-631. 10.1534/genetics.112.146290.
50. Zhou L., Ding X., Zhang Q., Wang Y., Lund M.S., Su G. Consistency of linkage disequilibrium between Chinese and Nordic Holsteins and genomic prediction for Chinese Holsteins using a joint reference population. Genet. Select. Evol. 2013, 45:7. 10.1186/1297-9686-45-7.
51. Zhou L., Heringstad B., Su G., Guldbrandtsen B., Meuwissen T., Svendsen M., Grove H., Nielsen U.S., Lund M.S. Genomic predictions based on a joint reference population for the Nordic Red cattle breeds. J. Dairy Sci 2014, 10.3168/jds.2013-7580, in press.
52. Zhou L., Lund M.S., Wang Y., Su G. Genomic predictions across Nordic Holstein and Nordic Red using the GBLUP model with different relationship matrices. J. Anim. Breed. Genet 2014.