Short communication: Genotype imputation within and across Nordic cattle breeds

Journal of Dairy Science

Volumn 95, Issue 11, 2012, Pages 6795-6800

  Brondum R F ^a   Ma, P ^a,b   Lund, M S ^a   Su, G ^a  

^a AARHUS UNIVERSITY   (Denmark)

^b CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

Combined reference population; Genotype imputation

Indexed keywords

ANIMAL; ARTICLE; BREEDING; CATTLE; DAIRYING; DENMARK; FINLAND; GENE LINKAGE DISEQUILIBRIUM; GENETICS; GENOTYPE; MALE; QUANTITATIVE TRAIT; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICS; SWEDEN;

ANIMALS; BREEDING; CATTLE; DAIRYING; DENMARK; FINLAND; GENOTYPE; LINKAGE DISEQUILIBRIUM; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT, HERITABLE; SWEDEN;

ANIMALIA; BOS;

EID: 84867742940     PISSN: 00220302     EISSN: 15253198     Source Type: Journal    
DOI: 10.3168/jds.2012-5585     Document Type: Article

References (13)

1. Brøndum R.F., Rius-Vilarrasa E., Stranden 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.
2. Browning B.L., Browning S.R. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am. J. Hum. Genet. 2009, 84:210-223.
3. Dassonneville R., Brondum R.F., Druet T., Fritz S., Guillaume F., Guldbrandtsen B., Lund M.S., Ducrocq V., Su G. Effect of imputing markers from a low-density chip on the reliability of genomic breeding values in Holstein populations. J. Dairy Sci. 2011, 94:3679-3686.
4. Dassonneville R., Brøndum R.F., Druet T., Fritz S., Guillaume F., Guldbrandtsen B., Lund M.S., Ducrocq V., Su G. Effect of imputing markers from a low-density chip on the reliability of genomic breeding values in Holstein populations. J. Dairy Sci. 2011, 94:3679-3686.
5. 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 SNP panels. J. Dairy Sci. 2012, 95:4114-4129.
6. Hayes B.J., Bowman P.J., Daetwyler H.D., Kijas J.W., van der Werf J.H.J. Accuracy of genotype imputation in sheep breeds. Anim. Genet. 2012, 43:72-80.
7. Hickey J.M., Crossa J., Babu R., de los Campos G. Factors affecting the accuracy of genotype imputation in populations from several maize breeding programs. Crop Sci. 2012, 52:654-663.
8. Huang L., Li Y., Singleton A.B., Hardy J.A., Abecasis G., Rosenberg N.A., Scheet P. Genotype-imputation accuracy across worldwide human populations. Am. J. Hum. Genet. 2009, 84:235-250.
9. Huang L., Wang C.L., Rosenberg N.A. The relationship between imputation error and statistical power in genetic association studies in diverse populations. Am. J. Hum. Genet. 2009, 85:692-698.
10. Lund M.S., De Roos A.P., 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. Mulder H.A., Calus M.P.L., Druet T., Schrooten C. Imputation of genotypes with low-density chips and its effect on reliability of direct genomic values in Dutch Holstein cattle. J. Dairy Sci. 2012, 95:876-889.
12. 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.
13. Zhang Z., Druet T. Marker imputation with low-density marker panels in Dutch Holstein cattle. J. Dairy Sci. 2010, 93:5487-5494.