Short communication: Genotype imputation within and across Nordic cattle breeds

被引：30

作者：

Brondum, R. F. ^{[1
]}

Ma, P. ^{[1
,2
]}

Lund, M. S. ^{[1
]}

Su, G. ^{[1
]}

机构：

[1] Aarhus Univ, Dept Mol Biol & Genet, Ctr Quantitat Genet & Genom, DK-8830 Tjele, Denmark

[2] China Agr Univ, Coll Anim Sci & Technol, Dept Anim Genet, Beijing 100193, Peoples R China

来源：

JOURNAL OF DAIRY SCIENCE | 2012年 / 95卷 / 11期

关键词：

genotype imputation; combined reference population; DUTCH HOLSTEIN CATTLE; DIRECT GENOMIC VALUES; POPULATIONS; ACCURACY; RELIABILITY; PREDICTIONS; PANELS;

D O I：

10.3168/jds.2012-5585

中图分类号：

S8 [畜牧、动物医学、狩猎、蚕、蜂];

学科分类号：

0905 ;

摘要：

This study investigated the accuracies of imputation from 50K genotypes to high-density genotypes for animals from the Danish, Swedish, or Finnish Red dairy cattle populations, using either a national, combined Red, or combined Red and Holstein reference population. Combining the Red populations increased the imputation accuracy for all 3 populations compared with using single-nationality references. Including Holstein animals in the reference further increased the imputation accuracy for Danish Red.

引用

页码：6795 / 6800

页数：6

共 12 条

[1] Reliabilities of genomic prediction using combined reference data of the Nordic Red dairy cattle populations [J].

Brondum, R. F. ;

Rius-Vilarrasa, E. ;

Stranden, I. ;

Su, G. ;

Guldbrandtsen, B. ;

Fikse, W. F. ;

Lund, M. S. .

JOURNAL OF DAIRY SCIENCE, 2011, 94 (09) :4700-4707

[2] A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals [J].

Browning, Brian L. ;

Browning, Sharon R. .

AMERICAN JOURNAL OF HUMAN GENETICS, 2009, 84 (02) :210-223

[3] Effect of imputing markers from a low-density chip on the reliability of genomic breeding values in Holstein populations [J].

Dassonneville, R. ;

Brondum, R. F. ;

Druet, T. ;

Fritz, S. ;

Guillaume, F. ;

Guldbrandtsen, B. ;

Lund, M. S. ;

Ducrocq, V. ;

Su, G. .

JOURNAL OF DAIRY SCIENCE, 2011, 94 (07) :3679-3686

[4] Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels [J].

Erbe, M. ;

Hayes, B. J. ;

Matukumalli, L. K. ;

Goswami, S. ;

Bowman, P. J. ;

Reich, C. M. ;

Mason, B. A. ;

Goddard, M. E. .

JOURNAL OF DAIRY SCIENCE, 2012, 95 (07) :4114-4129

[5] Accuracy of genotype imputation in sheep breeds [J].

Hayes, B. J. ;

Bowman, P. J. ;

Daetwyler, H. D. ;

Kijas, J. W. ;

van der Werf, J. H. J. .

ANIMAL GENETICS, 2012, 43 (01) :72-80

[6] Factors Affecting the Accuracy of Genotype Imputation in Populations from Several Maize Breeding Programs [J].

Hickey, John M. ;

Crossa, Jose ;

Babu, Raman ;

de los Campos, Gustavo .

CROP SCIENCE, 2012, 52 (02) :654-663

[7] The Relationship between Imputation Error and Statistical Power in Genetic Association Studies in Diverse Populations [J].

Huang, Lucy ;

Wang, Chaolong ;

Rosenberg, Noah A. .

AMERICAN JOURNAL OF HUMAN GENETICS, 2009, 85 (05) :692-698

[8] Genotype-Imputation Accuracy across Worldwide Human Populations [J].

Huang, Lucy ;

Li, Yun ;

Singleton, Andrew B. ;

Hardy, John A. ;

Abecasis, Goncalo ;

Rosenberg, Noah A. ;

Scheet, Paul .

AMERICAN JOURNAL OF HUMAN GENETICS, 2009, 84 (02) :235-250

[9] A common reference population from four European Holstein populations increases reliability of genomic predictions [J].

Lund, Mogens S. ;

de Roos, Adrianus P. W. ;

de Vries, Alfred G. ;

Druet, Tom ;

Ducrocq, Vincent ;

Fritz, Sebastien ;

Guillaume, Francois ;

Guldbrandtsen, Bernt ;

Liu, Zenting ;

Reents, Reinhard ;

Schrooten, Chris ;

Seefried, Franz ;

Su, Guosheng .

GENETICS SELECTION EVOLUTION, 2011, 43

[10] Imputation of genotypes with low-density chips and its effect on reliability of direct genomic values in Dutch Holstein cattle [J].

Mulder, H. A. ;

Calus, M. P. L. ;

Druet, T. ;

Schrooten, C. .

JOURNAL OF DAIRY SCIENCE, 2012, 95 (02) :876-889

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