Single-step methods for genomic evaluation in pigs

被引:274
作者
Christensen, O. F. [1 ]
Madsen, P. [1 ]
Nielsen, B. [2 ]
Ostersen, T. [2 ]
Su, G. [1 ]
机构
[1] Aarhus Univ, Dept Mol Biol & Genet, DK-8830 Tjele, Denmark
[2] Danish Agr & Food Council, Pig Res Ctr, DK-1609 Copenhagen V, Denmark
关键词
breeding value; genetic parameters; genomic selection; mixed model methods; pigs; RELATIONSHIP MATRICES; FULL PEDIGREE; PREDICTIONS; INFORMATION; SELECTION; TRAITS; ACCURACY;
D O I
10.1017/S1751731112000742
中图分类号
S8 [畜牧、 动物医学、狩猎、蚕、蜂];
学科分类号
0905 ;
摘要
Genetic evaluation based on information from phenotypes, pedigree and markers can be implemented using a recently developed single-step method. In this paper we compare accuracies of predicted breeding values for daily gain and feed conversion ratio (FCR) in Danish Duroc pigs obtained from different versions of single-step methods, the traditional pedigree-based method and the genomic BLUP (GBLUP) method. In particular, we present a single-step method with an adjustment of the genomic relationship matrix so that it is compatible to the pedigree-based relationship matrix. Comparisons are made for both genotyped and non-genotyped animals and univariate and bivariate models. The results show that the three methods with marker information (two single-step methods and GBLUP) produce more accurate predictions of genotyped animals than the pedigree-based method. In addition, single-step methods provide more accurate predictions for non-genotyped animals. The results also show that the single-step method with adjusted genomic relationship matrix produce more accurate predictions than the original single-step method. Finally, the results for the bivariate analyses show a somewhat improved accuracy and reduced inflation of predictions for FCR for the two single-step methods compared with the univariate analyses. The conclusions are: first the methods with marker information improve prediction compared with the pedigree-based method; second, a single-step method, contrary to GBLUP provides improved predictions for all animals compared to the pedigree-based method; and third, a single-step method should be used with an adjustment of the genomic relationship matrix.
引用
收藏
页码:1565 / 1571
页数:7
相关论文
共 22 条
[1]   Hot topic: A unified approach to utilize phenotypic, full pedigree, and genomic information for genetic evaluation of Holstein final score [J].
Aguilar, I. ;
Misztal, I. ;
Johnson, D. L. ;
Legarra, A. ;
Tsuruta, S. ;
Lawlor, T. J. .
JOURNAL OF DAIRY SCIENCE, 2010, 93 (02) :743-752
[2]   Implications of avoiding overlap between training and testing data sets when evaluating genomic predictions of genetic merit [J].
Amer, P. R. ;
Banos, G. .
JOURNAL OF DAIRY SCIENCE, 2010, 93 (07) :3320-3330
[3]  
[Anonymous], 2010, A User's Guide to DMU. Version 6
[4]  
Brune T, 2011, THESIS HOCHSCHULE OS
[5]   Accuracy of multi-trait genomic selection using different methods [J].
Calus, Mario P. L. ;
Veerkamp, Roel F. .
GENETICS SELECTION EVOLUTION, 2011, 43
[6]   Effect of different genomic relationship matrices on accuracy and scale [J].
Chen, C. Y. ;
Misztal, I. ;
Aguilar, I. ;
Legarra, A. ;
Muir, W. M. .
JOURNAL OF ANIMAL SCIENCE, 2011, 89 (09) :2673-2679
[7]   Genomic prediction when some animals are not genotyped [J].
Christensen, Ole F. ;
Lund, Mogens S. .
GENETICS SELECTION EVOLUTION, 2010, 42
[8]   COMPARISON OF TESTS OF EQUALITY OF DEPENDENT CORRELATION COEFFICIENTS [J].
DUNN, OJ ;
CLARK, V .
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 1971, 66 (336) :904-908
[9]   Different genomic relationship matrices for single-step analysis using phenotypic, pedigree and genomic information [J].
Forni, Selma ;
Aguilar, Ignacio ;
Misztal, Ignacy .
GENETICS SELECTION EVOLUTION, 2011, 43
[10]   Deregressing estimated breeding values and weighting information for genomic regression analyses [J].
Garrick, Dorian J. ;
Taylor, Jeremy F. ;
Fernando, Rohan L. .
GENETICS SELECTION EVOLUTION, 2009, 41