Single-step methods for genomic evaluation in pigs

TY - JOUR

T1 - Single-step methods for genomic evaluation in pigs

AU - Christensen, Ole Fredslund

AU - Madsen, Per

AU - Nielsen, Bjarne

AU - Ostersen, Tage

AU - Su, Guosheng

PY - 2012/10

Y1 - 2012/10

N2 - 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.

AB - 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.

KW - breeding value

KW - genetic parameters

KW - genomic selection

KW - mixed model methods

KW - pigs

U2 - 10.1017/S1751731112000742

DO - 10.1017/S1751731112000742

M3 - Journal article

C2 - 22717310

SN - 1751-7311

VL - 6

SP - 1565

EP - 1571

JO - Animal

JF - Animal

IS - 10

ER -