Single-step methods for genomic evaluation in pigs.
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.
Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark. OleF.Christensen@agrsci.dk
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Christensen
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Madsen
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Nielsen
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Ostersen
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D000822:Animal Husbandry / Q000379:methods*; D000818:Animals; D001947:Breeding; D005260:Female; D023281:Genomics / Q000379:methods*; D005838:Genotype; D008297:Male; D008957:Models, Genetic; D010375:Pedigree; D034421:Sus scrofa / Q000235:genetics* / Q000502:physiology; D015430:Weight Gain