title: Accounting for genetic architecture in single- and multipopulation genomic prediction using weights from genomewide association studies in pigs.
abstract: We studied the effect of including GWAS results on the accuracy of single- and multipopulation genomic predictions. Phenotypes (backfat thickness) and genotypes of animals from two sire lines (SL1, n = 1146 and SL3, n = 1264) were used in the analyses. First, GWAS were conducted for each line and for a combined data set (both lines together) to estimate the genetic variance explained by each SNP. These estimates were used to build matrices of weights (D), which was incorporated into a GBLUP method. Single population evaluated with traditional GBLUP had accuracies of 0.30 for SL1 and 0.31 for SL3. When weights were employed in GBLUP, the accuracies for both lines increased (0.32 for SL1 and 0.34 for SL3). When a multipopulation reference set was used in GBLUP, the accuracies were higher (0.36 for SL1 and 0.32 for SL3) than in single-population prediction. In addition, putting together the multipopulation reference set and the weights from the combined GWAS provided even higher accuracies (0.37 for SL1, and 0.34 for SL3). The use of multipopulation predictions and weights estimated from a combined GWAS increased the accuracy of genomic predictions.
authors.affiliation: Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, Brazil.|Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands.
authors.forename: R
authors.initials: R
authors.lastname: Veroneze
authors.affiliation: Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, Brazil.
authors.forename: P S
authors.initials: PS
authors.lastname: Lopes
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands.|Topigs Norsvin Research Center, Beuningen, the Netherlands.
authors.forename: M S
authors.initials: MS
authors.lastname: Lopes
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands.|Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
authors.forename: A M
authors.initials: AM
authors.lastname: Hidalgo
authors.affiliation: Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, Brazil.
authors.forename: S E F
authors.initials: SE
authors.lastname: Guimarães
authors.affiliation: Topigs Norsvin Research Center, Beuningen, the Netherlands.
authors.forename: B
authors.initials: B
authors.lastname: Harlizius
authors.affiliation: Topigs Norsvin Research Center, Beuningen, the Netherlands.
authors.forename: E F
authors.initials: EF
authors.lastname: Knol
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands.
authors.forename: J A M
authors.initials: JA
authors.lastname: van Arendonk
authors.affiliation: Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, Brazil.
authors.forename: F F
authors.initials: FF
authors.lastname: Silva
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands.
authors.forename: J W M
authors.initials: JW
authors.lastname: Bastiaansen
mesh_terms: D000273:Adipose Tissue; D000818:Animals; D001835:Body Weight; D055106:Genome-Wide Association Study; D020641:Polymorphism, Single Nucleotide; D034421:Sus scrofa / Q000145:classification / Q000235:genetics* / Q000502:physiology
keywords: accuracy; genetic variance; genomic relationship; single nucleotide polymorphisms