Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 504004
Title Accounting for genetic architecture in single- and multipopulation genomic prediction using weights from genomewide association studies in pigs
Author(s) Veroneze, R.; Lopes, P.S.; Lopes, M.S.; Hidalgo, A.M.; Guimarães, S.E.F.; Harlizius, B.; Knol, E.F.; Arendonk, J.A.M. van; Silva, F.F.; Bastiaansen, J.W.M.
Source Journal of Animal Breeding and Genetics 133 (2016)3. - ISSN 0931-2668 - p. 187 - 196.
Department(s) Animal Breeding and Genetics
Publication type Refereed Article in a scientific journal
Publication year 2016
Keyword(s) Accuracy - Genetic variance - Genomic relationship - Single nucleotide polymorphisms

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.

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