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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.,
Silva F.F.,
Bastiaansen J.W.M.
Publication year - 2016
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1111/jbg.12202
Subject(s) - genome wide association study , genetic architecture , population , sire , mathematics , set (abstract data type) , statistics , biology , genetics , genotype , single nucleotide polymorphism , computer science , quantitative trait locus , medicine , zoology , gene , environmental health , programming language
Summary 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 ( SL 1, n = 1146 and SL 3, 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 SL 1 and 0.31 for SL 3. When weights were employed in GBLUP , the accuracies for both lines increased (0.32 for SL 1 and 0.34 for SL 3). When a multipopulation reference set was used in GBLUP , the accuracies were higher (0.36 for SL 1 and 0.32 for SL 3) 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 SL 1, and 0.34 for SL 3). The use of multipopulation predictions and weights estimated from a combined GWAS increased the accuracy of genomic predictions.