title: Genomic best linear unbiased prediction method reflecting the degree of linkage disequilibrium.
abstract: The degree of linkage disequilibrium (LD) between markers differs depending on the location of the genome; this difference biases genetic evaluation by genomic best linear unbiased prediction (GBLUP). To correct this bias, we used three GBLUP methods reflecting the degree of LD (GBLUP-LD). In the three GBLUP-LD methods, genomic relationship matrices were conducted from single nucleotide polymorphism markers weighted according to local LD levels. The predictive abilities of GBLUP-LD were investigated by estimating variance components and assessing the accuracies of estimated breeding values using simulation data. When quantitative trait loci (QTL) were located at weak LD regions, the predictive abilities of the three GBLUP-LD methods were superior to those of GBLUP and Bayesian lasso except when the number of QTL was small. In particular, the superiority of GBLUP-LD increased with decreasing trait heritability. The rates of QTL at weak LD regions would increase when selection by GBLUP continues; this consequently decreases the predictive ability of GBLUP. Thus, the GBLUP-LD could be applicable for populations selected by GBLUP for a long time. However, if QTL were located at strong LD regions, the accuracies of three GBLUP-LD methods were lower than GBLUP and Bayesian lasso.
authors: NARO Institute of Livestock and Grassland Science, Tsukuba, Japan.
authors: M
authors: M
authors: Nishio
authors: NARO Institute of Livestock and Grassland Science, Tsukuba, Japan.
authors: M
authors: M
authors: Satoh
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D005819:Genetic Markers / Q000235:genetics; D023281:Genomics / Q000379:methods*; D016014:Linear Models; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci
chemical_list: D005819:Genetic Markers
keywords: Genomic relationship matrix; genomic selection; linkage disequilibrium; predictive ability; simulation