Genomic Prediction Using Multi-trait Weighted GBLUP Accounting for Heterogeneous Variances and Covariances Across the Genome

Abstract

Implicit assumption of common (co)variance for all loci in multi-trait Genomic Best Linear Unbiased Prediction (GBLUP) results in a genomic relationship matrix (G) that is common to all traits. When this assumption is violated, Bayesian whole genome regression methods may be superior to GBLUP by accounting for unequal (co)variance for all loci or genome regions. This study aimed to develop a strategy to improve the accuracy of GBLUP for multi-trait genomic prediction, using (co)variance estimates of SNP effects from Bayesian whole genome regression methods. Five generations (G1-G5, test populations) of genotype data were available by simulations based on data of 2,200 Danish Holstein cows (G0, reference population). Two correlated traits with heritabilities of 0.1 or 0.4, and a genetic correlation of 0.45 were generated. First, SNP effects and breeding values were estimated using BayesAS method, assuming (co)variance was the same for SNPs within a genome region, and different between regions. Region size was set as one SNP, 100 SNPs, a whole chromosome or whole genome. Second, posterior (co)variances of SNP effects were used to weight SNPs in construction of G matrices. In general, region size of 100 SNPs led to highest prediction accuracies using BayesAS, and wGBLUP outperformed GBLUP at this region size. Our results suggest that when genetic architectures of traits favor Bayesian methods, the accuracy of multi-trait GBLUP can be as high as the Bayesian method if SNPs are weighted by the Bayesian posterior (co)variances.

Keywords: GenPred; Genetic architecture; Genomic prediction; Genomic relationship matrix; Region size; SNP weight; Shared Data Resources.

Figure 1

Change in prediction accuracy for weighted GBLUP over generations with varying regions sizes of genome regions, for 200 QTL scenario. L and H: low (0.1) and high (0.4) heritability traits, respectively; different colors represent different region sizes; Chr: chromosome; WG: whole genome (or equivalently, GBLUP).

Figure 2

Change in prediction accuracy for weighted GBLUP over generations with varying regions sizes of genome regions, for 500 QTL scenario. L and H: low (0.1) and high (0.4) heritability traits, respectively; different colors represent different region sizes; Chr: chromosome; WG: whole genome (or equivalently, GBLUP).