Technical note: Automatic scaling in single-step genomic BLUP

Abstract

Single-step genomic BLUP (ssGBLUP) requires compatibility between genomic and pedigree relationships for unbiased and accurate predictions. Scaling the genomic relationship matrix (G) to have the same averages as the pedigree relationship matrix (i.e., scaling by averages) is one way to ensure compatibility. This requires computing both relationship matrices, calculating averages, and changing G, whereas only the inverses of those matrices are needed in the mixed model equations. Therefore, the compatibility process can add extra computing burden. In the single-step Bayesian regression, the scaling is done by including a mean (μg) as a fixed effect in the model. The parameter μg can be interpreted as the average of the breeding values of the genotyped animals. In this study, such scaling, called automatic, was implemented in ssGBLUP via Quaas-Pollak transformation of the inverse of the relationship matrix used in ssGBLUP (H), which combines the inverses of the pedigree and genomic relationship matrices. Comparisons involved a simulated data set, and the genomic relationship matrix was computed using different allele frequencies either from the current population (i.e., realized allele frequencies), equal among all the loci, or from the base population. For all of the scenarios, we computed bias [defined as the average difference between true breeding values (TBV) and genomic estimated breeding values (GEBV)], accuracy (defined as the correlation between TBV and GEBV), and dispersion (defined as the regression coefficient of GEBV on TBV). With no scaling, the bias expressed in terms of genetic standard deviations was 0.86, 0.64, and 0.58 with realized, equal, and base population allele frequencies, respectively. With scaling by averages, which is currently used in ssGBLUP, bias was 0.07, 0.08, and 0.03, respectively. With automatic scaling, bias was 0.18 regardless of allele frequencies. Accuracies were similar among scaling methods, but about 0.1 lower in the scenario without scaling. The GEBV were more inflated without any scaling, whereas the automatic scaling performed similarly to the scaling by averages. The average dispersion for those methods was 0.94. When μg was treated as random, with the variance equal to differences between pedigree and genomic relationships, the bias was the same as with the scaling by averages. The automatic scaling is biased, especially when μg is treated as a fixed effect. The bias may be small in real data with fewer generations, when traits are undergoing weak selection, or when the number of genotyped animals is large.