The estimation of genomic relationships using breedwise allele frequencies among animals in multibreed populations.

Different approaches of calculating genomic measures of relationship were explored and compared with pedigree relationships (A) within and across base breeds in a crossbreed population, using genotypes for 38,194 loci of 4,106 Nordic Red dairy cattle. Four genomic relationship matrices (G) were calculated using either observed allele frequencies (AF) across breeds or within-breed AF. The G matrices were compared separately when the AF were estimated in the observed and in the base population. Breedwise AF in the current and base population were estimated using linear regression models of individual genotypes on breed composition. Different G matrices were further used to predict direct estimated genomic values using a genomic BLUP model. Higher variability existed in the diagonal elements of G across breeds (standard deviation=0.06, on average) compared with A (0.01). The use of simple observed AF across base breeds to compute G increased coefficients for individuals in distantly related populations. Estimated breedwise AF reduced differences in coefficients similarly within and across populations. The variability of the current adjusted G matrix decreased from 0.055 to 0.035 when breedwise AF were estimated from the base breed population. The direct estimated genomic values and their validation reliabilities were, however, unaffected by AF used to compute G when estimated with a genomic BLUP model, due to inclusion of breed means in the model. In multibreed populations, G adjusted with breedwise AF from the founder population may provide more consistency among relationship coefficients between genotyped and ungenotyped individuals in an across-breed single-step evaluation.