A single-step genomic BLUP method (ssGBLUP) has been successfully developed and applied for purebred and crossbred performance in pigs. However, it requires phasing the genotypes and inferring the breed origin of alleles in crossbred animals, which is somewhat inconvenient. Recently, a new concept of metafounders that considers the relationship within and across base populations was developed. With this concept of metafounders, regular methods to build and invert the pedigree relationships matrix can be used with only minor modifications and, moreover, genomic relationships and pedigree-based relationships are automatically compatible in the ssGBLUP. In this study, data for the total number of piglets born in Danish Landrace, Yorkshire, and 2-way crossbred pigs and models for purebred and crossbred performance were revisited by use of ssGBLUP with 2 metafounders. Genetic variances and genetic correlations between purebred and crossbred performances were first reestimated. Then, model-based reliabilities of purebred boars for their crossbred performance and predictive abilities for crossbred animals were compared in different scenarios. Results in this study were compared to those in a previous study with identical data but with models that required known breed origin of crossbred genotypes. Results show that relationships for base individuals within Landrace and within Yorkshire are similar and that the ancestor populations for Landrace and Yorkshire are related. In terms of model-based reliabilities and predictive abilities, ssGBLUP with metafounders performs at least as well as the single-step method requiring phasing at a lower complexity.

The partition of the total genetic variance into its additive and non-additive components can differ from trait to trait, and between purebred and crossbred populations. A quantification of these genetic variance components will determine the extent to which it would be of interest to account for dominance in genomic evaluations or to establish mate allocation strategies along different populations and traits. This study aims at assessing the contribution of the additive and dominance genomic variances to the phenotype expression of several purebred Piétrain and crossbred (Piétrain × Large White) pig performances. A total of 636 purebred and 720 crossbred male piglets were phenotyped for 22 traits that can be classified into six groups of traits: growth rate and feed efficiency, carcass composition, meat quality, behaviour, boar taint and puberty. Additive and dominance variances estimated in univariate genotypic models, including additive and dominance genotypic effects, and a genomic inbreeding covariate allowed to retrieve the additive and dominance single nucleotide polymorphism variances for purebred and crossbred performances. These estimated variances were used, together with the allelic frequencies of the parental populations, to obtain additive and dominance variances in terms of genetic breeding values and dominance deviations. Estimates of the Piétrain and Large White allelic contributions to the crossbred variance were of about the same magnitude in all the traits. Estimates of additive genetic variances were similar regardless of the inclusion of dominance. Some traits showed relevant amount of dominance genetic variance with respect to phenotypic variance in both populations (i.e. growth rate 8%, feed conversion ratio 9% to 12%, backfat thickness 14% to 12%, purebreds-crossbreds). Other traits showed higher amount in crossbreds (i.e. ham cut 8% to 13%, loin 7% to 16%, pH semimembranosus 13% to 18%, pH longissimus dorsi 9% to 14%, androstenone 5% to 13% and estradiol 6% to 11%, purebreds-crossbreds). It was not encountered a clear common pattern of dominance expression between groups of analysed traits and between populations. These estimates give initial hints regarding which traits could benefit from accounting for dominance for example to improve genomic estimated breeding value accuracy in genetic evaluations or to boost the total genetic value of progeny by means of assortative mating.