Abstract
BackgroundGenomic prediction of purebred animals for crossbred performance can be based on a model that estimates effects of single nucleotide polymorphisms (SNPs) in purebreds on crossbred performance. For crossbred performance, SNP effects might be breed-specific due to differences between breeds in allele frequencies and linkage disequilibrium patterns between SNPs and quantitative trait loci. Accurately tracing the breed-of-origin of alleles (BOA) in three-way crosses is possible with a recently developed procedure called BOA. A model that accounts for breed-specific SNP effects (BOA model), has never been tested empirically on a three-way crossbreeding scheme. Therefore, the objectives of this study were to evaluate the estimates of variance components and the predictive accuracy of the BOA model compared to models in which SNP effects for crossbred performance were assumed to be the same across breeds, using either breed-specific allele frequencies ({text{G}}_{text{A}} model) or allele frequencies averaged across breeds ({text{G}}_{text{B}} model). In this study, we used data from purebred and three-way crossbred pigs on average daily gain (ADG), back fat thickness (BF), and loin depth (LD).ResultsEstimates of variance components for crossbred performance from the BOA model were mostly similar to estimates from models {text{G}}_{text{A}} and {text{G}}_{text{B}}. Heritabilities for crossbred performance ranged from 0.24 to 0.46 between traits. Genetic correlations between purebred and crossbred performance ({text{r}}_{text{pc}}) across breeds ranged from 0.30 to 0.62 for ADG and from 0.53 to 0.74 for BF and LD. For ADG, prediction accuracies of the BOA model were higher than those of the {text{G}}_{text{A}} and {text{G}}_{text{B}} models, with significantly higher accuracies only for one maternal breed. For BF and LD, prediction accuracies of models {text{G}}_{text{A}} and {text{G}}_{text{B}} were higher than those of the BOA model, with no significant differences. Across all traits, models {text{G}}_{text{A}} and {text{G}}_{text{B}} yielded similar predictions.ConclusionsThe BOA model yielded a higher prediction accuracy for ADG in one maternal breed, which had the lowest {text{r}}_{text{pc}} (0.30). Using the BOA model was especially relevant for traits with a low {text{r}}_{text{pc}}. In all other cases, the use of crossbred information in models {text{G}}_{text{A}} and {text{G}}_{text{B}}, does not jeopardize predictions and these models are more easily implemented than the BOA model.
Highlights
Genomic prediction of purebred animals for crossbred performance can be based on a model that estimates effects of single nucleotide polymorphisms (SNPs) in purebreds on crossbred performance
The correlation between PB and CB performance for grain yield (GY) is lower than that for grain dry matter content (GDMC), and it was observed that models that do not include CB information failed to predict the performance of CB for GY but for GDMC yielded a high prediction accuracy [14]
S Synthetic boar, LR Landrace, LW Large White, CB three-way crossbred pigs ADG average daily gain, BF back fat thickness, LD loin depth a breed-of-origin of alleles (BOA) model, model with breed-specific relationship matrices b GA model, model with genomic relationship matrix by allele frequencies obtained across the genotyped population c GB model, model with genomic relationship matrix by breed-specific allele frequencies * Average from the three bivariate models ** (0.5σa2S + 0.25σa2LR + 0.25σa2LW)/(0.5σa2S + 0.25σa2LR + 0.25σa2LW + σu2CB* + σe2CB*)
Summary
Genomic prediction of purebred animals for crossbred performance can be based on a model that estimates effects of single nucleotide polymorphisms (SNPs) in purebreds on crossbred performance. A model that accounts for breed-specific SNP effects (BOA model), has never been tested empirically on a three-way crossbreeding scheme. The objectives of this study were to evaluate the estimates of variance components and the predictive accuracy of the BOA model compared to models in which SNP effects for crossbred performance were assumed to be the same across breeds, using either breed-specific allele frequencies (GA model) or allele frequencies averaged across breeds (GB model). GS using CB information could benefit from models that estimate the effects on CB performance of markers that segregate within the parental breeds, as suggested by Dekkers [7], Ibáñez-Escriche et al [15], Kinghorn et al [16] and Christensen et al [17, 18] in the context of animal breeding, and by Schrag et al [14] in the context of hybrid performance in maize
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
