Genomic Selection of Purebred Animals for Crossbred Performance in the Presence of Dominant Gene Action

Abstract

Background: Genomic selection is an appealing method to select purebreds for crossbred performance. In the case of crossbred records, single nucleotide polymorphism (SNP) effects can be estimated using an additive model or a breed-specific allele model. In most studies, additive gene action is assumed. However, dominance is the likely genetic basis of heterosis. Advantages of incorporating dominance in genomic selection were investigated in a two-way crossbreeding program for a trait with different magnitudes of dominance. Training was carried out only once in the simulation. Results: When the dominance variance and heterosis were large and overdominance was present, a dominance model including both additive and dominance SNP effects gave substantially greater cumulative response to selection than the additive model. Extra response was the result of an increase in heterosis but at a cost of reduced purebred performance. When the dominance variance and heterosis were realistic but with overdominance, the advantage of the dominance model decreased but was still significant. When overdominance was absent, the dominance model was slightly favored over the additive model, but the difference in response between the models increased as the number of quantitative trait loci increased. This reveals the importance of exploiting dominance even in the absence of overdominance. When there was no dominance, response to selection for the dominance model was as high as for the additive model, indicating robustness of the dominance model. The breed-specific allele model was inferior to the dominance model in all cases and to the additive model except when the dominance variance and heterosis were large and with overdominance. However, the advantage of the dominance model over the breed-specific allele model may decrease as differences in linkage disequilibrium between the breeds increase. Retraining is expected to reduce the advantage of the dominance model over the alternatives, because in general, the advantage becomes important only after five or six generations post-training. Conclusion: Under dominance and without retraining, genomic selection based on the dominance model is superior to the additive model and the breed-specific allele model to maximize crossbred performance through purebred selection. Background Numerous studies have shown encouraging results of applying genomic selection (GS) in purebred populations [1-6]. However, except for dairy cattle, most animals used in livestock production systems are crossbreds, with advantages of heterosis and breed complementarity. For

Modeling additive and non-additive effects in a hybrid population using genome-wide genotyping: prediction accuracy implications

“…They differed from the parent models because they were defined using the female-and male-origin haplotypes of each progeny inferred by long-range phasing. Such models were implemented in previous studies (Ibánez-Escriche et al, 2009;Kinghorn et al, 2010;Zeng et al, 2013) while only considering additive effects in the model. We extended this approach by including dominance and epistatic effects.…”

“…This is especially the case regarding animal breeding, when purebred animals are evaluated for their crossbred performance, where models that take the allele origin into account are implemented. Some rely on the relationship among purebred parents (Lo et al, 1997), which are referred to as 'parent models' in the following, while others are based on the relationship among crossbred progenies estimated by their gametotype (haplotype of each parental gamete) (Ibánez-Escriche et al, 2009;Kinghorn et al, 2010;Zeng et al, 2013), which are referred to as 'progeny models' hereafter. Although both parent and progeny models have been fully studied in assessing the performance of crossbreeds, they have mainly been focused on genetic additive effects.…”

Genome Properties and Prospects of Genomic Prediction of Hybrid Performance in a Breeding Program of Maize

“…In simulation studies on genomic prediction with training sets consisting of crossbred individuals (Ibánez-Escriche et al 2009;Zeng et al 2013) or single-cross hybrids (Technow et al 2012), it was found that genomic prediction models that fitted specific marker effects for the parental populations (i.e., purebred breed or heterotic group) had little or no advantage over simpler models that assumed marker effects to be the same across parental populations. One explanation the authors gave for this was that the linkage phase consistency across populations was sufficiently high at high marker densities.…”

Quantitative genetics theory for genomic selection and efficiency of genotypic value prediction in open-pollinated populations

“…of the relevance of predicting genotypic value based on markers in animal and plant breeding. Zeng et al (2013) concluded that genomic selection based on the dominance model maximized the cumulative response to selection of purebred animals for crossbred performance.…”