Abstract
BackgroundIn livestock production, many animals are crossbred, with two distinct advantages: heterosis and breed complementarity. Genomic selection (GS) can be used to select purebred parental lines for crossbred performance (CP). Dominance being the likely genetic basis of heterosis, explicitly including dominance in the GS model may be an advantage to select purebreds for CP. Estimated breeding values for CP can be calculated from additive and dominance effects of alleles that are estimated using pure line data. The objective of this simulation study was to investigate the benefits of applying GS to select purebred animals for CP, based on purebred phenotypic and genotypic information. A second objective was to compare the use of two separate pure line reference populations to that of a single reference population that combines both pure lines. These objectives were investigated under two conditions, i.e. either a low or a high correlation of linkage disequilibrium (LD) phase between the pure lines.ResultsThe results demonstrate that the gain in CP was higher when parental lines were selected for CP, rather than purebred performance, both with a low and a high correlation of LD phase. For a low correlation of LD phase between the pure lines, the use of two separate reference populations yielded a higher gain in CP than use of a single reference population that combines both pure lines. However, for a high correlation of LD phase, marker effects that were estimated using a single combined reference population increased the gain in CP.ConclusionsUnder the hypothesis that performance of crossbred animals differs from that of purebred animals due to dominance, a dominance model can be used for GS of purebred individuals for CP, without using crossbred data. Furthermore, if the correlation of LD phase between pure lines is high, accuracy of selection can be increased by combining the two pure lines into a single reference population to estimate marker effects.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0099-3) contains supplementary material, which is available to authorized users.
Highlights
In livestock production, many animals are crossbred, with two distinct advantages: heterosis and breed complementarity
Since the initial allele frequencies were sampled from a uniform distribution, a kind of uniform distribution was expected with some fluctuations after 2000 generations of random mating, under a balance between mutation and random genetic drift due to finite population size
Since heterosis depends on the difference in allele frequencies between the two breeds, these results suggest that selection for crossbred performance (CP) moves allele frequencies in the two breeds in opposite directions and causes divergence in allele frequencies between both breeds
Summary
Many animals are crossbred, with two distinct advantages: heterosis and breed complementarity. Estimated breeding values for CP can be calculated from additive and dominance effects of alleles that are estimated using pure line data. The objective of this simulation study was to investigate the benefits of applying GS to select purebred animals for CP, based on purebred phenotypic and genotypic information. One of the main limitations of many livestock breeding programs is that selection is carried out in purebred nucleus lines or breeds that are housed in high-health environments, whereas the goal of selection is to improve crossbred performance (CP) under field conditions. In livestock production systems, many animals are crossbred, with two distinct advantages i.e. heterosis and breed complementarity. Dekkers [1] demonstrated that marker-assisted selection or GS with marker effects derived at the commercial crossbred level can lead to substantially higher gain in CP and a lower rate of inbreeding compared to CCPS when marker effects were estimated accurately
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