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A crossbred reference population can improve the response to genomic selection for crossbred performance.

Esfandyari H, Sørensen AC, Bijma P - Genet. Sel. Evol. (2015)

Bottom Line: A genomic selection (GS) model that includes dominance effects can be used to select purebreds for crossbred performance.Training on crossbred animals yielded a larger response to selection in crossbred offspring compared to training on both pure lines separately or on both pure lines combined into a single reference population.If both parental lines were distantly related, tracing the line origin of alleles improved genomic prediction, whereas if both parental lines were closely related and the reference population was small, it was better to ignore the line origin of alleles.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark. Hadi.esfandyari@mbg.au.dk.

ABSTRACT

Background: Breeding goals in a crossbreeding system should be defined at the commercial crossbred level. However, selection is often performed to improve purebred performance. A genomic selection (GS) model that includes dominance effects can be used to select purebreds for crossbred performance. Optimization of the GS model raises the question of whether marker effects should be estimated from data on the pure lines or crossbreds. Therefore, the first objective of this study was to compare response to selection of crossbreds by simulating a two-way crossbreeding program with either a purebred or a crossbred training population. We assumed a trait of interest that was controlled by loci with additive and dominance effects. Animals were selected on estimated breeding values for crossbred performance. There was no genotype by environment interaction. Linkage phase and strength of linkage disequilibrium between quantitative trait loci (QTL) and single nucleotide polymorphisms (SNPs) can differ between breeds, which causes apparent effects of SNPs to be line-dependent. Thus, our second objective was to compare response to GS based on crossbred phenotypes when the line origin of alleles was taken into account or not in the estimation of breeding values.

Results: Training on crossbred animals yielded a larger response to selection in crossbred offspring compared to training on both pure lines separately or on both pure lines combined into a single reference population. Response to selection in crossbreds was larger if both phenotypes and genotypes were collected on crossbreds than if phenotypes were only recorded on crossbreds and genotypes on their parents. If both parental lines were distantly related, tracing the line origin of alleles improved genomic prediction, whereas if both parental lines were closely related and the reference population was small, it was better to ignore the line origin of alleles.

Conclusions: Response to selection in crossbreeding programs can be increased by training on crossbred genotypes and phenotypes. Moreover, if the reference population is sufficiently large and both pure lines are not very closely related, tracing the line origin of alleles in crossbreds improves genomic prediction.

No MeSH data available.


Related in: MedlinePlus

Heterosis in crossbreds. Scenario 1: separate training in both breeds A and B; Scenario 2: training on a combined set of animals from both breeds A and B; Scenario 3: training on crossbred animals with phenotypes and genotype probabilities and it was assumed that the alternate heterozygotes Aa and aA were identical in crossbred animals; Scenario 4: training on crossbred animals with phenotypes and genotype probabilities and it was assumed that the alternate heterozygotes could be distinguished in crossbred animals. Scenario 5: training on crossbred animals with phenotypes and genotypes and it was assumed that the alternate heterozygotes were identical in crossbred animals. Scenario 6: training on crossbred animals with phenotypes and genotypes and it was assumed that the alternate heterozygotes could be distinguished in crossbred animals
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Fig3: Heterosis in crossbreds. Scenario 1: separate training in both breeds A and B; Scenario 2: training on a combined set of animals from both breeds A and B; Scenario 3: training on crossbred animals with phenotypes and genotype probabilities and it was assumed that the alternate heterozygotes Aa and aA were identical in crossbred animals; Scenario 4: training on crossbred animals with phenotypes and genotype probabilities and it was assumed that the alternate heterozygotes could be distinguished in crossbred animals. Scenario 5: training on crossbred animals with phenotypes and genotypes and it was assumed that the alternate heterozygotes were identical in crossbred animals. Scenario 6: training on crossbred animals with phenotypes and genotypes and it was assumed that the alternate heterozygotes could be distinguished in crossbred animals

Mentions: Heterosis refers to the superior performance of crossbred animals compared to the average performance of its purebred parents. Figure 3 shows the amount of heterosis over generations for the simulated scenarios. Total heterosis was calculated as the sum of heterosis at each locus based on , where is the dominance effect at QTL , is the allele frequency at QTL in breed A, and is the allele frequency at QTL in breed B [20]. In all scenarios, the amount of heterosis increased over generations, however, the rate of increase differed among scenarios. The amount of heterosis in Scenarios 1 and 2 increased a little from generation 1 to 5, whereas it increased much more sharply in the other scenarios in which training was on crossbreds. Since heterosis depends on the differences in allele frequencies between two breeds, this increase suggests that training on crossbreds together with selection for CP result in diverging allele frequencies between the two breeds. This could be caused by allele frequencies moving in different directions in both breeds or by selection acting on different loci in the two breeds.Fig. 3


A crossbred reference population can improve the response to genomic selection for crossbred performance.

Esfandyari H, Sørensen AC, Bijma P - Genet. Sel. Evol. (2015)

Heterosis in crossbreds. Scenario 1: separate training in both breeds A and B; Scenario 2: training on a combined set of animals from both breeds A and B; Scenario 3: training on crossbred animals with phenotypes and genotype probabilities and it was assumed that the alternate heterozygotes Aa and aA were identical in crossbred animals; Scenario 4: training on crossbred animals with phenotypes and genotype probabilities and it was assumed that the alternate heterozygotes could be distinguished in crossbred animals. Scenario 5: training on crossbred animals with phenotypes and genotypes and it was assumed that the alternate heterozygotes were identical in crossbred animals. Scenario 6: training on crossbred animals with phenotypes and genotypes and it was assumed that the alternate heterozygotes could be distinguished in crossbred animals
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4587753&req=5

Fig3: Heterosis in crossbreds. Scenario 1: separate training in both breeds A and B; Scenario 2: training on a combined set of animals from both breeds A and B; Scenario 3: training on crossbred animals with phenotypes and genotype probabilities and it was assumed that the alternate heterozygotes Aa and aA were identical in crossbred animals; Scenario 4: training on crossbred animals with phenotypes and genotype probabilities and it was assumed that the alternate heterozygotes could be distinguished in crossbred animals. Scenario 5: training on crossbred animals with phenotypes and genotypes and it was assumed that the alternate heterozygotes were identical in crossbred animals. Scenario 6: training on crossbred animals with phenotypes and genotypes and it was assumed that the alternate heterozygotes could be distinguished in crossbred animals
Mentions: Heterosis refers to the superior performance of crossbred animals compared to the average performance of its purebred parents. Figure 3 shows the amount of heterosis over generations for the simulated scenarios. Total heterosis was calculated as the sum of heterosis at each locus based on , where is the dominance effect at QTL , is the allele frequency at QTL in breed A, and is the allele frequency at QTL in breed B [20]. In all scenarios, the amount of heterosis increased over generations, however, the rate of increase differed among scenarios. The amount of heterosis in Scenarios 1 and 2 increased a little from generation 1 to 5, whereas it increased much more sharply in the other scenarios in which training was on crossbreds. Since heterosis depends on the differences in allele frequencies between two breeds, this increase suggests that training on crossbreds together with selection for CP result in diverging allele frequencies between the two breeds. This could be caused by allele frequencies moving in different directions in both breeds or by selection acting on different loci in the two breeds.Fig. 3

Bottom Line: A genomic selection (GS) model that includes dominance effects can be used to select purebreds for crossbred performance.Training on crossbred animals yielded a larger response to selection in crossbred offspring compared to training on both pure lines separately or on both pure lines combined into a single reference population.If both parental lines were distantly related, tracing the line origin of alleles improved genomic prediction, whereas if both parental lines were closely related and the reference population was small, it was better to ignore the line origin of alleles.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark. Hadi.esfandyari@mbg.au.dk.

ABSTRACT

Background: Breeding goals in a crossbreeding system should be defined at the commercial crossbred level. However, selection is often performed to improve purebred performance. A genomic selection (GS) model that includes dominance effects can be used to select purebreds for crossbred performance. Optimization of the GS model raises the question of whether marker effects should be estimated from data on the pure lines or crossbreds. Therefore, the first objective of this study was to compare response to selection of crossbreds by simulating a two-way crossbreeding program with either a purebred or a crossbred training population. We assumed a trait of interest that was controlled by loci with additive and dominance effects. Animals were selected on estimated breeding values for crossbred performance. There was no genotype by environment interaction. Linkage phase and strength of linkage disequilibrium between quantitative trait loci (QTL) and single nucleotide polymorphisms (SNPs) can differ between breeds, which causes apparent effects of SNPs to be line-dependent. Thus, our second objective was to compare response to GS based on crossbred phenotypes when the line origin of alleles was taken into account or not in the estimation of breeding values.

Results: Training on crossbred animals yielded a larger response to selection in crossbred offspring compared to training on both pure lines separately or on both pure lines combined into a single reference population. Response to selection in crossbreds was larger if both phenotypes and genotypes were collected on crossbreds than if phenotypes were only recorded on crossbreds and genotypes on their parents. If both parental lines were distantly related, tracing the line origin of alleles improved genomic prediction, whereas if both parental lines were closely related and the reference population was small, it was better to ignore the line origin of alleles.

Conclusions: Response to selection in crossbreeding programs can be increased by training on crossbred genotypes and phenotypes. Moreover, if the reference population is sufficiently large and both pure lines are not very closely related, tracing the line origin of alleles in crossbreds improves genomic prediction.

No MeSH data available.


Related in: MedlinePlus