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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

Cumulative response to selection for varying sizes of training populations. Training on crossbred animals with phenotypes and genotypes. Scenario 5: alternate heterozygotes Aa and aA were assumed identical in crossbred animals; Scenario 6: alternate heterozygotes could be distinguished in crossbred animals; TS stands for training population size of 500, 2000 and 8000; standard errors of phenotypic means ranged from 0.02 to 0.03
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Fig4: Cumulative response to selection for varying sizes of training populations. Training on crossbred animals with phenotypes and genotypes. Scenario 5: alternate heterozygotes Aa and aA were assumed identical in crossbred animals; Scenario 6: alternate heterozygotes could be distinguished in crossbred animals; TS stands for training population size of 500, 2000 and 8000; standard errors of phenotypic means ranged from 0.02 to 0.03

Mentions: Figure 4 shows the cumulative response to selection in Scenarios 5 and 6 for varying sizes of the training population. To evaluate the impact of training population size on the relative ranking of Scenarios 5 and 6, 200 generations of divergence between breeds A and B were considered, since response to selection for these two scenarios was almost the same for this time since divergence and a training population size of 2000. As expected, response to selection with both scenarios increased as the size of the training population increased. However, the relative ranking of Scenarios 5 and 6 changed as the size of training population increased. If the size of the training population was 500, response to selection was greater for Scenario 5 than for Scenario 6, but with a 4- and 16-fold increase, response to selection was greater for Scenario 6 than for Scenario 5. Thus, these results showed that being able to distinguish between alternate heterozygotes Aa and aA was beneficial when the training population was large.Fig. 4


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

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

Cumulative response to selection for varying sizes of training populations. Training on crossbred animals with phenotypes and genotypes. Scenario 5: alternate heterozygotes Aa and aA were assumed identical in crossbred animals; Scenario 6: alternate heterozygotes could be distinguished in crossbred animals; TS stands for training population size of 500, 2000 and 8000; standard errors of phenotypic means ranged from 0.02 to 0.03
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig4: Cumulative response to selection for varying sizes of training populations. Training on crossbred animals with phenotypes and genotypes. Scenario 5: alternate heterozygotes Aa and aA were assumed identical in crossbred animals; Scenario 6: alternate heterozygotes could be distinguished in crossbred animals; TS stands for training population size of 500, 2000 and 8000; standard errors of phenotypic means ranged from 0.02 to 0.03
Mentions: Figure 4 shows the cumulative response to selection in Scenarios 5 and 6 for varying sizes of the training population. To evaluate the impact of training population size on the relative ranking of Scenarios 5 and 6, 200 generations of divergence between breeds A and B were considered, since response to selection for these two scenarios was almost the same for this time since divergence and a training population size of 2000. As expected, response to selection with both scenarios increased as the size of the training population increased. However, the relative ranking of Scenarios 5 and 6 changed as the size of training population increased. If the size of the training population was 500, response to selection was greater for Scenario 5 than for Scenario 6, but with a 4- and 16-fold increase, response to selection was greater for Scenario 6 than for Scenario 5. Thus, these results showed that being able to distinguish between alternate heterozygotes Aa and aA was beneficial when the training population was large.Fig. 4

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