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Reliability of pedigree-based and genomic evaluations in selected populations.

Gorjanc G, Bijma P, Hickey JM - Genet. Sel. Evol. (2015)

Bottom Line: The aim of this study was to quantify the effect of selection on these two measures of reliability and to show how this affects comparison of breeding programs using pedigree-based or genomic evaluations.The base PEV reliabilities of these EBV were compared to the corresponding reliabilities of selection.The two measures of reliability matched when the reductions in additive genetic variance due to the Bulmer effect, selection, and inbreeding were taken into account.

View Article: PubMed Central - PubMed

Affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK. gregor.gorjanc@roslin.ed.ac.uk.

ABSTRACT

Background: Reliability is an important parameter in breeding. It measures the precision of estimated breeding values (EBV) and, thus, potential response to selection on those EBV. The precision of EBV is commonly measured by relating the prediction error variance (PEV) of EBV to the base population additive genetic variance (base PEV reliability), while the potential for response to selection is commonly measured by the squared correlation between the EBV and breeding values (BV) on selection candidates (reliability of selection). While these two measures are equivalent for unselected populations, they are not equivalent for selected populations. The aim of this study was to quantify the effect of selection on these two measures of reliability and to show how this affects comparison of breeding programs using pedigree-based or genomic evaluations.

Methods: Two scenarios with random and best linear unbiased prediction (BLUP) selection were simulated, where the EBV of selection candidates were estimated using only pedigree, pedigree and phenotype, genome-wide marker genotypes and phenotype, or only genome-wide marker genotypes. The base PEV reliabilities of these EBV were compared to the corresponding reliabilities of selection. Realized genetic selection intensity was evaluated to quantify the potential of selection on the different types of EBV and, thus, to validate differences in reliabilities. Finally, the contribution of different underlying processes to changes in additive genetic variance and reliabilities was quantified.

Results: The simulations showed that, for selected populations, the base PEV reliability substantially overestimates the reliability of selection of EBV that are mainly based on old information from the parental generation, as is the case with pedigree-based prediction. Selection on such EBV gave very low realized genetic selection intensities, confirming the overestimation and importance of genotyping both male and female selection candidates. The two measures of reliability matched when the reductions in additive genetic variance due to the Bulmer effect, selection, and inbreeding were taken into account.

Conclusions: For populations under selection, EBV based on genome-wide information are more valuable than suggested by the comparison of the base PEV reliabilities between the different types of EBV. This implies that genome-wide marker information is undervalued for selected populations and that genotyping un-phenotyped female selection candidates should be reconsidered.

No MeSH data available.


Equilibrium reliability and reliability of selection of different types of estimated breeding values in generation 20. Breeding values estimated using (a) pedigree and phenotype information in males (EBVP&Y,m), (b) marker and phenotype information in males (EBVM&Y,m), and (c) pedigree and phenotype information in females (EBVP&Y,f). Equilibrium reliabilities are shown with contours, as a function of the proportions of males and females selected, while reliability of selection is shown as a point at the proportions selected used in this study
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Fig3: Equilibrium reliability and reliability of selection of different types of estimated breeding values in generation 20. Breeding values estimated using (a) pedigree and phenotype information in males (EBVP&Y,m), (b) marker and phenotype information in males (EBVM&Y,m), and (c) pedigree and phenotype information in females (EBVP&Y,f). Equilibrium reliabilities are shown with contours, as a function of the proportions of males and females selected, while reliability of selection is shown as a point at the proportions selected used in this study

Mentions: The effect of changes in variances (Figs. 1 and 2) on the reliability of selection was quantified in detail in generations 20 and 21 by calculating the PEV reliability with different values of additive genetic variance (Table 4). In the random selection scenario, the reliability of selection tended to be lower than the base PEV reliabilities. Taking into account the reduction in variance due to inbreeding, or using the additive genetic variance from generation 20 or 21, gave a PEV reliability that matched the reliability of selection within the bounds of sampling. In the BLUP selection scenario, the base PEV reliabilities considerably overestimated the reliability of selection, as previously noted (Table 2). This overestimation was, due to the reduction in additive genetic variance, as caused by several underlying processes (Table 4). Inbreeding, and to a small extent selection, reduced the additive genic variance and therefore also the additive genetic variance by changing the allele frequencies of causative loci. More importantly, the additive genetic variance was also reduced by the generation of gametic phase disequilibrium between the causative loci by selection, i.e., the Bulmer effect. These reductions in additive genetic variance due to inbreeding, selection, and the Bulmer effect were used to gradually reduce the base additive genetic variance to the additive genetic variance in generation 20 or 21 and to recalculate the PEV reliabilities for each reduction. The resulting PEV reliabilities matched the reliability of selection within the bounds of sampling. These results not only show which processes contribute to the reduction of the reliability of selection in selected populations but also that the base PEV reliabilities overestimate the reliability of selection in such populations by using the base additive genetic variance instead of actual additive genetic variance of selection candidates. Finally, the equilibrium reliabilities matched the reliability of selection for EBVP and EBVP&Y (Table 4 and Figs. 3 and 4, while there were minor discrepancies for EBVM&Y and EBVM. Figures 3 and 4 show contours of equilibrium reliabilities for the different proportion of selected males and females and a dot for the reliability of selection obtained in this study (Table 4). The discrepancies for EBVM&Y and EBVM arose because, in this study, selection was on EBVP&Y and calculating the equilibrium reliabilities with the higher EBVM&Y or EBVM base PEV reliabilities, as if selection was on the EBVM&Y or EBVM, leads to underestimation of the equilibrium reliabilities. Changing the proportion of selected males and females when calculating the equilibrium reliability for EBVP&Y and EBVM&Y in generation 20 (Fig. 3) and for EBVP and EBVM in generation 21 (Fig. 4) showed that the observed base PEV reliabilities were recovered when selection was absent, i.e., the equilibrium reliabilities from the bottom-left corners of Figs. 3 and 4 matched the base PEV reliabilities corrected for inbreeding in Table 4.Table 4


Reliability of pedigree-based and genomic evaluations in selected populations.

Gorjanc G, Bijma P, Hickey JM - Genet. Sel. Evol. (2015)

Equilibrium reliability and reliability of selection of different types of estimated breeding values in generation 20. Breeding values estimated using (a) pedigree and phenotype information in males (EBVP&Y,m), (b) marker and phenotype information in males (EBVM&Y,m), and (c) pedigree and phenotype information in females (EBVP&Y,f). Equilibrium reliabilities are shown with contours, as a function of the proportions of males and females selected, while reliability of selection is shown as a point at the proportions selected used in this study
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4536753&req=5

Fig3: Equilibrium reliability and reliability of selection of different types of estimated breeding values in generation 20. Breeding values estimated using (a) pedigree and phenotype information in males (EBVP&Y,m), (b) marker and phenotype information in males (EBVM&Y,m), and (c) pedigree and phenotype information in females (EBVP&Y,f). Equilibrium reliabilities are shown with contours, as a function of the proportions of males and females selected, while reliability of selection is shown as a point at the proportions selected used in this study
Mentions: The effect of changes in variances (Figs. 1 and 2) on the reliability of selection was quantified in detail in generations 20 and 21 by calculating the PEV reliability with different values of additive genetic variance (Table 4). In the random selection scenario, the reliability of selection tended to be lower than the base PEV reliabilities. Taking into account the reduction in variance due to inbreeding, or using the additive genetic variance from generation 20 or 21, gave a PEV reliability that matched the reliability of selection within the bounds of sampling. In the BLUP selection scenario, the base PEV reliabilities considerably overestimated the reliability of selection, as previously noted (Table 2). This overestimation was, due to the reduction in additive genetic variance, as caused by several underlying processes (Table 4). Inbreeding, and to a small extent selection, reduced the additive genic variance and therefore also the additive genetic variance by changing the allele frequencies of causative loci. More importantly, the additive genetic variance was also reduced by the generation of gametic phase disequilibrium between the causative loci by selection, i.e., the Bulmer effect. These reductions in additive genetic variance due to inbreeding, selection, and the Bulmer effect were used to gradually reduce the base additive genetic variance to the additive genetic variance in generation 20 or 21 and to recalculate the PEV reliabilities for each reduction. The resulting PEV reliabilities matched the reliability of selection within the bounds of sampling. These results not only show which processes contribute to the reduction of the reliability of selection in selected populations but also that the base PEV reliabilities overestimate the reliability of selection in such populations by using the base additive genetic variance instead of actual additive genetic variance of selection candidates. Finally, the equilibrium reliabilities matched the reliability of selection for EBVP and EBVP&Y (Table 4 and Figs. 3 and 4, while there were minor discrepancies for EBVM&Y and EBVM. Figures 3 and 4 show contours of equilibrium reliabilities for the different proportion of selected males and females and a dot for the reliability of selection obtained in this study (Table 4). The discrepancies for EBVM&Y and EBVM arose because, in this study, selection was on EBVP&Y and calculating the equilibrium reliabilities with the higher EBVM&Y or EBVM base PEV reliabilities, as if selection was on the EBVM&Y or EBVM, leads to underestimation of the equilibrium reliabilities. Changing the proportion of selected males and females when calculating the equilibrium reliability for EBVP&Y and EBVM&Y in generation 20 (Fig. 3) and for EBVP and EBVM in generation 21 (Fig. 4) showed that the observed base PEV reliabilities were recovered when selection was absent, i.e., the equilibrium reliabilities from the bottom-left corners of Figs. 3 and 4 matched the base PEV reliabilities corrected for inbreeding in Table 4.Table 4

Bottom Line: The aim of this study was to quantify the effect of selection on these two measures of reliability and to show how this affects comparison of breeding programs using pedigree-based or genomic evaluations.The base PEV reliabilities of these EBV were compared to the corresponding reliabilities of selection.The two measures of reliability matched when the reductions in additive genetic variance due to the Bulmer effect, selection, and inbreeding were taken into account.

View Article: PubMed Central - PubMed

Affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK. gregor.gorjanc@roslin.ed.ac.uk.

ABSTRACT

Background: Reliability is an important parameter in breeding. It measures the precision of estimated breeding values (EBV) and, thus, potential response to selection on those EBV. The precision of EBV is commonly measured by relating the prediction error variance (PEV) of EBV to the base population additive genetic variance (base PEV reliability), while the potential for response to selection is commonly measured by the squared correlation between the EBV and breeding values (BV) on selection candidates (reliability of selection). While these two measures are equivalent for unselected populations, they are not equivalent for selected populations. The aim of this study was to quantify the effect of selection on these two measures of reliability and to show how this affects comparison of breeding programs using pedigree-based or genomic evaluations.

Methods: Two scenarios with random and best linear unbiased prediction (BLUP) selection were simulated, where the EBV of selection candidates were estimated using only pedigree, pedigree and phenotype, genome-wide marker genotypes and phenotype, or only genome-wide marker genotypes. The base PEV reliabilities of these EBV were compared to the corresponding reliabilities of selection. Realized genetic selection intensity was evaluated to quantify the potential of selection on the different types of EBV and, thus, to validate differences in reliabilities. Finally, the contribution of different underlying processes to changes in additive genetic variance and reliabilities was quantified.

Results: The simulations showed that, for selected populations, the base PEV reliability substantially overestimates the reliability of selection of EBV that are mainly based on old information from the parental generation, as is the case with pedigree-based prediction. Selection on such EBV gave very low realized genetic selection intensities, confirming the overestimation and importance of genotyping both male and female selection candidates. The two measures of reliability matched when the reductions in additive genetic variance due to the Bulmer effect, selection, and inbreeding were taken into account.

Conclusions: For populations under selection, EBV based on genome-wide information are more valuable than suggested by the comparison of the base PEV reliabilities between the different types of EBV. This implies that genome-wide marker information is undervalued for selected populations and that genotyping un-phenotyped female selection candidates should be reconsidered.

No MeSH data available.