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Accuracy of whole-genome prediction using a genetic architecture-enhanced variance-covariance matrix.

Zhang Z, Erbe M, He J, Ober U, Gao N, Zhang H, Simianer H, Li J - G3 (Bethesda) (2015)

Bottom Line: Predictive ability of BLUP/GA was validated with three model traits in a dairy cattle dataset and 11 traits in three public datasets with a variety of genetic architectures and compared with GBLUP and other approaches.Further analyses showed that the difference of accuracies for BLUP/GA and GBLUP significantly correlate with the distance between the T: and G: matrices.Applying BLUP/GA in WGP would ease the burden of model selection.

View Article: PubMed Central - PubMed

Affiliation: National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China Department of Animal Sciences, Animal Breeding and Genetics Group, Georg-August-Universität Göttingen, Göttingen 37075, Germany.

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Regression of absolute increased accuracy of best linear unbiased prediction -given genetic architecture (BLUP/GA) over genomic best linear unbiased prediction (∆) on the distance between T and G matrices (σ).
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fig6: Regression of absolute increased accuracy of best linear unbiased prediction -given genetic architecture (BLUP/GA) over genomic best linear unbiased prediction (∆) on the distance between T and G matrices (σ).

Mentions: The results suggest that the advantage of BLUP/GA over GBLUP is the more pronounced the more the T and G matrices differ from each other. Therefore, we quantified the distance between T and G by calculating the standard deviation of the element-wise difference between the two matrices, i.e., . Next we calculated the linear regression of absolute increased accuracy of BLUP/GA over GBLUP (termed ∆ in the following) on σ. The scatter plots and regression lines for each dataset are shown in Figure 6. The intercepts were set to zero for all regressions since zero is the expectation when T = G. All regression coefficients are significant (P < 0.01). The largest regression coefficient was observed for the cattle dataset (2.17) while the smallest one was observed for the pine dataset (0.84).


Accuracy of whole-genome prediction using a genetic architecture-enhanced variance-covariance matrix.

Zhang Z, Erbe M, He J, Ober U, Gao N, Zhang H, Simianer H, Li J - G3 (Bethesda) (2015)

Regression of absolute increased accuracy of best linear unbiased prediction -given genetic architecture (BLUP/GA) over genomic best linear unbiased prediction (∆) on the distance between T and G matrices (σ).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390577&req=5

fig6: Regression of absolute increased accuracy of best linear unbiased prediction -given genetic architecture (BLUP/GA) over genomic best linear unbiased prediction (∆) on the distance between T and G matrices (σ).
Mentions: The results suggest that the advantage of BLUP/GA over GBLUP is the more pronounced the more the T and G matrices differ from each other. Therefore, we quantified the distance between T and G by calculating the standard deviation of the element-wise difference between the two matrices, i.e., . Next we calculated the linear regression of absolute increased accuracy of BLUP/GA over GBLUP (termed ∆ in the following) on σ. The scatter plots and regression lines for each dataset are shown in Figure 6. The intercepts were set to zero for all regressions since zero is the expectation when T = G. All regression coefficients are significant (P < 0.01). The largest regression coefficient was observed for the cattle dataset (2.17) while the smallest one was observed for the pine dataset (0.84).

Bottom Line: Predictive ability of BLUP/GA was validated with three model traits in a dairy cattle dataset and 11 traits in three public datasets with a variety of genetic architectures and compared with GBLUP and other approaches.Further analyses showed that the difference of accuracies for BLUP/GA and GBLUP significantly correlate with the distance between the T: and G: matrices.Applying BLUP/GA in WGP would ease the burden of model selection.

View Article: PubMed Central - PubMed

Affiliation: National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China Department of Animal Sciences, Animal Breeding and Genetics Group, Georg-August-Universität Göttingen, Göttingen 37075, Germany.

Show MeSH
Related in: MedlinePlus