RT Journal Article
SR Electronic
T1 Shrinkage Estimation of the Realized Relationship Matrix
JF G3: Genes|Genomes|Genetics
FD Genetics Society of America
SP 1405
OP 1413
DO 10.1534/g3.112.004259
VO 2
IS 11
A1 Endelman, Jeffrey B.
A1 Jannink, Jean-Luc
YR 2012
UL http://www.g3journal.org/content/2/11/1405.abstract
AB The additive relationship matrix plays an important role in mixed model prediction of breeding values. For genotype matrix X (loci in columns), the product XX′ is widely used as a realized relationship matrix, but the scaling of this matrix is ambiguous. Our first objective was to derive a proper scaling such that the mean diagonal element equals 1+f, where f is the inbreeding coefficient of the current population. The result is a formula involving the covariance matrix for sampling genomic loci, which must be estimated with markers. Our second objective was to investigate whether shrinkage estimation of this covariance matrix can improve the accuracy of breeding value (GEBV) predictions with low-density markers. Using an analytical formula for shrinkage intensity that is optimal with respect to mean-squared error, simulations revealed that shrinkage can significantly increase GEBV accuracy in unstructured populations, but only for phenotyped lines; there was no benefit for unphenotyped lines. The accuracy gain from shrinkage increased with heritability, but at high heritability (> 0.6) this benefit was irrelevant because phenotypic accuracy was comparable. These trends were confirmed in a commercial pig population with progeny-test-estimated breeding values. For an anonymous trait where phenotypic accuracy was 0.58, shrinkage increased the average GEBV accuracy from 0.56 to 0.62 (SE < 0.00) when using random sets of 384 markers from a 60K array. We conclude that when moderate-accuracy phenotypes and low-density markers are available for the candidates of genomic selection, shrinkage estimation of the relationship matrix can improve genetic gain.