Estimation of variance components due to imprinting effects with DFREML and VCE: results of a simulation study

Treating gametes as homozygous diploid individuals, TIER and SÖLKNER (Theor. Appl. Genet. 85: 868–872, 1993) proposed a method which manages the use of available computer programs with a common animal model to estimate variance components caused by imprinting effects. Despite some relevant model restrictions, this approach has already been used in some field data analyses by an adapted version of the widely used DFREML computer program, subsequently indicated by DFREML ^a. The main objective of this study was to ascertain the properties of DFREML ^a by computer simulation and to examine other alternative estimation approaches. The most important results may be summarized as follows: (1) Treating gametes as homozygous diploid individuals has the consequence that one‐half of the actually realized gametic effect is totally abstracted in variance component estimation. Thus, an additional adjustment of the phenotypic variance calculated by DFREML ^a is necessary to get correct values of estimated variance component ratios. (2) Adjusted DFREML ^a estimates yielded correct results when animals were unselected and only maternal or paternal imprinting (not both simultaneously) occurred. (3) When the model did not adequately account for the additive genetic component within a maternal lineage, significant upward biases for the cytoplasmic component were observed. (4) The use of a simple dam and sire model with appropriate relationship matrices can be recommended when only the difference of maternal and paternal imprinting effects is of primary interest and the covariance between maternal halfsibs is not substantially increased by common environmental effects. (5) An adequate estimation of variance components for all possible imprinting situations requires the use of an animal model augmented by both maternal and paternal gametic effects. Unfortunately, a computer program on the basis of such a model does not yet exist.