Data #
Single nucleotide polymorphisms (SNP) are analyzed using the Illumina Bovine Genotyping BeadChip platform. When selecting SNPs for evaluation, polymorphisms that exhibit more than 10% missing genotypes or whose frequency of the rarer allele is less than 0.01 are excluded.
Phenotypic data are derived from deregressed conventional breeding values (EBV – Estimated Breeding Value), supplemented with effective daughter contribution (EDC) and relatedness of individuals.
Model #
Direct genomic evaluation (DGV) #
Direct genomic evaluation (Direct Genomic Value) is based on a single-trait linear mixed model with a random additive effect of SNP, using deregressed conventional breeding values as dependent variables and SNP genotypes specified for individuals as independent variables, as described in section 4.1, either directly or by imputation from other genotyping platforms. Evaluations are weighted by effective daughter contribution (EDC).
Genomic Enhanced Breeding Value (DEBV) #
Genomic Enhanced Breeding Value (GEBV) is calculated as an index composed of the conventional breeding value (EBV) or, in its absence, the pedigree index (PI), and the direct genomic evaluation (DGV), weighted by their accuracy.
Repeatability of evaluation #
Accuracy of direct genomic evaluation (DGV).
The accuracy (repeatability) of direct genomic evaluation is approximated by the accuracy achieved through Interbull validation.
Accuracy of combined breeding value (GEBV).
The accuracy (repeatability) of combined breeding value (GEBV) for evaluated animals is estimated based on the accuracy calculated for DGV and EBV or pedigree index (PI).
Index and subindexes #
Genomic breeding values are combined into sub-indices and a selection index according to the rules described in the section on conventional evaluation.
Conditions for evaluation acceptance #
An international combined genomic breeding value is published, and in its absence, a national genomic breeding value is published. The condition for publication is an accuracy value of at least 0.5 for production traits.