Modeling identical twins and clones in genetic evaluations

Abstract

Identical animals cause more complex relationships to model in genetic evaluations. The USA evaluation currently includes 4,762 pairs of natural identical twins, 1,776 split embryos, and 530 nuclear transfer clones from cells of other embryos, calves, or adults, plus 7 million other genotyped animals. Genetic effects for the 7,068 animals reported to be a clone or copy of another animal were linked to the source animal, and their own effects were removed from the relationship matrix. The model retained separate permanent environmental effects for each cow. For progeny of clones, the source animals are substituted as their sires and dams. After completing the evaluation, the reverse process restored the actual sires and dams and duplicated the evaluations of source animals to their clones for publication. Pedigree inbreeding coefficients increased slightly for animals with a paternal ancestor and a maternal ancestor that were clones of each other. Genomic predictions improved by estimating just 1 polygenic effect instead of modeling the copies as full sibs. Milk production of adult clones was not significantly affected, but their fertility and health traits were below expected. Several AI companies now market cloned bulls. The revised model better evaluates identical twins, cloned animals, and their progeny.