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The mouse at bottom is heterozygous with a mutant gene that gives it a spotted tail. The two mice above it are paramutated; they also have spotted tails even though they do not carry the gene for this trait.

Although no complete knowledge of the genetic makeup of any breed of livestock exists yet, genetic variations can be used for improving stock. Researchers partition total genetic variation into additive, dominance, and epistatic types of gene action, which are defined in the following paragraphs. Additive variation is easiest to use in breeding because it is common and the effect of each allele at a locus just adds to the effect of other alleles at that same locus. Genetic gains made using additive genetic effects are permanent and cumulate from one generation to the next.

Although dominance variation is not more complex in theory, it is more difficult to control in practice because of how one allele masks the effect of another. For example, let a indicate a locus, with a1 and a2 representing two possible alleles at that location. Then a1a1, a1a2 (which is identical to a2a1), and a2a2 are the three possible genotypes. If a1 dominates a2, the genotypes a1a2 and a1a1 cannot be outwardly distinguished. Thus, the inability to observe differences between a1a2 and a1a1 presents a major difficulty in using dominance variance in selective breeding.

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Additive and dominance variations are caused by genes at one locus. Epistatic variation is caused by the joint effects of genes at two or more loci. There has been little deliberate use of this type of genetic variation in breeding because of the complex nature of identifying and controlling the relevant genes.