Quantitative Genetics of Genomic Imprinting: A Comparison of Simple Variance Derivations, the Effects of Inbreeding, and Response to Selection

The level of expression of an imprinted gene is dependent on the sex of the parent from which it was inherited. As a result, reciprocal heterozygotes in a population may have different mean phenotypes for quantitative traits. Using standard quantitative genetic methods for deriving breeding values, population variances, and covariances between relatives, we demonstrate that although these approaches are equivalent under Mendelian expression, this equivalence is lost when genomic imprinting is acting. Imprinting introduces both parent-of-origin-dependent and generation-dependent effects that result in differences in the way additive and dominance effects are defined for the various approaches. Further, imprinting creates a covariance between additive and dominance terms absent under Mendelian expression, but the expression for this covariance cannot be derived using a number of the standard approaches for defining additive and dominance terms. Inbreeding also generates such a covariance, and we demonstrate that a modified method for partitioning variances can easily accommodate both inbreeding and imprinting. As with inbreeding, the concept of breeding values has no useful meaning for an imprinted trait. Finally, we derive the expression for the response to selection under imprinting, and conclude that the response to selection for an imprinted trait cannot be predicted from the breeder’s equation, even when there is no dominance.