Great progress has been made in understanding the genetic architecture of phenotypic variation, but it is almost entirely focused on how the genotype of an individual affects the phenotype of that same individual. However, in many species the genotype of the mother is a major determinant of the phenotype of her offspring. Therefore, a complete picture of genetic architecture must include these maternal genetic effects, but they can be difficult to identify because maternal and offspring genotypes are correlated and therefore, partially confounded. We present a conceptual framework that overcomes this challenge to separate direct and maternal effects in intact families through an analysis that we call "statistical cross-fostering." Our approach combines genotype data from mothers and their offspring to remove the confounding effects of the offspring's own genotype on measures of maternal genetic effects. We formalize our approach in an orthogonal model and apply this model to an experimental population of mice. We identify a set of six maternal genetic effect loci that explain a substantial portion of variation in body size at all ages. This variation would be missed in an approach focused solely on direct genetic effects, but is clearly a major component of genetic architecture. Our approach can easily be adapted to examine maternal effects in different systems, and because it does not require experimental manipulation, it provides a framework that can be used to understand the contribution of maternal genetic effects in both natural and experimental populations.
MATERNAL effects occur when mothers have an indirect causal influence on the expression of traits in their offspring independent of genes passed from mothers to offspring (see Cheverud and Wolf 2009;Wolf and Wade 2009). These maternal effects, which arise from a diversity of factors such as maternally derived mRNA (Berleth et al. 1988), maternal provisioning (Bowen 2009), and maternally determined dispersal (Donohue 1998), have been shown to have important influences on offspring development across a diversity of taxa (Mousseau and Fox 1998;Maestripieri and Mateo 2009). The importance of maternal effects in evolution and ecology has become more broadly recognized (Mousseau and Fox 1998), where maternal effects have been shown to play a role in the evolutionary response to selection (see Kirkpatrick and Lande 1989), mate choice and sexual selection (Wolf et al. , 1999, adaptive evolution (e.g., Badyaev et al. 2002), dynamics of population size (Ginzburg 1998), and niche construction (Odling-Smee et al. 2003). Genetically based maternal effects ("maternal genetic effects") are of particular importance to many processes because they contribute to the genetic architecture of traits and can, as a result, contribute in nonintuitive ways to evolutionary change (Kirkpatrick and Lande 1989;Cheverud and Wolf 2009). For example, maternal genetic effects can contribute "hidden" variation that can allow for rapid evolution (e.g., Badyaev et al. 2002) and ca...