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Research article2008Peer reviewedOpen access

Defining the assumptions underlying modeling of epistatic QTL using variance component methods

Ronnegard, Lars; Pong-Wong, Ricardo; Carlborg, Orjan


Variance component models are commonly used to detect quantitative trait loci (QTL) in general pedigrees. The variance-covariance structure of the random QTL effect is given by the identity by descent (IBD) between genotypes. Epistatic effects have previously been modeled, both for unlinked and linked loci, as a random effect with a variance-covariance structure given by the Hadamard product between the IBD matrices of the direct QTL effects. In the original papers, the model was given but not derived. Here, we identify the underlying assumptions of this previously proposed model. It assumes that either an unlinked QTL or a fully informative marker (i.e., all marker alleles are unique in the base generation) is located between the loci. We discuss the need of developing a general algorithm to estimate the variance-covariance structure of the random epistatic effect for linked loci.

Published in

Journal of Heredity
2008, Volume: 99, number: 4, pages: 421-425

      UKÄ Subject classification

      Veterinary Science
      Animal and Dairy Science

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