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Journal of Heredity Advance Access published online on March 15, 2008
Journal of Heredity, doi:10.1093/jhered/esn017
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© The American Genetic Association. 2008. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org.

Brief Communication

Defining the Assumptions Underlying Modeling of Epistatic QTL Using Variance Component Methods

Lars Rönnegård, Ricardo Pong-Wong, and Örjan Carlborg

From the Linnaeus Centre for Bioinformatics, SE-75124 Uppsala, Sweden (Rönnegård and Carlborg); Roslin Institute, Midlothian, UK (Pong-Wong); Örjan Carlborg is now at the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden

Address correspondence to Lars Rönnegård at the address above, or e-mail: lars.ronnegard{at}lcb.uu.se.

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.

Corresponding Editor: Jerry Dodgson

Received November 6, 2007
Accepted January 25, 2008


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