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Defining the assumptions underlying modeling of epistatic QTL using variance component methods
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.ORCID iD: 0000-0002-2722-5264
2008 (English)In: Journal of Heredity, ISSN 0022-1503, E-ISSN 1465-7333, Vol. 99, no 4, 421-425 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2008. Vol. 99, no 4, 421-425 p.
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-149368DOI: 10.1093/jhered/esn017ISI: 000256761200011PubMedID: 18344528OAI: oai:DiVA.org:uu-149368DiVA: diva2:404889
Available from: 2011-03-18 Created: 2011-03-18 Last updated: 2017-12-11

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Carlborg, Örjan

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