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Separation of base allele and sampling term effects gives new insights in variance component QTL analysis
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
2007 (English)In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 8, 1- p.Article in journal (Refereed) Published
Abstract [en]

Background

Variance component (VC) models are commonly used for Quantitative Trait Loci (QTL) mapping in outbred populations. Here, the QTL effect is given as a random effect and a critical part of the model is the relationship between the phenotypic values and the random effect. In the traditional VC model, each individual has a unique QTL effect and the relationship between these random effects is given as a covariance structure (known as the identity-by-descent (IBD) matrix).

Results

We present an alternative notation of the variance component model, where the elements of the random effect are independent base generation allele effects and sampling term effects. The relationship between the phenotypic vales and the random effect is given by an incidence matrix, which results in a novel, but statistically equivalent, version of the traditional VC model. A general algorithm to estimate this incidence matrix is presented. Since the model is given in terms of base generation allele effects and sampling term effects, these effects can be estimated separately using best linear unbiased prediction (BLUP). From simulated data, we showed that biallelic QTL effects could be accurately clustered using the BLUP obtained from our model notation when markers are fully informative, and that the accuracy increased with the size of the QTL effect. We also developed a measure indicating whether a base generation marker homozygote is a QTL heterozygote or not, by comparing the variances of the sampling term BLUP and the base generation allele BLUP. A ratio greater than one gives strong support for a QTL heterozygote.

Conclusion

We developed a simple presentation of the VC QTL model for identification of base generation allele effects in QTL linkage analysis. The base generation allele effects and sampling term effects were separated in our model notation. This clarifies the assumptions of the model and should also enhance the development of genome scan methods.

Place, publisher, year, edition, pages
2007. Vol. 8, 1- p.
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-23490DOI: 10.1186/1471-2156-8-1ISI: 000243659800001PubMedID: 17210073OAI: oai:DiVA.org:uu-23490DiVA: diva2:51264
Available from: 2007-01-29 Created: 2007-01-29 Last updated: 2017-12-07

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Rönnegård, LarsCarlborg, Örjan

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