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Non-iterative variance component estimation in QTL analysis
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
2009 (English)In: Journal of Animal Breeding and Genetics, ISSN 0931-2668, E-ISSN 1439-0388, Vol. 126, no 2, 110-116 p.Article in journal (Refereed) Published
Abstract [en]

In variance component quantitative trait loci (QTL) analysis, a mixed model is used to detect the most likely chromosome position of a QTL. The putative QTL is included as a random effect and a method is needed to estimate the QTL variance. The standard estimation method used is an iterative method based on the restricted maximum likelihood (REML). In this paper, we present a novel non-iterative variance component estimation method. This method is based on Henderson's method 3, but relaxes the condition of unbiasedness. Two similar estimators were compared, which were developed from two different partitions of the sum of squares in Henderson's method 3. The approach was compared with REML on data from a European wild boar x domestic pig intercross. A meat quality trait was studied on chromosome 6 where a functional gene was known to be located. Both partitions resulted in estimated QTL variances close to the REML estimates. From the non-iterative estimates, we could also compute good approximations of the likelihood ratio curve on the studied chromosome.

Place, publisher, year, edition, pages
2009. Vol. 126, no 2, 110-116 p.
Keyword [en]
Henderson's method 3, minimized mean square error, quantitative trait loci analysis, restricted maximum likelihood, variance components
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-148711DOI: 10.1111/j.1439-0388.2008.00780.xISI: 000264241300004PubMedID: 19320767OAI: oai:DiVA.org:uu-148711DiVA: diva2:402807
Available from: 2011-03-09 Created: 2011-03-09 Last updated: 2017-12-11Bibliographically approved

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