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doi:10.1534/genetics.105.048108
A more recent version of this article appeared on July 1, 2006.
REGULAR RESEARCH PAPERS |
On Locating Multiple Interacting Quantitative Trait Loci in Intercross Designs
Andreas Baierl 1*, Malgorzata Bogdan 2, Florian Frommlet 1 and Andreas Futschik 1
1 University of Vienna
2 Wroclaw University of Technology
* To whom correspondence should be addressed. E-mail: andreas.baierl{at}univie.ac.at.
Submitted on July 12, 2005
Revised on September 7, 2005
Accepted on 10 April 2006
A modified version (mBIC) of the Bayesian Information Criterion (BIC) has been previously proposed for backcross designs to locate multiple interacting quantitative trait loci. In this paper, we extend the method to intercross designs. We also propose two modifications of the mBIC. First we investigate a two-stage procedure in the spirit of empirical Bayes methods involving an adaptive ( i.e. data based) choice of the penalty. The purpose of the second modification is to increase the power of detecting epistasis effects at loci where main effects have already been detected. We investigate the proposed methods by computer simulations under a wide range of realistic genetic models, with non-equidistant marker spacings and missing data. In case of large intermarker distances we use imputations according to Haley and Knott regression to reduce the distance between searched positions to not more than 10 cM. Haley and Knott regression is also used to handle missing data. The simulation study as well as real data analyses demonstrate good properties of the proposed method of QTL detection.
Key Words: BIC, Bayesian model, QTL mapping, epistasis, intercross design
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