Issue |
Genet. Sel. Evol.
Volume 35, Number 5, September-October 2003
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Page(s) | 513 - 532 | |
DOI | https://doi.org/10.1051/gse:2003037 |
DOI: 10.1051/gse:2003037
Linkage disequilibrium fine mapping of quantitative trait loci: A simulation study
Jihad M. Abdallaha, Bruno Goffinetb, Christine Cierco-Ayrollesb and Miguel Pérez-Encisoaa Station d'amélioration génétique des animaux, Institut national de la recherche agronomique, Auzeville BP 27, 31326 Castanet-Tolosan Cedex, France
b Unité de biométrie et intelligence artificielle, Institut national de la recherche agronomique, Auzeville BP 27, 31326 Castanet-Tolosan Cedex, France
(Received 27 June 2002; accepted 17 January 2003)
Abstract
Recently, the use of linkage disequilibrium (LD) to locate genes which
affect quantitative traits (QTL) has received an increasing
interest, but the plausibility of fine mapping using linkage
disequilibrium techniques for QTL has not been well studied. The main
objectives of this work were to (1) measure the extent and pattern of
LD between a putative QTL and nearby markers in finite populations and
(2) investigate the usefulness of LD in fine mapping QTL in simulated
populations using a dense map of multiallelic or biallelic marker
loci. The test of association between a marker and QTL and the power
of the test were calculated based on single-marker regression
analysis. The results show the presence of substantial linkage
disequilibrium with closely linked marker loci after 100 to 200
generations of random mating. Although the power to test the
association with a frequent QTL of large effect was satisfactory, the
power was low for the QTL with a small effect and/or low
frequency. More powerful, multi-locus methods may be required to map
low frequent QTL with small genetic effects, as well as combining both
linkage and linkage disequilibrium information. The results also
showed that multiallelic markers are more useful than biallelic
markers to detect linkage disequilibrium and association at an equal
distance.
Key words: linkage disequilibrium / quantitative trait locus / fine mapping
Correspondence and reprints: Jihad M. Abdallah
e-mail: abdallah@germinal.toulouse.inra.fr
© INRA, EDP Sciences 2003