Genet. Sel. Evol. 35 (2003) 513-532
DOI: 10.1051/gse:2003037

Linkage disequilibrium fine mapping of quantitative trait loci: A simulation study

Jihad M. Abdallah^a, Bruno Goffinet^b, Christine Cierco-Ayrolles^b and Miguel Pérez-Enciso<sup>a

a</sup>  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