Linkage Disequilibrium Fine Mapping of Quantitative Trait Loci: A Simulation Study
Publication Type
Original research
  • Jihad M. Abdallah
  • Bruno Goffinet
  • Christine Cierco-Ayrolles
  • Miguel Pérez-Enciso

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. Themain objectives of thiswork were to (1)measure the extent and pattern of LD between a putativeQTL 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 amarker and QTL and the power of the test were calculated based on singlemarker 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.

Genet. Sel. Evol. Volume 35, Number 5, P: 513 - 532
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Both (Printed and Online)