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Genetics Selection Evolution

, 35:513 | Cite as

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

  • Jihad M AbdallahEmail author
  • Bruno Goffinet
  • Christine Cierco-Ayrolles
  • Miguel Pérez-Enciso
Open Access
Research

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.

Keywords

linkage disequilibrium quantitative trait locus fine mapping 

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Copyright information

© INRA, EDP Sciences 2003

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Authors and Affiliations

  • Jihad M Abdallah
    • 1
    Email author
  • Bruno Goffinet
    • 2
  • Christine Cierco-Ayrolles
    • 2
  • Miguel Pérez-Enciso
    • 1
  1. 1.Station d'amélioration génétique des animauxInstitut national de la recherche agronomique, AuzevilleCastanet-Tolosan CedexFrance
  2. 2.Unité de biométrie et intelligence artificielleInstitut national de la recherche agronomique, AuzevilleCastanet-Tolosan CedexFrance

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