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This article is part of the supplement: Proceedings of the 13th European workshop on QTL mapping and marker assisted selection

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QTL detection for a medium density SNP panel: comparison of different LD and LA methods

Olivier Demeure12*, Nicola Bacciu12, Olivier Filangi12 and Pascale Le Roy12

Author Affiliations

1 INRA, UMR 598 Génétique Animale, F-35000 Rennes, France

2 Agrocampus-Ouest, UMR Génétique Animale, F-35000 Rennes, France

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BMC Proceedings 2010, 4(Suppl 1):S10  doi:10.1186/1753-6561-4-S1-S10

Published: 31 March 2010



New molecular technologies allow high throughput genotyping for QTL mapping with dense genetic maps. Therefore, the interest of linkage analysis models against linkage disequilibrium could be questioned. As these two strategies are very sensitive to marker density, experimental design structures, linkage disequilibrium extent and QTL effect, we propose to investigate these parameters effects on QTL detection.


The XIIIth QTLMAS workshop simulated dataset was analysed using three linkage disequilibrium models and a linkage analysis model. Interval mapping, multivariate and interaction between QTL analyses were performed using QTLMAP.


The linkage analysis models identified 13 QTL, from which 10 mapped close of the 18 which were simulated and three other positions being falsely mapped as containing a QTL. Most of the QTLs identified by interval mapping analysis are not clearly detected by any linkage disequilibrium model. In addition, QTL effects are evolving during the time which was not observed using the linkage disequilibrium models.


Our results show that for such a marker density the interval mapping strategy is still better than using the linkage disequilibrium only. While the experimental design structure gives a lot of power to both approaches, the marker density and informativity clearly affect linkage disequilibrium efficiency for QTL detection.