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Open Access Open Badges Methodology article

Statistical properties of interval mapping methods on quantitative trait loci location: impact on QTL/eQTL analyses

Xiaoqiang Wang12, Hélène Gilbert34, Carole Moreno5, Olivier Filangi12, Jean-Michel Elsen5 and Pascale Le Roy12*

Author affiliations

1 INRA, UMR 1348, PEGASE, 35042 Rennes cedex, France

2 Agrocampus Ouest, UMR 1348, PEGASE, 35042 Rennes cedex, France

3 INRA, UMR 1313, GABI, 78352 Jouy en Josas cedex, France

4 INRA, UMR 444, LGC, 31326 Castanet Tolosan cedex, France

5 INRA, UMR 631, SAGA, 31326 Castanet Tolosan cedex, France

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Citation and License

BMC Genetics 2012, 13:29  doi:10.1186/1471-2156-13-29

Published: 20 April 2012



Quantitative trait loci (QTL) detection on a huge amount of phenotypes, like eQTL detection on transcriptomic data, can be dramatically impaired by the statistical properties of interval mapping methods. One of these major outcomes is the high number of QTL detected at marker locations. The present study aims at identifying and specifying the sources of this bias, in particular in the case of analysis of data issued from outbred populations. Analytical developments were carried out in a backcross situation in order to specify the bias and to propose an algorithm to control it. The outbred population context was studied through simulated data sets in a wide range of situations.

The likelihood ratio test was firstly analyzed under the "one QTL" hypothesis in a backcross population. Designs of sib families were then simulated and analyzed using the QTL Map software. On the basis of the theoretical results in backcross, parameters such as the population size, the density of the genetic map, the QTL effect and the true location of the QTL, were taken into account under the "no QTL" and the "one QTL" hypotheses. A combination of two non parametric tests - the Kolmogorov-Smirnov test and the Mann-Whitney-Wilcoxon test - was used in order to identify the parameters that affected the bias and to specify how much they influenced the estimation of QTL location.


A theoretical expression of the bias of the estimated QTL location was obtained for a backcross type population. We demonstrated a common source of bias under the "no QTL" and the "one QTL" hypotheses and qualified the possible influence of several parameters. Simulation studies confirmed that the bias exists in outbred populations under both the hypotheses of "no QTL" and "one QTL" on a linkage group. The QTL location was systematically closer to marker locations than expected, particularly in the case of low QTL effect, small population size or low density of markers, i.e. designs with low power. Practical recommendations for experimental designs for QTL detection in outbred populations are given on the basis of this bias quantification. Furthermore, an original algorithm is proposed to adjust the location of a QTL, obtained with interval mapping, which co located with a marker.


Therefore, one should be attentive when one QTL is mapped at the location of one marker, especially under low power conditions.

QTL; linkage analysis; QTL location; bias