Open Access

Comparison of three multitrait methods for QTL detection

Genetics Selection Evolution200335:281

DOI: 10.1186/1297-9686-35-3-281

Received: 30 April 2002

Accepted: 18 November 2002

Published: 15 May 2003


A comparison of power and accuracy of estimation of position and QTL effects of three multitrait methods and one single trait method for QTL detection was carried out on simulated data, taking into account the mixture of full and half-sib families. One multitrait method was based on a multivariate function as the penetrance function (MV). The two other multitrait methods were based on univariate analysis of linear combination(s) (LC) of the traits. One was obtained by a principal component analysis (PCA) performed on the phenotypic data. The second was based on a discriminate analysis (DA). It calculates a LC of the traits at each position, maximising the ratio between the genetic and the residual variabilities due to the putative QTL. Due to its number of parameters, MV was less powerful and accurate than the other methods. In general, DA better detected QTL, but it had lower accuracy for the QTL effect estimation when the detection power was low, due to higher bias than the other methods. In this case, PCA was better. Otherwise, PCA was slightly less powerful and accurate than DA. Compared to the single trait method, power can be improved by 30% to 100% with multitrait methods.


multitrait QTL sib families simulations

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Authors’ Affiliations

Institut national de la recherche agronomique, Station de génétique quantitative et appliquée


© INRA, EDP Sciences 2003