Genet. Sel. Evol. 35 (2003) 281-304
DOI: 10.1051/gse:2003009

Comparison of three multitrait methods for QTL detection

Hélène Gilbert and Pascale Le Roy

Institut national de la recherche agronomique, Station de génétique quantitative et appliquée, 78352 Jouy-en-Josas Cedex, France
(Received 30 April 2002; accepted 18 November 2002)

Abstract
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.

Key words: multitrait / QTL / sib families / simulations

Correspondence and reprints: Hélène Gilbert
    e-mail: helene.gilbert@dga.jouy.inra.fr

© INRA, EDP Sciences 2003