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Open Access Research

Comparison of three multitrait methods for QTL detection

Hélène Gilbert* and Pascale Le Roy

Author Affiliations

Institut national de la recherche agronomique, Station de génétique quantitative et appliquée, 78352 Jouy-en-Josas Cedex, France

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Genetics Selection Evolution 2003, 35:281-304  doi:10.1186/1297-9686-35-3-281


The electronic version of this article is the complete one and can be found online at: http://www.gsejournal.org/content/35/3/281


Received:30 April 2002
Accepted:18 November 2002
Published:15 May 2003

© 2003 INRA, EDP Sciences

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.

Keywords:
multitrait; QTL; sib families; simulations

Research

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