Plant & Animal Genomes XIV Conference Plant & Animal Genomes XIV ConferenceJanuary 14-18, 2006
Town & Country Convention Center
San Diego, CA
David Delannoy , Marie M Jourjon , Sylvain Jasson , Brigitte Mangin
The aim of MCQTL software package is to perform QTL mapping in multi-cross design.
It allows the analysis of the usual populations derived from inbred lines and can link the families by assuming that the QTL locations are the same in all of them. Moreover, a diallel modeling of the QTL genotypic effect is allowed in multiple related families.
The implemented model is a linear regression model using the probabilities of QTL genotypes given marker information are used as regressors. A composite interval mapping and an iterative QTL mapping are implemented to deal with multiple QTL model. Marker cofactor selections by forward or backward stepwise methods are implemented as well as computation of threshold test value by permutation.
MCQTL is a local UNIX application. The package is composed of three software components. The first component, TranslateData, reads the data from MAPMAKER or MAPQTL files. The second component, ProbaPop, computes QTL genotype probabilities at specific chromosome location given multiple marker data in each family and stores them in XML formatted files. The last component, Multipop, builds the pooled model and fits the observations on genotype probabilities.
There are two independent ways of operating the MCQTL software, either using the Command Line applications (TranslateData, ProbaPop, and MultiPop) or using a java Graphical User Interface (GUI). The GUI has been built to provide a friendly and useful tool for inexperienced users.
The TranslateData application was developed in Java and runs using a 1.4 or later JVM. ProbaPop and MultiPop, being computationally intensive, are coded in C++. A Sun-OS and a Linux archive respectively tested on Sun OS 5.9 sparc Ultra-Entreprise and Linux 2.4.4 Intel computers are available. Gnuplot 3.7 or latter version (available from http://www.gnuplot.info ) is required.
The program is available on request after signing a license agreement; free of charge for academic and non-profit organizations at http://www.genoplante.com (Bioinformatics products).
Contact: Brigitte Mangin
Jourjon M. F., Jasson S., Marcel J., Ngom B., Mangin B. 2005. MCQTL: multi-allelic QTL mapping in multi-cross design. Bioinformatics, 21, 128-130.