French (Fr)English (United Kingdom)
 

BioMercator: genetic maps and QTL integration

BioMercator V2.1: genetic maps and QTL integration

 

Project team Johann Joets, Matthieu Falque, Alain Charcosset
Project previous members Anne Arcade, Fabien Chardon
Project collaborators Aymeric Labourdette, Bruno Goffinet, Brigitte Mangin (INRA, BIA, Toulouse, France)

 

UPDATE (01/2011): This version is not maintained any more. We are developing the third version, please visit the new page here.

 

A new challenge in breeding programs is to integrate information from genomics and that from quantitative trait loci (QTL) analysis, in order to identify sequences controlling the variation of important traits. Despite the outburst of genomic databases, constructing an integrative genetic map compiling genes, QTLs and other loci gathered from multiple maps remains a manual and tedious task. Yet, consensus maps are very useful to reveal co-locations between candidate genes and QTLs.
The increasing number of QTL experiments delivers an important corpus of results which must be synthesized. It seems interesting to determine whether QTLs detected in independent experiments and located in a same region of a chromosome might be in fact several estimations of the position of one single QTL. This assertion can be verified by means of appropriate statistical tools such as meta-analysis, which consists in combining data from diverse sources in a single study. Meta-analysis therefore represents a useful tool to synthesize dense QTL information and to refine QTL position.

 

BioMercator is a stand-alone application which automatically performs these tasks. (1) BioMercator offers a user-friendly graphical map browser. Genetic map and QTL data are loaded from text files. (2) BioMercator performs automatic compilations of several genetic maps. A consensus genetic map can be built from multiple individual maps by iterative projection of QTLs, genes and other loci. (3) BioMercator computes meta-analysis of QTLs (Goffinet and Gerber, 2000). This statistical method determines the most likely number of "real" QTLs represented by N QTLs detected in independent experiments for the same trait or related ones. Finally, the graphical interface allows to visualize co-locations between consensus QTLs and genes.

 

This software is a graphical interface written in Java (1.5) language. It was developed with the support of Génoplante projects "Integrative tools for genetic mapping" and "Maize bioinformatics". Biomercator is furnished "as is" without warranties of any kind nor associated service.

 

Availability

BioMercator is a licensed product available free of charge for non-profit activities here and on request from Genoplante-Valor otherwise (see the Genoplante web site).


References

Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A, Joets J. BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics. (2004) Sep 22;20(14):2321-6.

Goffinet B, Gerber S. Quantitative trait loci: a meta-analysis. Genetics. (2000) May,155(1):463-73

 

Funding

This programme was funded by Génoplante and the Génération Challenge Programme.