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BioMercator V3

BioMercator V3: a software for genetic map compilation, QTL meta-analyses

 

Project team

Olivier Sosnowski, Marion Truntzler (GQMS), Alain Charcosset (GQMS), Johann Joets



Collaborating groups

UR AGPF, INRA,  Orléans : Véronique Jorge

UR GI, INRA, Versailles : Dorothée Valdenaire, Erik Kimmel, Delphine Steinbach

UMR BIOGECO, INRA-Université Bordeaux 1, Cestas: Catherine Bodenes, Antoine Kremer

UMR GDEC, INRA-Université Blaise Pascal, Clermont-Ferrand: Jacques Le Gouis

UMR GDPP, INRA-Bordeaux 2, Villenave d'Ornon; Véronique Decroocq

Syngenta Seeds, Saint Sauveur: Florence Louis, Mark Sawkins

Biogemma, Clermont-Ferrand: Frédéric Sapet, Olivier Dugas

Summarize

 

Over several years, large efforts have been made to produce crop genetic and genomic data at genome scale. To take full advantage of these data, integration is required at various levels of resolution. QTL mapping can generally be undertaken on different populations and levels of inbreeding (e.g., F3; RILs). Integrative QTL meta-analysis methods have been developed to take full advantage of existing results to more accurately predict the most probable location of QTL. Methods have also been devised to build consensus map by integrating genetic map and QTL map positions and making it easier to search for co-localization between genes and QTL. These methods have been implemented into the BioMercator V2.1 software thanks to the previous support of Génoplante and The Generation Challenge program.

 

Compared to the previous versions, BioMercator V3 will include several new map compilation and meta-analysis algorithms from the MetaQTL package. The graphical user interface has also been improved and offers new display options (compact information representation) and zooming tools. BioMercator V3 will be fully connected to the URGI GnpMap databases.

 

The software will be released freely in 2011

image BM
Figure 1 : Map overview Figure 2 : Map comparison Figure 3 : Map zoom

 

References

Olivier Sosnowski, Alain Charcosset and Johann Joets. BioMercator V3: an upgrade of genetic map compilation and QTL meta-analysis algorithms Bioinformatics (2012); doi: 10.1093/bioinformatics/bts313

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

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.

Jean-Baptiste Veyrieras, Bruno Goffinet and Alain Charcosset. MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments. BMC Bioinformatics (2007), 8:49

 

Funding

BioMercator V3 is developed with funding from ANR projet ANR-PCS-08-GENO-126 (PI Johann Joets) .