Prsentation PowerPoint

1
GnpMap the mapping database update  the
cytogenetic map view
1INRA Unité de recherche en Génomique-Info, 523
place des terrasses 91000 Evry 2Laboratoire de
Génomique et Bioinformatique, Biogemma, 1 rue
Pierre Fontaine, 91058 Evry Cedex 3Bayer
BIOSCIENCE Technologiepark  38 B-9052 Zwijnaarde
Belgium 4INRA 234 Avenue du Brèzet, Domaine de
Crouelle 63100 Clermont Ferrand 5INRA URGV, UMR
INRA 1165 - CNRS 8114- 2, Rue Gaston Crémieux,
91057 Evry Cedex 6INRA Station d'Amélioration
des Plantes, BP 29, 35653 Le Rheu Cedex 7INRA UMR
Genetique vegetale, Ferme du Moulon 91190
Gif-sur-Yvette, France 8Limagrain Verneuil
Holding, 77390 Verneuil l'etang
GnpMap the mapping database 2005 and 2006
updates  the cytogenetic map view Michael
Alaux1, Farid Chetouani1, Delphine
Steinbach-Samson1, Philippe Leroy4, Matthieu
Falque7, Anne-Francoise Adam-Blondon5, Regine
Delourme6, Laurent Hanneton8, Emmanuelle
Karsenty1, Erik Kimmel1, Fabrice Legeai1, Bruce
Thomas2, Laurent Viau3, Denis Scala2, Francois
Artiguenave1.
GnpMap is a database containing genetic maps,
markers, QTLs and all related information, as
well as an interface to query and compare maps.
Web textual interface and graphical interface
(MapComparator) allow the biologists to query and
visualize the data and navigate through them.
GnpMap database was modeled in UML and in
relational database SQL description. Last release
of GnpMap is now supporting cytogenetic maps and
makes the identification of new loci and markers
easier. Furthermore, an extension of the
graphical interface MapComparator has been
developed to give an interactive overview of the
chromosome loci organization and allows
comparisons between maps.

• Technology
• RDBMS Oracle 8.1.7
• Database modeling UML (Rational Rose, Poseidon)
• Object relational Mapping Hibernate
• Data upload and integration tool Perl/CGI
• Web interface Java J2EE servlets and JSP under
  the Struts framework
• Graphical Interface Java J2EE, RMI, Swing

Data insertion in DB
2005-2006 database achievements

• Insertion or update of 5 Génoplante genetic maps
  (ARE, AXO, CtCs, RER, TXO).
• Insertion of a public genetic map (ITMI) and 3
  public cytogenetic maps (DEL, Ditelo,
  Nullitetra).
• Insertion of a public genetic map (Sar10).
• Insertion of 4 public genetic maps (Grenache,
  Riesling, SG, Syrah).
• Update of 2 Génoplante genetic maps (LHRE,
  REFMAP).
• Insertion of 2 Génoplante genetic maps (DY_Q5,
  Rapid/NSL9625).
• Update of the GnpMap public database to add new
  species Wheat, Grape and Sorghum.

GnpMap
Visit GnpMap at https//genoplante.infobiogen.
fr/GnpMap (private site) http//urgi.infobiogen.f
r/GnpMap (public site)
Aster is the integrated database schema composed
by the common tables of the different GnpIS
schemas. It enables links to clones, sequences,
genomes.
New the cytogenetic map interface
Deletion bin are regrouped into colored box
arranged in order along the map.
Common loci between map can be identified by a
blue coloration
or linked to enhance chromosomal organization.
Find your region by querying marker or loci, and
visualize the data of your cytogenetic map in an
adhoc form.
In progress

• Management of marker anchoring into BAC clones
  libraries, either from individual or pooling
  experiments.
• Direct link from marker to other GnpIS modules
  (GnpGenome, GnpSeq) or public databanks.
• Physical mapping data storage and display in
  order to link genetic, physical maps and genomes
  (partially based on WebFPC software).

Physical mapping with WebFPC.
Genetic map
QTL
Genomic sequence
BAC contigs
Crosslinks informations for marker, clone or
sequences.
Anchoring data from pooling experiments.
Colocalization
Acknowledgements We are very grateful to
Génoplante mapping workgroup. In particular we
would like to express our gratitude towards Alain
Charcosset, Johan Joets, Alain Murigneux,
Philippe Lessard, Jean-Pierre Martinant. Thanks
to Judith Burstin and Brigitte Courtois for data
submission.
Dépot APP (Génoplante Valor) GnpMap Deposit
number IDDN.FR.001.260001.001.D.P.2003.000.10300 U
RGI Contact urgi-contact_at_versailles.inra.fr INRA
URGI and Génoplante public Web site
http//urgi.infobiogen.fr Publication Falque et
al.Linkage Mapping of 1454 New Maize Candidate
Gene Loci Genetics, Vol. 170,
1957-1966, August 2005