Data

Mapping data

This genetic mapping database schema contains about 80 entities which store genetic maps of markers of differents types: RFLP, microsatellites (with PCR information, primers), CAPS, EST and all the corresponding loci.

The database stores also QTL data with their associated traits and all information describing a QTL experiment detection: the experiment itself, the measures, the effects and the population studied. Positions of QTL are stored with classical parameters: LOD, r2 and confidence interval.

GnpMap query interface is composed of a text query interface which allows extended interrogations in the mapping database and a Java applet entitled MapComparator for graphical map drawing and comparative analysis. From the textual interface, web forms provide different ways to query the database by loci, QTLs, markers, maps and traits.

Locus interrogations include searches according to map's name, linkage group, locus name, marker's or sequence's information. For chromosomic region analysis, loci mapped between two input named loci or two absolute chromosomic positions may be retrieved. For neighbourhood studies, the regions displayed around the loci, returned by the query, can be restricted according to an input maximal distance before and after the loci. QTL's interrogations include searches according to map's name, linkage groups, QTL's name, traits, keywords, and by locus name for colocalization studies.

GnpMap allows to colocalize QTL with ESTs mapped and is linked to GnpSeq database module to get all information concerning the EST, its library, samples and its experimental conditions.

GnpMap is able to store data that has to be kept confidential before publication. For that, ask urgi-support for a group and tell which user can access the data on Private URGI Web server.

GnpMap data information

Most of the mapping data available in this database were generated in the frame of the french Genoplante plant genomics consortium .

The objective of Genoplante cDNA mapping project was to map candidate genes identified by the consortium, so that their map locations can be confronted with QTL positions. So framework maps were built, cDNA loci were placed on them, and all loci were integrated on a consensus map together with loci from other public sources.

In addition to cDNA loci, anonymous markers were also mapped from segregation data generated by Genoplante, kindly provided by Mike Lee (Iowa State University), or downloaded from MaizeGDB . These anonymous markers provide a dense coverage of of links between the Genoplante consensus map and any other Maize map. The main framework map used for Genoplante cDNA mapping is IBM_Gnp2004. It is based on the 94 IBM (Intermated B73xMo17) lntermated Recombinant Inbred Lines chosen as international community mapping resource and distributed by the Maize Genetics Cooperation Stock Center.

In case of no polymorphism on IBM, the LHRF_Gnp2004 map was used. It is based on 94 LHRF (Intermated F2xF252) intermated Recombinant Inbred Lines developed at INRA Le Moulon, Gif-sur-Yvette, France (contact: charcos@moulon.inra.fr). All mapped loci were pooled on the IBMconsensus_Gnp2004 map. This map is based on IBM_Gnp2004, on which loci from other maps were projected based on shared markers. Loci from LHRF_Gnp2004, from IBM2 neighbors (see MaizeGDB ), and from other public maps were then integrated to IBMconsensus_Gnp2004 to provide a comprehensive Maize linkage map. Intermated Recombinant Inbred Lines used for IBM_Gnp2004 and LHRF_Gnp2004 were obtained by performing four generations of random intermating between F2 stage and subsequent selfing generations. this results in more frequent recombinations, and a higher potential of map resolution as compared to RILs. For distance calculations with such lines, two different estimates are providede in this database: distances computed with MapMaker (Lander et al. 1987, Genomics 2: 174-181) as for RILs with the "RI self Haldane" parameter. This calculation is inappropriate for intermated RILs, but ensures cross-compatibility with previous public maps. A consensus map was done in 2005 that contains markers, QTLs and that is used for metaQTL analysis.

It contains also :

• grape genetic maps:
  • contact data: Anne Francoise Blondon, INRA URGV Evry , adam[[at]]evry.inra.fr, urgi-contact[at]versailles.inra.fr
• Two rice genetic maps:
  • contact data: Brigitte Courtois, CIRAD Montpellier , brigitte.courtois[at]cirad.fr, urgi-contact[at]versailles.inra.fr
• A sorgho map
  • contact data: Monique Deu, CIRAD Montpellier , monique.deu[at]cirad.fr, urgi-contact[at]versailles.inra.fr

Since 2009, Barley maps from TriticaeGenome projects (Nils Stein and collaborators).

Data submission

To submit data to GnpMap, go to URGI datasubmission Web page to get and fill exchange format files. An excel version of these files are available: ask urgi-contact[at]versailles.inra.fr to get it.

A new version of GnpMap was developped in the frame of ANR MetaQTL project and allow the management of metaQTL analysis data.  A new graphical interface based on BioMercattor V3 software, was developped.

New Pea markers and QTL maps from current ANR GenoPea

New wheat data from TriticaeGenome project