TropGeneDB: an information system for tropical crops

TropGeneDB is an information system initially developed by CIRAD (French Agricultural Research Centre for International Development) to manage various kinds of data on tropical crops. It is a Web application based on MySQL databases (one per crop) that can be queried using Java customizable interfaces automatically generated to fit the databases contents.

TropGeneDB can record crop information on:
- molecular markers, QTLs, genetic and physical maps
- genetic diversity, association and linkage disequilibrium studies
- phenotypic diversity studies based on agro-morphological traits or traits measuring the susceptibility/resistance to aggression (diseases, salinity, drought)
- geographic origin, parentage, collection, ecology

See User Interface Documentation.

The TropGeneDB project [1] was initiated by P. Lagoda and L.M. Raboin in 1996 using the DBMS ACEDB but the databases were later migrated to the MySQL DBMS in order to follow the evolution of the computer technology [2].

Data on the following 11 crops are currently recorded in TropGeneDB: banana, breadfruit, citrus, cocoa, coconut, coffee, cotton, oil palm, rice, rubber tree, sugarcane. All the data in TropGeneDB are public and generally linked to published scientific papers. Links to the GMOD CMAP viewer (the Comparative Map Viewer) have been integrated.

People wishing to submit data may download submission templates which consist of Microsoft Excel files.
See instructions
for filling in the templates and contact us at TropgeneDB.

TropGeneDB is a component of the South Green Bioinformatics Platform.

[1] Ruiz M, Rouard M, Raboin LM, Lartaud M, Lagoda P, Courtois B., (2004) TropGENE-DB, a multi-tropical crop information system, Nucleic Acids Res. Jan 1;32(1):D364-7

[2] Chantal Hamelin, Guilhem Sempere, Vincent Jouffe and Manuel Ruiz, (2012) TropGeneDB, the multi-tropical crop information system updated and extended, Nucl. Acids Res. (2012) doi: 10.1093/nar/gks1105

Contact: TropgeneDB