TropGENE DB : a tropical crop database

At CIRAD, plant genomics is aimed at assisting tropical crops breeding programs. TropGENE DB database has been conceived to manage genetic and genomic information on these crops.

In accordance with its mandate, CIRAD has undertaken varietal improvement for a wide range of crops and a large array of environments:

- rational use of genetic diversity available from germplasm collections,
- refinement of gene incorporation or introgression methodologies through accurate genome mapping,
- marker-assisted selection,
- genetic transformation.
The strength of these activities rests on efficient collaborations with partners from the South, in both the public and private sectors, and integrated research on stations in the tropics. Research into genomic was undertaken within this framework. The first genetic maps for cocoa, banana and sugarcane cultivar were developped and published by scientists from CIRAD.[1] [2] [3]

The TropGENE DB project has been initiated by P. Lagoda and L.M. Raboin in 1996 to store the increasing amount of molecular genetic data. TropGENE DB was used internally until the development of the Web version in 2003 [4].

The TropGENE DB database was developed using the AceDB system and is currently organized on a crop basis. AceDB is an object-oriented system able to store and seek complex biological information. AceDB is currently used by many databases : WormBase [5], various plant-related databases such as Maize DB, Cotton DB, CocoaGenDB [6], pathogen-related database such MagnaportheDB [7], etc...
AceDB provides an intuitive object-oriented view of biological data, and a graphical user interface with many specialized data visualization tools, such as a genetic map viewer and a sequence annotation display. A set of Perl CGI scripts (AceBrowser, WebAce) have been yet implemented to allow to any AceDB databases for being browsed via World Wide Web pages, using different database search interfaces [8].

The Perl object package, Tropgene [9], developed at CIRAD, uses modules of the AcePerl API (Application Programming Interface) and the AceBrowser generic web interface [8]. This package makes it possible to carry out complex queries (combined requests, use of arithmetic and comparison operators, etc.) and a synthetic display of results.

References

[1] Lanaud C, Risterucci AM, N'Goran J, Clément D, Flament MH, Laurent V, Falque M, (1995) A genetic map of theobroma cacao L, Theor Appl Genet 91: 987-993

[2] Faure S, Noyer JL, Horry JP, Bakry F, Lanaud Claire, Gonzalez De Léon D, (1993) A molecular marker-based linkage map of diploid bananas, Theor Appl Genet 87: 517-526

[3] Grivet L, D'Hont A, Roques D, Feldmann P, Lanaud C, Glaszmann JC, (1996) RFLP mapping in cultivated sugarcane (Saccharum spp.): genome organization in a highly polyploid and aneuploid interspecific hybrid, Genetics 142(3):987-1000

[4] 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.

[5] Stein L, Sternberg P, Durbin R, Thierry-Mieg J, Spieth J, (2001) WormBase: network access to the genome and biology of Caenorhabditis elegans, Nucleic Acids Res, 82-6

[6] Ruiz, M, Rouard, M, Turnbull, CJ, Orain, R, Ford, C, Raboin, LM, Lartaud, M, Lanaud, C, Clément, D, Petithuguenin, P, Wilkinson, MD, Hadley, P, Brown, S, Rosenquist, E, and Courtois, B (2003) A new international cocoa genetic database. In 14th International Cocoa Research Conference (Accra, Ghana)

[7] Martin SL, Blackmon BP, Rajagopalan R, Houfek TD, Sceeles RG, Denn SO, Mitchell TK, Brown DE, Wing RA, Dean RA, (2002) MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea, Nucleic Acids Res, 121-4

[8] Stein LD, Thierry-Mieg J, (1998) Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases, Genome Res, 1308-15

[9] Rouard, M, and Ruiz, M (2003) Tropgene: quick implementation of new web interfaces for ACEDB databases. In ECCB'2003 European Conference on Computational Biology (Paris, France), pp. 71