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CIRAD’s Manuel Ruiz on Building a Genomic Resource for Tropical Crops

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Manuel Ruiz
researcher
France’s Centre de Coopération Internationale en Recherche Agronomique pour le Développement
Manuel Ruiz, a researcher at France’s Centre de Coopération Internationale en Recherche Agronomique pour le Développement, coordinates the informatics and scientific development of TropGene, a genomic database that is focused specifically on tropical crops.   
 
Ruiz recently discussed his group’s research with BioInform via e-mail. An edited version of the discussion follows.
 
TropGene is a database for plant research. What can you tell me about it beyond that?
 
TropGene … is an information system that manages genetic and genomic information about tropical crops.
 
TropGene is organized into crop-specific modules. Each module includes data on genetic resources (agro-morphological data, parentages, and allelic diversity), information on molecular markers, genetics maps, result of QTL (quantitative trait loci) analyses, data from physical mapping, sequences, etc. Currently TropGene has modules for banana, cocoa, coconut, coffee, cotton, oil palm, rice, rubber tree, and sugarcane. We plan to create additional modules for taro, yam, and citrus.
 
CIRAD is part of a multi-national consortium to study three types of bacteria. The European Union has funneled a great amount of money into that. How is your group funded?
 
We have two types of funds — funds related to projects specific to a given plant (rice, cocoa, sugarcane), and funds related to the informatics development of our information system.   
 
EU is not our main sponsor in the case of TropGene, but we have some EU funds for projects related to the genetics and genomics of rice. We also had support from the French joint program in plant genomics, Genoplante. In this context, we developed a lot of tools in the domain of rice functional genomics.  
 
We have funds from the United States Department of Agriculture for the expansion of the cocoa module of TropGene, mainly focused on the links between genetic and phenotypic information.  
 
With the sponsorship of the International Consortium for Sugarcane Biotechnology, we are developing TropGene modules to store and analyze diversity array technology and linkage disequilibrium data.
 
We are also highly involved in the Generation Challenge Program, which is a large international consortium whose goal is to use plant genetic diversity and advanced genomic science to develop tools and technologies that help plant breeders in the developing world. GCP's major funders are the EU, the UK's Department for International Development, and the World Bank. They jointly contribute about 90 percent of the GCP total income. In this project, we are connecting TropGene to a global coherent platform called Pantheon, which will integrate different crop databases and a lot of bioinformatics tools.
 
How many people are involved in this project?
 
The core of the TropGene team is composed of seven people. But we have to include a lot of external collaborating biologists, from CIRAD or other institutions, for submission and curation of the data.
 
For the TropGene banana module, we interact closely with the bioinformatics team of the Bioversity Center, which is a partner of the Global Musa Genomics Consortium.
 
Whose idea was TropGene? When did it first come into being?
 
CIRAD researchers generate a lot of various data on the genetic, molecular, and phenotypic characteristics of tropical plants. Quickly it seemed important to allow researchers to store and query this huge amount of data. We began the project in 2002, and the first version of TropGene was online in 2003.
 
Plants don’t seem to have the cachet of their human counterparts in terms of biomolecular study. Why do you think that is?
 
Maybe we can see that as a consequence of the medical importance of the human biomolecular studies (and animal models). However the consequences of the molecular studies in plants can also have major economical, social, and ecological impacts, as important as the green revolution.
 
What are the goals of this project?
 
Our goal is to develop a highly integrated information system combining dynamically various crop datasources and bioinformatic tools. Indeed, researchers can compare sequences (or maps) of a plant of agronomic interest with sequences (or maps) of a plant model (such as Arabidopsis) in order to find important genes or loci. Or researchers can determine the function of a new gene using orthologous prediction, expression data, or mutant information. Or users can find new plant varieties of interest by combining polymorphism (alleles) and phenotypic information.
 
Describe the interfaces for the web site and how they work.
 
Web interfaces have been designed to allow quick consultations as well as complex queries. Each crop module has several interfaces to carry out specific requests. We connected our interface to generic viewers like Cmap for displaying genetic and physical comparative maps, and Gbrowse for displaying genome annotations.
 
Describe any other technology required for users to interact/gain data/research with TropGene.
 
Our informatics development is focused on Web applications. So generally users need only to use generic Web browsers to interact with TropGene.
 
Who is using TropGene?
 
TropGene is running and consulted by plant researchers (geneticists, physiologists, breeders, etc.) from different part of the world.
 
What’s next for your group at CIRAD?
 
More and more tropical plant genomes will be entirely sequenced. We have to be prepared for integrating quickly all these sequences with the different levels of automatic and manual annotation (structural, functional, and relational). We plan to be more involved in these annotation tasks and in the development of corresponding bioinformatics integrative and generic solutions.

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