A Biological Resource Centre dedicated to plant genomes

Genomics has seen extraordinary growth since the 1990s and constitutes a major scientific challenge. The numerous genomics programmes carried out on plants led to the creation and proliferation of gene and genome fragment collections. The cloning of genomes into bacterial artificial chromosome (BAC) libraries is an invaluable tool for genome analysis, physical mapping, map-based cloning and sequencing projects. The french Ministry of Research acknowledged the strategic importance of these genomic resources and commissioned INRA (French National Institute for Agricultural Research) to set up a Biological Resource Centre (BRC). BRCs are an essential part of the infrastructure underpinning biotechnology. They consist of service providers and repositories of biological material. dedicated to plant genome. In this context, the French Plant Genomic Resources Centre (CNRGV), unique in France, has been set up in 2004. CNRGV is a non-for-profit service centre for plant genomic resources. A new building dedicated to this centre has been officially inaugurated in September 2007 (see figure 1) in the presence of Marion Guillou, President of the Institute, Guy Riba (Deputy Director General, in charge of scientific programmes, resources and evaluation) and Hélène Lucas (head of a the research division of Plant Breeding and Genetics).

The activities of this national organisation are to ensure that this important genomic material and their descriptions are maintained and available for the benefit of science and biotechnology.

The missions of the CNRGV

CNRGV holds the most relevant BAC and cDNA libraries from top public-sector laboratories (INRA, CNRS, American laboratories) and private laboratories (e.g. arising from Génoplante - programmes) for model and crop plants: Arabidopsis thaliana, Medicago truncatula, tomato, wheat, pepper, grapevine, rapeseed, maize, pea and sunflower. The objectives are to gather, to conserve and to manage genomic collections and to provide high throughput molecular tools to the scientific community. More than 5 millions clones are yet available. These BAC libraries are an invaluable tool for genome analysis, physical mapping, map-based cloning and sequencing projects, they facilitated gene cloning and contributed to rapidly identify homoeologous genes in polyploid species.

The main missions of CNRGV are:

• Centralize and maintain all the plant genomic resources for model and crop plants
• Distribute these genomic resources and their related data at the international level.
• Provide high quality research material
• Provide high throughput technology

Hosting genomic material from additional species is a permanent requirement. We have developed particular relations with several laboratories in order to enrich our libraries with additional clones but also to exchange experience and libraries.

CNRGV is not only a repository centre for all these plant genomic libraries but also a service provider dedicated to the scientific community. CNRGV offers a wide range of services for the study of plant genomics collections:

• Production of high quality plant BAC libraries
• Distribution of clones and libraries
• High density colony arrays production
• DNA Pools Production
• Custom screening (for macroarrays and DNA pools)
• Robotic services (rearraying, automated colony picking …)

CNRGV benefits from leading-edge technologies and automated equipment which guarantees high throughput and standardised processing of the collections. The main equipment is represented by: freezers (-80°C), various automates for clones handling, liquid handling, spotting on macroarrays, high throughput PCR machines, real time PCR machine and automated DNA electrophoresis system, macroarrays scanners. Information systems and traceability of clones and experiments have been optimised with the set up of powerful and adapted data bases.

Ordering on-line clones and services are possible thanks to our website. Fees for services are calculated according to the users’ status. The legal status of collections before dissemination to different partners, including public and industry, are carefully checked according to the current regulation. CNRGV has set up a Quality Management System and has obtained certification under ISO 9001:2000 quality standards in 2005.

Local environment :

A European positioning

From the very beginning, this platform was anticipated as largely opened to the European plant academic community and to industry with a rapid development toward the international community. Indeed, service platform dealing with plant species of economical interest are unique in France and very rare worldwide. CNRGV already supplies laboratories throughout the world with genomic resources. CNRGV is a member of the IWGSC (International Wheat Genomic Sequencing Consortium) coordinating committee and is dedicated to serve as resource center (storage, distribution) for the wheat genomic collections that have been created by various laboratories, providing access to these resources to the international wheat community ( http://www.wheatgenome.org/)

CNRGV is also a member of the Medicago Stock Center project ( http://medicago.toulouse.inra.fr/cgi-bin/Mt/medicagoo.cgi) . It is dedicated to serve as European resource center (storage, distribution) for the M. truncatula genomic collections that have been created by various laboratories, providing access to these resources to the european legume community. It also houses the world reference collections of tomato ( http://www.sgn.cornell.edu/about/tomato_sequencing.pl) and grapevine ( http://www.vitaceae.org/index.php/Genome_Sequencing) BAC libraries used by their respective sequencing international consortium.

Technical development

CNRGV aims not only at being a repository centre for plant genomic resources but also a service provider dedicated to the scientific community. One of our objectives is to produce efficient tools to facilitate the use of BAC libraries in various applications such as genome analysis, physical mapping, map-based cloning and sequencing projects.

Within this context, we have developed an efficient method to create and screen three dimensional pools (3D-pools) of BAC libraries, in order to resolve high-density filter hybridization limitations. Using smart pooling strategy, large-scale DNA amplification enzyme and RealTime-PCR technology, we have developed a high-throughput pipeline from the 3D-pool construction to the acquisition of screening results (see description of the pooling strategy on figure 2). This reliable method is able to minimize the number of PCR reactions needed to screen a BAC library. It can be adapted to different library size and coverage and produces an unlimited quantity of DNA matrix. It could be widely used for isolation of genes of interest, construction of physical map, genomic studies between crop and model species, in alternative to macroarray hybridization.

3D pools are yet available for various libraries ie for wheat, tomato and pepper BAC libraries, and other BAC libraries are under process of being pooled. These pools are available to the scientific community, as well as screening services.

Partners :