GARNet, Genomic Arabidopsis Resource Network

Karin van de Sande

Functional genomics are changing the way research is approached at a rapid pace. To enable UK researchers to make use of these new technologies, the BBSRC started the IGF (Investigating Gene Function) initiative. Within this initiative different programmes are carried out, developing tools and resources of functional genomics. Drosophila, microbial eukaryotes, Streptomyces, farm animals, cereals, Brassica and Arabidopsis comprise the range of organisms currently covered by the IGF initiative. The Arabidopsis programme, GARNet (Genomic Arabidopsis Resource Network) consists of a wide range of services and resources. GARNet is service based only: there is no biological research being carried out as part of GARNet apart from what is required for development of the project. GARNet is funded by the BBSRC for a period of three years, and received 5 million pounds.

Tools of forward and reverse genetics are being created at the Sainsbury Laboratory and the John Innes Institute. Ian Bancroft is constructing and screening libraries in large insert binary vectors. This service is ready to start, and applications for this service can be submitted to the steering committee, through the GARNet webpage at http://garnet.arabidopsis.org.uk. Jonathan Jones is creating a population of transposon mutagenised lines, with high insertion copy numbers. ATIS, the Arabidopsis Transposon Insertion Service run by Mike Bevan and Jonathan Jones will sequence insertion sites from single insertion mutant populations.

Transcriptome analysis is carried out in a collaboration between Sean May at the Nottingham Arabidopsis Stock Centre (NASC), David Lonsdale at the JIC, Norwich and Jim Beynon at HRI Wellesbourne. David and Jim will produce primers and clones to complement the existing EST collection and ultimately cover the entire transcriptome, while Sean will provide the community with arrays in macro (filter) and micro (slide) format. The service will consist of a complete labelling/ hybridisation/ analysis/ data-ÕminingÕ service that will be available from the first half of 2001. Proteome analysis, carried out by Paul Dupree at Cambridge University will analyse protein samples by 2D PAGE for the selection of proteins with altered abundance between samples. MS polypeptide identification will lead to gene identification. Metabolite profiling, (Mike Beale, IACR Long Ashton), will lead to the construction of a library of spectra of metabolites in Arabidopsis. The service is aimed at screening of mutants, tagged lines, or different treatments for changes in metabolite profiles.

GARNet will be organising three annual meetings, the first of which will take place at the University of York on October 2 and 3, 2000. The first meeting is aimed at introducing the different techniques and resources to people interested in functional genomics. This meeting is organised in collaboration with the Brassica IGF project. Some speakers have been invited, to show what sort of data they got, using similar tools. Similarly, to stimulate co-operation with international projects, and give participants of the meeting the chance to be informed about international efforts in functional genomics, several guests have been invited, from the American Arabidopsis Functional Genomics Consortium, AFGC, and from the German and French projects GABI and Genoplante. The meeting program and registration forms are available at the GARNet website http://garnet.arabidopsis.org.uk. We would like to stimulate attendance of post graduate students to this meeting and are offering a number of reduced fee places, on a first come, first served basis.