Draft Report

International Workshop “Towards Building a Global Rice Gene Machine”

CSIRO Plant Industry, 11-12 November 2002

Report on the Workshop by N.M. Upadhyaya (Workshop Convenor)

 

 

Following the success of the rice genome sequencing, the next emphasis is on determining the function of the predicted 40,000 rice genes. We organised an international workshop “Towards Building a Global Rice Gene Machine” on rice functional genomics, focussing on insertional mutagenesis as a resource for assignment of gene function. The main objective of this workshop was to ensure greater collaboration between groups to share resources and tools to accelerate progression towards a unified database. Initial discussions were held on a framework for web based complete rice functional genomics database and stock centres.

 

31 overseas delegates, 81 Australians including 47 from CSIRO Plant Industry and 73 remote online observers participated in this workshop. We have set up a workshop website http://www.pi.csiro.au/grgm02/home.htm. We also have a Media Server installed at http://grgm.pi.csiro.au/home.htm and a download centre at http://grgm.pi.csiro.au/dload.htm for recorded web telecast of the workshop for the benefit of online observers. We have also set up a bulletin board (http://www.pi.csiro.au/grgm02/
participantshome/forum/) for active communication among participants during and after the workshop.

 

The workshop was comprised of 12 sessions. The first three sessions dealt directly with gene knockouts using different systems and the fourth session was on “Gene Silencing”. We did include other functional genomics tools - “Expression Profiling”, “Activation Tagging” and “TraitMill” in sessions 5 and 6. Session 7 was devoted to case studies of gene identification using gene knockouts. As bioinformatics is an integral part of functional genomics in general and the “Global Rice Gene Machine” in particular, session 8 was a presentation-cum-panel discussion to facilitate common ground for intra- and inter-system unification and information sharing. In session 9, the logistics of a possible “Global Rice Gene Machine” were discussed by panel members representing different research groups. As we had more than 70 remote online observers registered to this workshop, session 10 was devoted to questions and feedback from these remote observers. We also had a session devoted to other new initiatives and possible new comers to the field of functional genomics (session 11). The last session (session 12) was a panel discussion “Where to from here?” to discuss strategies required for the efficient delivery of a “Global Rice Gene Machine”  

 

This Workshop was partially funded by the Australian Government Department of Education, Science and Training's Frontiers of S&T Missions and Workshops component of the Innovation Access Program, administered by the Australian Academy of Technological Sciences and Engineering and we greatly appreciate the support. We also wish to acknowledge the support from Rural Industries Research and Development Corporation (Canberra, Australia), CRC for Sustainable Rice Production (Yanco, Australia), NSW Agricultural Genomics Centre (Wagga Wagga, Australia) and the French Embassy (Canberra, Australia).

 

High lights of the workshop:

 

  1. There are more than ~150,000 T-DNA tagged lines (with ~2 copies of T-DNA/line), 40,000 Ds tagged lines and 50,000 tos17 lines (with ~10 copies of tos17/line) in existence.
  2. Only 5% of the flanking sequences have been rescued so far.
  3. Ds tagging efficiencies are  ~4-5% in any screening population.
  4. Unification of flanking sequence tag (FST) databases is probably not possible unless some sort of filtering is put in place to unify different databases for easy back tracing.
  5. A need for a unified way of describing the mutant phenotypes or gene ontology was felt by all the participating groups.
  6. Bioinformatics requirements for the Global Rice Gene Machine were also discussed. The need for an open source system was stressed by Bill Crosby. Possibility of incorporating FST data into INE was discussed. RGP’s Bal Antonio said that RGP is trying to set up a new project to do this.
  7. Logistics of a possible “Global Rice Gene Machine” was discussed and the recommendations were:-

(a) individual groups are to deposit their FSTs to public databases,

(b) individual groups are to put the information on FSTs on their respective websites only if they can supply the corresponding seed materials for research use by the scientific community,

(c) There should be several stock centres ideally maintained by the insertion line producers,

(d) Each group to setup committees for lobbying for government funding for support for the “Global Rice Gene Machine”.

(d) As a publicly funded research organization IRRI to push forward the agenda for an “International Consortium on Rice Functional Genomics”.