4th International Rice Genetics Symposium (IRGS)

Rice Functional Genomics Workshop

Introduction

A Functional Genomics Workshop was held 25 October 2000 as part of the Fourth International Rice Genetics Symposium (IRGS) at IRRI. Mike Gale and Hei Leung served as moderators. More than 200 people attended the 90-minute meeting. The objective was to develop details of collaboration on the three activities brought forward during the San Diego meeting: (1) developing an information node, (2) promoting the sharing of genetic stocks, and (3) developing microarray resources.

Mike Gale opened the workshop indicating the need for more international collaboration in rice functional genomics because of the uniqueness of rice as a food crop and as a model system. Furthermore, due to the scale and costs of many genomics technologies and the emerging need for phenotyping, there are many incentives for the research community to share resources and combine expertise.

Topics discussed

Web site information node

Hei Leung reported on the creation of a Web site (http://www.cgiar.org/irri/genomics/ (April 2003 - site changed to www.iris.irri.org/IRFGC, i.e., this site) to facilitate communication and called for active participation. Research groups with interest in participating in the working group were requested to post a summary of their research interest on the Web site and provide links to their own Web sites. The information flow and database linkages are expected to improve the usefulness of the site.

Genetic stocks

At the IRGS, representatives of research laboratories from Asia, Australia, Europe, and the United States reported on the development of mutant stocks for functional genomics research. With the growing wealth of genetic stocks, the group felt that it would be useful to have a general inventory of these resources posted on the Web site. Research groups will be contacted to gather information on their mutant stocks that will be of general interest to the research community.

The group also identified several factors that potentially limit the sharing and distribution of genetic materials, particularly for transgenic insertion mutants. Several research group representatives (Gynheung An of Pohang University of Science and Technology, Korea; Andy Pereira of Plant Research International, the Netherlands; and Andrzej Kilian of CAMBIA, Australia) pointed out the obstacles concerning the distribution of the insertion mutants:

Limited seed
Distribution costs
Special conditions needed to propagate transgenic materials
Regulatory and quarantine requirements in the movement of rice seeds between countries

These concerns together represent a significant burden on the providers of genetic stocks on a large scale. Hei Leung proposed two steps to initiate the sharing process. First, collaborating laboratories can consider exchanging a small amount of seed with specific traits in mind. For example, insertion lines with known flanking sequences at the insertion sites can be shared among collaborators to conduct selective phenotyping. Second, the working group can develop a network system to propagate and distribute selective stocks.

Gurdev Khush indicated that since IRRI routinely distributes rice germplasm and has considerable experience in the safe movement of rice seed, IRRI can explore extending this service to mutant stocks. However, in the case of transgenic mutants, IRRI must also assess its capacity to handle a large quantity of materials. IRRI will report to the group on its ability to assist in the propagation and distribution of available mutant stocks.

Development of Microarray Resources

Several research groups reported on the development and applications of microarray analysis in rice at the IRGS. For example, Hans Bohnert of the University of Arizona described the progress made in using microarray to analyze gene expression under abiotic stresses. Shoshi Kikuchi of the National Institute of Agrobiological Resources, Japan, discussed the microarray project under the Japan Rice Genome Program. Novartis Agriculture Discovery Institute Inc. (NADII) announced that a rice gene chip carrying 23,000 unique genes will be available for research by January 2001.

The group discussed the timeliness and benefits of developing microarray facilities that would be made available to the research community. Three main points emerged from the discussion:

Microarray technology is still far from routine and technically demanding. It may be too early for an institute like IRRI to invest at this point unless strong technical support is available.
The technology has multiple applications and significant technical improvements have been made over the past year. It would be a worthy investment to broaden access to this technology.
Microarray technology requires an abundant supply of cDNA and ESTs. Thus, it is important for the research community to collaborate to make this resource available.

To study the issues of access, an ad hoc discussion group—Hans Bohnert, Andrzej Kilian, Qifa Zhang, Susan McCouch, Akhilesh Tyagi—was formed to further analyze the costs and benefits of developing a publicly accessible microarray facility and how to promote sharing of needed resources. Hans Bohnert will continue to lead the group discussion and report back to the working group with recommendations. This will be particularly useful to IRRI as it is considering investment in a microarray facility with the goal of providing research support to many collaborating partners in Asia.

Overall Impression

A growing interest and commitment by the public and private research communities toward collaboration are evident. Throughout the IRGS, many research groups expressed interest in participating in the working group. The three activities defined at the San Diego workshop have provided the focal points for the Working Group to concentrate its efforts on. The discussion at the IRGS workshop has provided important guidance toward sharing genetic stocks and microarray resources.

This brief summary captures the key points raised at the workshop. If you see important points missing, please let us know by email (h.leung@cgiar.org) or through the “comments and opinions” mailbox (genomics@cgiar.org) on the working group WWW site. A final version of the summary report will be included in the proceedings of the IRGS.

We wish to thank all the participants of the workshop for their active participation and thoughtful discussion. Your continuing inputs and ideas are important to advance the agenda of the working group. Thanks for your support.

Prepared by Hei Leung and Mike Gale