By Salvatore Salamone
March 10, 2003 | The role of bioinformatics in plant molecular biology is being elevated to higher levels of importance, thanks to new funding priorities of federal and international plant genomic groups.
"We are going to require that every project [the U.S. National Plant Genome Initiative (NPGI)] supports must have an informatics component," said Mary Clutter, co-chair of the Interagency Working Group (IWG) for Plant Genomes, the group that establishes NPGI funding and research priorities. Clutter's comments came in a speech at the Plant and Animal Genomics XI Conference held in San Diego, Calif., earlier this year.
The long-term goal of the NPGI is to understand the structure and function of genes in plants that are important to agriculture, environmental management, energy, and health. The directive to require an informatics component in all future research proposals is a new provision set out in the NPGI's five-year plan (covering 2003 to 2008), which was released earlier this year.
Currently, federal funding for the NPGI is about $100 million a year. About two-thirds comes from the National Science Foundation; other agencies in the IWG include the U.S. Department of Agriculture,National Institutes of Health, Department of Energy, Office of Science and Technology Policy, and Office of Management and Budget.
To get a sense of exactly what type of informatics work the agencies are looking for in new proposals, one need only look at the specifications spelled out by the National Science Foundation for its Plant Genome Research Program. The NSF tells researchers applying for grants: "This year's competition focuses on functional genomics, the identification of functions of a pathway or a cluster of genes at a genomic scale, and new informatics tools to disseminate, access and analyze massive dispersed datasets."
This increased emphasis on plant bioinformatics is not confined to the U.S. Earlier this yearthe Australian government set aside $18 million to build the National Centre for Plant Functional Genomics.
The center will be based at Adelaide University, will employ about 100 scientists to start, and will focus on developing molecular breeding technology for wheat, barley, and other grains. Details on the center's timetable and the specific informatics technologies it will use are not yet available.
To date, plant genomic efforts have focused on sequencing Arabidopsis and plants that feed the world, like rice, wheat, legumes, the tomato, and maize. Rice sequencing is probably the furthest along. Two private efforts that used the shotgun approach to sequencing rice have already been published in Science (Vol. 296, April 2002). With Arabidopsis, there is an international effort under way called Arabidopsis 2010 that seeks to fully sequence the plant by the end of the decade.
Gleaning from New Fields
Besides the emphasis on informatics in the new NPGI plan, Clutter noted that there is also need for more education, training, and collaboration in the field. And the NSF guidelines for grant submissions mention that the agency is looking for the "development of research resources and tools that would enable a broad community of investigators to participate in plant genome research."
Specifically, the type of collaboration that is desired will bring together traditional plant biologists with bioinformaticians. A good example of this type of collaboration is the
New York Plant Genomics Consortium (NYPGC), which includes the New York Botanical Garden (NYBG), New York University, Cold Spring Harbor Laboratory, and the American Museum of Natural History.
In such collaborative environments there are benefits to all parties. Bioinformatics techniques like high-throughput sequencing "can be used to expand the repertoire in the lab when doing plant molecular biology," said Dennis Stevenson, NYBG’s vice president of botanical science, at a recent conference at the Botanical Garden.
To make such technology available to more plant biologists, the NYPGC brings together some unique resources. For example, even though the New York Botanical Garden is building a new state-of-the-art laboratory to replace its current 50-year-old lab, NYBG's staff might still need to run some tests that would benefit from high-throughput bioinformatics technology available only at Cold Spring Harbor.
And similarly, "Cold Spring Harbor isn't going to go out and [acquire] its own 7-million plant collection," Stevenson said.