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National Center for Genome Resources Launches Agricultural Database Project


SANTA FE, NM--When public funding for plant and animal genomics research catches up with that for the human genome, which Bruno Sobral is counting on, one inevitable consequence will be "data poisoning." That's what Sobral, a geneticist hired last year to lead agricultural genomics at the National Center for Genome Resources here, calls the deluge of genomic information ramped up research will generate.

Already, scientists face insuperable banks of unintegrated agricultural data. Proposed 1999 federal Department of Agriculture and National Science Foundation budgets indicate they'll get support to product more data soon. Plop $200 million a year into the public research coffers, and you're instigating an overload, Sobral said.

Sobral's team at NCGR is getting a head start controlling the storm by coordinating bioinformatics support and creating a cross-referenced database for agricultural genomics projects worldwide. "We're developing a plan in anticipation of the deluge," Sobral told BioInform.

In January, NCGR launched a phytophthora genome initiative (PGI), the first of many international agricultural genomics collaborations, Sobral said. So far, five phytophthora research groups, hailing from Peru, Holland, Argentina, California, and Ohio, have joined the PGI consortium, with NCGR bioinformatics at the core.

One Late Blight Databank

NCGR aims to put agricultural genomic data in the public domain so researchers can access it all at once, Sobral explained. "Databases of agricultural data that exist now don't talk to each other," Sobral said. "Our program will allow access in one place."

But the project's significance doesn't end there. Ultimately Sobral sees agricultural genomics research minimizing needs for fertilizer and pesticide chemicals, securing a safer, cleaner food supply, promoting less environmentally degrading farming techniques, and boosting worldwide food production.

"Agricultural genomics is just as much about human health as the human genome project," Sobral said. It's why he's confident increases in public funding for agricultural genomics will render his project vital.

The phytophthora initiative will gather information from labs around the world studying late blight, the pathogenic fungus famous for causing the Irish potato famine, and still responsible for billions of dollars worth of damage annually to potatoes--the world's fourth-largest crop.

An ongoing, successful New Mexico State University National Biotechnology Informa tion Facility collaboration is a model for Sobral's team.

Through that arrangement, underway more than a year now, NCGR formed a plant secondary metabolic archive (PlaSMA)--an integrated system to allow storage and query of data from secondary metabolism--that will be posted on the internet. It also taught bioinformatics courses.

For phytophthora and genomes selected for future projects, NCGR will develop AGDB, a software series that will make data accessible via the World Wide Web (at ) and allow users to cross-reference organisms with any browser. And NCGR will provide its consortiums with an education. "It's in our interest that the people we work with understand bioinformatics," Sobral said.

But for the most part, NCGR's role will be information handling. "That's our strength, and that's where the huge deficit is," said Sobral.

Funding and the Future

To date, the PGI consortium includes: the University of Cali fornia, Davis; the International Potato Center in Peru; Holland's Wagenin gen Agricultural Univer sity; Ohio State University; and Argentina's Instituto Nacion al de Tecnologia Agropecuaria. Sobral selects collaborators based on compatibility with the center's goals, and based on the economic or industrial appeal of their projects.

"The groups that form their questions best are the ones we'll answer first. We need to be choosy. Economically more important projects will become first choice. Big industrial interests will be a priority," he said.

Sobral said the center has close ties among industry leaders who will be invited to sit on a steering committee. The project will offer leading corporations in agricultural genomics--Monsanto, DuPont, and Novartis--the opportunity to make their discoveries public, Sobral said.

Aside from current US Depart ment of Defense and New Mexico State University grants, NCGR relies on a large endowment set up with proceeds from the center's sale of Molecular Informatics to Perkin-Elmer in November, 1997. Still, Sobral is busy writing grant proposals with the PSI consortium: one went already to the World Bank; another will be sent to the National Science Foun dation, he said.

Beyond a five-year plan, Sobral said he can only guess how the project will evolve. He shared this "pie in the sky" projection: "Some day technology could allow someone who breeds corn to walk inside a virtual plant and idealize--from the time it takes to mature, to the type of starch it's made of--what kind of plant they want; the system would show what the end DNA would look like, and the breeder would generate the blue print."

Sobral said he has had preliminary discussions about providing bioinformatics support for consortiums of poplar, cotton, and shrimp genome researchers. As technology advances, he said, "Who knows? It will be an evolving project."

One thing is for sure: NCGR's staff will more than double over the next few years. At press time the center was in negotiations to move across town into office space three times its current capacity. A spokeswoman said the center has been "interviewing nonstop" in recent weeks to fill 10 positions in the agriculture project. Sobral said another 12 slots will open up in the spring, and by the project's third year he said he expects to add 40 staff.

The possibilities seem endless: "There are all the animals, plants, and aquaculture, and then all the pests and pathogens that cause problems for people trying to grow them," Sobral said. "Agriculture genomics is more broad and diverse than human."

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