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Clickable genomics
Plans for virtual plant posted
  
By
Edward R. Winstead



We are not talking about seed money. Millions of dollars probably will be spent trying to create the first virtual plant, an Internet tool that scientists might use to study the role of every gene and protein in the life of a plant. The goal of developing and posting the tool on the Web by the year 2010 is perhaps unrealistic, but the project's planners know this. They don't care.

"We decided to think big," says Joanne Chory, a Howard Hughes Medical Institute investigator at The Salk Institute for Biological Studies. "The ultimate goal is a 'clickable' plant." The idea is that researchers can visit a Web site and click through every stage of plant development from when a seed germinates to when the next generation falls off the mother plant. Along the way, they witness the inner workings of cells in the plant Arabidopsis thaliana. This species has served as the laboratory mouse of botanical research. see What Makes Plants Grow?


Click through a plant's life

The complete sequence of the Arabidopsis genome is expected this summer. Then begins the monumental task of identifying the function of some 25,000 Arabidopsis genes, an effort that could lead to innovations in agricultural research. After genes come proteins, whose precise roles will have to be defined if researchers are to use the tool for studying protein-protein interactions in the virtual Arabidopsis cells.

The strategy for achieving the clickable plant grew out of an international workshop meeting at The Salk Institute in January. The workshop, which was led by Chory and Joseph Ecker, of the University of Pennsylvania, produced a draft report called The Project 2010. The draft is posted on the Internet (see below) and appears in the June issue of the journal Plant Physiology.

In recent weeks, project leaders have sought comment on the paper through e-mail, scientific meetings and message boards. Anyone with an opinion is invited to attend a plant genomics meeting in Madison, Wisconsin, in late June.

The final report will be submitted later this year to the National Science Foundation, which has taken the lead in funding plant genome research, according to Chory. The NSF sponsored the January workshop and essentially asked plant scientists where the field ought to be in a decade. "The clickable plant is where we want to be in ten years," says Chory.


Plant genomics: reality becomes virtual

National Science Foundation officials will use the report to raise funds. Chory predicts that financial support will ultimately come from a multi-agency coalition involving the NSF, the US Department of Agriculture, and Department of Energy. As with the sequencing of the Arabidopsis genome, building the virtual plant will be a collaborative effort involving laboratories around the world.

The authors of the report break the project into what the collaborators might be able to accomplish in three-year increments. Nonetheless, building a user-friendly device that allows scientists to track the activity of a single gene in all cell types over the course of a plant's life cycle is a tall order. Especially over the course of just ten years. Determining the roles of thousands of genes and proteins, how they interact, and creating the software to turn databases into the virtual plant will take time. Still, if anyone knows that the biggest redwood tree was once a seed in the soil, plant scientists do.

For the draft Project 2010 report visit http://www.arabidopsis.org/workshop1.html

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Chory, J. et al. Functional genomics and the virtual plant: a blueprint for understanding how plants are built and how to improve them. Plant Physiol 123 (June 2000).
 

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