Salk news: Gene chips and crop yield

October 31, 2003

La Jolla, Calif. -- A study led by the Salk Institute and the University of California at Berkeley has found new methods to identify functional genes in the common mustard weed Arabidopsis. This technology may lead to the development of new ways to modify plants to grow faster, produce more food and resist disease.

The study, which appears in the Oct. 31 issue of Science, led by Joe Ecker, Salk professor of plant biology, and Athanasios Theologis, adjunct professor at UC Berkeley and senior scientist at the Plant Gene Expression Center of the USDA's Agricultural Research Service, identified directly the existence of protein-encoding genes, in an advance over previous work that relied on computer predictions of what genes may exist in Arabidopsis. This identification for the first time confirmed experimentally the existence of nearly 6,000 genes, about one third of the genes that computer models could only suggest existed in Arabidopsis.

For plant researchers, the tiny mustard weed has become the equivalent of the fruit fly for their genetics research. Knowing these plant genes and how they work can allow researchers -- in a short period of time -- to use them to change the characteristics of other plants.

The findings also changed our understanding of computer-based genome projects, including the Human Genome Project as well as the ongoing effort to sequence every gene in Arabidopsis. These projects used computer analysis to point to likely genes and to estimate how large the genome would be. Scientists now are taking the next step; using direct experimental methods to determine whether the computerized estimates were correct.

"By putting the entire genome on gene chips, we found that the computers were wrong about a third of the time in identifying genes," said Ecker. "But we also found other genes we had not seen before."

The research teams placed the entire Arabidopsis genome, consisting of about 25,000 suspected genes, on six gene chips, and then analyzed the chips for any protein-making activity, the primary function of genes. They isolated one-third of the plant's genes, which will be publicly available for researchers to fix errors in the current blueprint of the genome.

"Arabidopsis has all the genes a plant needs," said Ecker. "All flowering plants are closely related, so the genes that produce various traits also are shared. It's possible, then, to take a gene for flowering from Arabidopsis and insert it into rice or poplar, and have that gene function."

"We eventually want to be able to understand the function of all the proteins within an organism," said Theologis. "If you know the correct gene structure, you can clone DNA to express and study proteins. This type of research eventually will lead to advances in proteomics."

Many of the researchers on this study were part of the team that sequenced the genome of Arabidopsis, nearly three years ago. The initial genome work and the current research are funded by the National Science Foundation, which established a project to identify an entire plant genome by 2010.

"Finding the genes that lurk in the DNA sequence sounds like an easy problem, but in fact is tremendously challenging," said Robert Last, program director of the NSF's plant genome research program. "Completion of the DNA sequence of a genome such as Arabidopsis is an important milestone towards understanding the function of every gene in the plant, and discovering the genes that can positively influence the productivity, nutritional and medical value of the plant to human beings."

Ecker and Theologis lead a team of 72 scientists from nine institutions in the United States and Japan on the project.
Sarah Yang, UC Berkeley

The Salk Institute for Biological Studies, located in La Jolla, Calif., is an independent nonprofit organization dedicated to fundamental discoveries in the life sciences, the improvement of human health and conditions, and the training of future generations of researchers. Jonas Salk, M.D., founded the institute in 1960 with a gift of land from the City of San Diego and the financial support of the March of Dimes Birth Defects Foundation.

Salk Institute

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