First Plant Genome Sequenced: Salk Scientists Part Of International Effort

December 13, 2000

First Plant Genome Sequenced: Salk Scientists Part Of International Effort

December 13, 2000

La Jolla, CA – The first complete genome sequence of a plant appears in the current issue of Nature. Salk Professor Joseph R. Ecker, co-director of one of six contributing sequencing groups, expects the sequence to greatly accelerate efforts to improve the yield and hardiness of crop plants.

“The organism we used – the small mustard Arabidopsis – is a plant, not a model for plants like flies or worms are models for humans,” Ecker said, referring to the animals sequenced thus far. “Therefore, scientists can open up the Arabidopsis ‘reference book’ and apply that information directly to crops like wheat or rice.”

Arabidopsis became the gold standard for plant research in the 1980s for several reasons.

“It does the basic things that all plants do – grow, flower and turn light into chemical energy,” said Joanne Chory, a Salk professor and co-author on the study. “In addition, Arabidopsis is easy to grow in the laboratory and reproduces quickly.

“Arabidopsis also turns out to have a relatively small genome, which made the sequencing project feasible,” said Ecker. Arabidopsis contains five chromosomes; Ecker’s group contributed to sequencing and analysis of chromosome number 1.

Many crop plants contain duplicate, triplicate or even higher multiple genomes, probably an artifact of years of selective breeding. Individual genes from many of those plants, however, are closely related to Arabidopsis genes. And frequently Arabidopsis genes function when added to other plants.

“This means that you can take a gene for cold-resistance, for example, from Arabidopsis and put it into a strain of wheat and confer resistance,” said Ecker. “This ability makes the Arabidopsis sequence a very powerful tool for agricultural engineering.”

The plant sequence is expected to have implications for human medicine as well. Many genes that are mutated in human diseases are found in plants, and Arabidopsis may prove to be an effective model for screening therapeutic compounds.

“Because experiments can be done so quickly and cheaply in plants – much more so than in mice – large pools of chemicals could be tested for effects on various disease genes,” said Ecker. “One would move into animals for definitive tests, of course, but plants could be very useful in the initial screening.”

He added that because many pharmaceuticals come from plants, understanding the genes that control their synthesis will probably point toward ways of producing new drugs or improved versions of existing drugs.

Now that sequencing is completed, Ecker and his colleagues are part of the next initiative in plant genomics – determining what all the genes are and what they do. This phase of the project, dubbed the 2010 Project, is a ten-year National Science Foundation funded drive to decipher the functions of Arabidopsis’s approximately 25,000 genes. Efforts already are underway in Ecker’s laboratory.

“I’m extremely happy to see the sequence completed,” said Ecker. “It’s one end, but it’s also an entirely new beginning.”

Ecker and Chory are co-author and contributing author, respectively, on the study, “Analysis of the genome sequence of the flowering plant Arabidopsis thaliana”. Salk co-authors include Huaming Chen, Meng Chen, Christopher Kim and Paul Shinn. Ecker is also lead co-author on a study in the same issue, “Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.” Salk co-authors include Huaming Chen, Rosa Cheuk, Christopher Kim and Paul Shinn. The work was supported by the National Science Foundation, the U.S. Dept. of Energy and the U.S. Dept. of Agriculture.

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