Arabidopsis--A Model Plant Genome
Tissue-cultured Arabidopsis thaliana.
An ambitious international venture to decode nearly all of the genetic
material in a flowering plant called Arabidopsis thaliana--a member of
the mustard family--is speeding ahead of schedule. And the project is already
hastening the discovery of important genes in crop plants.
A. thaliana, also known as mouse-ear cress or thale cress, has become
a workhorse of plant biotechnology because it has only a small amount of
genetic material. A small genome helps simplify the task of determining the
exact sequence, or order, of the four chemical subunits that make up genetic
material or DNA. Every plant gene is composed of a unique sequence of at least
a thousand of these subunits, or bases.
Scientists sleuthing Arabidopsis originally estimated that they would
finish their precedent-setting task by 2004, says molecular biologist
Athanasios Theologis. He directs the Arabidopsis sequencing project at
the ARS/University of California at
Berkeley Plant Gene Expression Center in Albany, California. Now, researchers
expect to finish by 2000, giving the world what has been described as "the
first essentially complete catalog of all the genes involved in the life cycle
of the typical plant, from seed to flower to fruit."
Theologis and colleagues at Stanford University in Stanford, California, and
the University of Pennsylvania in Philadelphia use an approach called
high-throughput DNA sequencing. It is among the newest, cheapest, and fastest
ways to find out the sequence of base units on the long strands of tightly
coiled DNA in the chromosomes of Arabidopsis.
Once the sequence of bases is known, it is promptly posted on GenBank, an
up-to-the-minute Internet compilation that also displays mouse, human, and
other sequences. Scientists can use GenBank to look for sequences other
organisms have in common. Because similarities in sequence often indicate
similarities in function, searching for sameness via computer quickens the
discovery of a gene's function.
Once biotechnologists discover the sequence and function of a gene, they may
be able to move useful genes into plants that lack them, such as a gene for
disease resistance, for example. Or they might be able to rebuild a gene to
boost its effectiveness.
Theologis and co-researchers have already discovered about 500
Arabidopsis genes. Currently, the team sequences about one gene a day.
High-throughput DNA sequencing offers that payoff because it focuses on finding
sequences first and leaves the question of a gene's function for later.
In contrast, the conventional approach begins by investigating a function or
trait first, then finds the gene responsible for the trait, and finally decodes
the gene's sequence. That one-by-one approach, says Theologis, costs millions,
while finding a gene with high-throughput DNA sequencing averages only a modest
$2,000 per gene. Theologis expects the price to drop even lower.
The National Science Foundation, U.S. Department of Energy, and ARS are
funding the work at Albany. Foundation and Energy Department funds are, in
addition, going to Stanford, Philadelphia, and four other U.S. labs. Scientists
in Japan and Europe are also part of the quest to unlock all of the sequences
in the Arabidopsis genome.--By
Marcia Wood, Agricultural
Research Service Information Staff.
Athanasios Theologis is at the
USDA-ARS/University of California at Berkeley
Plant Gene Expression Center, 800
Buchanan St., Albany, CA 94710; phone (510) 559-5911, fax (510) 559-5678.
Visit the Plant Gene
Expression Center's Genome Sequencing Laboratory
"Arabidopsis--A Model Plant Genome" was published in the
January 1999 issue of
Agricultural Research magazine.