A Small Plant's Genome Has Huge Impact
Completing the first-ever plant genome means knowing plants well, really well.
July 23, 2004
Most people would consider Arabidopsis thaliana nothing more than a white-flowered weed, something they might see growing in an empty lot or along the roadside. But this unimposing member of the mustard family has changed the world of biology. Arabidopsis is the first plant to have its entire genome mapped. The feat, accomplished by an international team of researchers, is providing insights into all the worlds' 250,000 species of higher plants.
Over the last two decades, the National Science Foundation (NSF) along with several other U.S. agencies and an international cadre of partners, has funded an unprecedented effort in plant genome research. The initiative brought together thousands of scientists from across the globe. NSF's coordination helped ensure the results from each laboratory were usable by all researchers. Aided by breakthroughs in sequencing technologies and computer science, as well as remarkable cooperation among scientific groups, the Arabidopsis thaliana Genome Sequencing Project finished in 2000, four years ahead of schedule.
Now, biologists have a map of this flowering plant's genes, and they already know what some of the genes do. They know which set of genes controls the shape of the flower. They know some of the genes that make the plant resilient to salt stress, and some of the genes that make it susceptible to fungus.
And because of this lowly mustard weed, biologists are now predicting changes in all plant sciences. Changes that may allow crops to be grown without pesticides, or to be grown in poorer soil. Changes that could help native plants fight invasive species. And changes that may well bring about new medicines for humans.
A Giant Puzzle
Mapping a genome is not unlike putting together a jigsaw puzzle, only a few thousand times more complex.
In the 1980s, Arabidopsis was one of many plant genomes being pursued in various laboratories across the country. But with NSF's support and encouragement, biologists came together, selecting Arabidopsis as the plant to focus on.
Arabidopsis, it turns out, has several traits that make it ideal for genetic research. For one thing, it's small and easy to cultivate. The plant grows to a height of about 20 centimeters, normally flowers in 3-4 weeks, produces many seeds and can be grown inexpensively on a table with a florescent light. Arabidopsis also has a small genome and numerous mutations are readily available.
In 1990, NSF helped launch the Multinational Coordinated Arabidopsis thaliana Genome Research Project. The goal was easily expressed if not easily attained: to understand a plant at its genetic level from roots to tips, and everything in between. The project involved hundreds of top biologists from around the world, all of whom shared their findings with each other and the public.
"Beyond the sequence itself, one of the real victories of this project was the challenge of coordination of this international effort," says Joe Ecker, a biologist at the Salk Institute and one of the lead investigators. "With NSF's support, a major international community-driven effort was launched to sequence the first plant genome. We had no idea that we could make it work. However, because we had a common goal for plant biology, it was relatively easy to change the culture to fit a single unified vision."
In 1996, further coordination was needed. At that point, international groups came together as the Arabidopsis Genome Initiative (AGI), and representatives met at NSF to agree on a collaborative approach. AGI divided up the plant by chromosomes, the cellular structures that house the genes. Different groups sequenced the genes on different chromosomes. In total, biologists found more than 25,000 genes along the plant's five chromosomes.
"Completing the Arabidopsis genome was a tremendous accomplishment that was only a dream five years earlier," says Chris Town, associate investigator at The Institute for Genomic Research (TIGR). TIGR laboratories completed the sequencing of chromosome 2 and later parts of chromosomes 1 and 3. "Much more important than the technical challenges of the assembly is the wealth of information that comes from the delineation of genes and their functions."
Arabidopsis thaliana is not only an ideal laboratory plant, it turns out to be an ideal reference for other plants. All higher plants evolved only about 150 million years ago, so at a genetic level, they are still very similar.
The Arabidopsis genome provides the raw material to learn about fundamental aspects of all plant growth including flowering, root growth, hormone action and response to environmental signals.
For example, Rick Amasino of the University of Wisconsin is using Arabidopsis to study vernalization. There are many plant species that require vernalization -- the exposure to the long cold of winter -- to flower. Amasino's group discovered a gene in Arabidopsis encoding a flower repressor. "The expression of the gene keeps this strain of Arabidopsis from flowering in its first year," he explains. "Winter turns the gene off." When spring arrives, the gene is still turned off and the plant flowers. Amasino knows that other plants in the cabbage family have a similar gene. He is beginning to look at other plant families.
Eduardo Blumwald of the University of California-Davis, is using the genome information to identify and manipulate Arabidopsis' salt tolerance gene. This gene, when turned on, allows Arabidopsis to grow in salty soil. Blumwald found the corresponding gene in tomato plants. When the gene is turned on, tomatoes are suddenly a viable crop in salt-filled areas, such as the Fertile Crescent of the Middle East.
Shauna Somerville of the Carnegie Institute of Stanford University is investigating Arabidopsis' infection with a powdery mildew disease, learning how the host interacts with that fungus to contract the disease.
And environmental biologists at the University of Montana are looking at how Arabidopsis stands up to invasive species, such as knapweed.
While some of these projects started as part of the original Genome Research Project, they continue as the NSF-funded Multinational Coordinated Arabidopsis thaliana Functional Genomics Project. The project's aim is to identify the function of all Arabidopsis genes by 2010, but the overall mission for the little mustard weed is even bigger.
By understanding Arabidopsis, the Arabidopsis 2010 biologists write in their mission statement, we can start to understand other plants. And by understanding other plants, we can start to address the big issues, such as food for an expanding world population and ways of protecting our environment for future generations.
-- Amy S. Hansen
Plant Genome Research Program
Dept. of Energy
U.S. Dept. of Agriculture
The Arabidopsis Information Resource (TAIR): http://www.arabidopsis.org
Plant Genome Research Outreach Portal: http://www.plantgdb.org/pgrop/pgrop.php
View a video explaining the project: http://www.nsf.gov/od/lpa/news/press/00/pr0094.htm
America's Investment in the Future-Arabidopsis: http://www.nsf.gov/od/lpa/news/publicat/nsf0050/start.htm
NSF Directorate for Biological Sciences Arabidopsis thaliana Progress Reports: http://www.nsf.gov/bio/reports.htm