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What Makes Plants Grow?
The Arabidopsis genome knows
By Bijal P. Trivedi

Featured Article.

It is an unremarkable spindly weed, with tiny, white, four-petalled flowers. It has no immediate agricultural importance, is not thought to cure any disease, and certainly has no future as a culinary delight, yet scientists in Japan, Europe and the United States are spending time and $70 million to complete the sequence of its genome by July.

Arabidopsis thaliana will provide scientists with an overview of the basic toolbox of genes needed for a flowering plant to grow. Researchers expect they will find genes they can tweak to increase the nutritional content and yields of food crops. These genes might also be used to coax plants to grow in salty or metallic soils, or in very hot or very cold climates.

Arabidopsis thaliana

The Arabidopsis Genome Initiative (AGI) began in 1996 when Japanese, European and American scientists established a plan to dissect the plant at the molecular level and identify all of its genes. About 84 percent of the genome is sequenced and the rest should be completed in the next four months, according to Samir Kaul, Project Leader of the Arabidopsis Sequencing Project at The Institute of Genome Research (TIGR) in Rockville, Maryland.

“In the old days, two or three years ago, we would find an interesting Arabidopsis mutant in the lab, and then there was the year-long haul to find the gene responsible for those physical characteristics,” says Steve Rounsley, formerly of TIGR, where Arabidopsis chromosome 2 was sequenced. Now, with the nearly complete Arabidopsis genome stored in a database, tracking down a gene responsible for a specific trait and doing the genetic experiments in the lab can all be done by one person in around a month, says Rounsley, of Cereon Genomics in Cambridge, Massachusetts.

Having the entire genome sequence of any organism accelerates the pace of biological research. While in graduate school, Rounsley recounted, it took four people five years to find and characterize 12 genes that were members of the same family. Today, using a database and bioinformatics, identifying genes will take only minutes—leaving more time for actually understanding the function of the gene.

Arabidopsis is a genomic minimalist

The DNA of Arabidopsis is made up of about 140 million bases, or genetic letters—adenine (A), guanine (G), and thymine (T) and cytosine (C)—which are parceled into five chromosomes arbitrarily numbered one through five. It is the arrangement of these bases into genes that make up the genetic instruction manual to create an organism. While 140 million pieces might sound like a lot, Arabidopsis has the smallest genome of any flowering plant, which is the main reason it was selected as a model organism for genome sequencing. Major crop plants like wheat and corn have genomes that are billions of bases long. Arabidopsis, by comparison, is a genomic minimalist.

Researchers believe genes found in Arabidopsis will be used to improve crops like rapeseed.

Evolutionarily speaking, Arabidopsis is considered to be a genetic model for more than 200,000 species of flowering plants, each of which shares a basic architectural foundation and similar biochemical processes. However, it is the different versions of these genes that determine when and where a plant will grow best and how it will look. Scientists have used Arabidopsis for the past 40 years as the model for finding a gene and have used it as a guide to find equivalent genes in other plants, such as rice, corn, potatoes or tomatoes. Researchers have already found genes in Arabidopsis that may be used to improve other crops.

Chromosomes 2 and 4 have been completely sequenced and combed by gene prediction computer programs. The two chromosomes, which represent about 30 percent of the Arabidopsis genome, contain an estimated 7781 genes. The function of about half these genes is unknown. The remaining genes bear a strong resemblance to genes found in other plants, animals and bacteria, giving a good indication of their role in the plant cell.

TIGR has classified 51 percent of the 4,037 genes found on Chromosome 2, based on comparisons to known genes. Of these, early estimates suggest that about 100 genes directly influence growth and development, 80 affect responses to pathogens like insects and fungi, and around 40 control responses to environmental stresses.

One use of these genes might be to insert them into other crop plants to provide “disease resistance, or to make them grow bigger and faster,” says Kaul. The other use is to provide basic knowledge on how plants grow and protect themselves from pathogens.

One of Arabidopsis’ most valuable features is its amenability to genetic tinkering—adding or subtracting genes. “Most of what you want to do is to disable genes one at a time,” and then examine what happens to the organism, says David W. Meinke, a plant geneticist at Oklahoma State University in Stillwater.

But knocking out specific genes, or creating random genetic mutations using chemicals like EMS, and examining the results are approaches that “have been done to death,” says Martin Yanofsky, of the University of California, San Diego, in La Jolla. The approach has been very productive but now with the genome sequence of Arabidopsis, “we are going to see a real revolution—the second wave of genetics,” says Yanofsky, whose team recently reported on SHATTERPROOF genes that may be of great value to farmers.

Many genes have eluded characterization because there is more than one copy in the genome, Yanofsky notes. One particularly surprising finding observed in sequences from chromosomes 2 and 4 was the amount of gene duplication. A huge piece of DNA, between four and five million letters long, was common to chromosomes 2 and 4. Thus, these two chromosomes share several hundred genes.

Geneticists often knock out only one of several copies of a gene, producing no noticeable change in the plant. When all the genes are sequenced, researchers will be able to seek and knock out all copies of a gene and determine its function, according to Yanofsky.

“The wonderful thing about this simple little plant is that it does almost everything that a more complex plant does—but it is a plant where one can really dissect a single process, do the tedious work, understand the basic science, and then ask what are the practical applications of this,” says Meinke.

Arabidopsis is small—it can be grown in a petri dish or flower pot. It has a short life cycle; within six weeks the seed germinates, grows to a height of up to 20cm, flowers, is pollinated and produces up to 5000 offspring—seeds. Given that today much of plant genetics focuses on altering genes and examining the offspring, it makes sense to use organisms with a short life span.

Genes that protect against heat, cold, and salt

One area of Arabidopsis research with broad applications is the search for genes that confer resistance to environmental stresses such as heat, cold, salty or metallic soils, or high ozone levels to name a few. Salt buildup from years of continual irrigation is a widespread problem for farmers; most plants will not grow in salty soils and finding a gene that provides salt tolerance would allow the land to become fruitful.

Researchers have also found mutated Arabidopsis plants that can withstand four times the level of aluminum that would cripple normal plants. Aluminum is the most common metal in the Earth’s crust and is a problem for up to 12 percent of the Earth’s cultivated land. The metal prevents root growth, and with stunted roots the plant is unable to absorb enough nutrients from the soil and dies. Using genetic maps, scientists know that the mutated gene responsible for this tolerance lies on chromosome 1, now they just need to find it.

Rising levels of ozone is a big and growing problem because it weakens a plant’s immune system, producing brown spots on leaves. High levels of the gas kill plants, says Nina Federoff, of Pennylvania State University in University Park. Federoff’s team is studying Arabidopsis to find out which genes are turned on or off by different levels of ozone.

“With unexpected climatic [and environmental] changes, how do we arm ourselves best for changes we can’t predict,” asks Federoff. One way is to first “understand what allows plants to survive in different environments” and then create plants which are more resistant, she says.

“Given the rate of population growth and no new agricultural land, you need to get more from what you have,” says Federoff.

See related GNN article
»SHATTERPROOF genes in Arabidopsis are good news for agriculture

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Lin, X. et al. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402, 761-768 (December 16, 1999).
Mayer, K. et al. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature 402, 769-777 (December 16, 1999).

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