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THALE cress, Arabidopsis thaliana, occupies a unique position in plant
science. Having enjoyed for decades the attentions of classical geneticists,
this unshowy, weedy relative of the cabbage is now set to play a key role
in efforts to understand the plant genome. Arabidopsis will be the first
higher plant to be systematically dissected at the molecular level.

With its unassuming ways, Arabidopsis seems an unlikely pioneer. Yet
several qualities render it exquisitely adapted to life in the genetics
laboratory. It is easy to grow and it thrives at a density that would choke
any less hardy plant. Under the right conditions, it sprints through its
life cycle in five weeks, setting seed with obliging liberality. Small wonder
that it has earned itself the nickname of the botanist’s fruit fly.

Arabidopsis achieves these feats with a degree of genetic economy bordering
on the miraculous. Its cells contain just 10 chromosomes arranged in five
pairs (wheat, by contrast, has 42 chromosomes). Each set of five contains
70 million building blocks (base pairs), according to the studies of Elliot
Meyerowitz and colleagues at the California Institute of Technology, Pasadena.
Cell for cell, Arabidopsis has a seventh of the DNA of the tomato, a seventieth
of the DNA of a pea. It sprouts from the earth with just five times as much
DNA as the lowly yeast cell. Such brevity makes it a superb model for research.

Decoding its entire genome is nevertheless a massive venture – a venture
that is ideally suited to international cooperation. At the moment collaboration
remains informal. ‘All the groups involved know each other and have talked
– and there’s an effort being made to avoid direct duplication,’ says Chris
Somerville at Michigan State University. Somerville believes that a more
formal structure for coordination will emerge later this year.

Some elements of the project are already at an advanced stage. Research
into patterns of inheritance in Arabidopsis has generated an excellent map
of its chromosomes, showing the position of 100 or so genes. More recently,
several teams have drawn highly detailed maps showing the whereabouts of
restriction fragment length polymorphisms (RFLPs). RFLPs are idiosyncrasies
in DNA that can be detected with chemical probes. For the genetic cartographer,
they act as chemical landmarks, pointing the way to genes. Because Arabidopsis
has such a small genome, many of its genes are close to a suitable landmark
– a circumstance that makes the genes easier to track down. To keep a sense
of scale, it should be said that ‘close’ means something like within 140
000 base pairs – a sizeable stretch of DNA, but a manageable one nevertheless.
Several of its genes have already been cloned.

Work is also under way to produce reference libraries made up of cloned
pieces of Arabidopsis DNA. The ideal is a complete set of overlapping fragments
covering the entire genome. Howard Goodman and his colleagues at Massachusetts
General Hospital have made such a library in the form of artificial ring-shaped
structures called cosmids, which can be propagated inside the standard biochemical
workhorse, the bacterium Escherichia coli. At Michigan State University,
Somerville has made a ‘YAC’ library – a library whose ‘books’ are in the
form of artificial yeast chromosomes. In this technique, researchers weld
very long segments of DNA from Arabidopsis to a scaffolding of yeast DNA
and introduce them into yeast cells, where they behave as extra chromosomes.
Somerville’s next task is to put the library in order, that is, to decide
how the cloned fragments of DNA are arranged along the chromosomes of the
living plant. Various groups around the world, including the one under Caroline
Dean at the AFRC’s Institute of Plant Science Research in Norwich, are collaborating
in this task as well as making additional YAC libraries.

Although such libraries are an essential prerequisite for methodical
sequencing, today’s researchers are more interested in scouring the libraries
for specific genes. Among the genes of interest to researchers at Norwich,
for example, are some of the most basic in plant biology – the genes that
control flowering and responses to daylength or temperature, or even the
structure of flowers and fruits.

Two ingenious techniques will help researchers to track down their genetic
quarry. Arabidopsis DNA mutates readily when seeds of the plant are dosed
with certain chemicals. When the seeds germinate, they grow into novel strains
with defective genetic equipment. Such mutants can be rescued, so to speak,
by using genetic engineering to provide them with an unmutated version of
the gene in question. If researchers have cloned a gene and need confirmation
of its function, they can install it in a suitable mutant and see whether
normality is restored.

A second way of creating mutations is to employ the services of transposable
elements – stretches of DNA that jump around genomes, disrupting any gene
that they happen to land upon. Researchers can then locate the disrupted
gene by searching for the chemical signature of the transposable element.

As Arabidopsis yields up its genetic secrets, there will be major implications
for agriculture. Researchers believe that Arabidopsis has much in common
at the molecular level with other higher plants, including major food crops
such as wheat, rice or maize. ‘It doesn’t have corn kernels,’ says Goodman,
‘but it is a flowering plant and many of its properties presumably are similar
– and that’s certainly been true with structural genes.’

And then there is the prospect of deciphering the complete genetic code
of Arabidopsis. The signs are that this will eventually happen. At Massachusetts,
Goodman is already organising some preliminary studies. ‘We’re starting
a fairly sizeable programme on that now, trying to look at methodology.
We’re certainly doing it now in regions of interest.’