Adaptation to the environment has a stronger effect on the genome than
anticipated
Faster growth, darker leaves, a different way of branching - wild
varieties of the plant Arabidopsis thaliana are often substantially
different from the laboratory strain of this small mustard plant, a favorite
of many plant biologists. Which detailed differences distinguish the genomes
of strains from the polar circle or the subtropics, from America, Africa or
Asia has been investigated for the first time by research teams from
Tübingen, Germany, and California led by Detlef Weigel from the Max Planck
Institute for Developmental Biology. The results were surprising: The extent
of the genetic differences far exceeds the expectations for such a
streamlined genome, as the scientists write in this week?s edition of
Science magazine.

To track down the variation in the genome of the different Arabidopsis
strains, the researchers compared the genetic material of 19 wild strains
with that of the genome of the lab strain, which was sequenced in the year
2000. Using a very elaborate procedure, they examined every one of the
roughly 120 million building blocks of the genome. For their molecular
sleuthing they used almost one billion specially designed DNA probes. "All
together, these probes would have seven times the length of human genome,"
illustrates Weigel the extent of the project. The data were evaluated with
several specially designed statistical methods, including a variant of
machine learning.

The result of this painstaking analysis: on average, every 180th DNA
building block is variable. And about four percent of the reference genome
either looks very different in the wild varieties, or cannot be found at
all. Almost every tenth gene was so defective that it could not fulfill its
normal function anymore!

Results such as these raise fundamental questions. For one, they
qualify the value of the model genomes sequenced so far. "There isn?t such a
thing as the genome of a species," says Weigel. He adds "The insight that
the DNA sequence of a single individual is by far not sufficient to
understand the genetic potential of a species also fuels current efforts in
human genetics."

Still, it is surprising that Arabidopsis has such a plastic genome. In
contrast to the genome of humans or many crop plants such as corn, that of
Arabidopsis is very much streamlined, and its size is less than a twentieth
of that of humans or corn?even though it has about the same number of genes.
In contrast to these other genomes, there are few repeats or seemingly
irrelevant filler sequences. "That even in a minimal genome every tenth gene
is dispensable, has been a great surprise," admits Weigel.

Detailed analyses showed that genes for basic cellular functions such
as protein production or gene regulation rarely suffer knockout hits. Genes
that are important for the interaction with other organisms, on the other
hand, such as those responsible for defense against pathogens or infections,
are much more variable than the average gene. "The genetic variability
appears to reflect adaptation of local circumstances," says Weigel. It is
likely that such variable genes allow plants to withstand dry or wet, hot or
cold conditions, or make use of short and long growing seasons.

Such genome analyses of unprecedented details will allow a much better
understanding of local adaptation, and this was indeed one of the main
reasons for conduction the study. "By extending these types of studies to
other species we hope to help breeders to produce varieties that are
optimally adapted to rapidly changing environmental conditions," explains
Weigel. He is already collaborating with the International Rice Research
Institute (IRRI) in the Philippines to apply the methods and experience
gathered with Arabidopsis to twenty different rice varieties.

How environment and genome interact is also the goal of new, even more
powerful methods. While the technology used so far can only identify genes
that have changed or are lost relative to the reference genome, direct
sequencing of the genome of wild strains will allow the detection of new
genes. The plan is to decipher the genomes of at least 1001 Arabidopsis
varieties. A new instrument, with which the entire genome of a plant can be
read in just a few days, is already available. Still missing are the
computational algorithms to interpret the anticipated flood of data.

Researchers from Tübingen who contributed to the study include Richard
Clark, Stephan Ossowski and Norman Warthmann from the MPI for Developmental
Biology, Georg Zeller and Gunnar Rätsch from the Friedrich Miescher
Laboratory of the Max Planck Society, Gabriele Schweikert and Bernhard
Schölkopf from the MPI for Biological Cybernetics, and Daniel Huson from the
University Tübingen.

Researchers from California who contributed to this study include
Huaming Chen, Paul Shinn and Joseph Ecker from the Salk Institute,
Christopher Toomajian, Tina Hu and Magnus Nordborg from the University of
Southern California, and Glenn Fu, David Hinds and Kelly Frazer from
Perlegen Sciences, Inc.

Original work:

Richard M. Clark, Gabriele Schweikert, Christopher Toomajian, Stephan
Ossowski, Georg Zeller, Paul Shinn, Norman Whartmann, Tina T. Hu, Glenn Fu,
David A. Hinds, Huaming Chen, Kelly A. Frazer, Daniel H. Huson, Bernhard
Schölkopf, Magnus Nordborg, Gunnar Rätsch, Joseph R. Ecker, Detlef Weigel
Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis
thaliana
Science, July 20, 2007

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