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Colorado State University, The Institute for Genomic Research, Perlegen
Sciences, Inc. and the International Rice Research Institute are joining
forces to unlock the genetic secrets of rice, information that could improve
rice crops and help address hunger and malnutrition for millions of people,
May 2006.

Rice is the world's top food crop and the principal source of nourishment
for nearly half the world's population, particularly people in the poorest
but fastest growing nations.

The study will focus on the genetic basis underlying important agricultural
traits such as the nutritional value and disease resistance of 21 diverse
lines, or varieties, of rice, by identifying and comparing differences in
DNA sequences. This information will accelerate development of hardier, more
productive types of rice. The U.S. Department of Agriculture's Cooperative
State Research, Education and Extension Service - National Research
Initiative competitive grants plant genome program provided $715,000 for the
U.S. group's contribution to the collaboration. Additional funding for
international collaboration will be provided by other sources.

"This collaboration will produce a powerful resource to investigate the
patterns of molecular variation across the rice genome, assess evolutionary
forces shaping rice and discover genes controlling important traits such as
disease resistance, drought tolerance and nutritional value," said Jan
Leach, the lead U.S. researcher on the study and a professor of
bioagricultural sciences and pest management at Colorado State University.
"In the long term, this information will be used to improve rice, and it
will also help scientists better understand how to improve other crop
plants."

As populations boom in countries with limited availability of productive
land, the need for additional information about agriculture and crops that
can improve production and nutritional values have become key in preventing
hunger and malnutrition. Much of the information scientists need may reside
in the genomes of wild species of rice.

DNA sequence variation accounts for many differences between individual
plants and different varieties of the same plant, such as how the plant
develops, how much a crop plant yields, the nutritional value and how well
the plant tolerates stresses such as drought or exposure to diseases. Much
of the variation in genomes is represented by single nucleotide
polymorphisms, known as SNPs, which are changes at single base positions in
DNA.

This collaboration will identify SNPs from across the whole genome of 21
rice strains using methodologies developed by Perlegen Sciences. Wild
species of rice are a rich resource of diverse traits, and analysis of their
genomic variations may provide valuable information regarding phenotypic
variation between different rice strains.

SNPs are a marker of genetic variation between individuals of a species, and
they allow scientists to identify regions of genetic variation that may be
linked to traits. By identifying differences in SNPs among major rice
varieties, the study will help uncover the genetic basis behind important
agricultural traits.

"In addition to their importance in understanding genome evolution, studying
the SNPs of rice is valuable for several reasons," Leach said. "First, it
reveals DNA variation among different varieties of rice, which provides
information for developing better varieties. It also provides the ultimate
anchor to relate the study of rice and other crops."

The International Rice Research Institute is a non-profit agricultural
research and training center that was established to improve the wellbeing
of present and future generations of rice farmers and consumers,
particularly those with low incomes. It helps farmers in developing
countries produce more food on limited land, using less water, labor and
chemicals. The institute has helped to develop about 1,000 modern varieties
of rice, which has increased the availability of rice to populations in need
and reduced the price.

Perlegen will perform the microarray experiments. Perlegen uses microarray
technology to quickly assess DNA variations and compare whole genomes in an
effort to identify those variations associated with human diseases and to
explain and predict the efficacy and adverse effects of prescription drugs.

"Rice is an important crop for world agriculture and an excellent candidate
for DNA variation study," said Kelly Frazer, vice president of genomic
biology at Perlegen. "The combination of the methodologies and experience
our company can provide and the initial genomic research that has been
conducted by the International Rice Research Institute will give scientists
the opportunity to improve the quality of one of the most critical human
food sources in the world."

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