Blacksburg, Virginia
May 25, 2007
The Virginia Bioinformatics Institute (VBI) at Virginia Tech
today announced that it has completed the largest ever
Affymetrix GeneChip®
microarray study for a plant experimental system in an academic
research setting. The 2600-chip experiment explores the
counter-play of plant and pathogen genes during infection of
soybean with the root-rot pathogen Phytophthora sojae,
with a focus on mechanisms of long-lasting disease resistance.
P. sojae causes severe damage in
soybean crops and results in $100-200 million annually in losses
for commercial farmers in the United States alone.
Much information has been obtained
by careful study of single resistance genes in plants. However,
this "low hanging fruit" approach has not resulted in
significant long-lasting resistance of crops. Plants in which a
single gene has been modified are quickly overcome by new
strains of pathogens. The GeneChip experiment is part of a
project aimed at understanding and improving a more long-lasting
form of disease resistance called quantitative or multigenic
resistance.
Adam Jerauld, Affymetrix Team
Leader in the Core Laboratory Facility (CLF) remarked: "Our
facility was able to successfully complete the data generation
stage for this 2600-chip experiment within a six-month period.
This was possible due to a highly effective collaboration
between the research scientists and the ability of our team to
scale-up our array processing capabilities. We also received
first-rate technical support from
Affymetrix."
Clive Evans, CLF Manager at VBI,
commented: "The Affymetrix GeneChip® microarrays used in the
study comprise probes for 38 000 soybean genes and 15 800
P.sojae genes. We increased the productivity of our Affymetrix
processing four-fold to accommodate the scale of this project."
"VBI is a National Customer Array
Center with world class scientists working in the plant and
biomedical sciences. It is an ideal place to conduct the largest
Affymetrix agriculture microarray experiment to date by a
not-for- profit facility," said Fredrick Pollock, Director of
Strategic Business at Affymetrix. "We worked with the soybean
research community to develop the content for the Soybean Genome
Array. Affymetrix currently produces 17 arrays as part of its
GeneChip(r) Consortia Program and we are excited about working
with the leading agricultural researchers on further projects
designed to improve crop yields and the nutritional value of the
food we eat."
The Affymetrix microarray
experiment combines two approaches, transcriptional profiling
and quantitative trait locus (QTL) mapping. These approaches are
well suited for dissecting complex biological processes that
involve the interactions of many genes. The information obtained
from this study will be valuable for understanding how legumes
may be protected from a wide variety of pathogens, and how many
hosts may be protected against oomycete pathogens. Project team
leader and VBI Professor Brett Tyler said: "With the massive
data set from the CLF now in hand, the data-analysis phase of
the project will begin and is expected to take 18 months."
VBI's CLF is a multi-user resource
providing various high-throughput technologies and other
state-of-the-art technology-related services. The CLF currently
provides analysis platforms for DNA sequencing and genotyping,
gene expression analysis, and proteomics.
The project is supported by
cooperative agreement DBI-0211863 from the National Science
Foundation Plant Genome Research Program. The project is a
multidisciplinary collaboration involving Saghai Maroof
(Department of Crop and Soil Environmental Sciences, Virginia
Tech), Ina Hoeschele (VBI), Anne Dorrance (Ohio State
University) and Steve St. Martin (Ohio State University).
The Virginia Bioinformatics
Institute (VBI) at Virginia Tech has a research platform
centered on understanding the "disease triangle" of
host-pathogen-environment interactions in plants, humans and
other animals. By
successfully channeling innovation into transdisciplinary
approaches that combine information technology and biology,
researchers at VBI are addressing some of today's key challenges
in the biomedical, environmental
and plant sciences.
Affymetrix Inc. (Nasdaq:AFFX)
scientists invented the world's first high- density microarray
in 1989 and began selling the first commercial microarray in
1994. The microarray technology is used by the world's top
pharmaceutical, diagnostic and biotechnology companies, as well
as leading academic, government and not-for-profit research
institutes.
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