www.czu.cz ; www.raupp.info

A technology that uses "gene chips," which can help analyze tens of
thousands of different DNA elements in a cotton plant, could lead to cotton
varieties with superior traits and improved fiber quality; by Blair Fannin .

Dr. Jeff Chen, a Texas Agricultural Experiment Station scientist, is
working on a $5.7 million National Science Foundation project led by Thomas
Osborn at the University of Wisconsin, and a project funded by the National
Institutes of Health on translating gene expression mechanisms using plants
as a model system.

Chen's work involves DNA microarrays or "gene chips." In his laboratory, by
spotting DNA elements directly onto 1X3-inch glass slides, one chip can
potentially contain all annotated genes (approximately 30,000) of an animal
or plant genome.

"DNA microarrays have broad applications in studying changes in gene
expression and genomic structure in many biological contexts, including
genetics, physiology, development and environment," Chen said. "With the
help of computational and statistical tools, these changes can be
incorporated into understanding of biological networks that regulate plant
growth and production traits."

The technology "provides a high-throughput tool for practical applications,"
Chen said. Those include a wide variety from medical diagnostics to plant
breeding programs.

The work was initially funded by Cotton Incorporated and the Texas Higher
Education Coordinating Board. Collaborators include Barbara Triplett, a
fiber biologist with the U.S. Department of Agriculture-Agricultural
Research Service in New Orleans, and the Texas A&M University staff of David
Stelly, a molecular cytogeneticist, Peggy Thaxton, a cotton breeder, and
Sing-Hoi Sze, a computer scientist.

They recently received a five-year award of $2.5 million from the National
Science Foundation Plant Genome Research Program for their ongoing studies
of physiological and genetic effects on early stages of cotton fiber
development.

Chen's team is collaborating with Jonathan Wendel, project leader of the
National Science Foundation-funded Cotton Evolution Genome Project at Iowa
State University. The two research groups will collectively develop a
high-quality DNA microarray resource that is open and accessible to the
cotton community.

The microarrays will eventually include all favorable genes from cotton
researchers so they can be used in cotton breeding and field applications.

"This project represents a clear example where Cotton Incorporated and
state-funded research initiatives have had a ?multiplier-effect' on
garnering substantial federal funding for cotton research," Chen said. "In
the current era of genome biology, plant researchers are working together in
groups to share expertise necessary to generate large amounts of genomic
resources for the entire research community and to the cotton industry.

"Genomic resources generated in rice, corn and wheat have produced
tremendous impacts on the plant research community and plant production
agriculture. Cotton researchers are establishing new information and
technologies that will enhance cotton's share of competitive federal
research support for genomic research." Chen said he would like to expand
genome biotechnology education outside the university setting.

"We would like to build an outreach program where middle school teachers can
bring their classes to our laboratories so they can learn about genome
biotechnology," he said. "It would give students an opportunity for a
hands-on look at how to extract DNA from plants and amplify DNA in test
tubes. They would be exposed to how science and technology programming
involves not only agriculture, but biotechnology and engineering as well."

[agnews.tamu.edu]

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