'Gene chips' research in cotton could lead to superior variety


COLLEGE STATION 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.

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."

Source: Eurekalert & others

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