News Release

'Knockout' research eases study of plant gene functions

Peer-Reviewed Publication

North Carolina State University

A North Carolina State University geneticist has helped create a powerful new tool to assist plant researchers in their studies of individual gene functions in the so-called lab rat of plant research – Arabidopsis thaliana, or mustard weed.

That's important, says Dr. Jose Alonso, assistant professor of genetics at NC State, because knowing the functions of specific genes in Arabidopsis gives researchers the ability to apply that knowledge to gene studies in other plants. Genetically, Arabidopsis has a great deal in common with other plants, Alonso says.

Alonso's work led to the creation of lines of Arabidopsis plants that have certain genes knocked out, or turned off. The seeds of these plants are held at a seed stock center at the Arabidopsis Biological Resource Center at The Ohio State University and are publicly available to researchers all over the world, making it much simpler for a scientist to study specific gene function in his or her own lab.

The research is presented in a paper published in the Aug. 1 issue of Science. Alonso is the paper's lead author.

To arrive at the findings, Alonso and his colleagues used a method called insertional mutagenesis, in which foreign DNA was randomly inserted into the Arabidopsis genome. When the foreign DNA hit a gene, that specific gene was turned off.

Of the predicted 29,454 genes in Arabidopsis – the genome of the plant has already been sequenced, so scientists were able to accurately map the locations of the inserted DNA – 21,799, or 74 percent of the genes, were knocked out using insertional mutagenesis, the paper states.

Now, libraries of Arabidopsis seeds with specific single genes knocked out have been compiled and are available for public consumption. Researchers studying a specific gene can quickly and easily search for an Arabidopsis plant that has a particular gene turned off, and order it from the Arabidopsis Resource Center.

Alonso started the project and set up the protocols while working as a research associate at the Salk Institute for Biological Studies in La Jolla, Calif.

The study was done in collaboration with researchers at The Salk Institute, the National Research Council Plant Biotechnology Institute in Canada and the University of California– San Diego.

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Note to editors: An abstract of the paper follows.

"Genomewide Insertional Mutagenesis of Arabidopsis thaliana"
Authors: Jose M. Alonso and Anna Stepanova, North Carolina State University; Joseph R. Ecker, The Salk Institute for Biological Studies, et al. Published: Aug. 1, 2003 in Science

Abstract: Over 225,000 independent Agrobacterium transferred DNA (T-DNA) insertion events in the genome of the reference plant Arabidopsis thaliana have been created that represent near saturation of the gene space. The precise locations were determined for more than 88,000 T-DNA insertions, which resulted in the identification of mutations in more than 21,700 or the ~29,454 predicted Arabidopsis genes. Genomewide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels. Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene.

Media Contacts:
Dr. Jose Alonso, 919-515-2292
Tim Lucas, News Services, 919-515-3470


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