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United States Department of Agriculture

Agricultural Research Service


Location: Sunflower and Plant Biology Research

2011 Annual Report

1a. Objectives (from AD-416)
1. Implement 454 sequencing technology to compare gene expression impacted by ecological factor affecting invasiveness. 2. To use this technology to also identify regulatory regions and potential targets for future manipulation of invasive perennial weeds.

1b. Approach (from AD-416)
Ecological factors have an impact on invasiveness of perennial weeds of the Northern plains; for example, Canada thistle and leafy spurge. These ecological factors cause changes in gene expression that are regulated by cis-acting elements. Advances in 454 sequencing technology now make it uniquely suited for the rapid and efficient quantification of both 1) gene expression, and 2) the identification of the cis-acting elements that control gene expression. Quantification of gene expression will be accomplished by 454 sequencing of biological samples collected from various ecological settings. This information will be analyzed and compared to obtain a dataset of genes linked to invasive traits. Further, 454 sequencing will be used to characterize genomic DNA to identify the specific cis-acting elements regulating the genes from our dataset.

3. Progress Report
The Canada thistle EST-database produced from the 454 sequencing project conducted in collaboration with the W.M. Keck Center, University of Illinois-Urbana, has been assembled, annotated, and parsed against existing databases to identify 15,232 unique transcripts. In silico and bioinformatics analysis of the data further identified physiological processes, expression targets and binding partners for genes, and pathways involved in paradormancy release. Results of this project were presented at the 2011 Plant and Animal Genome Meeting in San Diego, CA, the 2011 WSSA Annual Meeting in Portland, OR, the University of California-Davis, and a manuscript related to the project is in preparation. A Material Transfer Agreement (MTA) between ARS and the University of British Columbia, Vancouver, B.C. allowed the Canada thistle EST-database to be used for development of Canada thistle microarrays, and to study hybridization and introgression in Compositae weeds; a manuscript related to this project has been submitted. The ADODR actively monitors these projects, reviews accomplishments, and provides technical advice with cooperating personnel through e-mail and conference calls.

4. Accomplishments

Last Modified: 2/23/2016
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