Progress 09/01/08 to 08/31/13
Outputs
Progress Report 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. 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. The objectives of this SCA have been completed and no further research is planned. The outcomes from this SCA have been presented at numerous conferences, workshops, and meetings, and published in numerous international, peer-reviewed journals over the life of the project. In summary, this SCA provided important information on how simulated tillage impacts cross-talk among hormones to drive molecular networks regulating cell cycle processes leading to cell division, differentiation, and vegetative outgrowth. This information will be valuable for developing strategies for next-generation, integrated weed management practices.
Impacts
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Progress 10/01/11 to 09/30/12
Outputs
Progress Report 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. 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. This SCA resulted in the identification of 15,232 unique Canada thistle transcripts from root tissue covering a time scale involving the transition from para-dormancy to growth-induction. Bioinformatic analysis of differentially-expressed transcripts, based on this time scale, identified processes involved in plant hormone signaling networks, which led us to examine hormone profiles in root sections of Canada thistle. Results from the transcriptome and hormone profiling data helped us to propose a model where sectioning-induced changes in polar auxin transport alters ABA metabolism and signaling, which further impacts gibberellic acid signaling involving interactions between ABA and FUSCA3. Reduced auxin- and ABA-signaling, in conjunction with increased cytokinin biosynthesis or perception, also supports our model, which indicates that cross-talk among hormones drive molecular networks impacting cell cycle processes leading to cell division, differentiation, and vegetative outgrowth. Results of this project were presented at the 2012 Plant and Animal Genome Meeting in San Diego, CA, the 2012 American Society of Plant Biologists Annual Meeting in Auxin, TX, and have been documented in three peer-reviewed publications in 2012 including the American Journal of Botany, Journal of Biogeography, and Functional and Integrative Genomics.
Impacts
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Progress 10/01/10 to 09/30/11
Outputs
Progress Report 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. 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. 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.
Impacts
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Progress 10/01/09 to 09/30/10
Outputs
Progress Report 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. 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. A Canada thistle EST-database produced from a 454 sequencing project conducted in collaboration with the W.M. Keck Center, University of Illinois-Urbana, generated nearly 2.5 million reads. After assembly, 67, 358 sequences were identified of which 42,549 had hits to known Arabidopsis homologues while 24,810 had no hits. Annotation of the Canada thistle sequence data against the Arabidopsis database indicated the presence of at least 15,232 unique transcripts. Preliminary MIPs analysis indicated that transcripts belonging to functional categories involved in cell cycle and DNA processing, biogenesis of cellular components, and systemic interaction with environment were over-represented (p<0.05) and up-regulated (>3-fold) in paradormant root sections, while amino acid metabolism, energy, protein fate and binding, cellular transport and communication, cell rescue/defense, and subcellular localization were over-represented among up-regulated transcripts during paradormancy release. Sub-network analysis further help to identify physiological processes, expression targets and binding partners for genes, and pathways involved in paradormancy release. Data from this project were presented at the 2010 WSSA Annual Meeting in Denver, CO, and a manuscript related to the project is being drafted. The ADODR actively monitors the project, reviews accomplishments, and provides technical advice with cooperating personnel through e-mail and conference calls.
Impacts
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Progress 10/01/08 to 09/30/09
Outputs
Progress Report 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. 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. Significant Activities that Support Special Target Populations At the USDA-ARS, BRL in Fargo, ND, RNA samples were isolated from roots sections of greenhouse propagated Canada thistle (monoculture NW22-1) collected at 0, 1, 2, and 3 days of incubation at 25oC under 16:8 h light:dark conditions. The RNA samples were sent to the W.M. Keck Center, University of Illinois-Urbana for the successful construction of four MID- tagged cDNA libraries. 454 next generation sequencing of the four libraries generated nearly 1 giga-base of DNA from approximately 2.5 million ESTs with an average read length of 362 bases. Bioinformatics analysis is currently underway at the W.M. Keck Center to assemble and annotate the sequence information into a unigene set that can be used for a virtual in silico analysis, and for future construction of Canada thistle oligoarrays. The ADODR actively monitors the project, reviews accomplishments, and provides technical advice with cooperating personnel through e-mail and conference calls.
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