Progress 11/26/03 to 09/30/08
Outputs
Progress Report Objectives (from AD-416) 1-construct three normalized cDNA libraries using cassava and leafy spurge; 2-develop an expressed sequence tag (EST)-database from the three libraries; 3-identify unigenes within the EST-database for development of DNA microarrays. Approach (from AD-416) Three normalized cDNA libraries (one for environmentally challenged above- ground tissue of cassava variety TME 117, one for root tissue of cassava variety TME 117, and one for whole plant of leafy spurge) will be constructed by Dr. Alvaro Hernandez at the University of Illinois. The normalization of the cDNA libraries will reduce the number of abundant cDNA and enhance the ability to identify rare and novel cDNAs. Clones within the three normalized cDNA libraries will be robotically isolated and sequenced from the 5' ends using an ABI3730XL DNA sequencer. DNA sequence data will be analyzed using bioinformatics software under the direction of Dr. Lei Liu at the University of Illinois. The bioinformatics service will include redundancy checks and Genbank submissions. Contigs identified within the EST-database will be used to generate unigene sets that can be used as templates for future development of Euphorbiaceae-specific DNA microarrays. Significant Activities that Support Special Target Populations Research on this project was completed on 09/30/2008. See the annual report for FY 2008 (October 31, 2007-September 30, 2008) which details the progress of this agreement. Administrative close-out procedures have now been completed.
Impacts
(N/A)
Publications
|
Progress 10/01/06 to 09/30/07
Outputs
Progress Report Objectives (from AD-416) 1-construct three normalized cDNA libraries using cassava and leafy spurge; 2-develop an expressed sequence tag (EST)-database from the three libraries; 3-identify unigenes within the EST-database for development of DNA microarrays. Approach (from AD-416) Three normalized cDNA libraries (one for environmentally challenged above- ground tissue of cassava variety TME 117, one for root tissue of cassava variety TME 117, and one for whole plant of leafy spurge) will be constructed by Dr. Alvaro Hernandez at the University of Illinois. The normalization of the cDNA libraries will reduce the number of abundant cDNA and enhance the ability to identify rare and novel cDNAs. Clones within the three normalized cDNA libraries will be robotically isolated and sequenced from the 5' ends using an ABI3730XL DNA sequencer. DNA sequence data will be analyzed using bioinformatics software under the direction of Dr. Lei Liu at the University of Illinois. The bioinformatics service will include redundancy checks and Genbank submissions. Contigs identified within the EST-database will be used to generate unigene sets that can be used as templates for future development of Euphorbiaceae-specific DNA microarrays. Significant Activities that Support Special Target Populations This report documents a Specific Cooperative Agreement between ARS and the W.M. Keck Center, University of Illinois-Urbana. Additional information can be found in the report of the parent project 5442-21220- 017-00D. The objectives of this collaboration are to develop state-of-the- art genomics technologies, such as DNA microarrays, to be used for marker- assisted and genome-wide biology discovery, for accelerating plant breeding in cassava, and for identifying other important traits related to food quality and vegetative reproduction in related Euphorbiaceae- family members. We have used normalized cDNA libraries from cassava genotype TME 117 (drought-tolerant) and whole plant leafy spurge to development an EST- (expressed sequence tag) database for Euphorbiaceae. This project has generated 45,314 high quality leafy spurge ESTs and 18, 325 high quality cassava ESTs. The leafy spurge EST-database was assembled into 23,472 unique sequences representing 19,015 unigenes (10, 293 clusters and 8,722 singletons) whereas the 18,166 cassava ESTs assembled into 8,577 unique gene clusters (3,194 clusters and 5,383 singletons). The ESTs have all been annotated and data related to this project can be accessed through the National Center for Biotechnology Information (NCBI) and a web site maintained by the Bioinformatics Department at the W.M. Keck Center. Bioinformatic analysis was further used to identify a set of 23,000 unique sequences within this Euphorbiaceae EST-dataset which have successfully been used to generate the first round of high-density Euphorbiaceae-specific DNA microarrays. The ESTs and microarrays are providing a valuable resource for breeding programs working on improving genetic stocks of desirable species and for assisting scientist involved in developing methods to control the growth of undesirable species. The ADODR actively monitors the project by discussing project plans, providing technical advice, and frequently reviewing accomplishments with cooperating personnel.
Impacts
(N/A)
Publications
|
Progress 10/01/05 to 09/30/06
Outputs
Progress Report 4d Progress report. This report documents a Specific Cooperative Agreement between USDA-ARS and the W.M. Keck Center, University of Illinois-Urbana. Additional information can be found in the report of the parent CRIS 5442-21220-017- 00D, Biologically Based Weed Management: Fundamental Research on Dormancy and the Genetics of Weeds. The objectives of this collaboration are to develop state-of-the-art genomics technologies, such as DNA microarrays, to be used for marker-assisted and genome-wide biology discovery, for accelerating plant breeding in cassava, and for identifying other important traits related to food quality and vegetative reproduction in related Euphorbiaceae-family members. We have used normalized cDNA libraries from cassava genotype TME 117 (drought-tolerant) and whole plant leafy spurge to development an EST- (expressed sequence tag) database for Euphorbiaceae. This project has generated 45,314 high quality leafy spurge ESTs and 18,325
high quality cassava ESTs. The ESTs have all been annotated and data related to this project can be accessed through the National Center for Biotechnology Information (NCBI) and a web site maintained by the Bioinformatics Department at the W.M. Keck Center. Bioinformatic analysis was used to identify a set of 23,000 unique sequences from Euphorbiaceae which are currently being used to generate the first round of DNA microarrays. The ESTs and microarrays are providing a valuable resource for breeding programs working on improving genetic stocks of desirable species and for assisting scientist involved in developing methods to control the growth of undesirable species.
Impacts
(N/A)
Publications
|
Progress 10/01/04 to 09/30/05
Outputs
4d Progress report. This report documents a Specific Cooperative Agreement between USDA-ARS and the W.M. Keck Center, University of Illinois-Urbana. Additional information can be found in the report of the parent CRIS 5442-21220-011- 00D. The objectives of this collaboration are to develop state-of-the-art genomics technologies, such as DNA microarrays, to be used for marker- assisted and genome-wide biology discovery, for accelerating plant breeding in cassava, and for identifying other important traits related to food quality and vegetative reproduction in related Euphorbiaceae- family members. We have used normalized cDNA libraries from cassava genotype TME 117 (drought-tolerant) and whole plant leafy spurge to development an EST- (expressed sequence tag) database for Euphorbiaceae. This project has generated 46,197 high quality leafy spurge ESTs and 18, 325 high quality cassava ESTs. The ESTs have all been annotated and data related to this project can be accessed
through a password protected web site generated and maintained by the Bioinformatics Department at the W.M. Keck Center. Bioinformatics analysis has identified greater than 30,000 unique sequences for Euphorbiaceae which will be used to generate future cDNA microarrays. The ESTs and future microarrays should provide a valuable resource for breeding programs working on improving genetic stocks of desirable species and for scientist involved in developing methods to control the growth of undesirable species.
Impacts
(N/A)
Publications
|
Progress 10/01/03 to 09/30/04
Outputs
4. What were the most significant accomplishments this past year? This report documents a Specific Cooperative Agreement between USDA-ARS and the W.M. Keck Center, University of Illinois-Urbana. Additional information can be found in the report of the parent CRIS 5442-21220-011- 00D. The objectives of this collaboration are to develop state-of-the-art genomics technologies, such as DNA microarrays, to be used for marker- assisted and genome-wide biology discovery, for accelerating plant breeding in cassava, and for identifying other important traits related to food quality and vegetative reproduction in related Euphorbiaceae- family members. As a first step towards accomplishing our objectives, we have constructed normalized cDNA libraries from cassava genotype TME 117 (drought-tolerant) and whole plant leafy spurge that are being used for development of an EST- (expressed sequence tag) database. The first phase of this project will provide 8,000-10,000 unigenes that
will be used for future fabrication of DNA microarrays. The ESTs and future microarrays should provide a valuable resource for breeding programs working on improving genetic stocks of desirable species and for scientist involved in developing methods to control the growth of undesirable species.
Impacts
(N/A)
Publications
|
|