Progress 04/16/03 to 03/23/08
Outputs
Progress Report Objectives (from AD-416) In FY 2003, the NSF Plant Genome Research Program funded two new projects (total of $10,300,000 over two years) to enable high-throughput DNA sequencing of the 'gene space' of maize, and to construct a high-quality physical map of the maize genome. The preceding research will generate new information about the maize genome that ARS should incorporate into its research programs on maize biology/genetics/genomics: in particular, into the existing strong programs in maize genetics at the PGEC and other Bay Area institutions. Effective utilization of this new information requires development of effective bioinformatics tools and algorithms for the analysis, visualization, and public dissemination of information derived from studies of crop genomes, especially maize and other grains. In FY03 two projects were funded by NSF to enable high-throughput DNA sequencing of "gene space" of maize and construct a high-quality physical map of the maize genome. This new project will transition that genome information into research programs on maize biology/genetics/genomics and to leverage very significant strengths in maize at PGEC and other Bay Area institutions. Funding is for new bioinformatics personnel, staff and operating costs which will enhance PGEC's capabilities for analyzing, managing, and integrating data derived from the study of maize (and other important agricultural) genomes, including genetic and physical maps, genome and EST sequence and functional genomic (microarray, proteomic) data. Provide important leadership for the agency in maize genomics and bioinformatics, through interactions with other key agency sites (e.g., Ames, Iowa; Columbia, Missouri; Ithaca, New York, and its collaborators at Cold Spring Harbor Laboratory; Urbana, Illinois), and academic institutions involved in large-scale genome sequencing and functional analysis of the maize genome. Approach (from AD-416) These funds will augment FY2003's $357,660 increase, providing additional resources to defray operating costs for this ARS project, which will enhance PGEC's capability to analyze, manage, and integrate data derived from the study of the maize genome and other important agricultural genomes. These data include genetic and physical maps, genome and EST sequence, and functional genomic (microarray, proteomic) information. FY04 Program Increase $161,044. Significant Activities that Support Special Target Populations This project was initiated upon the hiring of a new investigator at the beginning of FY2006. Initially, the investigator equipped the lab and set up the physical space to support the research activities of newly hired staff. At the same time, the investigator recruited new staff to carry out research and trained them to meet the defined research goals. The current personnel in the laboratory include two postdoctoral researchers, one staff laboratory assistant, and five undergraduate research assistants from University of California, Berkeley. The investigator also collected the biological resources required to begin the research. In addition, collaborations were established with scientists at ARS units in Ithaca and Raleigh who will be an important source of maize inbred phenotype and genotype data. Finally, the investigator established a Cooperative Research and Development Agreement (CRADA) with Pioneer Hi-Bred � A DuPont Company to enable the identification and exchange of potential null mutants that affect key aspects of circadian clock function and/or flowering time in maize. The fundamental goal of the research program developed by the investigator is to define the maize circadian system and assess its impact on key agronomic traits in cereals, including flowering time and abiotic stress responses. This research program will lead to the formulation and application of novel paradigms and tools for manipulating the environmental response of crop plants. Ultimately, this work will lead to improvements in crop production. This work directly addresses the NP 301 Action Plan, Component 2, Problem Statement 2C: Genetic Analysis and Mapping of Important Traits. As this project is expiring, the objectives conceived by the investigator will be instituted in the replacement project 5335-21000-026-00D.
Impacts
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Publications
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Progress 10/01/06 to 09/30/07
Outputs
Progress Report Objectives (from AD-416) In FY 2003, the NSF Plant Genome Research Program funded two new projects (total of $10,300,000 over two years) to enable high-throughput DNA sequencing of the 'gene space' of maize, and to construct a high-quality physical map of the maize genome. The preceding research will generate new information about the maize genome that ARS should incorporate into its research programs on maize biology/genetics/genomics: in particular, into the existing strong programs in maize genetics at the PGEC and other Bay Area institutions. Effective utilization of this new information requires development of effective bioinformatics tools and algorithms for the analysis, visualization, and public dissemination of information derived from studies of crop genomes, especially maize and other grains. In FY03 two projects were funded by NSF to enable high-throughput DNA sequencing of "gene space" of maize and construct a high-quality physical map of the maize genome. This new project will transition that genome information into research programs on maize biology/genetics/genomics and to leverage very significant strengths in maize at PGEC and other Bay Area institutions. Funding is for new bioinformatics personnel, staff and operating costs which will enhance PGEC's capabilities for analyzing, managing, and integrating data derived from the study of maize (and other important agricultural) genomes, including genetic and physical maps, genome and EST sequence and functional genomic (microarray, proteomic) data. Provide important leadership for the agency in maize genomics and bioinformatics, through interactions with other key agency sites (e.g., Ames, Iowa; Columbia, Missouri; Ithaca, New York, and its collaborators at Cold Spring Harbor Laboratory; Urbana, Illinois), and academic institutions involved in large-scale genome sequencing and functional analysis of the maize genome. Approach (from AD-416) These funds will augment FY2003's $357,660 increase, providing additional resources to defray operating costs for this ARS project, which will enhance PGEC's capability to analyze, manage, and integrate data derived from the study of the maize genome and other important agricultural genomes. These data include genetic and physical maps, genome and EST sequence, and functional genomic (microarray, proteomic) information. FY04 Program Increase $161,044. Accomplishments Initiate Program to Identify Null Alleles of Maize Flowering Time Genes Understanding the genetic basis of flowering time control in maize is important for crop productivity. PGEC scientists established a cooperative agreement with Pioneer, A DuPont Company, to enable identification of transposon insertion lines in specific genes from the Pioneer TUSC collection. Research will ultimately lead to the identification of maize loci contributing to flowering time and a better understanding of fundamental processes in environmental responses and genes with which to improve crop productivity. This work addresses the NP 301 Action Plan, Component 2, Problem Statement 2C:Genetic Analysis and Mapping of Important Traits. Technology Transfer Number of New CRADAS and MTAS: 1 Number of Web Sites managed: 1 Number of Non-Peer Reviewed Presentations and Proceedings: 1
Impacts
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Publications
- Faigon-Soverna, A., Harmon, F.G., Storani, L., Karayekov, E., Staneloni, R. J., Gassmann, W., Mias, P., Casal, J.J., Kay, S.A., Yanovsky, M.J. 2006. A Constitutive Shade-Avoidance Mutant Implicates TIR-NBS-LRR Proteins in Arabidopsis Photomorphogenic Development. The Plant Cell 18(11):2919-2928.
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Progress 10/01/04 to 09/30/05
Outputs
1. What major problem or issue is being resolved and how are you resolving it (summarize project aims and objectives)? How serious is the problem? What does it matter? A major problem to be solved is the analysis of complex genome data of agriculturally important crops. Understanding how plants perceive the daily circadian rhythm has implications for all aspects of plant growth, including time to flowering, photosynthesis, nitrogen fixation, etc. The development of bioinformatics tools to examine gene expression during a circadian cycle will provide users increased capacity to utilize a growing body of data. 2. List the milestones (indicators of progress) from your Project Plan. Project plan not developed yet Newly hired scienist begins work in September 2005. 6. What science and/or technologies have been transferred and to whom? When is the science and/or technology likely to become available to the end- user (industry, farmer, other scientists)? What are the
constraints, if known, to the adoption and durability of the technology products? Project will be initiated upon recruitment of scientist.
Impacts
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Publications
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Progress 10/01/03 to 09/30/04
Outputs
1. What major problem or issue is being resolved and how are you resolving it (summarize project aims and objectives)? How serious is the problem? What does it matter? The major problem to be solved is the analysis of complex genome data of agriculturally important crops. The development of bioinformatics tools will provide users increased capacity to utilize a growing body of data. 2. List the milestones (indicators of progress) from your Project Plan. Agriculture is of the utmost importance and as the poplulation continues to increase, while usable land descreases, it will only become more important to have effective tools for the enhancement of agriculture. 3. Milestones: National Program 301: Plant, Microbial & Insect Genetic Research, Genomics & Genetic Improvement (100%). Bioinformatics tools will be needed to move the knowledge gained from sequencing genomes to practical use. 6. What science and/or technologies have been transferred and to whom? When is the
science and/or technology likely to become available to the end- user (industry, farmer, other scientists)? What are the constraints, if known, to the adoption and durability of the technology products? Project will be initiated upon recruitment of scientist.
Impacts
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Publications
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