Progress 10/01/08 to 09/30/09
Outputs
Progress Report Objectives (from AD-416) The Agricultural Research Service (ARS) and the Regents of the University of California (Cooperator) desire to collaborate in plant gene expression research. To accomplish this objective, ARS and the Cooperator have established an entity called the Plant Gene Expression Center (PGEC). The mission of the PGEC is to perform fundamental research using modern molecular and genetic strategies to understand the basic processes and mechanisms controlling plant growth, development and survival, and based on that understanding, to develop the molecular tools and materials that can be exploited by plant geneticists and breeders to generate superior crop plants and address agriculturally important problems. To accomplish this mission, PGEC scientists will interface with individuals and organizations who propose to utilize the molecular tools and materials developed at the PGEC. Approach (from AD-416) 1. The PGEC conducts research in the complex biology of plant gene expression and to develops the technology required by plant geneticists and breeders for the timely production of superior crop plants. Formerly 5335-21000-023-02N (6/06). 2. The PGEC is comprised of a Director, a University of California, Berkeley (UCB) Scientific Director, a core of Principal Investigators who are ARS employees, and support staff. The Director is an ARS employee who is responsible for the ARS program and resources and reports to the ARS Pacific West Area Director. The UCB Scientific Director is a University of California at Berkeley faculty member who is responsible for the UCB program and resources and reports to the Dean, College of Natural Resources, UCB. 3. The research program of the PGEC shall be determined by mutual consent of ARS, based on the mandate of Congress and the ARS National Programs, and the Cooperator through their respective representatives. The Principal Investigators shall select the research strategies, methodological procedures, and research organisms deemed most appropriate on scientific grounds to accomplish the mission of the PGEC. Documents NFCA with UC Berkeley. Significant Activities that Support Special Target Populations 5335-21000-028-00D 5335-21000-027-00D 5335-22000-007-00D 5335-21000-016-00D 5335-21000-026-00D 5335-21000-030-00D 5335-21000-031-00D 5335-21430-007-00D ARS scientist determined the expression patterns of 24 members of the CLE family of putative signaling molecules throughout Arabidopsis development. She found that most Arabidopsis tissues express multiple CLE genes during the life cycle, and detected dynamic CLE gene expression patterns during developmental processes such as lateral root initiation, stamen maturation and fruit formation. ARS scientist determined that the hormone gibberellin is directly regulated by the KNOTTED1 transcription factor and that the regulatory sequences of the GA-2-oxidase gene are conserved in the grasses. She has also identified a number of other direct targets using chromatin sequencing. ARS scientist identified a substantial number of maize transcripts under circadian regulation and discovered several likely maize clock components. Microarray analysis showed 10% of maize transcripts exhibit a circadian rhythm; a clear illustration of the maize circadian oscillator�s broad transcriptional regulatory purview. ARS scientist showed that mutants which carry truncated versions of a protein disulfide isomerase have embryo sac maturation and disrupted pollen tube guidance, whereas gene knockouts in this gene had no effect.. ARS scientist analyzed plants regenerated from calluses generated in FY08 and showed that site specific integration mediated by the Bxb1 recombination system occurred at a ~10% frequency. This is practical for commercial developers to obtain site-specifically integrated transgenes, and will help speed the development of more precisely engineered transgenic varieties. ARS scientist has discovered a novel complexity in phytochrome (phy)- mediated light signaling, whereby bHLH signaling partners function as transcription factors in regulating early gene-expression, but as direct feedback modulators of phy-protein abundance in regulating later visible seedling morphogenesis. ARS scientist is concluding 10 years of research on the function of the ACC synthase enzymes encoded by 9 genes in Arabidopsis. The results have revealed a critical role for ACC and is soon to be published. ARS scientist investigated the functional and evolutionary properties of three pathogen disease resistance loci of wild Solanum species using comparative genomics. Research at the PGEC provides an essential knowledge base for biotechnology's impact on agriculture. The knowledge has moved from determining the function of single genes to elucidation of entire networks. This information can be used to understand the function of developmental processes in crop processes. Monitoring of activities is carried out by weekly seminars and monthly meetings.
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Progress 10/01/06 to 09/30/07
Outputs
Progress Report Objectives (from AD-416) The Agricultural Research Service (ARS) and the Regents of the University of California (Cooperator) desire to collaborate in plant gene expression research. To accomplish this objective, ARS and the Cooperator have established an entity called the Plant Gene Expression Center (PGEC). The mission of the PGEC is to perform fundamental research using modern molecular and genetic strategies to understand the basic processes and mechanisms controlling plant growth, development and survival, and based on that understanding, to develop the molecular tools and materials that can be exploited by plant geneticists and breeders to generate superior crop plants and address agriculturally important problems. To accomplish this mission, PGEC scientists will interface with individuals and organizations who propose to utilize the molecular tools and materials developed at the PGEC. Approach (from AD-416) 1. The PGEC conducts research in the complex biology of plant gene expression and to develops the technology required by plant geneticists and breeders for the timely production of superior crop plants. Formerly 5335-21000-023-02N (6/06). 2. The PGEC is comprised of a Director, a University of California, Berkeley (UCB) Scientific Director, a core of Principal Investigators who are ARS employees, and support staff. The Director is an ARS employee who is responsible for the ARS program and resources and reports to the ARS Pacific West Area Director. The UCB Scientific Director is a University of California at Berkeley faculty member who is responsible for the UCB program and resources and reports to the Dean, College of Natural Resources, UCB. 3. The research program of the PGEC shall be determined by mutual consent of ARS, based on the mandate of Congress and the ARS National Programs, and the Cooperator through their respective representatives. The Principal Investigators shall select the research strategies, methodological procedures, and research organisms deemed most appropriate on scientific grounds to accomplish the mission of the PGEC. Documents NFCA with UC Berkeley Formerly 5335-21000-017-02N (10/05) BSL-1; 7/3/06. Significant Activities that Support Special Target Populations This report serves to document research conducted under this Non-Funded Cooperative Agreement between ARS and UC Berkeley. Additional details of research can be found in the reports for the parent projects: Baker - 5335-22000-006-00D Fletcher - 5335-21000-029-00D Harmon - 5335-21000-025-00D Hake - 5335-21000-028-00D McCormick - 5335-21000-030-00D Ow - 5335-21000-031-00D Theologis - 5335-21430-006-00D Quail - 5335-21000-027-00D Scientists in the PGEC, Albany, CA cloned & characterized BOP1 and BOP2, two genes that act as key regulators of leaf & flower development. The McCormick lab demonstrated that a pollen protein called KPP (for kinase partner protein) interacts with receptor protein kinases and that its overexpression causes aberrant pollen tube growth. The Theologis lab has implemented system biological approaches to define the protein network of the auxin signalling components (Aux/IAA-ARF-F-box auxin receptor proteins). Similar approaches led to the discovery that ethylene produced by specific ACS isozymes control flowering time. The Hake lab used positional cloning to isolate three genes in maize that regulate the inflorescence & one gene that regulates leaf development. The Quail lab determined that PIF3, a key gene in photomorpho-genesis, is regulated by phosphorylation. The Baker lab investigated the functional & evolutionary properties of three pathogen disease resistance loci of wild Solanum species using comparative genomics. Their NSF Potato Genome Project has generated comprehensive & widely used public genomic resources for basic research & breeding for disease resistance in Solanaceae & fosters science education & public awareness of plant genomics. The Ow lab identified a transcription factor that regulates stress-induced reproduction. In addition, in collaboration with WRRC, the Ow lab has characterized new site-specific recombination systems for use as tools in plant genetic engineering. Research at PGEC provides an essential knowledge base for biotechnology's impact on agriculture. PGEC scientists have taken advantage of the model species, Arabidopsis, to determine the function of genes important in growth, development & responses to abiotic and biotic stress. The knowledge has moved from determining the function of single genes to elucidation of entire networks. This information can be used to understand the function of developmental processes in crop processes. Monitoring of activities is carried out by weekly seminars and monthly meetings. Accomplishments This report documents research conducted under a specific cooperative agreement between ARS and the University of Californa at Berkeley. Additional details of research can be found in reports for the in-house associated projects: Baker - 5335-22000-006-00D Fletcher - 5335-21000-029-00D Harmon - 5335-21000-025-00D Hake - 5335-21000-028-00D McCormick - 5335-21000-030-00D Ow - 5335-21000-031-00D Theologis - 5335-21430-006-00D Quail - 5335-21000-027-00D Significant Activities that Support Special Target Populations See individual projects: Baker - 5335-22000-006-00D Fletcher - 5335-21000-029-00D Harmon - 5335-21000-025-00D Hake - 5335-21000-028-00D McCormick - 5335-21000-030-00D Ow - 5335-21000-031-00D Theologis - 5335-21430-006-00D Quail - 5335-21000-027-00D Technology Transfer Number of New CRADAS and MTAS: 33 Number of Active CRADAS and MTAS: 6 Number of Patent Applications filed: 1 Number of Web Sites managed: 9 Number of Non-Peer Reviewed Presentations and Proceedings: 27 Number of Newspaper Articles,Presentations for NonScience Audiences: 1
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Progress 10/01/05 to 09/30/06
Outputs
Progress Report 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? Why does it matter? This report documents the formal non-funded cooperative agreement between the ARS and the University of California Berkeley (#58-5335-4-0531N) that constitutes the entity called the Plant Gene Expression Center, Albany CA. Research under the formal agreement between the ARS and the University of California Berkeley fall under NP 301 (1 project), NP 302 (6) and NP 303 (1 project). The Objectives and Approach as outlined in this Agreement are: OBJECTIVE The Agricultural Research Service (ARS) and the Regents of the University of California (Cooperator) desire to collaborate in plant gene expression research. To accomplish this objective, ARS and the Cooperator have established an entity called the Plant Gene Expression Center (PGEC). The mission of the PGEC is to perform fundamental
research using modern molecular and genetic strategies to understand the basic processes and mechanisms controlling plant growth, development and survival, and based on that understanding, to develop the molecular tools and materials that can be exploited by plant geneticists and breeders to generate superior crop plants and address agriculturally important problems. To accomplish this mission, PGEC scientists will interface with individuals and organizations who propose to utilize the molecular tools and materials developed at the PGEC. APPROACH 1. The PGEC conducts research in the complex biology of plant gene expression and develops the technology required by plant geneticists and breeders for the timely production of superior crop plants. 2. The PGEC is comprised of a Director, a University of California, Berkeley (UCB) Scientific Director, a core of Principal Investigators who are ARS employees, and support staff. The Director is an ARS employee who is responsible for the ARS
program and resources and reports to the ARS Pacific West Area Director. The UCB Scientific Director is a University of California at Berkeley faculty member who is responsible for the UCB program and resources and who reports to the Dean, College of Natural Resources, UCB. 3. The research program of the PGEC shall be determined by mutual consent of ARS, based on the mandate of Congress and the ARS National Programs, and the Cooperator through their respective representatives. The Principal Investigators shall select the research strategies, methodological procedures, and research organisms deemed most appropriate on scientific grounds to accomplish the mission of the PGEC. 4d Progress report. This report serves to document research conducted under this Non-Funded Cooperative Agreement between ARS and UC Berkeley. Additional details of research can be found in the reports for the parent projects: Baker - 5335-22000-006-00D Fletcher - 5335-21000-029-00D Harmon - 5335-21000-025-00D
Hake - 5335-21000-028-00D McCormick - 5335-21000-030-00D Ow - 5335-21000-031-00D Theologis - 5335-21430-006-00D Quail - 5335-21000-027-00D); 5335-21000-027-03S (current SCA w/UCB) The Fletcher lab cloned and characterized BOP1 and BOP2, two genes that act as key regulators of leaf and flower development. The McCormick lab demonstrated that a pollen protein called KPP (for kinase partner protein) interacts with receptor protein kinases and that its overexpression causes aberrant pollen tube growth. This finding directly links receptor kinase signaling, via KPP, to cytoplasmic remodeling necessary for polar growth. The Theologis lab has implemented System biological approaches to define the protein network of the auxin signalling components (Aux/IAA- ARF-F-box auxin receptor proteins). In addition, similar approaches led to the discovery that ethylene produced by specific ACS isozymes control flowering time. The Hake lab used positional cloning to isolate three genes in maize that
regulate the inflorescence and one gene that regulates leaf development. The Quail lab has discovered that photoactivated phytochromes induce rapid intranuclear phosphorylation of a transcription factor as an early step in the signaling pathway that leads to light-regulated seedling development. The Baker lab investigated the functional and evolutionary properties of three pathogen disease resistance loci of wild Solanum species using comparative genomics. Their NSF Potato Genome Project has generated comprehensive and widely used public genomic resources for basic research and breeding for disease resistance in Solanaceae and fosters science education and public awareness of plant genomics. The Ow lab identified a transcription factor that regulates stress-induced reproduction. In addition, in collaboration with WRRC, the Ow lab has characterized new site-specific recombination systems for use as tools in plant genetic engineering.
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Progress 10/01/04 to 09/30/05
Outputs
4a What was the single most significant accomplishment this past year? The phytochrome (phy) family of sensory photoreceptors transduce informational light signals to selected nuclear genes, inducing plant growth and developmental responses appropriate to the environment. Existing data suggest that one signaling pathway by which this occurs involves direct, intranuclear interaction of the photoactivated phy molecule with PIF3, a basic helix-loop-helix transcription factor. We have provided evidence from newly identified pif3 mutant alleles that PIF3 is necessary for early chloroplast greening, and rapid phy-induced expression of nuclear genes encoding chloroplast components, upon first exposure of seedlings to light. The data indicate, therefore, that PIF3 functions to transduce phy signals to genes involved in a critical facet of the early seedling deetiolation process, the generation of a functional photosynthetic apparatus. Using transgenically expressed GUS:PIF3
fusion-protein constructs, we have found that PIF3 protein levels are rapidly and reversibly modulated by the photoreceptor over diurnal cycles in Arabidopsis seedlings. The PIF3 protein declines rapidly to a basal steady-state level upon initial light exposure, but reaccumulates to pre-irradiation levels in darkness during the subsequent night period. The data suggest that PIF3 may function in early phy signaling at the dark-to-light transition, not only during initial seedling deetiolation, but daily at dawn under diurnal light-dark cycles (Monte et al. (2004) Proc. Natl. Acad. Sci. 101: 16091-16098). 4d Progress report. This report serves to document research conducted under a Non-Funded Cooperative Agreement between ARS and UC Berkeley. Additional details of research can be found in the report for the parent project (5335-21000- 017-00D). Progress has been made in deciphering the function of genes that are required for growth and reproduction and in response to environmental
signals. Two genes that function in maize inflorescence development were cloned based on their chromosomal position. One encodes a LOB domain protein and one encodes a microRNA. A gene that regulates meristem size was cloned in Arabidopsis. It functions to organize the stem cells of the meristem. A function for a pollen receptor kinase was determined from overexpression studies. The results link the kinase, which functions at the cell surface to the actin cytoskeleton inside the cell. The function of an Arabidopsis protein, OXS2, was found to be a novel transcription factor. The cytoplasmic form promotes vegetative growth and represses flowering whereas the stress-dependent nuclear form triggers stress tolerance and floral transition. The function of SUN1 in tomato was determined. It mediates resistance signaling for a number of pathogens, including bacterial, fungal and viral pathogens. The results show that R gene-mediated pathways and general resistance pathways intersect or
overlap. The Bs4 gene, which provides resistance against Xanthomonas campestris pv. vesicatoria (Xcv), was also cloned. The ACS genes encode enzymes in the ethylene biosynthetic pathway. A pentuple mutant was constructed in Arabidopsis using single T-DNA insertions lines in five different ACS genes. The mutant plant is taller, bolts earlier but its resistance to diseases is the same compared to the wild type plants. Finally, the function of PHYTOCHROME INTERACTING FACTOR 3 (PIF3) was determined by reverse genetics. It is necessary for early chloroplast greening, and rapid phy-induced expression of nuclear genes encoding chloroplast components, upon first exposure of seedlings to light. Progress has been made in identifying promoters that function at specific developmental times. We have identified promoters that function in sperm and egg cells. Progress has also been made in developing alternative recombination systems for transgenic plants. Identification of genes that regulate the
maize inflorescence.
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