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United States Department of Agriculture

Agricultural Research Service

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Research Project: Non-Funded Cooperative Agreement Between University of California, Berkeley and U.S. Department of Agriculture,agricultural Research Service

Location: Plant Gene Expression Center Albany_CA

2012 Annual Report


1a.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.


1b.Approach (from AD-416):
1. The Plant Gene Expression Center (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 comprises 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 who reports to the Dean, College of Natural Resources, UCB, and who shall be appointed by the Dean for a five-year term.

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.


3.Progress Report:

This research contributes to all objectives of the research projects being carried out by PGEC scientists. This project relates to plants responding to light signals informing them of imposed or impending vegetative shade, via the phytochrome (phy) photoreceptor system, by adaptive changes in growth and development, collectively termed the shade avoidance syndrome (SAS). To examine the roles of the Phy-Interacting bHLH Factors, PIF1, 3, 4 and 5, in relaying this perceived information to the transcriptional network, we compared the genome-wide transcription profiles of wild-type and quadruple pif (pifq) mutants in response to shade. The data identify a subset of genes, enriched in transcription-factor-encoding loci, that respond rapidly (within 1 h), in a PIF-dependent manner, to the shade signal, and that contain promoter-located G-box-sequence motifs (CACGTG), known to be preferred PIF binding sites. These genes are thus potential direct targets of phy-PIF signaling that function in the primary transcriptional circuitry that controls downstream response elaboration. A second subset of PIF-dependent, early-response genes, lacking G-box motifs, are enriched for auxin-responsive loci, suggestive of being indirect targets of phy-PIF signaling involved in the rapid cell-expansion responses known to be induced by shade. A meta-analysis comparing deetiolation- and shade-responsive transcriptomes identifies a further subset of G-box-containing genes that reciprocally display rapid repression and induction in response to light and shade signals at the inception of deetiolation and shade-avoidance, respectively. These data define a core set of transcriptional and hormonal (auxin, cytokinin) processes that appear to be dynamically poised to react rapidly to changes in the light environment in response to perturbations in the mutually antagonistic regulatory activities of the phys and PIFs. Data from comparative analysis of the quadruple pifq and all triple pif-mutant combinations in response to light and shade, confirm that the PIF-quartet members act with overlapping redundancy on seedling morphogenesis and transcriptional regulation, but that the individual PIFs contribute differentially to these responses.


Last Modified: 7/30/2014
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