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United States Department of Agriculture

Agricultural Research Service

Research Project: Agricultural Crop Improvement Through Genomic and Molecular Research on Mechanisms of Plant Growth and Adaption to a Changing Environment

Location: Plant Gene Expression Center Albany_CA

2009 Annual Report


1a.Objectives (from AD-416)
Determine the molecular mechanisms by which plants perceive and respond to developmental, biotic and abiotic signals throughout the life cycle to enhance the quality and production efficiency of agriculturally important crops.


1b.Approach (from AD-416)
A combination of modern molecular, genetic, genomic, proteomic and bioinformatic approaches will be used to address this multifaceted problem. Particular emphasis will be placed on identifying signaling components, regulatory genes and transcriptional networks involved in controlling plant responses to developmental, biotic and abiotic signals. Genes that respond to light under control of the phytochrome photosensory system will be identified and the regulatory mechanisms defined. Genes involved in regulating the circadian clock will be identified and functionally defined. Genes controlling vegetative and reproductive development will be identified and characterized. Plant hormone function in mediating growth and developmental responses will be explored. Genes involved in plant responses to biotic and abiotic challenges will be identified and characterized. On an ongoing basis, cutting-edge strategies and technologies in areas such as targeted reverse-genetic gene disruption, high-density microarray analysis, and biocomputational approaches, will be assimilated and will be identified and characterized. Documents SCA with UC Berkeley.


3.Progress Report

An 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.

An 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.

An 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.

An 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..

An 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.

An 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.

An 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.

An 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.


Last Modified: 7/28/2014
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