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Genomic Science Program

Systems Biology for Energy and the Environment

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Genomic Science Program

2007 Awardee

Analysis of Small RNAs and mRNAs Associated with Abiotic Stress Responses in Brachypodium distachyon

INVESTIGATOR: Pamela J. Green

INSTITUTION: University of Delaware

NON-TECHNICAL SUMMARY: MicroRNAs (miRNAs) and siRNAs are small RNAs that regulate genes under certain conditions or in certain tissues. In plants, they usually act by decreasing the levels of the first product of the genes, the mRNAs. This project will examine the small RNAs and mRNAs associated with stresses such as drought, temperature and nutrient deprivation in Brachypodium dystachion, thus enhancing its value as a functional genomic model for energy crops and temperate grasses.

OBJECTIVES: 1) Identify and determine abundance information for millions of Brachypodium small RNAs and mRNAs from stressed and control plants,and from plants deficient in the production of most miRNAs (dcl1) or most siRNAs (rdr2). 2) Characterize the regulation and mRNA cleavage products of selected miRNAs that are related to specific stresses. 3) Compare the Brachypodium data to more limited information from switchgrass to identify conserved and nonconserved miRNAs. 4) Provide public access to the data through a web interface.

APPROACH: 1) Small RNA and mRNA libraries will be constructed and subjected to Sequencing by Synthesis (SBS) to a depth of about one million reads. Mutants deficient in miRNA or siRNA production will identified from among T-DNA insertion lines or constructed with RNAi. 2) Regulation of selected miRNAs and their cleaved targets will be examined gel blots and 5’ RACE, respectively. 3) Bioinformatics approaches will facilitate sequence comparisons between Brachypodium and related plants such as switchgrass. 4) A database will be constructed and a user-friendly web interface will be developed to make the data publicly available.

PROJECT CONTACT:
Name: Pamela J. Green
Email: green@dbi.udel.edu

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