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Genomic Science Program

2007 Awardee

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

INVESTIGATOR: Pamela J.Green

INSTITUTION: University of Delaware

NON-TECHNICAL SUMMARY: MicroRNAs (miRNAs) and siRNAs aresmall 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 thegenes, the mRNAs. This project will examine the small RNAs and mRNAs associatedwith stresses such as drought, temperature and nutrient deprivation in Brachypodium dystachion , thus enhancing its value as a functional genomicmodel for energy crops and temperate grasses.

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

APPROACH: 1) Small RNA and mRNA libraries will be constructedand subjected to Sequencing by Synthesis (SBS) to a depth of about one millionreads.Mutants deficient in miRNA or siRNA production will identified from amongT-DNA insertion lines or constructed with RNAi. 2) Regulation of selectedmiRNAs and their cleaved targets will be examined gel blots and 5’ RACE,respectively. 3) Bioinformatics approaches will facilitate sequence comparisonsbetween Brachypodium and related plants such as switchgrass. 4) A databasewill be constructed and a user-friendly web interface will be developedto make the data publicly available.

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

 

Funding Announcement DE-FOA-0001865:
Systems Biology of Bioenergy-Relevant Microbes to Enable Production of Next-Generation Biofuels and Bioproducts.
Pre-App required 01/08/2018, 5 PM Eastern [12/17]

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