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Genomic Science Program

Systems Biology for Energy and the Environment

Department of Energy Office of Science. Click to visit main DOE SC site.

Genomic Science Program

2006 Awardee

Genomic Knowledgebase for Facilitating the Use of Woody Biomass for Fuel Ethanol Production


INSTITUTION: North Carolina State University

NON-TECHNICAL SUMMARY: Situation and Problem: (A) Wood in forest trees is a major, potential lignocellulosic material for ethanol. (B) Trees can potentially be modified with a genome-wide approach for traits to overcome virtually any major biomass conversion barrier to ethanol production. (C) Gene expression and regulation of plant traits suited to ethanol production is poorly understood. Purpose: (A) This project examines, at the genome level, gene expression and regulation of lignocellulosic formation in Populus trichocarpa, a targeted energy tree crop. (B) The purpose of this project is to establish a knowledgebase about the possible genes and transcription factor genes involved in lignocellulosic formation and those genes that may enable effective manipulation of lignocellulosic traits to facilitate ethanol production.

OBJECTIVES: We propose a 3-year project to accomplish the following four objectives. (1) Chemical, biochemical and morphological profiling of TW development in Populus. (2) Oligo-microarray profiling of transgenics and TW development in Populus. (3) In vitro functional analysis of putative Populus xylan synthase genes. (4) Gene functional analysis in transgenic P. trichocarpa.

APPROACH: (1) Chemical, biochemical andmorphological profiling of TW development in Populus: Wildtype and transgenics will be propagated for array characterization. For the TW system, we will profile cell wall trait changes at several different stages along the development of TW in Nisqually-1. These include cellulose, xylan, and lignin contents, lignin S/G ratios, xylansynthase activity, key lignin pathway gene transcript levels and enzyme activities, vessel/fiber ratios and TW fiber formation. These profiles reflecting changes due to preferential processes for the particular cell wall traits will guide microarray analyses to identify the involving genes and transcription factor genes and their contributions to these processes. (2) Oligo-microarray profiling of transgenics and TW development in Populus:RNAs from developing xylem of wildtype and selected transgenic P. tremuloides lines will be characterized by the updated full Populus transcriptome oligo-microarrays. RNAs from the developing xylem of the TW development stages with known cell wall trait/property profiles, will be characterized by the full genome microarrays. These RNAs will also be analyzed by miRNA oligo-microarrays designed with probes for detecting mature miRNAs that are mostly related to xylem development. Three biological replicates will be used in all array experiments. Differentially expressed genes will be determined and their transcript variation profiles between distinct transgenic levels or various TW developmental states will be correlated with the cell wall trait profiles to identify the proposed genes and genes encoding transcription regulators. (3) In vitro functional analysis of putative Populus xylan synthase genes: The array-selected and qRT-PCR confirmed putative xylan synthase genes will be expressed in our established Drosophila S2 cell system and the gene products will be characterized for biochemical functions. (4) Gene functional analysis in transgenic P. trichocarpa: We will select three transcription factor genes that may coordinate lignocellulosic accumulation and two miRNA genes that may regulate vessel and fiber cell development for overexpression in transgenic Nisqually-1 to determine their functions.


Name: Vincent Chiang
Phone: 919-513-0098
Fax: 919-515-7801


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