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Genomic Science Program

2006 Awardee

Genomic Knowledgebase for Facilitating the Useof Woody Biomass for Fuel Ethanol Production


INSTITUTION: North Carolina StateUniversity

NON-TECHNICAL SUMMARY: Situation andProblem: (A) Wood in forest trees is a major, potentiallignocellulosic material for ethanol. (B) Trees canpotentially be modified with a genome-wide approach fortraits to overcome virtually any major biomass conversionbarrier to ethanol production. (C) Gene expression andregulation of plant traits suited to ethanol production ispoorly understood. Purpose: (A) This project examines, atthe genome level, gene expression and regulation oflignocellulosic formation in Populus trichocarpa, atargeted energy tree crop. (B) The purpose of this projectis to establish a knowledgebase about the possible genesand transcription factor genes involved in lignocellulosicformation and those genes that may enable effectivemanipulation of lignocellulosic traits to facilitateethanol production.

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

APPROACH: (1) Chemical, biochemical andmorphological profiling of TW development in Populus :Wildtype and transgenics will be propagated for arraycharacterization. For the TW system, we will profile cellwall trait changes at several different stages along thedevelopment of TW in Nisqually-1. These include cellulose,xylan, and lignin contents, lignin S/G ratios, xylansynthase activity, key lignin pathway gene transcriptlevels and enzyme activities, vessel/fiber ratios and TWfiber formation. These profiles reflecting changes due topreferential processes for the particular cell wall traitswill guide microarray analyses to identify the involvinggenes and transcription factor genes and theircontributions to these processes. (2) Oligo-microarrayprofiling of transgenics and TW development in Populus :RNAs from developing xylem of wildtype and selectedtransgenic P. tremuloides lines will be characterized bythe updated full Populus transcriptome oligo-microarrays.RNAs from the developing xylem of the TW development stageswith known cell wall trait/property profiles, will becharacterized by the full genome microarrays. These RNAswill also be analyzed by miRNA oligo-microarrays designedwith probes for detecting mature miRNAs that are mostlyrelated to xylem development. Three biological replicateswill be used in all array experiments. Differentiallyexpressed genes will be determined and their transcriptvariation profiles between distinct transgenic levels orvarious TW developmental states will be correlated with thecell wall trait profiles to identify the proposed genes andgenes encoding transcription regulators. (3) In vitrofunctional analysis of putative Populus xylan synthasegenes: The array-selected and qRT-PCR confirmed putativexylan synthase genes will be expressed in our establishedDrosophila S2 cell system and the gene products will becharacterized for biochemical functions. (4) Genefunctional analysis in transgenic P. trichocarpa : We willselect three transcription factor genes that may coordinatelignocellulosic accumulation and two miRNA genes that mayregulate vessel and fiber cell development foroverexpression in transgenic Nisqually-1 to determine theirfunctions.


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



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