USDA and DOE Fund 10 New Projects for Biomass Genomics Research

“Development of Genomic and Genetic Tools for Foxtail Millet, and Use of These Tools in the Improvement of Biomass Production for Bioenergy Crops”

University of Georgia, $1,295,000
Principal Investigator: Jeff Bennetzen
Co-Principal Investigators: Katrien Devos; Andrew Doust (Oklahoma State University); Janice Zale (University of Tennessee)
Project Goal: This project will generate a variety of genomic and genetic tools for foxtail millet, including SNPs, BAC libraries, optimized foxtail millet transformation technology, and a high density QTL and genetic map of foxtail millet for significant biomass traits. These resources will complement the DOE Joint Genome Institute whole genome sequencing of foxtail millet, enhancing its value as a functional genomic model for second generation bioenergy crops such as switchgrass.

“Identifying Genes Controlling Ferulate Cross-Link Formation in Grass Cell Walls”

Pennsylvania State University, $587,191
Principal Investigator: Marcia Maria de Oliveira Buanafina
Co-Principal Investigators: David Braun, Doug Archibald
Project Goal: This project will investigate the regulation of ferulic acid cross-linking in the cell walls of Brachypodium distachyon, and generate a saturated EMS mutant population for forward genetic studies in this model bioenergy crop.

“Computational Resources for Biofuel Feedstock Species”

Michigan State University, $540,000
Principal Investigator: C. Robin Buell
Co-Principal Investigator: Kevin Childs
Project Goal: This project will provide computational tools and resources for data-mining of genome sequence, genome annotation, and large-scale functional genomic datasets available for biofuel feedstock species.  Such species include candidates within the Poaceae, Pinaceae, and Salicaceae families, for which a diversity of genome sequence resources currently exist, ranging from whole genome sequences to modest EST transcriptome datasets.

“Translational Genomics for the Improvement of Switchgrass”

Purdue University, $1,200,000
Principal Investigator: Nick Carpita
Co-Principal Investigator: Maureen McCann
Project Goal: This project will study the cell walls of grass species, performing bioinformatics analyses on cell wall biosynthetic genes in maize, and annotation of switchgrass orthologs.  The project will also generate mutants in selected candidate cell wall-related genes, with direct analysis of saccharification of maize and switchgrass cell wall mutants.

“Identification of Genes That Regulate Phosphate Acquisition and Plant Performance During Arbuscular Mycorrhizal Symbiosis in Medicago Truncatula and Brachypodium Distachyon”

Boyce Thompson Institute for Plant Research, $882,000
Principal Investigator: Maria Harrison
Co-Principal Investigator: Matthew Hudson (University of Illinois)
Project Goal: This project will identify genes controlling arbuscular mycorrhizal symbiosis, as well as key factors regulating gene function and the acquisition of key nutrients such as phosphate. The results will provide mechanistic and molecular-level understanding of plant-fungal partnerships in natural ecosystems and their role in maintaining a terrestrial soil environment for sustainable biofuel production.

“Systems Level Engineering of Plant Cell Wall Biosynthesis to Improve Biofuel Feedstock Quality”

University of Massachusetts, $1,200,000
Principal Investigator: Samuel Hazen
Co-Principal Investigator: Todd Mockler (Oregon State University), Steve Kay (UC San Diego)
Project Goal: This project will identify and characterize cell wall biosynthetic regulatory genomic binding sites, using reverse and forward genetic approaches with candidate transcription factors in Brachypodium and Arabidopsis, two model plant systems.  The results will contribute to our understanding of key tissue-specific and developmental regulators of plant cell wall biosynthesis in monocot and dicot bioenergy crops.

“Identification of Genes that Control Biomass Production Using Rice”

Colorado State University, $1,500,000
Principal Investigator: Jan Leach
Co-Principal Investigators: Dan Bush, John McKay; Hei Leung (IRRI)
Project Goal: This project will provide an integrated breeding and genomics platform to identify biomass traits in rice, for translation to second generation bioenergy grasses such as switchgrass and Miscanthus.

“Genomics of Wood Formation and Cellulosic Biomass Traits in Sunflower”

University of Georgia, $1,200,000
Principal Investigator: Stephen Knapp
Co-Principal Investigators: Jeff Dean, Joe Nairn; Laura Marek (Iowa State University), Mark Davis (NREL)
Project Goal: This project will develop genomic resources for woody biomass trait identification in hybrid sunflower, a species that is extremely drought tolerant. This fundamental knowledge will complement the existing body of work on this species with respect to oilseed production.

“A Universal Genome Array and Transcriptome Atlas for Brachypodium Distachyon”

Oregon State University, $1,200,000
Principal Investigator: Todd Mockler
Co-Principal Investigator: Todd Michael (Rutgers University)
Project Goal: This project will develop an Affymetrix genome tiling array, based on the DOE Joint Genome Institute sequence of Brachypodium distachyon, and make the array available for broad community use. The investigators will use the array to generate an expression atlas representing major developmental stages or stress responses in Brachypodium, a model species for polyploid, perennial grasses with complex genomes, such as wheat and switchgrass.

“Epigenomics of Development in Populus”

Oregon State University, $1,200,000
Principal Investigator: Steven Strauss
Co-Principal Investigators: Todd Mockler, Michael Freitag
Project Goal: The project will study the role of chromatin modification (epigenetics) in the regulation of development and dormancy induction in poplar and other woody species. The investigators will characterize changes in DNA methylation patterns on specific tissues during dormancy induction and poplar development.

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