“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).

Foxtail millet, Setaria italica, has the full set of attributes that make it a model plant for basic and applied studies, particularly for its close relatives like switchgrass, an important bioenergy crop. 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.

Ferulic acid residues attached to arabinoxylans, a major component of cell wall of grasses, have the ability to form ferulate dimers functioning in cell wall cross-linking. They are also proposed to act as nucleation sites for the formation of lignin and for the linkage of lignin to the xylan/cellulose network. Such coupling reactions, which occur predominantly in grasses, significantly decrease cell wall degradability and thus work as a barrier against efficient utilization of cell walls as a source of biomass for bioenergy production.

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.

While current production of ethanol as a biofuel relies on starch and sugar inputs, it is anticipated that sustainable production of ethanol for biofuel use will utilize lignocellulosic feedstocks. Candidate plant species to be used for lignocellulosic ethanol production include a large number of species within the Grass, Pine and Birch plant families. For these biofuel feedstock species, there are variable amounts of genome sequence resources available, ranging from complete genome sequences (e.g. sorghum, poplar) to transcriptome data sets (e.g. switchgrass, pine). These data sets are not only dispersed in location but also disparate in content. It will be essential to leverage and improve these genomic data sets for the improvement of biofuel feedstock production.

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.

In the production of biofuels from lignocellulosic biomass, glucose, xylose and other sugars are released from plant cell walls by hydrolytic enzymes. Dramatic improvements in the rates and final yields of sugar release (saccharification potential) are required, as complex patterns of polysaccharide modification and cross-linking interfere with the ability of the hydrolytic enzymes to release sugars, and some modifications result in products inhibitory to fermentative bacteria.

Non-cellulosic polysaccharides of grass walls are potentially abundant sources of glucose and xylose if the structures are made more accessible by genetic manipulation. Switchgrass is targeted to become a future biomass crop, but the discovery of genes underlying biomass-relevant traits is compromised in switchgrass by the paucity of genetic resources. Maize provides a genetic resource for improvement of distinct cell walls of switchgrass and other energy grasses.

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).

Most vascular flowering plants have the ability to form symbiotic associations with arbuscular mycorrhizal (AM) fungi. The symbiosis develops in the roots and can have a profound effect on plant productivity, largely through improvements in plant mineral nutrition. Within the root cortical cells, the plant and fungus create novel interfaces specialized for nutrient transfer, while the fungus also develops a network of hyphae in the rhizosphere. Through this hyphal network, the fungus acquires and delivers phosphate and nitrogen to the root. In return, the plant provides the fungus with carbon. In addition, to enhancing plant mineral nutrition, the AM symbiosis has an important role in the carbon cycle, and positive effects on soil health.

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).

The cell wall is a distinguishing feature of plants. It is a complex composite of polysaccharides, proteins, and lignin, with lignin and cellulose representing two of the most abundant bio-organic compounds on the planet.

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).

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).

Sunflower is a North American native plant which thrives in semi-arid and arid habitats and produces high biomass yields in cultivation when water and other inputs are non-limiting. While sunflower is a globally important oilseed grown on 24 million hectares worldwide, and is primarily known to US consumers as an ornamental and confectionery plant, this species has significant potential for biofuel production. Several wild species produce woody stems with chemical properties similar to poplar and are excellent sources of natural genetic diversity for enhancing cellulosic biomass yields and wood production in sunflower.

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).

Despite its obvious importance in plant development and stress responses, relatively little is known about how the global regulation of gene expression at the transcriptional level in plants is achieved. This project will pursue a hypothesis-generating approach to better understand the gene regulation networks underlying traits of major importance for both the quality and quantity of biomass. The exceptional recent developments of genomics resources in Brachypodium distachyon enables a new approach to discovery and manipulation of transcriptional control mechanisms in grasses including bioenergy feedstock crops.

The goals of this project are to design a Brachypodium genome array, make it available for commercial manufacture and distribution to any researcher, and then use these arrays to map major gene expression changes of relevance to important traits of grass crops.

“Epigenomics of Development in Populus”. Oregon State University, $1,200,000; Principal Investigator: Steven Strauss; Co-Principal Investigators: Todd Mockler, Michael Freitag.

Epigenetics is defined by long-lasting or heritable changes in gene expression that are not associated with changes in DNA sequence. It is mainly reflected in methylation of DNA and chemical changes in DNA-associated chromosomal proteins such as histones. Recognition of its importance as a means for control of plant development has increased significantly in recent years, however, little is known about epigenetic controls in the life of trees and other woody plants.

Many traits important to biomass growth and adaptability in trees may be under epigenetic control, thus may be useful for their breeding and biotechnology. This includes timing of flowering and flower structure; dormancy induction and release; shoot and leaf architecture; amenability to organ regeneration; stress tolerance; and phase-associated changes in wood structure.

This project will use poplar (genus Populus, including aspens and cottonwoods), because it has been designated as a model woody biomass species for genomic studies, and is a major source of wood, energy, and environmental services in the USA and throughout the world. It will characterize epigenetic changes in DNA methylation and two kinds of histone modification via a combination of antibody-based chromatin immunoprecipitation and DNA sequencing (“ChIP-sequencing”).