DOE-USDA Plant Feedstock Genomics for Bioenergy Program 2006-2018

The Department of Energy’s (DOE) Office of Biological and Environmental Research has teamed with the U.S. Department of Agriculture (USDA) National Institute of Food and Agriculture’s Agriculture and Food Research Initiative to fund projects that accelerate plant breeding programs and improve biomass feedstocks by characterizing the genes, proteins, and molecular interactions that influence biomass production.

Biomass feedstocks are fast-growing trees, shrubs, and grasses that are bred for the specific purpose of producing energy (electricity or liquid fuels) from all or part of the resulting plant. For biofuels to become economically viable as mainstream fuels, the total amount of lignocellulosic biomass produced per acre per year must be maximized, as does the amount of fuel produced per unit of biomass. At the same time, these crops must be environmentally sustainable, requiring far fewer inputs—pesticide and herbicide applications, fertilizer, water, and the use of energy-consuming farm equipment—than are needed, for example, for the corn and soybean crops currently used to produce ethanol and biodiesel.

Major agricultural crops grown today for food, feed, and fiber in the United States have not been bred for biofuels, so many carefully selected traits—such as a high ratio of seed to straw production—are disadvantageous in biofuel production. However, significant advances in breeding, molecular genetics, and genomic technologies provide an opportunity to build upon the existing knowledge base of plant biology to be able to confidently predict and manipulate the biological function of biomass feedstocks for bioenergy resources.

To capitalize on this potential, DOE and USDA initiated a competitive grant program in 2006 to support fundamental research in biomass genomics. Ultimately, the research seeks to develop and demonstrate environmentally acceptable crops and cropping systems for producing large quantities of low-cost, high-quality biomass feedstocks.

Program Goal

The overall goal is genomics-based research leading to improved use of biomass and plant feedstocks for the production of fuels, such as ethanol or renewable chemical feedstocks. Specific goals include:

  • Improve biomass characteristics, biomass yield, or sustainability, water and nitrogen use efficiency.
  • Understand carbon partitioning and nutrient cycling in feedstocks.
  • Enhance fundamental knowledge of structure, function, and organization of feedstock plant genomes.
  • Enable plants to be efficiently bred or manipulated for such use.

Evolution of the Program’s Scope

The USDA-DOE Joint Program supports basic research, including (1) regulation of gene networks, proteins, and metabolites; (2) comparative genomics; (3) systems biology; and (4) integration of genomics with more traditional approaches. With each funding year, the program’s scope has evolved to address different research areas. See focus areas by year(s) listed below.


  • Genomics-based research to identify and functionally characterize plant genes/alleles influencing plant response to pathogens, with a long-term focus on crop improvement.
  • Genomics-based research to identify and functionally characterize plant genes/alleles influencing agronomic, yield, and quality traits of non-food oilseed crops.


  • Discovery and characterization of key plant genes/alleles that confer disease resistance/tolerance.
  • Develop regionally adapted bioenergy feedstock cultivars with enhanced biomass yield and resistance/tolerance to pathogens.


  • Characterizing the genes, proteins, and molecular interactions that influence lignocellulosic biomass production and oil seed characteristics.
  • Complex interactions between bioenergy feedstocks and the environment.
  • Develop regionally adapted bioenergy feedstock cultivars.


  • Phenotyping for gene/allele discovery.
  • Phenomics (genotype-to-phenotype).


  • Regulatory mechanisms for carbon partitioning and nutrient cycling.


  • Regulatory mechanisms necessary for feedstock manipulation.
  • Sustainability and environmental stresses.
  • Comparative analysis and bioinformatics.


  • Regulatory mechanisms of lignocellulose and cell wall maintenance.
  • Genetic markers.
  • Genome organization.
  • Model plants.

Award Summaries by Year

2018: USDA and DOE Fund Six New Projects

Genetic Improvement of Seed Yield and Oil Content in Field Pennycress, a Nonfood Oilseed Feedstock

  • James Anderson, University of Minnesota, Minneapolis

Goal: Genetically improve seed size and seed oil content of field pennycress (Thlaspi arvense L.) for its use as a new winter annual cash cover crop for the U.S. Midwest. Pennycress is a winter hardy cover crop that provides ecosystem services such as reduced soil erosion and nutrient loss in between fall corn harvest and spring soybean planting. Unlike traditional cover crops, field pennycress produces a mature oilseed in late spring, allowing farmers to harvest two cash crops in one year. Wild-derived pennycress lines have been shown to yield 1,500 kilograms per hectare on average. Pennycress seeds contain about 33% oil by weight, and the oil is an excellent biofuels feedstock. After pressing, the remaining pennycress meal could be used as animal feed. However, despite these environmental and economic benefits, pennycress is currently limited by its seeds’ small size (1 milligram per seed), which can complicate planting, harvesting, and handling. With pennycress domestication well under way, the goal is to identify, characterize, and introgress into breeding lines the traits that will improve pennycress efficiency and utility as a biofuels feedstock, namely increased seed size and oil content. These two traits will be key for rapid commercialization of the species and will aid in the generation of high-yielding, elite pennycress varieties, greatly improving the economics of growing and processing pennycress.

Identifying Plant Genes Associated with Pathogen Antagonism in Populus trichocarpa

  • Posy Busby, Oregon State University, Corvallis

Goal: Manage plant microbiomes to promote disease antagonism, potentially complementing traditional methods of disease management and, thereby, enhancing productivity and sustainability in plant feedstock production for biofuels. Within plant leaves, beneficial microbes can reduce plant disease severity by enhancing the plant immune response or by combatting pathogens directly. This project will identify plant genes influencing the fungal species composition of the leaf microbiome of the feedstock crop Populus trichocarpa, focusing on fungi that reduce the severity of Melampsora leaf rust disease. The link between disease antagonism and plant genes will be tested explicitly using greenhouse manipulations and gene-knockout experiments. Results of this research will lay the groundwork for integrating disease antagonism into P. trichocarpa production for biofuels, while helping to develop a mechanistic understanding of host genetic control of disease antagonism in the leaf microbiome.

Breeding Resilient, Disease-Resistant Switchgrass Cultivars for Marginal Lands

  • John E. Carlson, Pennsylvania State University, University Park

Goal: Accelerate the development of superior, disease-resistant, climate-resilient switchgrass (Panicum virgatum L.) cultivars for expanding the range of biomass cultivation in the U.S. Northeast. Switchgrass is a fast-growing, perennial, warm-season grass native to much of North America, and it has great potential for development as a bioenergy crop. In the humid Northeast, however, fungal diseases are prevalent and may reduce crop yield and quality. This project will focus on anthracnose (caused by Colletotrichum navitas) and Bipolaris leaf spot (caused by Bipolaris oryzae), leveraging variation in mapping populations for these diseases. This research will be critical for future sustainable utilization of switchgrass in warm, humid northeastern environments that are prone to heavy disease pressure. The objectives are to (1) expand the breeding of superior, disease-resistant cultivars for high productivity in marginal environments in the Northeast; (2) discover genes for resistance to anthracnose and Bipolaris diseases and for biomass yield in switchgrass; and (3) identify associations between soil microbial communities, plant genotypes, and environmental factors that affect yield characteristics and disease susceptibility in switchgrass. The resources developed through this project will increase the efficiency of selection for disease resistance and, ultimately, improve plant health, biomass yield, and long-term bioenergy sustainability of switchgrass on marginal lands. The research also will improve understanding of the roles of both genotype and environmental factors on disease and plant productivity.

Uncovering Novel Sources of Anthracnose Resistance in Populations of Genetically Diverse Sorghums [Sorghum bicolor (L.) Moench]

  • Hugo Cuevas, USDA Agricultural Research Service Tropical Agriculture Research Station, Mayaguez, Puerto Rico

Goal: Build upon ongoing efforts to uncover additional anthracnose resistance loci present in the sorghum association panel (SAP) by using diverse sorghum germplasm available in two community resources: the U.S. National Plant Germplasm System (NPGS) exotic sorghum germplasm collection and the Nested Association Mapping (NAM) population. Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important grain crop after maize, wheat, rice, and barley. During the past decade, sorghum cultivation has expanded into the U.S. Southeast and the Caribbean, where it is of interest as a source of fermentable sugars for the production of renewable fuels and chemicals and of biomass for co-firing. Sorghum productivity and profitability are limited by several biotic constraints, most notably anthracnose caused by the fungal pathogen Colletotrichum sublineolum. The most cost-effective and environmentally benign strategy to control anthracnose is through the incorporation of resistance genes. Four previously identified resistance genes explain only a portion of the observed phenotypic variation in SAP, implying the presence of other resistance sources not detected due to their low frequency or because they were masked by overcorrection for population structure. Specifically, multi-location screening will be conducted for anthracnose resistance of 661 NPGS exotic tropical accessions tracing back to western and central Africa, and the set will be characterized by genotype-by-sequencing (GBS). Genomic data and anthracnose-resistance response data will then be merged with previously generated phenotypic and genomic data from SAP and two other core sets (from Ethiopia and Sudan) to identify novel resistance loci through a genome-wide association study of a combined ~1,200 accessions. In parallel, 449 Recombinant Inbred Lines (RILs) derived from two founder lines of the NAM population that are resistant to anthracnose will be evaluated against C. sublineolum pathotypes from Puerto Rico, Florida, Georgia, and Texas. High-density recombination linkage maps previously constructed based on GBS of the lines will be used to delimit genomic regions associated with resistance response. In addition, in-depth studies on the four newly identified novel resistance loci will be performed (1) by examining allelic variation at each locus among different resistant accessions and (2) by conducting high-throughput expression profiling studies of inoculated tissues harvested at different time points, followed by the identification of co-expressed genes to identify signaling cascades involved in the defense response. Lastly, this project will test the effects of each locus in providing anthracnose resistance by introgression of these four genes, alone or in different combinations, into a susceptible sweet sorghum. The ultimate goal of this project is to provide plant breeders with a catalog of resistance loci and informative molecular markers that enable breeders to select and use resistance sources providing maximum levels of resistance in the intended area of production to maximize yield potential.

Conserved Genetic Mechanisms for Biotic Stress in Sorghum

  • Tiffany Jamann, University of Illinois, Urbana-Champaign

Goal: Develop durable disease resistance for bioenergy crops, particularly crucial as the range of production expands and microbes evolve to become pathogens of these crops. Disease threats for new crops are expected to arise from contact with similar crop species. Setosphaeria turcica (synonomy, Exserohilum turcicum) can infect both maize and sorghum, yet isolates are host specific. Sorghum leaf blight (SLB), caused by S. turcica, is widespread and can decrease yields, reduce forage quantity and quality, and predispose plants to other diseases such as anthracnose (causal organism: Colletotrichum sublineolum). Host resistance is one of the most environmentally friendly and cost-effective methods of disease control, and resistance can be conserved across different plant species. By leveraging the knowledge of resistance in maize, this project will accelerate the improvement of resistance to S. turcica in sorghum, while also developing this as a system to understand how microbes evolve to become pathogens of bioenergy crops. Furthermore, genes can confer resistance to other pathogens when tested in new systems, and thus the team will assess the relationship between resistance to sorghum leaf blight and anthracnose. To achieve the overall objective of improving biotic stress resistance in sorghum, the project will use a paired strategy of identifying plant genes that will confer resistance and identifying fungal genes that are key deterrents of a host jump from corn to sorghum. Identifying the genes involved in this interaction will enhance the prospects for strategic deployment of sustainable host resistance-based approaches in bioenergy crops.

Enhanced Resistance Pines for Improved Renewable Biofuel and Chemical Production

  • Gary Peter, University of Florida, Gainesville

Goal: Increase constitutive terpene production to enhance loblolly and slash pine resistance to pests and pathogens. Today, the U.S. Southeast hosts the world’s largest biomass supply chain, annually delivering 17% of global wood products, more than any other country. This well-developed regional supply chain supports southern pine genetic improvement, seedling production and planting, silviculture, harvesting, and transportation, annually delivering ~250 million tons of pine wood to integrated manufacturing facilities. In the Southeast, 39 million acres of land not suited for food production are planted with genetically improved loblolly and slash pine seedlings selected and managed for fast growth and high wood yields. This region also houses the U.S. pine chemicals industry, the oldest and one of the largest renewable hydrocarbon chemical industries with favorable cost-competitiveness with petroleum-derived feedstocks. Enhanced resistance in these commercial species is critical to protect against widespread losses as biotic pressures increase due to global warming, land-use change and introduced exotic organisms. Pine terpenes evolved as a primary chemical and physical defense system and are a main component of a durable, quantitative defense mechanism against pests and pathogens. The terpene defense traits are under genetic control and can be improved by breeding and genetic engineering. The goal is to genetically increase constitutive terpene defenses of loblolly and slash pine to enhance protection against pests and pathogens and at the same time expand terpene supplies for renewable biofuels and chemicals. Objective one will integrate existing and new genome-wide association genetic results with RNA expression, quantitative trait locus mapping, and allele frequency information in known high-oleoresin flow selections and the project’s breeding populations to discover and validate loblolly and slash pine alleles and genes that are important for resistance. Objective two will use information from objective one to accelerate breeding for increased resistance in loblolly and slash pine through marker-assisted introgression, developing and testing genomic selection models to accelerate breeding of resistant slash pine.

2017: USDA and DOE Fund Six New Projects

Optimizing Tradeoffs Implicit During Bioenergy Crop Improvement: Understanding the Effect of Altered Cell Wall and Sugar Content on Sorghum-Associated Pathogenic Bacteria

  • Rebecca Bart, Donald Danforth Plant Science Center, St. Louis, MO
  • DOE BER–funded project $1,197,786

Goal: To establish the Sorghum-Xanthomonas pathosystem as a model for deducing how latent microbial pathogens might exploit key biofuel crop traits. This research will reveal the mechanisms underlying tolerance to pathogens that must be maintained during biofuel trait optimization, enhancing knowledge of the impact of bioenergy relevant traits on pathogen susceptibility. This is a necessary first step towards the development of novel routes for disease control that can be deployed in parallel with targeted alterations to sugar and cell wall composition during bioenergy crop improvement and breeding efforts.

Discovery and Characterization of Dosage-Dependent Disease Resistance Loci in Poplar

  • Luca Comai, University of California, Davis
  • USDA NIFA–funded project $1,000,000

Goal: To describe and characterize the genetic regulation of disease resistance in forest trees. The research will leverage a unique set of poplar hybrids containing defined insertions and deletions of specific chromosomal regions, enabling genome-wide scans for genes influencing susceptibility or resistance. Outputs will include a new, comprehensive description of the genetic regulation of disease response in poplar, identification of individual genes influencing disease response, and identification of potential genotypes and strategies for durable resistance.

Elucidating Mechanisms of Rust Pathogenesis for Engineering Resistance in Poplar

  • Edward Eisenstein, University of Maryland, College Park
  • DOE BER–funded project $1,088,771

Goal: To investigate the molecular basis for the virulence of Melampsora larici-populina towards Populus species. Genome-wide, high-throughput screens will be used to identify pathogen effectors that suppress host immunity, host factors that are targets of pathogen effectors, as well as the components of poplar nutrient homeostasis that are hijacked by the pathogen to establish disease. This information will shed new light on the mechanism of rust-poplar interactions, and will enable the construction of transgenic poplars as a resource for the research community to accelerate the evaluation of disease models.

Towards Durable Resistance to Septoria Stem Canker and Leaf Spot: A Molecular Understanding of Resistance

  • Jared LeBoldus, Oregon State University, Corvallis
  • DOE BER–funded project $1,197,892

Goal: To identify, validate, and functionally characterize alleles that confer resistance to Septoria canker and leaf spot in Populus. The proposed research will elucidate a major mechanism of resistance to Sphaerulina musiva, the major limiting factor to plantations in eastern North America. Genome-wide association mapping, CRISPR/Cas9, and protein-protein assays will be used, enabling marker-aided breeding, reducing costs, and accelerating development of resistant varieties.

Identification of Adaptive Fungal Pathogen Resistance Loci in Switchgrass

  • David Lowry, Michigan State University, East Lansing
  • DOE BER–funded project $1,144,104

Goal: To identify the genetic loci underlying switchgrass pathogen resistance and understand the distribution of pathogens across different ecoregions of the United States. This project will leverage existing plantings of switchgrass, from Texas to Michigan, to clarify the distribution of pathogen across latitudes and discover the loci responsible for resistance to those pathogens through quantitative trait locus (QTL) mapping and Genome Wide Association Studies (GWAS). Overall, this project will facilitate the development of regionally adapted switchgrass cultivars.

Advancing Field Pennycress as a New Oilseed Biofuels Feedstock That Does Not Require New Land Commitments

  • John Sedbrook, Illinois State University, Normal
  • USDA NIFA–funded project $1,000,000

Goal: To genetically improve the agronomic traits of Field Pennycress (Thlaspi arvense L.; pennycress) for its use as a new winter annual oilseed/meal/cover crop in the U.S. Midwest. Genes for desirable traits, including high seed yield, reduced glucosinolate, reduced seed coat fiber, and decreased time to maturity, will be identified, characterized, and introgressed into breeding lines to generate elite pennycress varieties for commercialization.

2016: USDA and DOE Fund Seven New Projects

Development of Resources and Tools to Improve Oil Content and Quality in Pennycress

  • Ana Alonso, Ohio State University, Columbus
  • DOE BER–funded project $1,165,226

Goal: To develop pennycress (Thlaspi arvense), a member of the Brassicaceae, as a bioenergy crop, taking advantage of its ability to produce seed oil that is ideally suited as a renewable source of biodiesel and aviation fuel. In this project, pennycress’ natural variation will be investigated to identify candidate genes and biomarkers associated with oil accumulation and fatty acid composition as well as metabolic engineering targets for improving oil content and composition. A public seed collection of pennycress mutants and transgenic lines will be developed as a community resource for accelerating research.

Developing Non-food Grade Brassica Biofuel Feedstock Cultivars with High Yield, Oil Content, and Oil Quality Suitable for Low Input Production Dryland Systems

  • Jack Brown, University of Idaho, Moscow
  • DOE BER–funded project $1,188,083

Goal: To develop oilseed Brassica cultivars with higher seed and oil yield, high oil quality, blackleg resistance, and low input costs. Novel genes for resistance to blackleg disease will be identified, and molecular marker assisted selection tools will be developed to accelerate Brassica breeding. Putative pattern recognition receptor (PRR) resistance genes so identified will be introgressed into adapted cultivar backgrounds to develop superior non-food grade oilseed cultivars with durable resistance, suitable for the Pacific Northwest and other U.S. regions.

Genomics and Phenomics to Identify Yield and Drought Tolerance Alleles for Improvement of Camelina as a Biofuel Crop

  • John Dyer, USDA Agricultural Research Service, Maricopa, AZ
  • USDA NIFA– funded project $1,000,000

Goal: Camelina sativa has received considerable attention as a potential nonfood biofuels crop, but significant challenges remain to develop stable, high-yielding, geographically adapted germplasm suitable for biofuels production. Advanced high-throughput phenotyping and genomics-based approaches will be used to discover useful gene/alleles controlling seed yield and oil content and quality in Camelina under water-limited conditions, and will identify high-yielding cultivars suitable for production in different geographical regions.

Genetics and Genomics of Pathogen Resistance in Switchgrass

  • Serge Edmé, USDA Agricultural Research Service, Lincoln, NE
  • DOE BER–funded project $1,019,326

Goal: To provide the genetic, molecular, physiological, and transcriptomic bases for imparting durable rust and viral disease resistance to switchgrass. This project leverages the differential performance of lowland (‘Kanlow,’ resistant) and upland (‘Summer,’ susceptible) cultivars under fungal rust (Puccinia emaculata, Uromyces graminicola) and viral (Panicum mosaic virus) disease pressures. Genomic selection will be applied across three generations of a ‘Summer’ x ‘Kanlow’ breeding population to develop prediction models for yield and disease traits, which will facilitate pyramiding key genes into released cultivars for durable resistance and ultimately improve the bioenergy potential of switchgrass through breeding and selection.

Resistance to Stalk Pathogens for Bioenergy Sorghum

  • Deanna Funnell-Harris, USDA Agricultural Research Service, Lincoln, NE
  • USDA NIFA–funded project $1,000,000

Goal: To discover host molecular pathways that enhance endophytic growth of stalk fungi and inhibit the developmental switch to pathogenic growth that frequently occurs under periods of prolonged abiotic stress in sorghum. Biomolecular markers for resistance will be identified that will significantly enhance efforts to develop superior bioenergy sorghum with resistance to increasing disease and environmental stresses.

Systems Biology to Improve Camelina Seed and Oil Quality Traits

  • Chaofu Lu, Montana State University, Bozeman
  • DOE BER–funded project $1,196,335

Goal: To increase Camelina seed size and oil content for improved seedling establishment and oil yield, and to optimize oil quality for satisfactory fuel properties. In this project, quantitative trait loci (QTLs) and molecular markers associated with these important traits will be identified using high-density genome maps and repeated field trials in Montana and Washington states. Modern genomics and biotechnological approaches will be employed to uncover novel molecular mechanisms (including genes and gene networks regulated by microRNAs and transcription factors) regulating fatty acid modification, oil accumulation and seed size in Camelina.

Introgression of Novel Disease Resistance Genes from Miscanthus into Energycane

  • Erik Sacks, University of Illinois, Champaign-Urbana
  • DOE BER–funded project $1,198,898

Goal: To improve energy cane productivity and sustainability by providing resistance to key diseases through introgression of novel genes from Miscanthus into a Saccharum background. In this project, F1 miscanes (Miscanthus x sugarcane) will be backcrossed to sugarcane several times, and molecular markers associated with the disease resistance will be identified. Genetics studies will be conducted to determine if the resistance is conferred by one or few genes of large effect, many genes of small effect, or a combination of both large and small effect genes, enabling an optimized marker-assisted selection strategy.

2015: USDA and DOE Fund Five New Projects

Physiological and Molecular-Genetic Characterization of Basal Resistance in Sorghum

  • Peter Balint-Kurti, North Carolina State University, Raleigh
  • DOE BER–funded project $890,800

Goal: To identify loci and alleles that will be helpful for breeders in producing more robust sorghum lines designed for biomass production. In this project, assays will be developed and used to screen diverse sorghum germplasm for variation in the defense response and disease resistance and to identify genes associated with this variation, which will be used to develop quantitative, durable disease resistance for improved bioenergy sorghum.

Genomic Dissection of Anthracnose Resistance Response in Sorghum [Sorghum bicolor (L.) Moench]

  • Hugo Cuevas, USDA ARS Mayaguez, Puerto Rico
  • DOE BER–funded project $856,200

Goal: To identify anthracnose resistance loci from diverse sorghum germplasm, establish against which pathotypes the resistance alleles at these loci protect, and determine the underlying disease resistance mechanism. This work will allow dissection of the anthracnose resistance response into its multiple gene components and further understanding of the host/pathogen relationship present in different sorghum types to accelerate breeding and provide plant breeders with a tool kit that provides maximum levels of resistance in the intended area of production.

Characterizing the Defense Hierarchy of Populus trichocarpa and its Hybrids

  • George Newcombe, University of Idaho, Moscow
  • DOE BER–funded project $1,200,000

Goal: To develop an integrative, hierarchical model of P. trichocarpa defense that integrates genetic resistance and defense mutualists. This study will test the placement of several factors that contribute to rust resistance under different circumstances, including major and minor plant resistance genes, plant defense compounds, direct competitors, and defense mutualists within the microbiome. The goal is to develop disease management strategies that harness both resistance genes and naturally occurring defense mutualists of P. trichocarpa, maximizing plant resistance and productivity while minimizing impacts on the surrounding ecological landscape.

Genomics-Assisted Breeding for Leaf Rust (Melampsora) Resistance in Shrub Willow (Salix) Bioenergy Crops

  • Larry Smart, Cornell University, Ithaca NY
  • USDA NIFA–funded project $1,000,0000

Goal: To identify genes involved in rust resistance in willow that may be introgressed into new, improved willow cultivars through hybridization. This study will also generate molecular markers linked to those rust resistance genes that can be used in the early selection of resistant seedlings in breeding programs. The ultimate goal is to develop willow cultivars with improved rust resistance that result in greater yields, wider adoption of willow bioenergy crops, and increased production of renewable energy.

Parallel analysis of Puccinia emaculata Virulence and Switchgrass Resistance Phenotypes

  • Shavannor Smith, University of Georgia, Athens
  • USDA NIFA–funded project $1,000,000

Goal: To identify candidate effector genes in P. emaculata that interact with specific switchgrass resistance genes, and to develop and to test models of these interactions on switchgrass cultivars infected with field rust isolates. This study will reveal new strategies for generating more durable resistance to P. emaculata and other pathogens. Moreover, it can provide the knowledge base for the development of diagnostic tools for rapidly assessing the nature of a field P. emaculata isolate, thus identifying the host resistance cultivars that will exhibit the optimal resistance to the field pathogen populations at any given location.

2014: USDA and DOE Fund Ten New Projects

Coordinated Genetic Improvement of Bioenergy Sorghum for Compositional and Agronomic Traits

  • Patrick Brown, University of Illinois, Urbana-Champaign
  • DOE BER–funded project $1,339,800

Goal: Discover and characterize novel genetic variants that affect lignocellulosic composition and saccharification yield in bioenergy feedstock grasses without compromising agronomic performance. This project will characterize genetic variation in compositional and agronomic traits in a panel of 600 diverse sorghum inbreds and identify useful traits and variants that will guide and accelerate the genetic improvement of both bioenergy sorghum and closely related perennial grasses.

Abiotic Stress Networks Converging on FT2 to Control Growth in Populus

  • Amy Brunner, Virginia Polytechnic Institute and State University, Blacksburg
  • DOE BER–funded project $1,430,400

Goal: Uncover divergent and convergent regulatory networks that control growth responses to daylength and nutrient stress in poplar. Regulation of growth and dormancy by such seasonal and episodic environmental factors is of central importance to productivity in temperate tree species. This project will characterize genome-wide gene expression changes in response to day length and nutrient stress and identify protein-protein and protein-DNA networks that are centered on FT2, a key integrator of multiple abiotic signaling pathways in Populus.

Exploiting Natural Diversity to Identify Alleles and Mechanisms of Cold Adaptation in Switchgrass

  • Robin Buell, Michigan State University, East Lansing
  • USDA NIFA–funded project $1,000,000

Goal: Identify metabolites, alleles, transcripts, and regulatory RNAs associated with cold hardiness in switchgrass that will advance understanding of the biochemical, physiological, and molecular mechanisms for cold adaptation and provide molecular tools to improve breeding efficiency. Switchgrass biomass yields could potentially be increased by extending the northern range in which lowland ecotypes are grown, but these types are not cold tolerant and have low survival rates outside their adapted range. This project will identify genes and alleles relevant to cold hardiness that can be incorporated rapidly into switchgrass breeding programs to increase biomass and survival in northern latitudes.

A Novel Poplar Biomass Germplasm Resource for Functional Genomics and Breeding

  • Luca Comai, University of California, Davis
  • DOE BER–funded project $1,274,800

Goal: Further develop the poplar indel germplasm collection and use it to investigate the role of gene dosage in poplar hybrid performance and contribution to bioenergy traits. This project will catalog dosage variation in ~500 Populus deltoides × P. nigra F1 individuals, use field trials to characterize variation for traits central to sustainable production of biomass with optimal feedstock properties, and identify specific regulatory or functional gene modules underlying phenotypes of interest, ultimately to produce new cultivars directly usable for bioenergy applications.

Genetic Dissection of AM Symbiosis to Improve the Sustainability of Feedstock Production

  • Maria Harrison, Boyce Thompson Institute for Plant Research, Ithaca, NY
  • DOE BER–funded project $864,400

Goal: Understand the genetic bases of arbuscular mycorrhizal (AM) symbiosis in feedstocks through studies of a model feedstock species, Brachypodium distachyon, and sorghum, a feedstock species. This project will utilize Brachypodium to evaluate the function of candidate proteins that potentially control development of the symbiosis and symbiotic P and N transport, and then evaluate AM symbiosis in diverse sweet and cellulosic (bioenergy) sorghum lines. This research will inform feedstock breeding programs and enhance the sustainability of feedstock production.

Advancing Field Pennycress as a New Oilseed Biodiesel

  • Michael Marks, University of Minnesota, Minneapolis
  • USDA NIFA–funded project

Goal: Genetically improve the agronomic traits of field pennycress (Thlaspi arvense L.) for its use as a new winter annual oilseed/meal/cover crop in the Upper Midwest. Pennycress can be double-cropped on the same land during the time between the traditional corn harvest and subsequent planting of soybeans the following spring. This oilseed plant holds much agronomic promise, but improved domesticated varieties remain to be developed. The project will lead to superior, higher-yielding pennycress varieties grown as a winter oilseed crop integrated within corn-soybean rotations throughout the Midwest.

Biofuels in the Arid West: Gemplasm Development for Sustainable Production of Camelina Oilseed

  • John McKay, Colorado State University, Fort Collins
  • DOE BER–funded project $1,487,200

Goal: Facilitate the development of Camelina as an oilseed feedstock crop that can be grown on marginal farmland with relatively low fertilizer inputs and no irrigation. Camelina has many optimal qualities as an oilseed feedstock, but its performance as a fuel with minimal processing can be improved. Leveraging the newly available genome sequence of Camelina sativa, this project will use forward and reverse genetics and natural variation to combine optimal qualities in Camelina as an oilseed feedstock for the Great Plains and Western United States.

The Brachypodium ENCODE Project—From Sequence to Function: Predicting Physiological Responses in Grasses to Facilitate Engineering of Biofuel Crops

  • Todd Mockler, Donald Danforth Plant Science Center, St. Louis, MO
  • DOE BER–funded project $1,498,600

Goal: Identify and characterize the functional elements associated with progressive drought response in the Brachypodium distachyon genome sequence and develop integrated genome feature maps that will enable advanced modeling of complex pathways in plants. Using a model grass, the Brachypodium ENCODE (for Encyclopedia of DNA Elements) project will elucidate the molecular mechanisms and gene regulatory networks underlying drought stress, information which will aid basic and applied research on a wide range of bioenergy grasses and accelerate deployment of improved bioenergy grass feedstocks.

Genomics of Energy Sorghum‘s Water Use Efficiency / Drought Resilience

  • John Mullet, Texas A&M University, College Station
  • DOE BER–funded project $1,230,600

Goal: Increase the water use efficiency, drought resilience, and yield of high biomass energy Sorghum and other C4 bioenergy grasses. This project will use field analysis to identify traits and molecular responses that improve water use efficiency and drought resilience of energy Sorghum and characterize genetic variation, and then test the utility of modulating these traits in energy Sorghum hybrids through marker-assisted breeding.

Quantifying Phenotypic and Genetic Diversity of Miscanthus sacchariflorus to Facilitate Knowledge of Directed Improvement of M.×giganteus (M. sinensis × M. sacchariflorus) and Sugarcane

  • Erik Sacks, University of Illinois, Urbana-Champaign
  • DOE BER–funded project $1,496,300

Goal: Facilitate the rapid development of Miscanthus as a bioenergy crop by obtaining fundamental knowledge about M. sacchariflorus (Msa) genetic diversity, population structure, and environmental adaptation. This project will conduct field trials with ~600 individuals of Msa from throughout its natural range to evaluate yield potential and adaptation. It will develop molecular markers associated with traits of interest that will enable plant breeders to quickly develop improved biomass cultivars of M×g as well as the closely related sugarcanes and energycanes.

2013: USDA and DOE Fund Seven New Projects

Functional Manipulation of Root Endophyte Populations for Feedstock Improvement

  • Jeffrey Dangl, University of North Carolina, Chapel Hill
  • DOE BER–funded project $1,543,490

Goal: Utilize genomics, genetics, and physiology to understand how endophytic bacteria alter plant growth and productivity, ultimately to manipulate plant performance for feedstock production. A variety of plant functions and traits are co-dependent on the surrounding microbial community, especially those associated with the plant root system (rhizosphere). This project will investigate whether plant performance phenotype in association with microbial communities translates across plant species in a predictable manner.

Unraveling the Genetics of Two Key Biomass Traits that Differentiate Upland and Lowland Tetraploid Switchgrass Ecotypes, Colonization by Mycorrhizal Fungi, and Frost Tolerance

  • Katrien Devos, University of Georgia, Athens
  • DOE BER–funded project $1,314,235

Goal: Develop strategies for increased frost tolerance of lowland switchgrass through (1) identifying the genetic pathway(s) that provide frost tolerance in upland switchgrass and (2) studying the potential of beneficial fungi to minimize host cold stress. This project seeks to leverage the high biomass yield of southern-adapted lowland types and the frost tolerance of northern-adapted upland types to identify candidate genes that can be exploited to enhance biomass production of switchgrass under cold stress.

Genetic Control of Flowering in Switchgrass

  • Yiwei Jiang, Purdue University, West Lafayette, IN
  • DOE BER–funded project $850,076

Goal: Elucidate the genetic mechanisms and identify candidate genes controlling flowering time in switchgrass. Late-flowering genotypes yield more biomass because the growing season is extended; having a better understanding of the genes that control flowering time will help to develop a rational strategy for creating improved switchgrass lines. The knowledge generated will aid breeding programs in developing late-flowering varieties of switchgrass that fully utilize the growing season and achieve high biomass yield.

Pyramiding Genes and Alleles for Improving Energy Cane Biomass Yield

  • Ray Ming, University of Illinois, Urbana-Champaign
  • DOE BER–funded project $998,564

Goal: Accelerate energy cane breeding and maximize biomass yield by utilizing the extraordinary segregation of true F2 populations to select high biomass-yielding genotypes. Sugarcane cultivars are mostly derived from hybridization between domesticated and wild species followed by backcrossing to recover the high biomass yield and sugar content of the domestic parent while retaining stress tolerance from the wild. Because sugar content is not a limiting factor for energy cane, this project will introduce a new breeding paradigm for more efficient cultivar improvement.

Global Analysis of Epigenetic Regulation of Gene Expression in Response to Drought Stress in Sorghum

  • A. S. N. Reddy, Colorado State University, Fort Collins
  • DOE BER–funded project $1,385,763

Goal: Investigate the impact of drought stress on epigenetic modifications and alternative splicing in sorghum. Using recently developed high-throughput tools, this project will examine genome-wide changes in the chromatin landscape and patterns of alternative splicing in cultivars that are sensitive and tolerant to drought under normal conditions and in response to drought stress. Understanding how plants respond and adapt to drought stress at the molecular level will help in developing plants that can grow under water-limiting conditions.

Accelerated Development of Optimal Pine Feedstocks for Bioenergy and Renewable Chemicals Using Genome-Wide Selection

  • Matias Kirst, University of Florida, Gainesville
  • USDA NIFA–funded project $1,000,000

Goal: Hyper-accelerate pine breeding using genome-wide selection, generating cultivars of loblolly and slash pine tailored to produce high energy yields that are ready for deployment. Traditional genetic improvement of pines is logistically complex and expensive, and a single breeding cycle takes almost two decades to complete. Thus, the project will develop and apply new breeding strategies that accelerate development of cultivars suitable for bioenergy production.

Structural Polymorphisms as Causes of Heterosis in Populus

  • Steven Strauss, Oregon State University, Corvallis
  • USDA NIFA–funded project $1,000,000

Goal: Characterize the extent of structural polymorphisms (SPs) between and within species of Populus that are used to produce wood and bioenergy, and examine their relationship to growth, stress tolerance, and breeding efficiency. This project will study wild black cottonwoods and interspecies hybrids important in plantations in the Pacific Northwest United States and other parts of the world, with a focus on the extent to which assay of SPs could improve hybrid breeding compared to alternative approaches.

2012: USDA and DOE Fund Nine New Projects

Functional Gene Discovery and Characterization of Genes and Alleles Affecting Wood Biomass Yield and Quality in Populus

  • Victor Busov, Michigan Technological University, Houghton
  • DOE BER–funded project $1,097,567

Goal: To discover and characterize novel genes and alleles that affect wood biomass yield and quality in Populus. By combining mutagenesis for functional identification of genes with next generation sequencing technologies for identification of alleles with breeding values, these discoveries can enable knowledge-based approaches for development of specialized bioenergy poplar cultivars.

Identifying Differences in Abiotic Stress Gene Networks between Lowland and Upland Ecotypes of Switchgrass

  • Kevin Childs, Michigan State University, East Lansing
  • DOE BER–funded project $1,246,093

Goal: Investigate response to drought and salt stress in a diverse collection of lowland and upland switchgrass ecotypes. Comparing differential gene expression between tolerant and sensitive lines will allow a better understanding of this response, as well as the identification of genes and germplasm that can be used to improve cultivated switchgrass to better tolerate these abiotic stresses.

Poplar Interactome for Bioenergy Research

  • Pankaj Jaiswal, Oregon State University, Corvallis
  • DOE BER–funded project $1,362,045

Goal: Identify genome-wide functional gene networks and subnetworks in poplar that are associated with abiotic stress tolerance and bioenergy related traits, as well as candidate genes which interact to produce abiotic stress resistant phenotypes.  Using a combination of computational projections, gene expression analysis, and experimental validation, this project will further development of poplar varieties that can thrive under abiotic stress on marginal land that is unsuitable for food crops.

The Genetics of Biofuel Traits in Panicum Grasses: Developing a Model System with Diploid Panicum hallii

  • Thomas Juenger, University of Texas, Austin
  • DOE BER–funded project $1,465,840

Goal: Utilize genetic and genomic analyses to better understand the growth and development of Panicum grasses, including the diploid Panicum hallii, and provide tools for predicting biomass and tissue related phenotypes from genotypes. This project will exploit natural variation to discover the genes important in biomass production, tissue quality, and stress tolerance under diverse environmental conditions, providing avenues for improving C4 perennial grasses for use as bioenergy crops.

Genomics of Bioenergy Grass Architecture

  • Andrew Paterson, University of Georgia, Athens
  • USDA NIFA–funded project $575,000

Goal: Understand the genetic determinants of plant architecture that are important to the design of sorghum genotypes optimized for biomass production in a range of environments. Optimal biomass productivity in temperate latitudes and/or under perennial production systems may require substantial changes to architecture of plants of tropical origin that have previously been adapted to annual cultivation. This project will further enhance the value of many existing resources while also adding new dimensions to scientific research capacity.

Deciphering Natural Allelic Variation in Switchgrass for Biomass Yield and Quality Using a Nested Association Mapping Populations

  • Malay Saha, Samuel Roberts Noble Foundation, Ardmore, OK
  • DOE BER–funded project $1,478,982

Goal: Understand the genetic basis of key biofeedstock traits in switchgrass by identifying genetic markers controlling important biomass traits. Most of these traits, such as biomass yield and cell wall composition, are complex and difficult to improve, but improvement can be obtained using traditional breeding augmented by marker-assisted selection. Validated markers cosegregating with bioenergy-relevant traits will be used to initiate a marker-assisted and/or genomic selection program to accelerate development of superior cultivars.

Genetic Architecture of Sorghum Biomass Yield Component Traits Identified Using High-Throughput, Field-Based Phenotyping Technologies

  • Patrick Schnable, Iowa State University, Ames
  • USDA NIFA–funded project $1,425,000

Goal: Test the hypothesis that variation in biomass growth rate can be explained by variation in photosynthetic rates and/or amounts of photo-protection. Data from a large, genetically diverse sorghum collection will be collected at multiple time points during the growing season using an automated high-throughput field-based plant phenotyping system. Identifying the genetic control of biomass growth rates will allow breeders to genetically “stack” genes that control maximal growth rates, thereby paving a path to producing higher yielding hybrids.

The Genomic Basis of Heterosis in High-Yielding Triploid Hybrids of Willow (Salix spp.) Bioenergy Crops

  • Lawrence Smart, Cornell University, Ithaca NY
  • DOE BER–funded project $1,365,673

Goal: Investigate how gene expression patterns in willow hybrids are related to yield potential and other traits important for biofuels production. Yield improvement in many crops has been based on capturing hybrid vigor (aka heterosis), but its complex genetic basis is poorly understood. In this project we will learn if there is a bias in the expression of key genes from one parent versus the other in species hybrids, and whether there is a gene dosage effect skewing gene expression patterns in triploid progeny compared with their diploid and tetraploid parents.

The Dual Effect of Tubulin Manipulation on Populus Wood Formation and Drought Tolerance

  • Chung-Jui Tsai, University of Georgia, Athens
  • DOE BER–funded project $1,496,000

Goal: Determine how tubulin levels and/or tubulin protein modifications affect wood development and water use in Populus. Tubulin proteins form microtubule scaffolds which participate in cell wall biogenesis as well as regulate stomatal guard cell movements for photosynthesis and transpiration. This project will allow dissection of the contribution of tubulins to two interdependent processes, water utilization and the development of lignocellulosic biomass, which are relevant to bioenergy crop improvement.

2011: USDA and DOE Fund Six New Projects

Association Mapping of Cell Wall Synthesis Regulatory Genes and Cell Wall Quality in Switchgrass

  • Laura E. Bartley, University of Oklahoma, Norman
  • DOE BER–funded project $1,282,913

Goal: Identify natural genetic variation in switchgrass that correlates with lignocellulose-to-biofuel conversion qualities. Most plant dry matter is composed of lignocellulose, and because switchgrass yields high amounts of this material and tolerates drought and other stresses it is an attractive candidate for development into a biofuel crop. This project should enhance understanding of the qualities that critically impact the conversion efficiency of lignocellulose into biofuels.

Functional Interactomics: Determining the Roles Played by Members of the Poplar Biomass Protein-Protein Interactome

  • Eric Beers, Virginia Polytechnic and State University, Blacksburg
  • DOE BER–funded project $1,493,869

Goal: Identify key interactions between proteins associated with wood formation in poplar, a woody biomass crop. Wood characteristics result from the coordinated actions of enzymes and structural proteins in the cells, which typically interact with other proteins to perform their roles. This project will uncover the potential of the biomass protein-protein interactome to contribute to the development of poplar trees with superior biomass feedstock potential.

Functional Genomics of Sugar Content in Sweet Sorghum Stems

  • David M. Braun, University of Missouri, Columbia
  • DOE BER–funded project $1,191,200

Goal: Improve sucrose accumulation in sweet sorghum through investigating the mechanisms regulating carbon allocation to stems. A rapidly growing, widely adaptable crop, sweet sorghum accumulates in the stem high concentrations of sucrose that can be efficiently converted to ethanol, making this a valuable candidate bioenergy feedstock. This research will use a combination of approaches to identify bioenergy-relevant genes and to understand their functions in carbon partitioning in sweet sorghum.

Creation and High-Precision Characterization of Novel Populus Biomass Germplasm

  • Luca Comai, University of California, Davis
  • DOE BER–funded project $1,128,800

Goal: Provide new genomic tools for poplar breeders to identify germplasm with unique genotypes and increased biomass yields, and develop techniques for creating poplar hybrids with unique combinations of chromosomal regions. Because such properties can confer faster growth, this project addresses a challenge posed by the long generation time of trees through fast and cost-effective nontransgenic genetic manipulation.

Genomic and Breeding Foundations for Bioenergy Sorghum Hybrids

  • Stephen Kresovich, University of South Carolina, Columbia
  • USDA NIFA–funded project $1,200,000

Goal: Build the germplasm, breeding, genetic, and genomic foundations necessary to optimize cellulosic sorghum as a bioenergy feedstock. This project will facilitate breeding sorghum lines optimized for energy production and selected to maximize energy accumulation per unit time, land area, and/or production input.

An Integrated Approach to Improving Plant Biomass Production

  • Jan Leach, Colorado State University, Fort Collins
  • DOE BER–funded project $1,350,000

Goal: Expedite discovery of genes controlling biomass productivity in switchgrass by leveraging results from rice, a well-studied model grass. Switchgrass and other perennial grasses are promising candidates for bioenergy feedstocks; however, the genetic resources necessary to develop these species are currently limited. This work will greatly expand the research tool box for switchgrass and advance its improvement as an energy crop.

Modulation of Phytochrome Signaling Networks for Improved Biomass Accumulation Using a Bioenergy Crop Model

  • Todd C. Mockler, Donald Danforth Plant Science Center, St. Louis
  • DOE BER–funded project $1,230,900

Goal: Identify genes involved in light perception and signaling in the model grass Brachypodium distachyon to increase yield and improve the composition of bioenergy grasses. Plant growth and development, including biomass accumulation, are affected by the light environment. Finding key genes involved in modulating light perception could be useful in targeted breeding or engineering efforts for improved bioenergy grass crops.

Quantifying Phenotypic and Genetic Diversity of Miscanthus sinensis as a Resource for Knowledge-Based Improvement of M. x giganteus (M. sinensis x M. sacchariflorus)

  • Erik J. Sacks, University of Illinois, Urbana-Champaign
  • DOE BER–funded project $1,484,595

Goal: Facilitate development of Miscanthus as a bioenergy crop by acquisition of fundamental information about genetic diversity and environmental adaptation. Miscanthus is among the most promising cellulosic biofuel crops, but its improvement as a feedstock will require a broader genetic base. Identification of molecular markers associated with traits of interest will improve Miscanthus breeding efforts.

Discovering the Desirable Alleles Contributing to the Lignocellulosic Biomass Traits in Saccharum Germplasm Collections for Energy Cane Improvement

  • Jianping Wang, University of Florida, Gainesville
  • DOE BER–funded project $1,069,712

Goal: Improve energy cane by identifying the genetic components contributing to biomass production. Energy cane (Saccharum complex hybrids) holds great potential as a bioenergy feedstock in the southern United States. This project will produce foundational genetic resources for energy cane breeders to efficiently develop cultivars with increased biomass production and reduced input requirements.

Sorghum Biomass Genomics and Phenomics

  • Jianming Yu, Kansas State University, Manhattan
  • USDA NIFA–funded project $800,000

Goal: Integrate key genomics-assisted approaches into biomass sorghum research, and combine with high-throughput and traditional field-based phenotyping methods to enable advanced breeding strategies. By both exploiting genetic diversity and understanding the genotype-phenotype relationship, predictive approaches for efficient and cost-effective breeding can be developed.

2010: USDA and DOE Fund Nine New Projects

Genome-Wide Analysis of miRNA Targets in Brachypodium and Biomass Energy Crops

  • Pamela J. Green, University of Delaware, Newark
  • DOE BER–funded project $868,794

Goal: Identify the targets of MicroRNAs (miRNAs) in different organs and under adverse environmental conditions in the model grass Brachypodium and in the energy crops switchgrass, Miscanthus, and sorghum. miRNAs are important regulatory molecules that repress selected “target” genes to enable normal development, stress responses, and other processes. This project should enhance understanding of regulatory networks and may suggest new strategies for improving biomass energy crops.

Organ and Tissue-Specific Sucrose Transporters: Important Hubs in Gene and Metabolite Networks Regulating Carbon Use in Wood-Forming Tissues of Populus

  • Scott A. Harding, University of Georgia, Athens
  • DOE BER–funded project $1,340,000

Goal: Investigate how sucrose transporter proteins (SUTs) function to facilitate the distribution of sucrose for transient storage and biosynthetic use among different pathways in the developing wood matrix. Wood for lignocellulosic feedstocks is synthesized from sucrose that is exported from leaves and then processed in the wood-forming organs. SUTs mediate the export and efficient movement of sucrose from source leaves to sink organs in all plant species.

The Role of Small RNA in Biomass Deposition and Perenniality in Andropogoneae Feedstocks

  • Matthew E. Hudson, Energy Bioscience Institute, University of Illinois at Urbana-Champaign
  • DOE BER–funded project $1,165,900

Goal: Investigate the role of small RNA molecules in biomass production and their importance in the regulation of cellulose and lignin biosynthesis. The tissues and organs of next-generation biofuel crops that provide biomass for energy production are primarily composed of lignin and cellulose. This research will focus on Miscanthus species as well as other biomass crops including switchgrass and prairie cordgrass.

Development of a Low Input and Sustainable Switchgrass Feedstock Production System Utilizing Beneficial Bacterial Endophytes

  • Chuansheng Mei, The Institute for Advanced Learning and Research
  • DOE BER–funded project $734,759

Goal: Understand the molecular and physiological mechanisms by which interaction with bacterial endophytes promotes growth in the promising bioenergy crop switchgrass. The use of naturally occurring beneficial bacterial endophytes with switchgrass represents a practical and feasible way to develop a low-input and sustainable feedstock production system.

Functional Analysis of Regulatory Networks Linking Shoot Maturation, Stem Carbon Partitioning, and Nutrient Utilization in Sorghum

  • Stephen Moose, University of Illinois at Urbana-Champaign
  • USDA NIFA–funded project $1,000,000

Goal: Determine if changes in the Glossy15 gene system of sorghum might contribute to current physiological differences among grain, sweet and biomass sorghums, and whether this gene can be used to convert superior sorghum grain hybrids to cultivars enhanced for bioenergy production.

Genomics of Energy Sorghum Biomass Accumulation

  • John Mullet, Texas A&M University, College Station
  • USDA NIFA–funded project $1,000,000

Goal: Identify the genetic and biochemical basis for increasing yield and improving the composition of high-biomass cellulosic energy sorghum. Select genotypes will be analyzed for stem biomass yield, structure, and composition. The resources developed will enable analysis of the genes that modulate these traits and facilitate improvement of energy sorghum and other bioenergy grasses.

Identification and Genetic Characterization of Maize Cell-Wall Variation for Improved Biorefinery Feedstock Characteristics

  • Markus Pauly, University of California, Berkeley
  • DOE BER–funded project $793,413

Goal: Identify and characterize maize lines with enhanced biorefinery feedstock characteristics, particularly those containing higher yields of fermentable sugars. Stover, the material from the corn plant that remains after removal of the grain, consists primarily of cellulose, hemicellulose, and lignin. Because corn stover is generated by U.S. agriculture in significant amounts, this lignocellulosic residue is desirable to use as a biofuel source.

Systems View of Root Hair Response to Abiotic Stress

  • Gary Stacey, University of Missouri, Columbia
  • DOE BER–funded project $1,106,656

Goal: Gain insight into the impacts of variations in temperature and water availability on nutrient uptake by root cells. Root hair cells function to increase root surface area and to mediate water and nutrient uptake. The data obtained in this project should provide a better understanding of the impacts of climate change (heat and water limitation) on plant root physiology.

Insertional Mutagenesis of Brachypodium distachyon

  • John P. Vogel, USDA Agricultural Research Service Western Regional Research Center, Albany, California
  • DOE BER–funded project $949,348

Goal: Generate 30,000 additional insertional mutants in the model grass Brachypodium distachyon and sequence DNA flanking the insertion sites. Insertional mutants are a powerful research tool that allow researchers to rapidly determine the function of specific genes. Mutants from outside collaborators will be integrated into this collection and made available through a public database.

2009: USDA and DOE Fund Seven New Projects

Accelerating the Domestication of Miscanthus for Biofuel Production

  • Andrew H. Paterson, University of Georgia, Athens, $1,200,000
  • Co-Principal Investigator: Erik J. Sacks (Mendel Biotechnology)

Goal: This project will provide genomic tools and resources for a promising cellulosic biofuel crop, Miscanthus, that will (a) foster innovative strategies for its improvement and (b) develop comparative and bioinformatic approaches to enhance fundamental knowledge of Miscanthus genome structure, function, and organization.

The Hunt for Green Every April: Factors Affecting Fitness in Switchgrass

  • Gautam Sarath, USDA-ARS-Lincoln, $1,182,000
  • Co-Principal Investigators: Kenneth P. Vogel; Christian M. Tobias (USDA-ARS, Albany); Soundararajan Madhavan (University of Nebraska, Lincoln); Paul Twigg (University of Nebraska, Kearney)

Goal: This project will investigate winter survival in switchgrass populations and individual plants specifically selected for greater yields and with known differences in winter survival. Molecular events occurring in the crowns and rhizomes will be studied over two growing seasons and winters.  The goal is to make a significant and lasting contribution to the future improvement of switchgrass as a bioenergy crop, and will also directly benefit researchers working on developing other perennial grasses into biomass energy crops.

Phenomic Analysis of Natural and Induced Variation in Brachypodium distachyon

  • John P. Vogel, USDA-ARS Western Regional Research Center, Albany, California, $1,300,000
  • Co-Principal Investigators: Michelle Watt, Robert Furbank (CSIRO, Canberra, Australia); Hikmet Budak (Sabanci University, Engineering and Natural Sciences Biological Sciences and Bioengineering Program, Tuzla-Istanbul, Turkey); Metin Tuna (Namik Kemal University, Faculty of Agriculture, Tekirdag, Turkey)

Goal: In this project, high-throughput phenotypic analysis (phenomics) of homozygous T-DNA mutants and natural accessions of the model grass Brachypodium distachyon will be conducted to accelerate the understanding of the basic biology underlying traits that control the utility of grasses as energy crops.

Mechanism of Carbon Partitioning Regulation by cpg13 in the Bioenergy Woody Crop Poplar

  • Matias Kirst, University of Florida, $643,000
  • Co-Principal Investigator: Gary F. Peter

Goal: This project will characterize genes that regulate the balance of carbon going to cellulosics or lignin, leading to the development of plant materials that are more suitable for biofuel production.

A Systems Biology Approach to Elucidate Regulation of Root Development in Populus

  • Victor Busov, Michigan Technological University, $900,000
  • Co-Principal Investigators: Yordan S. Yordanov , Hairong Wei; Erik A. Lilleskov, (USDA Forest Service, Northern Research Station, Houghton, MI); Robert J. Kodrzycki (Phenotype Screening Corporation); David J. Weston (Oak Ridge National Laboratory)

Goal: This project will identify key regulators of root architecture in relation to nitrogen and water use in the bioenergy crop Populus using an integrated systems biology approach.  This research will generate resources and innovations that can enable robust biomass productivity under marginal conditions for sustainable lignocellulosic biomass production.

Improving Alfalfa as a Biofuel Feedstock

  • E. Charles Brummer, University of Georgia, Athens, $705,000
  • Co-Principal Investigators: Steven J. Knapp; Maria J. Monteros (The Samuel Roberts Noble Foundation, Inc.); Gregory D. May (National Center for Genome Resources)

Goal: Biofuel crops must maximize the production of energy, which requires a high yield of biomass with optimum fuel quality. In this project, molecular markers that are associated with optimal biofuel characteristics will be identified in alfalfa and directly integrated into traditional field-oriented alfalfa breeding programs. The long-term goal of this project is to develop biofuel-ready alfalfa cultivars that have improved yield and quality.

Characterization of Nitrogen Use Efficiency in Sweet Sorghum

  • Ismail Dweikat, University of Nebraska, Lincoln, $390,000

Goal: Enhancing the ability of sweet sorghum to utilize nitrogen will increase its potential as a leading and cost-effective bioenergy crop. This project will identify novel nitrogen use efficiency alleles in wild sorghum germplasm that can be used to improve sweet sorghum.

2008: USDA and DOE Fund Ten New Projects

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

  • Jeff Bennetzen, University of Georgia, $1,295,000
  • Co-Principal Investigators: Katrien Devos; Andrew Doust (Oklahoma State University); Janice Zale (University of Tennessee)

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

  • Marcia Maria de Oliveira Buanafina, Pennsylvania State University, $587,191
  • Co-Principal Investigators: D.M. Brown

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. (Updated December 2008)

Computational Resources for Biofuel Feedstock Species

  • C. Robin Buell, Michigan State University, $540,000
  • Co-Principal Investigator: Kevin Childs

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

  • Nick Carpita, Purdue University, $1,200,000
  • Co-Principal Investigator: Maureen McCann

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

  • Maria Harrison, Boyce Thompson Institute for Plant Research, $882,000
  • Co-Principal Investigator: Matthew Hudson (University of Illinois)

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

  • Samuel Hazen, University of Massachusetts, $1,200,000
  • Co-Principal Investigator: Todd Mockler (Oregon State University), Steve Kay (UC San Diego)

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

  • Jan Leach, Colorado State University, $1,500,000
  • Co-Principal Investigators: Dan Bush, John McKay; Hei Leung (IRRI)

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

  • Steven Knapp, University of Georgia, $1,200,000
  • Co-Principal Investigators: Jeff Dean, Joe Nairn; Laura Marek (Iowa State University), Mark Davis (NREL)

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

  • Todd Mockler, Oregon State University, $1,200,000
  • Co-Principal Investigator: Todd Michael (Rutgers University)

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

  • Steven Strauss, Oregon State University, $1,200,000
  • Co-Principal Investigators: Todd Mockler, Michael Freitag

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.

2007: USDA and DOE Fund Eleven New Projects

Towards a Map of the Populus Biomass Protein-Protein Interaction Network

  • Eric Beers, Virginia Polytechnic Institute and State University, $1,200,000 for 36 months
  • Co-Principal Investigators: Amy Brunner, Allan Dickerman

Goal: Map protein-protein interactions relevant to biomass production by focusing on proteins coexpressed in poplar xylem, site of the majority of lignocellulose synthesis and hence biomass accumulation in poplar.

Developing Association Mapping in Polyploid Perennial Biofuel Grasses

  • Ed Buckler, USDA-Agricultural Research Service (Cornell University), $700,000 for 36 months
  • Co-Principal Investigators: Jerry Cherney, Michael Casler (USDA-Agricultural Research Service, Wisconsin)

Goal: Undertake an association-mapping study of two important biofuel grasses, switchgrass and reed canarygrass, to identify molecular markers tightly linked to biomass-related trait loci. This will enable marker-assisted selection and greatly accelerate breeding programs for enhanced biomass production.

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

  • Pam Green, University of Delaware, $600,000 for 36 months

Goal: Identify small RNAs related to stresses such as drought, temperature, and nutrient deprivation and relate them to the emerging genome sequence of Brachypodium distachyon, thus enhancing its value as a functional genomic model for energy crops and temperate grasses.

Linkage Analysis Appropriate for Comparative Genome Analysis and Trait Selection in Switchgrass

  • Christian Tobias, USDA Agricultural Research Service (Western Regional Research Center), $600,000 for 36 months
  • Co-Principal Investigators: Rongling Wu (University of Florida), Joe Bouton (Noble Foundation), Malay Saha (Noble Foundation)

Goal: Create a comprehensive marker set for switchgrass based principally on simple sequence repeats, and initiate development of a linkage map.

Genetic Dissection of Bioenergy Traits in Sorghum

  • Wilfred Vermerris, University of Florida, $750,000 for 36 months
  • Co-Principal Investigators: S. Kresovich, S. Murray, J. Pedersen, W. Rooney, Z. Xin, S. Sattler (Cornell University, Texas A&M University, USDA-ARS)

Goal: Maximize the amount of fermentable sugar in the whole sorghum plant by identifying and isolating genes that control the high stalk juice sugar trait and a decreased stalk lignin trait, with the aim of eventually combining both traits in a single germplasm. (Updated December 2008)

Insertional Mutagenesis of Brachypodium distachyon

  • John Vogel, Agricultural Research Service (Western Regional Research Center), $600,000 for 36 months
  • Co-Principal Investigators: Yong Gu, Gerard Lazo, Olin Anderson

Goal: Create a collection of insertional mutants in Brachypodium distachyon. This resource collection can then be used to identify mutations in genes predicted to affect biomass quality and agronomic characteristics of other perennial grass energy crops.

A Functional Genomics Approach to Altering Crown Architecture in Populus: Maximizing Carbon Capture in Trees Grown in Dense Plantings

  • Jerry Tuskan, Oak Ridge National Laboratory, $1,040,000 for 36 months
  • Co-Principal Investigators: Udaya Kalluri, Stan Wullschleger, Glenn Howe (Oregon State University), Stephen DiFazio (West Virginia University), Gancho Slavov (West Virginia University)

Goal: Gain a molecular understanding of phytochrome-mediated responses to competition in Populus and then use that knowledge to maximize carbon capture per unit of land area for increased biomass production.

Identification of Cell Wall Synthesis Regulatory Genes Controlling Biomass Characteristics and Yield in Rice (Oryza sativa)

  • Zhaohua Peng, Mississippi State University, $1,300,000 for 36 months
  • Co-Principal Investigators: Pamela Ronald (University of California, Davis), Guo-Liang Wang (Ohio State University)

Goal: Examine cell-wall synthesis in rice, a model grass bioenergy species and the source of rice stover residues, using reverse genetic and functional genomic and proteomic approaches.

Development of Genomic Tools to Improve Prairie Cordgrass (Spartina pectinata), a Highly Productive Bioenergy Feedstock Crop

  • Jose Gonzalez, South Dakota State University, $420,000 for 24 months
  • Co-Principal Investigators: Arvid Boe, XingYou Gu, Vance Owens

Goal: Develop PCR markers for this species and to construct an initial linkage map for prairie cordgrass, a native perennial high-biomass–yielding grass.

Resource Development in Switchgrass, an Important Bioenergy Crop for the U.S.A.

  • Katrien Devos, University of Georgia, $400,000 for 36 months
  • Co-Principal Investigators: Jeff Bennetzen, Charles Brummer, Joe Bouton (Noble Foundation), and Malay Saha (Noble Foundation)

Goal: Construct a detailed genetic map of switchgrass based on simple sequence repeats, and align it with maps produced in rice, maize, and sorghum. This will allow the exploitation of resources and sequence information generated for these well-studied cereals. The genetic maps also will serve as a framework for locating genes that control bioenergy traits.

Strategies for Using Molecular Markers to Simultaneously Improve Corn Grain Yield and Stover Quality for Ethanol Production

  • Rex Bernardo, University of Minnesota, $715,000 for 36 months
  • Co-Principal Investigators: Hans-Joachim Jung (USDA-Agricultural Research Service)

Goal: Optimize the use of DNA markers to simultaneously breed for high corn grain yield (for nonenergy and energy uses) and high stover quality for ethanol production.

2006: USDA and DOE Fund Nine New Projects

Manipulation of Lignin Biosynthesis to Maximize Ethanol Production from Populus Feedstocks

  • Clint Chapple, Purdue University, $1.4 million
  • Co-Principal Investigators: Richard Meilan, Michael Ladisch

Systematic Modification of Monolignol Pathway Gene Expression for Improved Lignocellulose Utilization

  • Richard Dixon, The Noble Foundation, Oklahoma, $800,000
  • Co-Principal Investigator: Fang Chen

Sorghum Biomass/Feedstock Genomics Research for Bioenergy

  • William Rooney, Texas A&M University, $800,000
  • Co-Principal Investigators: John Mullet; Steve Kresovich (Cornell University), Doreen Ware (Cold Spring Harbor Laboratory)

Streamlined Method for Biomass Whole-Cell–Wall Structural Profiling

  • John Ralph, USDA-Agricultural Research Service, University of Wisconsin, $333,000

Development of a Proteoglycan Chip for Plant Glycomics

  • Chris Somerville, Carnegie Institute of Washington, $359,100

Biochemical Genomics of Wood Formation: O-Acyltransferases for Alteration of Lignocellulosic Property and Enhancement of Carbon Deposition in Poplar

  • Chang-Jun Liu, Brookhaven National Laboratory, $300,000

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

  • Vincent Chiang, North Carolina State University, $700,000

Genetic Dissection of the Lignocellulosic Pathway of Wheat to Improve Biomass Quality of Grasses as a Feedstock for Biofuel

  • Bikram Gill, Kansas State University, $700,000
  • Co-Principal Investigator: Wanlong Li

Using Association Mapping to Identify Markers for Cell-Wall Constituents and Biomass Yield in Alfalfa

  • Charles Brummer, University of Georgia, $445,000
  • Co-Principal Investigators: Kenneth Moore (Iowa State University), Jeff Doyle (Cornell University)