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Systems Biology for Energy and the Environment

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Genomic Science Program

Plant Feedstock Genomics for Bioenergy



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USDA and DOE Fund Six New Projects in 2018 for Biomass Genomics Research

The U.S. Department of Energy's Office of Science, Office of Biological and Environmental Research, and the U.S. Department of Agriculture (USDA) National Institute of Food and Agriculture’s Agriculture and Food Research Initiative* have jointly selected six projects for awards totaling $6.4 million for biobased-fuel research. These awards continue a commitment begun in 2006 to conduct fundamental research in biomass genomics that will establish a scientific foundation to facilitate and accelerate the use of woody plant tissue for bioenergy and biofuel.

2018 Awards

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, multilocation 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-bysequencing (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.

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*formerly the Cooperative State Research, Education, and Extension Service (CSREES), National Research Initiative


Lignocellulosic Biomass for Advanced Biofuels and Bioproducts: Workshop Report [2/15]

Sustainable Bioenergy [05/14]


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