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United States Department of Agriculture

Agricultural Research Service

Related Topics


Location: Genomics and Gene Discovery

2009 Annual Report

1a.Objectives (from AD-416)
Develop the necessary range of knowledge and technologies to use plants to produce chemical feedstocks and fuels with more renewable and more enviromentally acceptable methods than current sources such as petrochemicals. Focus initially on the cereal crops (especially wheat and rice) and other grasses and non-grass species with potential for biofuel development. Coordinate with other ARS and non-ARS projects in specific approaches to biofuel research and development.

1b.Approach (from AD-416)
To achieve these objectives, an integrated plant molecular, genomics, bioinformatics, plant transformation approach will be developed for the production of biofuels from crops. Specifically:.
1)Determine parameters underlying ectopic expression of polysaccharides and proteins in plant leaf and stem tissue, to include stability of expressed products and plant response;.
2)Determine potential for altering plant architecture and cell wall structure for altered functions such as more efficient light gathering, storage capacity, and increased efficiency of post-harvest product processing as for straw/fiber conversion;.
3)Modify polysaccharide production to enhance ethanol production, to include both existing and novel polymer structures;.
4)Develop a repertoire of tissue and development specific promoters, initially concentrating on promoters efficient in the monocotyledonous plants. Formerly 5325-21000-009-00D (8/04).

3.Progress Report
The on-going research in this project has made significant progress in the development of genetic and genomic resources for Brachypodium distachyon (Brachypodium) and switchgrass. 

Efforts within the agency and with external collaborators led to the release of a draft genome sequence encompassing 99.6% of the Brachypodium genome. ARS scientists in Albany, CA and in St. Paul, MN identified thousands of single nucleotide polymorphisms and produced a high density linkage map of Brachypodium. The first use of this genetic map was to facilitate assembly of genome sequence data on a whole chromosome-scale. The whole genome shotgun sequence assembly has now been integrated with physical maps and genetic data to create a final sequence assembly contained within five scaffolds. Further annotation of cell wall genes is being accomplished by ARS scientists in Albany, CA.

To create a large germplasm collection for Brachypodium, collaboration with Turkish colleagues at Sabanci, and Namik Kemal University led to release of 200 new inbred lines which are being used to understand species diversity.  To identify genes required for cell wall composition, mutant screens were initiated and have identified 27 new mutants. More detailed characterization of these lines to identify which cell wall components have been modified is underway.

For switchgrass, collaborative efforts have utilized EST sequences that were produced by this project in previous years for genetic analysis.  Biomaterials that are being used for complete genome sequencing of this species were genotyped which assured that all materials submitted to the sequencing project were from the same biological source. Additional markers have been developed and used for linkage analysis as part of a subordinate project and for characterization of genetic diversity. ARS Scientists in Albany have developed switchgrass research lines and novel switchgrass genetic stocks through controlled crosses for the purposes of understanding reproductive biology in switchgrass, and for testing different potential breeding strategies. This work has generated several full sib family pedigrees and second generation inbred lines that will be useful genetic stocks.  Further phenotypic characterization of diploid switchgrass stocks has helped to produce a greater understanding of polyploidy in switchgrass.

Insertional mutagenesis in Brachypodium has led to isolation of mutants that contain defined fragments of DNA inserted throughout the genome. For switchgrass, as part of subordinate projects supported by cooperative research and development agreements, we have inserted genes predicted to increase biomass, alter cell wall composition or induce sterility.  A collaboration with scientists at the USDA-Plant Gene Expression Center resulted in production of transgenic switchgrass with altered architecture.  This results from mis-expression of a regulatory small RNA molecule from maize that is responsible for the "corngrass" mutation.

1. Brachypodium genome project. A simple model for studying grass cell walls is needed to allow more rapid progress in understanding the potential to alter the properties of cellulosic biomass. ARS scientists in Albany, CA are collaborating with Department of Energy (DOE) and other researchers to sequence the entire genome. A complete draft of the genome was released through the website Knowledge of the genome sequence of Brachypodium and the linear order of genes in the genome relative to other grasses will help to make this species useful to researchers studying important agricultural traits in energy crops and grain species.

2. Characterization of diversity in polyploid switchgrass. The genetic make-up of the energy crop switchgrass is not well understood. Using molecular markers, ARS scientists in Albany, CA are collaborating to identify those that are prevalent in certain populations. They will use them to help distinguish different switchgrass cultivars and populations from one another genetically. This information will be useful for preserving diversity, defining which populations are derived from common ancestors, and measuring the amount of interbreeding that has occurred between different populations.

3. Expanding available genetic resources for Brachypodium. A simple model for studying grass cell walls is needed to allow more rapid progress in understanding the potential to alter the properties of cellulosic biomass. ARS scientists in Albany, CA and collaborators at Namik Kemal University and Sabanci University, both in Turkey, have continued to characterize new Brachypodium accessions. Over 200 inbred lines have been developed and are all now freely available to researchers. Albany researchers have also created over 4,000 T-DNA lines and these will be made available to the public as soon as sufficient seed has been bulked up. This work will identify genes that can then be manipulated in bioenergy crops to improve cell wall properties for biofuel production.

4. Identification of Brachypodium mutants with altered cell wall composition. The plant cell wall is a complex composite of polysaccharide polymers, phenolic compounds and proteins. The genes that control cell wall composition are poorly understood. To identify some of these genes, ARS scientists in Albany, CA have used near infrared spectroscopy (NIR) to identify 27 mutants with altered cell wall composition. This work will identify genes that can then be manipulated in bioenergy crops to improve cell wall properties for biofuel production.

5. Alteration of switchgrass plant architecture. Through switchgrass genetic modification, misexpression of a small regulatory RNA from maize caused alteration of plant structure and growth habit. ARS scientists in Albany, CA demonstrated that the regulatory RNA is likely to function similarly in both switchgrass and maize. In maize, corngrass causes alterations to the plant cell wall that lead to a decrease in lignin (a barrier to using the plant for bioenergy), as well as increasing biomass. A similar effect in switchgrass may improve its qualities as a bioenergy crop.

6.Technology Transfer

Number of Active CRADAs2

Review Publications
Tobias, C.M., Sarath, G., Twigg, P., Lindquist, E., Pangilinan, J., Penning, B., Barry, K., Carpita, N., Lazo, G.R. 2008. Comparative Genomics in Switchgrass Using 61,585 High-Quality EST. The Plant Genome. 1:111-124

Tobias, C.M. 2009. A GENOME MAY REDUCE YOUR CARBON FOOTPRINT. The Plant Genome. 2:5-8.

Huo, N., Vogel, J.P., Lazo, G.R., You, F., Ma, Y., McMahon, S.A., Dvorak, J., Anderson, O.D., Luo, M., Gu, Y.Q. 2009. Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat. Plant Molecular Biology. 70: 47-61.

Vogel, J.P., Metin, T., Budak, H., Huo, N., Gu, Y.Q., Steinwand, M.A. 2009. Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon Biomed Central (BMC) Plant Biology. 9:Article 88. Available:

Last Modified: 7/30/2014
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