Page Banner

United States Department of Agriculture

Agricultural Research Service

Related Topics


Location: Genomics and Gene Discovery

2007 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 and switchgrass. Collaborative efforts within the agency and with external collaborators have produced enough sequence information to produce a draft genome sequence of Brachypodium that will be assembled in the upcoming year. We have also developed and genetically evaluated a switchgrass mapping population and demonstrated regions of collinearity with other grass genomes using DNA markers derived from gene sequences. Analysis of several informative markers provided support for a high degree of preferential pairing in switchgrass and also led to the discovery of a diploid switchgrass line. These markers can be used for a number of purposes to assist breeder’s efforts to improve switchgrass as an energy crop. The development of plant transformation technology within our research project is being applied in Brachypodium toward developing basic research tools such as T-DNA “tagged” mutant populations and hypotheses testing of individual gene’s specific functions. In switchgrass we have more applied goals for our plant transformation efforts aimed at specifically improving cell wall properties.

This year we have evaluated lines that were designed to silence gene function in the lignin pathway and thereby have less of this compound that inhibits enzymatic conversion of structural carbohydrates to ethanol. Transgenic lines with reduced cinnamyl alcohol dehydrogenase activity were evaluated for cell wall composition. However, using a number of different analytical techniques, no differences in cell wall properties were observed. This indicates that either the enzyme levels were not altered to a sufficient degree, or that the specific gene we chose for silencing was not the one primarily responsible for lignification in switchgrass. Further work in this area is being carried out through a subordinate project supported by a cooperative research and development agreement.

Brachypodium distachyon genome resources. 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 have collaborated on the generation of a structural assemblyphysical map of the entire genome of the model grass species Brachypodium distachyon. 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. This accomplishment furthers the energy crop componentIV of National Program 307 - Bioenergy and Energy Alternatives.

Development of switchgrass genetic resources. Breeding progress in switchgrass is slow and efficient breeding techniques taking advantage of genome sequence information is needed. ARS scientists in Albany CA, and Tifton GA have established a switchgrass linkage mapping population at multiple field locations in collaboration with the Forage Breeding Division of the Samuel Roberts Noble Foundation for the purposes of collecting morphological and phenotypic data that will help to identify genetic loci affecting traits relevant to biomass production from switchgrass. Many molecular markers developed from existing sequence information are being used on this population to develop a linkage map that will allow comparison with other grasses. This accomplishment aligns with the energy crop componentIV of National Program 307 -Bioenergy and Energy Alternatives.

Identification of a diploid switchgrass line. Working with polyploid species such as switchgrass complicates identification of beneficial genes and gene combinations that will affect biomass traits. ARS scientists in Albany CA have identified a single switchgrass line that has been confirmed as diploid. Until the present, diploid switchgrass lines have been unavailable. Availability of such lines is extremely useful in several respects. Whole genome sequencing would become more feasible. Genetic map construction would be simplified, and population structure with regard to origins of polyploidy could be determined. Breeders should be able to exploit this diploid line using a number of established breeding techniques to manipulate desirable traits. This accomplishment aligns with the energy crop componentIV of National Program 307 -Bioenergy and Energy Alternatives.

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, Turkey and in-house research have collected novel accessions of the model grass species Brachypodium distachyon from diverse environments and have utilized molecular markers for to measure genetic diversity. A mutagenized population has also been created to provide additional genetic resources. These lines can be used to study grass cell wall structure and other traits important for the production of cellulosic biomass. This accomplishment aligns with the energy crop componentIV of National Program 307 -Bioenergy and Energy Alternatives.

Brachypodium mapping and marker development. To identify the underlying genes that are responsible for traits relevant to biomass production in grasses, markers and linkage maps are needed to delimit the relevant genome regions. ARS scientists in Albany, CA and St. Paul Minnesota have contributed to marker development and linkage map construction through concerted genotyping efforts. Microsatellite markers were developed from existing sequence information and used to genotype a mapping population. In addition, a project to create 1,000 single nucleotide polymorphism (SNP) markers that will be used to link the genetic and physical maps of Brachypodium has been initiated. To date 234 SNP markers have been identified. These markers will help to produce a dense linkage map and enable map-based cloning approaches in this species. This accomplishment aligns with the energy crop componentIV of National Program 307 -Bioenergy and Energy Alternatives.

5.Significant Activities that Support Special Target Populations

6.Technology Transfer

Number of active CRADAs and MTAs6
Number of non-peer reviewed presentations and proceedings8
Number of newspaper articles and other presentations for non-science audiences1

Review Publications
Vorwerk, S., Schiff, C., Santamaria, M., Koh, S., Nishimura, M., Vogel, J., Somerville, C., Somerville, S. 2007 EDR2 negatively regulates salicylic acid-based defenses and cell death during powdery mildew infections of Arabidopsis thaliana. BMC Plant Biology. 7: Issue 35 (on-line journal).

Last Modified: 4/17/2014
Footer Content Back to Top of Page