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Genomic Science Program

Systems Biology for Energy and the Environment

Department of Energy Office of Science. Click to visit main DOE SC site.

Genomic Science Program

2007 Awardee

Insertional mutagenesis of Brachypodium distachyon

INVESTIGATORS: J.P. Vogel, Y.Q. Gu, G.R. Lazo, O.D.Anderson

INSTITUTION: USDA-ARS Western Regional Research Center

NON-TECHNICAL SUMMARY: Herbaceous energy crops, especially grasses, are poised to become a major source of energy in the United States. Despite their increasing importance, we know little about the basic biology underlying the traits that control the utility of grasses as energy crops. Better knowledge of basic grass biology (e.g. identification of the genes that control cell wall composition, plant architecture, cell size, cell division, reproduction, nutrient uptake, carbon flux, etc.) could be used to design rational strategies for crop improvement and shorten the time required to domesticate these species. The use of an appropriate model system is an efficient way to gain this knowledge. Brachypodium distachyon is a small grass with all the attributes needed to be a modern model organism including simple growth requirements, fast generation time, small stature, small genome size and self-fertility. Insertional mutants are a powerful research tool that allow researchers to rapidly determine the function of specific genes. We will create a collection of insertional mutants and sequence the flanking DNA. The mutant collection will be made publicly available through a searchable database to allow researchers to identify mutants in specific genes.

OBJECTIVES: The objectives of this proposal are: 1) generate >7,500 insertional mutants in the model grass Brachypodium distachyon, 2) sequence DNA flanking >6,000 insertion sites and annotate the genes affected using the genomic sequence and 3) establish a website where researchers can search the flanking sequence database and order knockouts in genes of interest.

APPROACH: Obj. 1. Using Agrobacterium-mediated transformation we will generate7,500 Brachypodium lines with a known DNA sequence randomly inserted into the Brachypodium genome. We will also test different strategies including the use of transposons to improve the efficiency of generating mutants.

Obj. 2. Using the known sequence of the inserted DNA as a starting point, we will sequence a small stretch of Brachypodium DNA flanking the inserted DNA. By comparing the flanking sequence to the Brachypodium genomic sequence we will determine if the inserted DNA lies within a gene. When the inserted DNA lands within a gene it disrupts the activity of that gene. By studying such lines researchers will be able to determine the effect of specific genes on the process they are studying.

Obj. 3. A searchable web site will be established that will allow users to identify genes that contain inserts. Data displayed will include: the annotation of the gene, the location of the insert within the gene and any phenotype noted for the mutant.

PROJECT CONTACT:
Name: J.P. Vogel
Phone: 510-559-6117
Fax: 510-559-5818
Email: jvogel@pw.usda.gov

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