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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, arepoised to become a major source of energy in the United States. Despitetheir increasing importance, we know little about the basic biology underlyingthe traits that control the utility of grasses as energy crops. Betterknowledge of basic grass biology (e.g. identification of the genes thatcontrol cell wall composition, plant architecture, cell size, cell division,reproduction, nutrient uptake, carbon flux, etc.) could be used to designrational strategies for crop improvement and shorten the time requiredto domesticate these species. The use of an appropriate model system isan efficient way to gain this knowledge. Brachypodium distachyon is asmall grass with all the attributes needed to be a modern model organismincluding simple growth requirements, fast generation time, small stature,small genome size and self-fertility. Insertional mutants are a powerfulresearch tool that allow researchers to rapidly determine the functionof specific genes. We will create a collection of insertional mutantsand sequence the flanking DNA. The mutant collection will be made publiclyavailable through a searchable database to allow researchers to identifymutants in specific genes.

OBJECTIVES: The objectives of this proposal are: 1) generate >7,500 insertionalmutants in the model grass Brachypodium distachyon , 2) sequence DNA flanking >6,000insertion sites and annotate the genes affected using the genomic sequenceand 3) establish a website where researchers can search the flanking sequencedatabase 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 intothe Brachypodium genome. We will also test different strategies includingthe 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 insertedDNA. By comparing the flanking sequence to the Brachypodium genomic sequencewe will determine if the inserted DNA lies within a gene. When the insertedDNA lands within a gene it disrupts the activity of that gene. By studyingsuch lines researchers will be able to determine the effect of specificgenes on the process they are studying.

Obj. 3. A searchable web site will be established that will allow usersto identify genes that contain inserts. Data displayed will include: theannotation of the gene, the location of the insert within the gene andany 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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