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Genomic Science Program

2010 Awardee

Insertional Mutagenesis of Brachypodium distachyon

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

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, nutrient uptake, carbon flux, etc.) could be used to design rational strategies for crop improvement. 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. In addition, numerous genomic tools have been developed for Brachypodium including a high-quality draft genome sequence, high–efficiency transformation methods and microarrays. Insertional mutants are a powerful research tool that allow researchers to rapidly determine the function of specific genes. During our initial grant term we optimized methods and created over 8,000 insertional mutants. We will continue to create insertional mutants and sequence DNA flanking the insertion sites. The mutant collection will be made publicly available through a BLAST searchable database (http://brachypodium.pw.usda.gov/TDNA/) to allow researchers to identify knockouts in specific genes.

OBJECTIVES: The objectives of this proposal are: 1) Generate 30,000 insertional mutants. 2) Sequence DNA flanking the insertion sites of all mutants to place the insertions in a genomic context. 3) Collaborate with other groups creating T-DNA lines to integrate their lines into our database.

APPROACH: Obj. 1. Using Agrobacterium -mediated transformation we will generate 30,000 Brachypodium lines with a known DNA sequence randomly inserted into the genome.

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 genome 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. To leverage our collection, we have established collaborations with an international group of researchers to create a larger collection of Brachypodium T-DNA lines. Groups from the United Kingdom, South Korea, China and Canada are included and we will welcome additional collaborators. We will support these groups by providing technical assistance, vectors and we will incorporate their flanking sequences into a common database to facilitate access by the research community.

PROJECT CONTACT:
Name: Vogel, J.P.
Phone: 510-559-6117
Fax: 510-559-5818
Email: john.vogel@ars.usda.gov

 

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