Page Banner

United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Foundations for Bioenergy Feedstocks Title: Generation and characterization of the Western Regional Research Center brachypodium T-DNA insertional mutant collection

Authors
item Bragg, Jennifer -
item Wu, Jiajie -
item Gordon, Sean
item Guttman, Mara
item Thilmony, Roger
item Lazo, Gerard
item Gu, Yong
item Vogel, John

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 29, 2012
Publication Date: September 17, 2012
Citation: Bragg, J., Wu, J., Gordon, S.P., Guttman, M.E., Thilmony, R.L., Lazo, G.R., Gu, Y.Q., Vogel, J.P. 2012. Generation and characterization of the Western Regional Research Center brachypodium T-DNA insertional mutant collection. PLoS One. 7(9):e41916. doi:10.1371/journal.pone.0041916.

Interpretive Summary: The model grass Brachypodium distachyon (Brachypodium) is an excellent system for studying the basic biology underlying traits relevant to the use of grasses as food, forage and energy crops. This paper describes the creation of over 8,000 transgenic Brachypodium lines that can be used to help assign function to genes. By sequencing the DNA adjacent to the sites of insertion of the DNA inserted into the genome, we were able to create a database of which genes were potentially inactivated by the insertions. Researchers can then order specific lines to study what effect the loss of a specific gene on plant growth and development. Information about the Western Regional Research Center Brachypodium insertional mutant population is available on a searchable website (http://brachypodium.pw.usda.gov) designed to provide researchers with a means to order T-DNA lines with mutations in genes of interest.

Technical Abstract: The model grass Brachypodium distachyon (Brachypodium) is an excellent system for studying the basic biology underlying traits relevant to the use of grasses as food, forage and energy crops. To add to the growing collection of Brachypodium resources available to plant scientists, we further optimized our Agrobacterium tumefaciens-mediated high-efficiency transformation method and generated 8,491 Brachypodium T-DNA lines. We used inverse PCR to sequence the DNA flanking the insertion sites in the mutants. Using these flanking sequence tags (FSTs) we were able to assign 7,389 FSTs from 4,402 T-DNA mutants to 5,285 specific insertion sites (ISs) in the Brachypodium genome. More than 29% of the assigned ISs are supported by multiple FSTs. T-DNA insertions span the entire genome with an average of 19.3 insertions/Mb. The distribution of T-DNA insertions is non-uniform with a larger number of insertions at the distal ends compared to the centromeric regions of the chromosomes. Insertions are correlated with genic regions, but are biased toward UTRs and non-coding regions within 1 kb of genes over exons and intron regions. More than 1,300 unique genes have been tagged in this population. Information about the Western Regional Research Center Brachypodium insertional mutant population is available on a searchable website (http://brachypodium.pw.usda.gov) designed to provide researchers with a means to order T-DNA lines with mutations in genes of interest.

Last Modified: 11/26/2014
Footer Content Back to Top of Page