title: Generation and characterization of the Western Regional Research Center Brachypodium T-DNA insertional mutant collection.
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.
authors.affiliation: United States Department of Agriculture- Agriculture Research Service, Western Regional Research Center, Albany, California, United States of America.
authors.forename: Jennifer N
authors.initials: JN
authors.lastname: Bragg
authors.forename: Jiajie
authors.initials: J
authors.lastname: Wu
authors.forename: Sean P
authors.initials: SP
authors.lastname: Gordon
authors.forename: Mara E
authors.initials: ME
authors.lastname: Guttman
authors.forename: Roger
authors.initials: R
authors.lastname: Thilmony
authors.forename: Gerard R
authors.initials: GR
authors.lastname: Lazo
authors.forename: Yong Q
authors.initials: YQ
authors.lastname: Gu
authors.forename: John P
authors.initials: JP
authors.lastname: Vogel
mesh_terms: D060054:Agrobacterium / Q000502:physiology; D058431:Brachypodium / Q000235:genetics* / Q000382:microbiology; D032461:Chromosomes, Plant; D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D018744:DNA, Plant; D030561:Databases, Nucleic Acid; D015870:Gene Expression; D023061:Gene Order; D005822:Genetic Vectors / Q000235:genetics; D018745:Genome, Plant; D005966:Glucuronidase / Q000235:genetics / Q000378:metabolism; D020407:Internet; D016254:Mutagenesis, Insertional; D009154:Mutation; D010641:Phenotype; D030821:Plants, Genetically Modified; D014170:Transformation, Genetic
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D018744:DNA, Plant; C036483:T-DNA; D005966:Glucuronidase