Generation and characterization of the Western Regional Research Center Brachypodium T-DNA insertional mutant collection

PLoS One. 2012;7(9):e41916. doi: 10.1371/journal.pone.0041916. Epub 2012 Sep 17.

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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Agrobacterium / physiology
  • Brachypodium / genetics*
  • Brachypodium / microbiology
  • Chromosomes, Plant
  • DNA Transposable Elements
  • DNA, Bacterial*
  • DNA, Plant*
  • Databases, Nucleic Acid
  • Gene Expression
  • Gene Order
  • Genetic Vectors / genetics
  • Genome, Plant
  • Glucuronidase / genetics
  • Glucuronidase / metabolism
  • Internet
  • Mutagenesis, Insertional*
  • Mutation
  • Phenotype
  • Plants, Genetically Modified
  • Transformation, Genetic

Substances

  • DNA Transposable Elements
  • DNA, Bacterial
  • DNA, Plant
  • T-DNA
  • Glucuronidase

Grant support

This work was supported by the Office of Science (BER), US Department of Energy, Interagency Agreement No. DE-AI02-07ER64452 and by USDA CRIS project 5325-21000-013-00. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.