Brachypodium

Brachypodium Research

B. sylvaticum was initially adopted as the “bridge” brachypodium species to agronomically important cereals, but B. Distachyon was later selected due to its self-fertilization and annual characteristics (8, 10).

Brachypodium Genome Resources Project (15)

Developed A successful Agrobacterium-mediated transformation system
Collaborating on genetic maps, sequence and physical maps
Developing mutant population
EST sequencing
Constructed two BAC libraries

IBS Plant Molecular Pathology Group (6)

Collection of over 50 ecotypes
Identifying differential responses to Pathogenic attack (Magnaporthe grisea, Puccinia striformis and P. recondita, Pseudomonas syringae pathovars).
Developing models for local and systemic signalling following infection or wounding
Construction of cDNA and genomic libraries
Isolation of functional promoter sequences
Transient and stable transformation - regeneration and propagation of transgenic lines
Establishing the phylogenetic relationship between B. distachyon and cereal species
Developing B. distachyon as a general model for functional genomic studies in grasses and cereals.

Department of Energy Joint Genome Institute (14)

Sequencing Brachypodium to build a tractable temperate grass model needed to address questions directly relevant both for improving grain crops and forage grasses that are indispensable to our food production systems, and for developing grasses into superior energy crops. A whole-genome shotgun sequence (WGS) of the Brachypodium Bd21 genome, supplemented by a complete set of expressed sequence tags (ESTs), will be a cornerstone resource for a vigorous research community seeking to promote the development of new energy crops and to contribute to global food security. Principal Investigators: Jeff Chang (Oregon State Univ.), Michael Bevan (John Innes Centre), David Garvin (USDA-ARS), Samuel Hazen (Scripps Research Inst.), Todd Michael (Salk Inst.), Todd Mockler (Oregon State University), and John Vogel (USDA-ARS)

International Brachypodium Initiative (IBI) (5)

The IBI should aim to foster a collaborative framework based on free access to biological materials and immediate access to sequence and databases with no encumbrances. The IBI aims to establish a long-term, inclusive and diverse research programme that includes the following objectives:

Develop a set of community standard lines that are genetically well-defined and distribute these to all researchers free of encumbrances.
Promote the development and distribution of genomic and genetic resources such as BAC libraries, genetic markers and mapping populations
Initiate a genome sequencing programme
Establish collaborative links with other researchers e.g. in comparative genomics of crops.
Develop a web portal and genome database to link the research community, promote discussion and provide access to data, lines and other information.

Notes from the first meeting of the International Brachypodium Initiative (IBI) (1/2006)

Brachypodium data is increasingly available for research. In dbEST is it the ranks 9th among grasses for number of EST's, and provides enough information to begin functional genomic experiments, as well as raw material for generating molecular markers (18).

In addition to the resources in the bibliography section, the following resources are recent publications on Brachypdium research.

Allwood, JL, Ellis, DI, Heald, JK, Goodacre, R, & Mur LA. 2006. Metabolomic approaches reveal that phosphatidic and phosphatidyl glycerol phospholipids are major discriminatory non-polar metabolites in responses by Brachypodium distachyon to challenge by Magnaporthe grisea. The Plant Journal : for cell and molecular biology 46: 351-368.
Christiansen P, Andersen, CH, Didion T, Folling M, & Nielsen KK. 2005. A rapid and efficient transformation protocol for the grass Brachypodium distachyon. Plant Cell Reports 23: 751-758.
Hasterok R., Marasek A, Donnison IS, Armstead I, Thomas A, King IP, Wolny E, Idziak D, Draper J, & Jenkins G. 2006. Alignment of the genomes of Brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization. Genetics173: 349-362.
Hsiao C, Chatteron NJ, Asay KH, & Jensen KB. 1994. Phylogenetic relationships of 10 grass species: an assessment of phylogenetic utility of the internal transcribed spacer region in nuclear ribosomal DNA in monocots. Genome / National Research Council Canada 37: 112-120.
Huo N, Gu YQ, Lazo GR, Vogel JP, Coleman-Derr D, Luo MC, Thilmony R, Garvin, DF, & Anderson OD. 2006. Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome / National Research Council Canada 49: 1099-1108.
Vogel JP, Garvin DF, Leong OM, & Hayden DM. 2006. Agrobacterium-mediated transformation and inbred line development in the model grass Brachypodium distachyon. Plant Cell, Tissue and Organ Culture 84: 199-211.

Databases and Genetic Information

References:

Bennett, MD & Leitch, IJ. 2005. Nuclear DNA Amounts in Angiosperms: Progress, Problems and Prospects. Annals of Botany 95, 45-90.
Board of Trustees, Royal Botanic Gardens, Kew. The Online World Grass Flora (GrassBase) http://www.kew.org/data/grasses-db.html. [Accessed 1/8/07].
California plant names: Latin and greek meanings and derivations: A dictionary of botanical etymology. Compiled by Michael Charters. Website http://www.calflora.net/botanicalnames/. [Accessed 1/8/07].
Catalan P, Shi Y, Armstrong L, Draper J, Stace CA. 1995. Molecular phylogeny of the grass genus Brachypodium P. Beauv. based on RFLP and RAPD analysis. Botanical Journal of the Linnean Society, 117, 4, pp. 263-280.
Center for Genome Research and Biocomputing, The. http://www.brachypodium.org/ [Accessed 10/08/06].
Dept. of Molecular Plant Pathology, University of Wales at Aberystwyth. Brachyomics. http://www.aber.ac.uk/plantpathol/brachyomics.htm.[Accessed February 28, 2007].
Dept of Rangeland Ecology and Management, Texas A&M University. S M Tracy Herbarium. http://www.csdl.tamu.edu/FLORA/taes/tracy/610/brachypodium.html. [Accessed 1/8/2007].
Draper J, Mur LA, Jenkins G, Ghosh-Biswas GC, Bablak P, Hasterok R, & Routledge AP. 2001. Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiology 127: 1539-1555.
Hasterok R, Draper J, & Jenkins G. 2004. Laying the cytotaxonomic foundations of a new model grass, Brachypodium distachyon (L.) Beauv. Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 12: 397-403.
Hasterok R, Marasek A, Donnison IS, Armstead I, Thomas A, King IP, Wolny E, Idziak D, Draper J, & Jenkins G. 2006. Alignment of the genomes of Brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization. Genetics 173: 349-362.
Hussey BMJ, Keighery GJ, Cousens RD, Dodd J & Lloyd SG. 1997. Western Weeds, A guide to the weeds of Western Australia. http://members.iinet.net.au/~weeds/pps_publications.htm.
ITIS - Integrated taxonomic information system on-line database. http://www.itis.gov. [Accessed 1/8/07].
Piep, Michael B. 2007. Brachypodium in North America north of Mexico. http://herbarium.usu.edu/webmanual/info2.asp?name=Brachypodium&type=treatment Based on treatment in M.E. Barkworth et al. (eds). 2007. Flora of North America north of Mexico, volume 24. Oxford University Press, New York. (to order online, see http://www.oup.com/us/catalog/general/series/FloraofNorthAmerica/?view=usa )
The Regents of the University of California. 2001. Why Sequence Brachypodium? http://www.jgi.doe.gov/sequencing/why/CSP2007/brachypodium.html. [Accessed Jan 8, 2007].
USDA, ARS. Brachypodium genome resources project. Website http://brachypodium.pw.usda.gov/. [Accessed 1/8/07].
USDA Forest Service, USDI Bureau of Land Management, Oregon Department of Agriculture, US Army Corps of Engineers, OSU College of Forestry, Institute for Applied Ecology, Starker Forests Inc., The Nature Conservancy, Native Plant Society of Oregon. 2003. Invasive Plant Alert False-brome (Brachypodium sylvaticum). Prepared by Thomas Kaye. http://www.appliedeco.org/Reports/BRSYbrochure.PDF.
USDA, NRCS. (2006). The PLANTS Database (http://plants.usda.gov), 16 October 2006. National Plant Data Center, Baton Rouge, LA 70874-4490 USA.
Vogel JP, Gu YQ, Twigg P, Lazo GR, Laudencia-Chingcuanco D, Hayden DM, Donze TJ, Vivian LA, B. Stamova B, & Coleman-Derr D. 2006. EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon. TAG.Theoretical and applied genetics. 113: 186-195.
Watson, L and Dallwitz, MJ. 1992 onwards. The grass genera of the world: descriptions, illustrations, identification, and information retrieval; including synonyms, morphology, anatomy, physiology, phytochemistry, cytology, classification, pathogens, world and local distribution, and references. Version: 28th November 2005. http://delta-intkey.com. [Accessed 8 January, 2007].
Wikipedia contributors, 'Brachypodium distachyon', Wikipedia, The Free Encyclopedia, 6 September 2006, 10:03 UTC, http://en.wikipedia.org/w/index.php?title=Brachypodium_distachyon&oldid=74106473. [Accessed 8 January, 2007].
Wilken DH. 1993. Brachypodium. From The Jepson Manual, Copyright © 2007 Regents of the University of California. Available online at http://ucjeps.berkeley.edu/cgi-bin/get_JM_treatment.pl?8738,8852,8853. [Accessed 1/8/07].