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Brachypodium Resources

Brachypodium distachyon is a small annual grass that researchers use as a model for the grasses used to produce biomass, food, feed and forage. Unlike the grasses grown as crops, B. distachyon is well suited to experimental manipulation in the laboratory because of its small size, compact genome, diploid nature, self compatibility, rapid generation time and simple growth requirements. In addition, numerous resources and methods (e.g. complete genome sequence, high efficiency transformation, large collections of natural accessions, many sequenced accessions and several RIL populations) are available that allow researchers to apply a suite of modern research methods to understand the unique aspects of grass biology. See here for a review of B. distachyon as a model system.

In addition to B. distachyon, other species in the genus are being used to study polyploidy (B. hybridum and B. stacei) and perenniality (B. sylvaticum).

Below are links to announcements and experimental resources and background information. If you have suggestions, please contact us.

Chemical and radiation mutants.

Announcements (updated 2-28-2019)

Let us know if you have an announcement

  • The 4th International Brachypodium Conference that will be held in Huesca, Spain from June 25-28, 2019. The deadline for submitting and abstract to be considered for an oral talk is March 31. The deadline to submit and abstract for posters is April 30. A preliminary program is available on the meeting website. Contact the organizer Pilar Catalan with any questions.
  • Over 1,200,000 SNP mutations are now searchable on Phytozome. Look in jbrowse on the Bd21-3 reference genome
  • T-DNA insertion sites have been updated to the Bd21-3 v1.1 assembly (they are also on the Bd21 v3.1 assembly) and are available through the T-DNA page or through jbrowse in Phytozome.
  • The reference genome for the allotetraploid B. hybridum has been released on Phytozome as an early release genome.
  • The pan-genome of B. distachyon has been published in Nature Communications and is available online.
  • BrachyPan, a pan-genome website is now available to download and interrogate 54  de novo assemblies that were used to create a B. distachyon pan-genome.
  • A second reference genome for B. distachyon is now available. The genome of line Bd21-3 was sequenced because it is the parent of the sequenced mutant populations. Note that Bd21-3 is a different inbred line than Bd21, the source of the first B. distachyon reference genome.
  • Reference genomes for Brachypodium stacei and B. sylvaticum are now available on Phytozome under early access terms.
  • The 3rd International Brachypodium Conference held in July 2017 in Beijing was big success thanks to Zhiyong Liu and the local organizing committee. The program is available at the meeting website. The abstract book can be downloaded here.
  • The first book on Brachypodium genomics has been published.
  • The election for the International Brachypodium Steering Committee (IBSC) has been completed. Click here to view the results.
  • An improved reference genome assembly (v3.0) and annotation are now available on Phytozome.
  • The abstract book from the third International Brachypodium conference held 16-19 June 2015, in Amherst Massachusetts can be downloaded from the meeting website.

Resources and methods

T-DNA mutants

A collection of 23,649 T-DNA mutants is available.

Chemical and radiation mutants

A CSP project “Creating a genome-wide sequence-indexed collection of grass mutants” to sequence populations of EMS, fast neutron and sodium azide B. distachyon mutants was initiated in 2015. This project is a collaboration with researchers in France (Richard Sibout, INRA, IJPB) and the United States (Debbie Laudencia-Chingcuanco, USDA-ARS, WRRC). To date, over 1,200,000 mutations from 859 lines have been identified and are available as a jbrowse track on the Bd21-3 reference genome on Phytozome. When completed, this will be an unprecedented resource for forward and reverse genetics. If you would like to be involved in the screening or characterizing of this collection, please contact us.

Reference genomes

An extremely high quality reference genome for B. distachyon Bd21 is available on Phytozome 12. Details of this highly improved assembly are available on Phytozome.

Additional reference genomes are available for B. distachyon Bd21-3 (parent of mutant populations), B. stacei , the allotetraploid B. hybridum and the perennial B. sylvaticum are also available on Phytozome.

Germplasm

A large collection of inbred lines from geographically diverse locations has been established. A large collection of lines from Turkey are described in “Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon” and “Molecular, Morphological, and Cytological analysis of diverse B. distachyon inbred lines“. Most of the Turkish lines can be ordered from the National Plant Germplasm System. Many lines have been also been collected from Spain.

Garvin lab stocks including RIL populations.

Pan-genome and resequenced lines

A B. distachyon pan-genome created from 54 de novo assemblies has been published and is available from the BrachyPan website. An additional 65 lines have been sequenced and assembled and will be available shortly. Download this spreadsheet for a complete list of sequenced lines and their status.

Protocols

Transformation:

Crossing:

EMS mutagensis:

Publications

Book

  • Genetics and Genomics of Brachypodium. 2016 Vogel, J.P. Ed., Springer, Switzerland. ISBN: 978-3-319-26942-9

Review

  • Fitzgerald, T. L., J. J. Powell, K. Schneebeli, M. M. Hsia, D. M. Gardiner, J. N. Bragg, C. L. McIntyre, J. M. Manners, M. Ayliffe, M. Watt, J. P. Vogel, R. J. Henry and K. Kazan (2015). “Brachypodium as an emerging model for cereal-pathogen interactions.” Annals of Botany 115(5): 717-731.
  • Brutnell TP, Bennetzen JL, Vogel JP. 2015 Brachypodium distachyon and Setaria viridis: model genetic systems for the grasses. Annu. Rev. Plant Biol. 66:In press. doi: 10.1146/annurev-arplant-042811-105528
  • Catalan P, Chalhoub B, Chochois V, Garvin DF, Hasterok R, Manzaneda AJ, Mur LAJ, Pecchioni N, Rasmussen SK, Vogel JP, Voxeur A 2014 Update on the genomics and basic biology of Brachypodium. Trends in Plant Science 19 (7), pp. 414-418
  • Chochois V, Vogel JP, Watt M 2012 Application of Brachypodium to the genetic improvement of wheat roots. J. of Exp. Bot. 63:3467-3474
  • Bragg, J. N., T. Ludmila and Vogel, J.P. 2012 Brachypodium distachyon, A Model for Bioenergy Grasses. Handbook of Bioenergy Crop Plants. Kole, C., Joshi, C.P. and Shonnard, D.R., Boca Rotan, Taylor & Francis Group. p 593-618
  • Brkljacic J, Grotewold E, Scholl R, Mockler T, Garvin DF, Vain P, Brutnell T, Sibout R, Bevan M, Budak H, Caicedo AL, Gao C, Gu Y, Hazen SP, Holt BF, Hong SY, Jordan M, Manzaneda AJ, Mitchell-Olds T, Mochida K, Mur LAJ, Park CM, Sedbrook J, Watt M, Zheng SJ, Vogel JP 2011 Brachypodium as a model for the grasses: Today and the future. Plant Phys. 157: 3-13
  • Mur LAJ, Allainguillaume J, Catalán P, Hasterok R, Jenkins G, Lesniewska K, Thomas I, Vogel J. 2011 Exploiting the Brachypodium tool box in cereal and grass research. New Phytologist 191: 334-347
  • Bevan, M.W., Garvin, D.F., Vogel, J.P. 2010 Brachypodium distachyon genomics for sustainable food and fuel production. Current Opinion in Biotechnology 21: 211-217
  • Vogel, J. P. and Bragg, J.N. 2009 Brachypodium distachyon, a New Model for the Triticeae. Genetics and Genomics of the Triticeae. Feuillet, C. and Muehlbauer, G. New York, Springer. 7: 427-449.
  • Vogel, J. 2008 Unique aspects of the grass cell wall. Current Opinion in Plant Biology. 11: 301-307
  • Garvin, D., Gu, Y., Hasterok, R., Hazen, S., Jenkins, G., Mockler, T., Mur, LJ., and Vogel, JP.  2008 Development of genetic and genomic research resources for Brachypodium distachyon, a new model for grass crop research. Crop Science 48: S69-S84

Research papers

  • Gordon, S.P., Contreras-Moreira, B., Woods, D.P., Des Marais, D.L., Burgess, D., Shu, S., Stritt, C., Roulin, A.C., Schackwitz, W., Tyler, L., Martin, J.,  Lipzen, A., Dochy, N., Phillips, J., Barry, K., Geuten, K., Budak, H., Juenger, T.E., Amasino, R., Caicedo, A.L., Goodstein, D., Davidson, P., Mur, L.A.J., Figueroa, M., Freeling, M., Catalan, P., and Vogel, J.P., 2017 Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nat. Comm. doi: 10.1038/s41467-017-02292-8
  • Sancho, R., Cantalapiedra, C.P., López-Alvarez, D., Sean P. Gordon, S.G., Vogel, J.P., Catalán, P., Contreras-Moreira, B., 2017 Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes.  New Phytologist doi: 10.1111/nph.14926
  • O’Connor DL, Elton S, Ticchiarelli F, Hsia MM, Vogel JP, Leyser T. 2017 Cross-species functional diversity within the PIN auxin efflux protein family. Elife 6
  • Hsia, M.M., O’Malley, R., Cartwright, A., Nieu, R., Gordon, S.P., Sandra Kelly, K., Williams, T.G., Wood, D.F., Zhao, Y., Bragg, J., Jordan, M., Markus Pauly, M., Joseph R. Ecker, J.R., Yong Gu, Y., Vogel, J.P., 2017 Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection.  Plant Journal 91(3): p. 361-370.
  • T Raissig, M.T., Matos, J.L., Gil, M.X.A., Kornfeld, A., Bettadapur, A., Abrash, E., Allison, H.R., Badgley, G., Vogel, J.P., Berry, J.A., Bergmann, D.C. 2017 Mobile MUTE specifies subsidiary cells to build physiologically superior grass stomata, Science 355: 1215-1218Liu L,
  • Hsia MM, Dama M, Vogel J, Pauly M., 2016A Xyloglucan Backbone 6-O-Acetyltransferase from Brachypodium distachyon Modulates Xyloglucan Xylosylation. Molecular Plant 2016, 9(4):615-617.
  • Bindics, J., Genenncher, B., Navarrete, F., Kellner, R., Ekker, H., Kumlehn, J., Vogel, J.P., Gordon, S.P., Marcel, T.C., Münsterkötter, M., Walter, M.C., Sieber, C.M.K., Mannhaupt, G., Güldener, U., Kahmann R., and A. Djamei, A. 2016 A complete toolset for the study of Ustilago bromivora and Brachypodium sp. as a fungal-temperate grass pathosystem. eLife 5(November2016).
  • Woods, D.P., Bednarek, R.,  Bouché, F., Gordon, S.P., Vogel, J.P., Garvin, D.F., and Amasino, R.M. 2017 Genetic architecture of flowering-time variation in Brachypodium distachyon. Plant Physiology 173(1): 269-279
  • Thi, V.H.D., Coriton, O., Clainche, I.L., Arnaud, D., Gordon, S.P., Linc, G., Catalan, P., Hasterok, R., Vogel, J.P., Jahier, J. and B. Chalhoub, B. 2016 Recreating stable Brachypodium hybridum allotetraploids by uniting the divergent genomes of B. distachyon and B. stacei. PLoS ONE 11(12).
  • Raissig, MT. Emily Abrash, Bettadapur, A. Vogel, J.P., Bergmann, D.C. 2016 Grasses use an alternatively wired bHLH transcription factor network to establish stomatal identity Proc. Natl. Acad. Sci. 113 (29), pp. 8326-8331
  • Collier, R., Bragg, J., Hernandez, B.T., Vogel, J.P., Thilmony, T., 2016 Use of Agrobacterium rhizogenes strain 18r12v and paromomycin selection for transformation of Brachypodium distachyon and Brachypodium sylvaticum. Frontiers in Plant Science Volume 7, Article number 716
  • Petrik, D.L., Cass, C.L., Karlen, S.D., Foster, C.E., Padmakshan, D., Vogel, J.P.,4 Ralph, J., 2,5, and Sedbrook, J.C., 2016 BdCESA7, BdCESA8, and BdPMT utility promoter constructs for targeting gene-of-interest expression to secondary cell wall forming cells of grasses. Frontiers in Plant Science Volume 7, Article number 55
  • Schneebeli, K., Mathesius, U., Zwart, A., Vogel, J.P., Bragg, J., Watt, M., 2015 Brachypodium distachyon genotypes vary in resistance to Rhizoctonia solani anastomosis group 8. Functional Plant Biology 43 (2), pp. 189-198
  • Rellán-Álvarez, R., Lobet, G., Lindner, H., Pradier, P., Sebastian, J., Yee, M., Geng, Y., Trontin, C., LaRue, T., Schrager-Lavelle, S., Haney, C.H., Nieu, R., Maloof, J., Vogel, J.P., José R Dinneny, J.R. 2015 GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems. eLife 10.7554/eLife.07597 DOI: http://dx.doi.org/10.7554/eLife.07597
  • Chochois, V., Vogel, J.P., Rebetzke, G., and Watt, M. 2015 Variation in Adult Plant Phenotypes and Partitioning among Seed and Stem-Borne Roots across Brachypodium distachyon Accessions to Exploit in Breeding Cereals for Well-Watered and Drought Environments. Plant Physiology Vol. 168: 953-967
  • Bragg, N.B., Anderton, A., Nieu, R., and Vogel, J.P. 2015 Brachypodium distachyon. Agrobacterium Protocols: Volume 1 (Methods in Molecular Biology vol. 1223) Wang. K., New York, Springer. 2015, pp 17-33
  • Gordon, S.P., Priest, H., Des Marais, D.L., Schackwitz, W., Figueroa, M., Martin, J., Bragg, J.N., Tyler, L., Lee, C.R., Bryant, D., Wang, W., Messing, J., Manzaneda, A.J., Kerrie, B., Garvin, D.F., Budak, H., Tuna, M., Mitchell-Olds, T., Pfender, W.F., Juenger, T.E., Mockler, T.C., and Vogel, J.P., 2014 Genome Diversity in Brachypodium distachyon: Deep Sequencing of Highly Diverse Inbred Lines 2014 Plant Journal 79: 361–374 DOI: 10.1111/tpj.12569
  • Poiré R., Chochois V., Sirault X.R.R., Vogel J.P., Watt M., Furbank R.T., 2014 Whole plant phenotypic variability in nitrogen and phosphorus response of Brachypodium distachyon Journal of Integrative Plant Biology 56 (8), pp. 781-796
  • Tyler L., Fangel J.U., Fagerström A.D., Steinwand M.A., Raab, T.K., Willats, W.G.T., Vogel, J.P. 2014 Selection and phenotypic characterization of a core collection of Brachypodium distachyon inbred lines BMC Plant Biology 14:25  doi:10.1186/1471-2229-14-25
  • O’Connor, D.L., Runions, A., Sluis, A., Bragg, J., Vogel, J.P., Prusinkiewicz, Hake, S. 2014 A Division in PIN-Mediated Auxin Patterning During Organ Initiation in Grasses PLoS Computational Biology DOI: 10.1371/journal.pcbi.1003447
  • Steinwand, M.A., Young, H.A., Bragg, J.N., Tobias, C.M., and Vogel, J.P. 2013 Brachypodium sylvaticum, a model for perennial grasses: transformation and inbred line development PLoS ONE 8(9): e75180. doi:10.1371/journal.pone.0075180
  • Wu, X., Wu, J., Luo, Y., Bragg, J., Vogel, J., Gu, Y.Q, 2013 Phylogenetic, Molecular, and Biochemical Characterization of Caffeic Acid o-Methyltransferase Gene Family in Brachypodium distachyon. International Journal of Plant Genomics 2013 Article ID 423189
  • Bragg, J.N., Wu, J., Gordon, S.P., Guttman, M.A., 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) art. no. e41916
  • Cui, Y., Lee, M.Y., Huo, N., Bragg, J., Yan, L., Yuan, C., Li, C., Holditch, S.J., Xie, J., Luo, M.C., Li, D., Yu, J., Martin, J., Schackwitz, W., Gu, Y.Q., Vogel, J.P., Jackson, A.O., Liu, Z., Garvin, D.F. 2012 Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLoS ONE 7 (6) art. no. e38333
  • Chuck, G.S., Tobias, C., Sun, L., Kraemer, F., Li, C., Dibble, D., Arora, R., Bragg, J.N., Vogel, J.P., Singh, S., Simmons, B.A., Pauly, M., Hake, S. 2011 Overexpression of the maize Corngrass1 microRNA prevents flowering, improves digestibility, and increases starch content of switchgrass. Proc. Natl. Acad. Sci. 108: 17550-17555
  • Huo, N., Garvin, D.F., You, F.M., McMahon, S., Luo, M.C., Gu, Y.Q., Lazo, G.R., Vogel, J.P. 2011 Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon. Theor. and Appl. Genet. 123: 455-464
  • Tyler, L., Bragg, J.N., Wu, J., Yang, X., Tuskan, G.A., Vogel, J.P. 2010 Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon. BMC Genomics. 11: 600
  • Vogel, J.P., Garvin, D.F., Mockler, T.C., Schmutz, J., Rokhsar, D., Bevan, M.W. et. al. (134 authors in total) 2010 Genome Sequencing and Analysis of The Model Grass Brachypodium distachyon. Nature. 463: 763-768
  • Vogel, J.P., Tuna, M., Budak, H., Huo, N., Gu, Y.Q., Steinwand, M.A. 2009 Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon. BMC Plant Biology. 9: Article No. 88
  • Gu, Y.Q., Ma, Y., Huo, N., Vogel, J.P., You, F.M., Lazo, G.R., Nelson, W.M., Soderlund, C., Dvorak, J., Luo, M.C. 2009 A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. BMC Genomics 10:496.
  • Garvin, D.F., McKenzie, N., Vogel, J.P., Mockler, T.C., Blankenheim, Z.J., Wright, J., Cheema, J.J.S., Dicks, J., Huo, N., Hayden, D.M., Gu, Y., Tobias, C., Chang, J.H., Chu, A., Trick, M., Michael, T.M., Bevan, M.W., and Snape, J.W. 2009 An SSR-based Genetic Linkage Map of the Model Grass Brachypodium distachyon. Genome 53: 1-13.
  • Filiz, E., Ozdemir, B.S., Budak, F., Vogel, J.P., Tuna, M., and Budak, H. 2009 Molecular, morphological, and cytological analysis of diverse Brachypodium distachyon inbred lines. Genome 52: 876-890.
  • Wei B., Cai T., Zhang R., Li A., Huo N., Li S., Gu Y.Q., Vogel J., Jia J, Qi Y., Mao, L. 2009 Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv. Functional and Integrative Genomics 9(4):499-511. 2009.
  • Huo, N., Vogel, J., Lazo, J., You, F., Ma, Y., McMahon, S., Dvorak, J., Anderson, O., Luo, M., and Gu, Y. 2008 Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat. Plant Molecular Biology 70: 47
  • Vogel, J., Hill, T. 2008 High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3. Plant Cell Rep. 27: 471-478.
  • Huo, N., Lazo, G., Vogel, J., You, F., Ma, Y., Hayden, D., Colemann-Derr, D., Hill, T., Dvorak, J., Anderson, O., Luo, M., Gu, Y. 2008 The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. Functional and Integrative Genomics 8: 135-147
  • Huo, N., Gu, Y., Lazo, G., Vogel, J., Coleman-Derr, D., Luo, M., Thilmony, R., Garvin, D., and Anderson, O. 2006 Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome 49:1099-1108