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United States Department of Agriculture

Agricultural Research Service

Related Topics

John Vogel
Genomics and Gene Discovery
Research Molecular Biologist

Phone: (510) 559-6117
Fax: (510) 559-5818
Room 2105
USDA, ARS, PWA, WRRC-GGD
800 BUCHANAN STREET
ALBANY, CA, 94710

Projects
Genetic Foundations for Bioenergy Feedstocks
Appropriated (D)
  Accession Number: 418493
Insertional Mutagenesis of Brachypodium Distachyon (FY 2012-FY 2014)
Reimbursable (R)
  Accession Number: 423230
Expanding the Breeder's Toolbox for Perennial Grasses
Reimbursable (R)
  Accession Number: 423725

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Phylogenetic, molecular, and biochemical characterization of caffeic aicd O-methyltransferase (COMT) gene family in Brachypodium distachyon - (Peer Reviewed Journal)
Wu, X., Ju, J., Bragg, J.N., Vogel, J.P., Anderson, O.D., Gu, Y.Q. 2013. Phylogenetic, molecular, and biochemical characterization of caffeic aicd O-methyltransferase (COMT) gene family in Brachypodium distachyon. International Journal of Plant Genomics. doi.org/10.1155/2013/423189.
Generation and characterization of the Western Regional Research Center brachypodium T-DNA insertional mutant collection - (Peer Reviewed Journal)
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.
Fine mapping of the Bsrl barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. - (Peer Reviewed Journal)
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 Bsrl barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLoS One. 7:e38333.
Application of Brachypodium to the genetic improvement of wheat roots - (Review Article)
Chochois, V., Vogel, J.P., Watt, M. 2012. Application of Brachypodium to the genetic improvement of wheat roots. Journal of Experimental Botany. 63:3467-3474.
Brachypodium as a model for the grasses: today and the future Reprint Icon - (Peer Reviewed Journal)
Brkljacic, J., Grotewold, E., Scholl, R., Mockler, T., Garvin, D.F., Vain, P., Brutnell, T., Sibout, R., Bevan, M., Budak, H., Caicedo, A.L., Gao, C., Gu, Y.Q., Hazen, S.P., Holt, B.F., Hong, S., Jordan, M., Manzaneda, A.J., Mitchell-Olds, T., Mochida, K., Mur, L.A., Park, C., Sedbrook, J., Watt, M., Zheng, S., Vogel, J.P. 2011. Brachypodium as a model for the grasses: today and the future. Plant Physiology. 157(1):3-13.
Exploiting the Brachypodium Tool Box in cereal and grass research - (Review Article)
Mur, L., Allainguillaume, J., Catalan, P., Hasaterok, R., Jenkins, G., Lesniewski, K., Thomas, I., Vogel, J.P. 2011. Exploiting the Brachypodium tool box in cereal and grass research. New Phytologist. DOI: 10.1111/j.1469-8137.2011.03748.x.
Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon - (Peer Reviewed Journal)
Huo, N., Garvin, D.F., You, F., McMahon, S.A., Luo, M., 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. Theoretical and Applied Genetics. 123(3):455-464.
Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon - (Peer Reviewed Journal)
Tyler, L., Bragg, J.N., Wu, J., Yng, X., Tuskan, G., Vogel, J.P. 2010. Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon. Biomed Central (BMC) Genomics. 11:600.
Brachypodium distachyon genomics for sustainable food and fuel production - (Review Article)
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.
Genome Sequencing and Analysis of the Model Grass Brachypodium Distachyon. - (Peer Reviewed Journal)
Vogel, J.P., Garvin, D.F., Gu, Y.Q., Lazo, G.R., Anderson, O.D., Bragg, J.N., Chingcuanco, D.L., Weng, Y., Belknap, W.R., Thomson, J.G., Dardick, C.D., Baxter, I.R. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 463:763-768.
A Bac-Based Physical Map of Brachypodium Distachyon and Its Comparative Analysis with Rice and Wheat - (Peer Reviewed Journal)
Gu, Y.Q., Ma, Y., Huo, N., Vogel, J.P., You, F., Lazo, G.R., Nelson, W., Soderlund, C., Dvorak, J. 2009. A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. Biomed Central (BMC) Genomics. 10:496
An SSR-Based Genetic Linkage Map of the Model Grass Brachypodium distachyon Reprint Icon - (Peer Reviewed Journal)
Garvin, D.F., Mckenzie, N., Vogel, J.P., Mockler, T.C., Blankenheim, Z., Wright, J., Huo, N., Cheema, J.J., Dicks, J., Hayden, D.M., Gu, Y.Q., Tobias, C.M., Chang, J.H., Chu, A., Trick, M., Michael, T.P., Bevan, M.W., Snape, J.W. 2010. An SSR-Based Genetic Linkage Map of the Model Grass Brachypodium distachyon. Genome. 53(1):1-13.
Molecular, morphological and cytological analysis of diverse Brachypodium distachyon inbred lines - (Peer Reviewed Journal)
Filiz, E., Ozdemir, B.S., Budak, F., Vogel, J.P., Metin, T., Budak, H. 2010. Molecular, morphological and cytological analysis of diverse Brachypodium distachyon inbred lines. Genome. 52:876-890
Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon - (Peer Reviewed Journal)
Vogel, J.P., Metin, T., 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 Biomed Central (BMC) Plant Biology. 9:Article 88. Available: http://www.biomedcentral.com/1471-2229/9/88/abstract
Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat - (Peer Reviewed Journal)
Huo, N., Vogel, J.P., Lazo, G.R., You, F., Ma, Y., McMahon, S.A., Dvorak, J., Anderson, O.D., Luo, M., Gu, Y.Q. 2009. Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat. Plant Molecular Biology. 70: 47-61.
Brachypodium distachyon, a New Model for the Grasses - (Book / Chapter)
Vogel, J.P., Bragg, J.N. 2009. Brachypodium distachyon, a New Model for the Grasses. p. 427-449. Genetics and Genomics of the Triticeae.
Unique aspects of the grass cell wall - (Review Article)
Vogel, J.P. 2008. Unique aspects of the grass cell wall. Current Opinion in Plant Biology. 11:301-307.
High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd 21-3 - (Peer Reviewed Journal)
Vogel, J.P., Hill, T.A. 2007. High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd 21-3. Plant Cell Reports. 27:471-478
The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. - (Peer Reviewed Journal)
Huo, N., Lazo, G.R., Vogel, J.P., You, F., Ma, Y., Hayden, D.M., Coleman-Derr, D., Hill, T., Dvorak, J., Anderson, O.D., Luo, M., Gu, Y.Q. 2007. Characterizing the nuclear genome structure of Brachypodium distachyon using BAC end sequences. Functional and Integrative Genomics. 8:135-147.
Development of genetic and genomic research resources for Brachypodium distachyon, a new model system for grass crop research Reprint Icon - (Peer Reviewed Journal)
Garvin, D.F., Gu, Y.Q., Hasterok, R., Hazen, S.P., Jenkins, G., Mockler, T.C., Mur, L.A., Vogel, J.P. 2008. Development of genetic and genomic research resources for Brachypodium distachyon, a new model system for grass crop research. The Plant Genome. 48:S69-S84.
Edr2 Negatively Regulates Salicylic Acid-Based Defenses and Cell Death During Powdery Mildew Infections of Arabidopsis Thaliana - (Peer Reviewed Journal)
Vorwerk, S., Schiff, C., Santamaria, M., Koh, S., Nishimura, M., Vogel, J., Somerville, C., Somerville, S. 2007 EDR2 negatively regulates salicylic acid-based defenses and cell death during powdery mildew infections of Arabidopsis thaliana. BMC Plant Biology. 7: Issue 35 (on-line journal).
Construction and Characterization of Two Bac Libraries from Brachypodium Distachypon, a New Model for Grass Genomics - (Peer Reviewed Journal)
Gu, Y., Lazo, G., Vogel, J., Coleman-Derr, D., Luo, M.C., Thilmony, R., Garvin, D., Anderson, O., Huo, N. 2006. Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome. 49(9):1099-1108.
Conserved Requirement for a Plant Host Cell Protein in Powdery Mildew Pathogenesis - (Peer Reviewed Journal)
Consonni, C., Humphry, M., Hartmann, A., Livaja, M., Durner, J., Westphal, L., Vogel, J.P., Lipka, V., Kemmerling, B., Schulze, L., Somerville, S., Panstruga, R. 2006. Conserved requirement for a plant host cell protein in powdery mildew pathogenesis. Nature Genetics. 38:716-720.
Est Sequencing and Phylogenetic Analysis of the Model Grass Brachypodium Distachyon - (Peer Reviewed Journal)
Vogel, J.P., Gu, Y.Q., Twigg, P., Lazo, G.R., Chingcuanco, D.L., Hayden, D.M., Donze, T., Vivia-Lindsay, A., Stamova, B., Coleman-Derr, D. 2006. EST sequencing and phylogenetic analysis of the model grass brachypodium distachyon. Theoretical and Applied Genetics. 113: 186-195.
Agrobacterium-Mediated Transformation and Inbred Line Development in the Model Grass Brachypodium Distachyon. - (Peer Reviewed Journal)
Vogel, J.P., Garvin, D.F., Leong, O.M., Hayden, D.M. 2006. Agrobacterium-mediated transformation and inbred line development in the model grass brachypodium distachyon. Plant Cell Tissue And Organ Culture. 84:199-211.
Mutations in Pmr5 Result in Powdery Mildew Resistance and Altered Cell Wall Composition. - (Peer Reviewed Journal)
Vogel, J.P., Raab, T.K., Somerville, S.C. 2004. Mutations in pmr5 result in powdery mildew resistance and altered cell wall composition. Plant Journal. 40:968-978.
Agrobacterium-Mediated Transformation of the Model Grass Brachypodium Distachyon - (Abstract Only)
Vogel, J.P., Leong, O.M. 2004. Agrobacterium-mediated transformation of the model grass Brachypodium distachyon (abstract). 2004. In Vitro Cellular and Developmental Biology. 40:29A.
Loss of a Callose Synthase Results in Salicylic Acid Dependent Disease Resistance. - (Peer Reviewed Journal)
Nishimura, M.T., Stein, M., Hou, B., Vogel, J.P., Edwards, H., Somerville, S.C. 2003. Loss of a callose synthase results in salicylic acid dependent disease resistance. Science. 301:969-972.
ARS News Articles
Last Modified: 4/21/2014
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