Projects

AN INTEGRATED DATABASE AND BIOINFORMATICS RESOURCE FOR SMALL GRAINS Appropriated (D)   Accession Number: 413153

GENETIC FOUNDATIONS FOR BIOENERGY FEEDSTOCKS Appropriated (D)   Accession Number: 418493

GENOMICS AND MOLECULAR APPROACHES TO WHEAT TRAITS Appropriated (D)   Accession Number: 413137

INSERTIONAL MUTAGENESIS OF BRACHYPODIUM DISTACHYON Reimbursable (R)   Accession Number: 412354

FUNCTIONAL AND REGULATORY ANALYSIS OF THE SCS GENE, A MAJOR LOCUS AFFECTING CRITICAL PLANT DEVELOPMENT PATHWAYS IN TETRAPLOID WHEAT Reimbursable (R)   Accession Number: 414164

DEVELOPMENT OF GRASS GENOMIC RESOURCES FOR CROP IMPROVEMENT AND BIOFUEL RESEARCH Specific Cooperative Agreement (S)   Accession Number: 412522

Publications

A Genetic Linkage Map of the Model Grass Brachypodium distachyon - (Peer Reviewed Journal) - (24-Sep-09)

Conserved globulin gene across eight grass genomes identify fundamental units of the loci encoding seed storage proteins - (Peer Reviewed Journal) - (08-Aug-09)

Genome Comparisons Reveal a Dominant Mechanism of Chromosome Number Reduction in Grasses and Accelerated Genome Evolution in Triticeae - (Peer Reviewed Journal)

Luo, M.C., Deal, K.R., Akhunov, E.D., Akhunova, A.R., Anderson, O.D., Anderson, J.A., Blake, N., Clegg, M.T., Coleman-Derr, D., Conley, E.E., Crossman, C.C., Dubcovsky, J., Gill, B.S., Gu, Y.Q., Hadam, J., Heo, H., Huo, N., Lazo, G.R., Lundy, K.E., Ma, Y., Matthews, D.E., Mcguire, P.E., Morrell, P.L., Nicolet, C.M., Qualset, C.O., Renfro, J., Tabano, D., Talbert, L.E., Tian, A., Toleno, D.M., Warburton, M.L., You, F.M., Zhang, W.J., Dvorak, J. 2009. Genome Comparisons Reveal a Dominant Mechanism of Chromosome Number Reduction in Grasses and Accelerated Genome Evolution in Triticeae. Proceedings of the National Academy of Sciences.

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

Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv - (Peer Reviewed Journal)

Bai, W., Cai, A., Rz, Z., Li, A., Huo, N., Li, S., Gu, Y.Q., Yabut, L., Jia, J., Qi, Y. 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. 9:532-541.

Structure of the omega-gliadin gene family - (Peer Reviewed Journal)

Anderson, O.D., Gu, Y.Q., Kong, K., Lazo, G.R., Wu, J. 2009. Structure of the omega-gliadin gene family. Functional and Integrative Genomics. 9: 397-410.

Saturation and comparative mapping of genomic region harboring Hessian fly resistance gene H26 in wheat - (Peer Reviewed Journal)

Tao, G., Cai, X., Harris, M., Gu, Y.Q., Luo, M., Xu, S.S. 2009. Saturation and comparative mapping of genomic region harboring Hessian fly resistance gene H26 in wheat. Theoretical and Applied Genetics. 118(8):1589-1599.

Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat - (Peer Reviewed Journal)

Wanjugi, H., Coleman-Derr, D., Huo, N., Kianian, S.F., Luo, M., Wu, J., Anderson, O.D., Gu, Y.Q. 2009. Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat. Genome. 52:576-587.

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.

Radiation hybrid mapping in crop plants - (Review Article)

Kalavachrla, V., Hossia, K., Gu, Y.Q., Maan, S., Kianian, S. 2009. Radiation hybrid mapping in crop plants. Advances in Agronomy. 102:199-219.

The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes - (Peer Reviewed Journal)

Bortiri, E., Coleman-Derr, D., Lazo, G.R., Anderson, O.D., Gu, Y.Q. 2008. The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes. BMC Research Notes. 1:61.

BatchPrimer3: A high throughput web application for PCR and sequencing primer design - (Peer Reviewed Journal)

You, F.M., Huo, N., Gu, Y.Q., Luo, M., Ma, Y., Hane, D., Lazo, G.R., Dvorak, J., Anderson, O.D. 2008. BatchPrimer3: A high throughput web application for PCR and sequencing primer design. BMC Bioinformatics. 9:253.

Characterizing the nuclear genome structure of Brachypodium distachyon using 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 - (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.

Rapid evolution and complex structural organization in genomic regions harboring multiple prolamin genes in the polyploid wheat genome - (Peer Reviewed Journal)

Gao, S., Gu, Y.Q., Wu, J., Huo, N., Crossman, C., Jia, J., Ren, Z., Anderson, O.D., Xiuying, K. 2007. Rapid evolution and complex structural organization in genomic regions harboring multiple prolamin genes in the polyploid wheat genome. Plant Molecular Biology. 65:189-203.

New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification - (Peer Reviewed Journal)

Zhang, S., Gu, Y., Singh, J., Coleman-Derr, D., Brar, D., Jiang, N., Lemaux, P. 2007. New Insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification. Plant Molecular Biology. 64:589-600.

Geno Profiler: Batch Processing of High Throughput Capillary Fingerprinting Data - (Peer Reviewed Journal)

You, F.M., Luo, M.C., Gu, Y.Q., Lazo, G.R., Thomas, C., McGuire, P.E., Dvorak, J., and Anderson, O.D. 2007. Genoprofiler: Automated processing of high throughput capillary fingerprinting data. Bioinformatics. 23:240-242.

Types and Rates of Sequence Evolution at Hmw-Glutenin Locus in Hexaploid Wheat and Its Ancestral Genomes - (Peer Reviewed Journal)

Gu, Y., Salse, J., Coleman-Derr, D., Dupin, A., Crossman, C., Lazo, G., Huo, N., Belcram, H., Ravel, C., Charmet, G., Charles, M., Anderson, O., Chalhoub, B. 2006. Types and Rates of Sequence Evolution at the HMW-Glutenin Locus in Hexaploid Wheat and Its Ancestral Genomes. Genetics. 174:1493-1504.

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.

High-Resolution Radiation Hybrid Map of Wheat Chromosome 1d - (Peer Reviewed Journal)

Kalavacharla, V., Hossain, K., Gu, Y.Q., Riera, L.O., Isabel, V.M., Bhamidimarri, S., Gonzalez-Hernandez, J., Maan, S., Kianian, S. 2006. High-resolution radiation hybrid map of wheat chromosome 1d. Genetics. 173:1-11.

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.

Subtractive Cdna Libraries Identify Differentially Expressed Genes in Dormant and Growing Buds of Leafy Spurge (Euphorbia Esula) - (Peer Reviewed Journal)

Jia, Y., Anderson, J.V., Horvath, D.P., Gu, Y.-Q., Lym, R.G., Chao, W.S. 2006. Subtractive cDNA libraries identify differentially expressed genes in dormant and growing buds of leafy spurge (Euphorbia esula). Plant Molecular Biology. 61:329-344.

Positional Relationship Between Photoperiod Response Qtl and Photoreceptor and Vernalization Genes in Barley - (Peer Reviewed Journal)

Szucs, P., Karsai, I., Von Zitzewitz, J., Meszaros, K., Copper, L., Gu, Y.Q., Chen, T., Hayes, P., Skinner, J. 2006. Positional relationship between photoperiod response qtl and photoreceptor and vernalization genes in barley. Theoretical and Applied Genetics. 112: 1,277-1,285.

Positional Relationship Between Photoperiod Response Qtl and Photoreceptor and Vernaliazation Genes in Barley - (Peer Reviewed Journal)

Szucs, P., Karsai, I., Von Zitzewitz, J., Meszaros, K., Cooper, L., Gu, Y.Q., Chen, T., Hayes, P., Skinner, J. 2006. Positional relationship between photoperiod response qtl and photoreceptor and vernaliazation genes in barley. Theoretical and Applied Genetics. 112: 1,277-1,285.

Subtractive Cdna Libraries Identify Differentially-Expressed Genes in Dormant and Growing Buds of Leafy Spurge (Euphorbia Esula) - (Abstract)

Jia, Y., Anderson, J.V., Horvath, D.P., Gu, Y.Q., Lym, R.G., Chao, W.S. 2006. Subtractive cDNA libraries identify differentially-expressed genes in dormant and growing buds of leafy spurge (Euphorbia esula). [Abstract]. Weed Science Society of America Abstracts 46:30.

Identification of Differentially-Expressed Genes in Dormant and Growing Buds of Leafy Spurge (Euphorbia Esula L.) - (Abstract)

Jia, Y., Gu, Y.Q., Horvath, D.P., Anderson, J.V., Chao, W.S. 2005. Identification of differentially-expressed genes in dormant and growing buds of leafy spurge (Euphorbia esula L.). [Abstract]. Annual Meeting of the American Society of Plant Biologists. Final Program and Abstract Supplement, Poster 670, Page 225.

Hybsweeper: a Resource for Detecting High-Density Plate Coordinates - (Peer Reviewed Journal)

Lazo, G.R., Lui, N., Gu, Y.Q., Kong, X., Coleman Derr, D., Anderson, O.D. 2005. Hybsweeper: a resource for detecting high-density plate coordinates. Biotechniques. 39:320-324.

Subtractive Hybridization As a Tool to Screen for Genes Involved in Dormancy and Growth in Underground Adventitious Buds of Leafy Spurge (Euphorbia Esula) - (Abstract)

Jia, Y., Gu, Y., Horvath, D.P., Anderson, J.V., Chao, W.S. 2005. Subtractive hybridization as a tool to screen for genes involved in dormancy and growth in underground adventitious buds of leafy spurge (Euphorbia esula). [Abstract]. Weed Science Society of America. Page No. 120.

Genomic Organization of the Complex a-Gliadin Gene Loci in Wheat - (Peer Reviewed Journal)

Gu, Y.Q., Crossman, C.C., Kong, X., Luo, M., You, F.M., Coleman Derr, D., Dubcovsky, J., Anderson, O.D. 2004. Genomic organization of the complex a-gliadin gene loci in wheat. Theoretical and Applied Genetics. 109:648-657.

Dynamics and Rapid Genome Evolution in Allopolyploid Wheat As Revealed by Comparative Sequence Analysis of the Complex Hmw-Glutenin Locus Regions. - (Peer Reviewed Journal)

Gu, Y.Q., Coleman-Derr, D., Kong, X., Anderson, O.D. 2004. Dynamics and rapid genome evolution in allopolyploid wheat as revealed by comparative sequence analysis of the complex hmw-glutenin locus regions. Plant Physiology. 135:459-470.

Dynamics of the Evolution of Orthologous and Paralogous Portions of a Complex Locus Region in Two Genomes of Allopolyploid Wheat - (Peer Reviewed Journal)

Kong, X., Gu, Y.Q., You, F.M., Dubcovsky, J., Anderson, O.D. 2004. Dynamics of the evolution of orthologous and paralogous portions of a complex locus region in two genomes of allopolyploid wheat. Plant Molecular Biology. 54:55-69.

Construction of Contigs of Aegilops Tauschii Genomic DNA Fragments Cloned in Bac and Bibac Vectors - (Proceedings/Symposium)

LUO, M., THOMAS, C.S., DEAL, K.R., YOU, F., ANDERSON, O.D., GU, Y.Q., LI, W., KURAPARTHY, V., GILL, B.S., MCGUIRE, P.E. 2003. CONSTRUCTION OF CONTIGS OF AEGILOPS TAUSCHII GENOMIC DNA FRAGMENTS CLONED IN BAC AND BIBAC VECTORS. WHEAT GENETICS INTERNATIONAL SYMPOSIUM PROCEEDINGS. 1:293-296.

Silencing of Subfamily I of Protein Phosphatase 2a Catalytic Subunits Results in Activation of Plant Defense Responses and Localized Cell Death. - (Peer Reviewed Journal)

He, X., Anderson, J.C., Del Pozo, O., Gu, Y.Q., Tang, X., Martin, G.B. 2004. Silencing of subfamily I of protein phosphatase 2A catalytic subunits results in activation of plant defense responses and localized cell death. Plant Journal. 38:563-577.

Assessment of the Insular Organization of the Wheat D Genome by Physical Mapping - (Abstract)

DVORAK, J., ANDERSON, O.D., GILL, B.S., LUO, M., ZHANG, H., DEAL, K., LI, W., YOU, F., GU, Y.Q., MCGUIRE, P.E. ASSESSMENT OF THE INSULAR ORGANIZATION OF THE WHEAT D GENOME BY PHYSICAL MAPPING. Annual International Plant & Animal Genome Conference. 2003.