Research Accomplishment Reports 2009

Advanced Genetic Technologies, KY

C.L. Schardl
Department of Plant Pathology

 

Non-Technical Summary

Agricultural productivity depends heavily on the genetic potential and general health of crops and livestock. The project aims are to enhance techniques of genetic analysis, and through such techniques, to increase understanding of plant and animal genomics, the genomics of microbial pathogens and symbionts of plants and animals. The project will integrate the modern laboratory methods of large-scale DNA sequencing with computational methods to interpret DNA sequences and identify genes and key features of genomes. Personnel will be hired in both the life science and computer science areas to work together on enhancing the data flow and processing of all data generated in the Advanced Genetic Technologies Center at the University of Kentucky. Pilot studies will be conducted to obtain sequences from an important symbiont of tall fescue, the most widely planted forage grass in the U.S.A., and also from an important horse parasite. Other pilot studies will be invited, and undergraduate interns will be trained in genomics techniques and concepts.

2009 Project Description

The aim of this proposal was to bring to the University of Kentucky College of Agriculture the capabilities for, and a strong track record in, modern high-throughput genetic technologies, and to enhance prospects to leverage nationally competitive extramural grant support in these important areas of agricultural research. Preliminary data obtained in this project led directly to a grant to sequence the genome of Sarcocystis neurona, a protozoan parasite of horses, and to another grant involving genome sequence of the endophytic fungus, Neotyphodium coenophialum. Students on this grant provided crucial bioinformatic support to implement the new sequencing technology: pyrosequencing, which generates approximately 400 million bases of sequence data per run. Using this technology, the genome of the symbiotic fungus, Epichloe festucae was resequenced, leading to correction of predicted gene models. Finally, four undergraduate interns were introduced to genomic and high-throughput sequencing in the Advanced Genetic Technologies Center.

2009 Impact

Agricultural productivity depends on the genetic potential of the crops and livestock, and their interactions with the agro-ecosystem. The results of this project have enhanced techniques of genetic analysis, and through such techniques, increased understanding genomes of plants, fungal symbionts of plants, and animal parasites. The increased capacity and capabilities of the facility now make feasible genome sequencing for numerous microorganisms that are pathogenic or symbiotic with agricultural plants and livestock. The data obtained in pilot projects have been used to leverage major competitive grants, with considerable success.

2009 Publications

Bryant, M.K., Schardl, C.L., Hesse, U., and Scott, B. (2009) Evolution of a subtilisin-like protease gene family in the grass endophytic fungus Epichloe festucae. BMC Evolutionary Biology 9: 168.

Fitzpatrick, B.M., Shaffer, H.B., Johnson, J.J., Kump, K., and Voss, S.R. (2009) Genome-wide SNP-typing shows rapid allele fixation in a tiger salamander hybrid zone. BMC Evolutionary Biology 9: 176.

Florea, S., Andreeva, K., Machado, C., Mirabito, P.M., and Schardl, C.L. (2009). Elimination of marker genes from transformed filamentous fungi by unselected transient transfection with a Cre-expressing plasmid. Fungal Genetics and Biology 46: 721-730.

Fu, D., Ghabrial, S.A., and Kachroo, A. (2009) GmRAR1 and GmSGT1 are required for basal, R gene-mediated and systemic acquired resistance in soybean. Molecular Plant-Microbe Interactions 22: 86-95.

Gaji, R.Y., and Howe, D.K. (2009) The heptanucleotide motif GAGACGC is a key component of a cis-acting element that is critical for SnSAG1 expression in Sarcocystis neurona. Molecular and Biochemical Parasitology 166: 85-88.

Hajimorad, M.R., Ghabrial, S.A., and Roossinck, M.J. (2009) De novo emergence of a novel satellite RNA of Cucumber mosaic virus following serial passages of the virus derived from RNA transcripts. Archives of Virology 154: 137-140.

Iannone, L.J., Cabral, D., Schardl, C.L., and Rossi, M.S. (2009) Phylogenetic divergence, morphological and physiological differences distinguish a new Neotyphodium endophyte species in the grass Bromus auleticus from South America. Mycologia 101: 340-351.

Jia, X., Wang, W.-X., Ren, L., Chen, Q.-J., Mendu, V., Willcut, B., Dinkins, R., Tang, X., and Tang, G. (2009) Differential and dynamic regulation of miR398 in response to ABA and salt stress in Populus tremula and Arabidopsis thaliana. Plant Molecular Biology 71: 51-59.

Kurepa, J., Wang, S., Li, Y., Zaitlin, D., Pierce, A.J., and Smalle, J. (2009) Loss of 26S proteasome function leads to increased cell size and decreased cell number in Arabidopsis shoot organs. Plant Physiology 150, 178-189. http://www.plantphysiol.org/cgi/content/full/150/1/178.

Liu, H., Fu, Y., Jiang, D., Li, G., Xie, J., Peng, Y., Yi, X., and Ghabrial, S.A. (2009) A novel mycovirus that is related to the human pathogen Hepatitis E virus and rubi-like viruses. Journal of Virology 83: 1981-1991.

Liu, M., Panaccione, D.G., and Schardl, C.L. (2009) Phylogenetic analyses reveal monophyletic origin of the ergot alkaloid gene dmaW in fungi. Evolutionary Bioinformatics 5: 15-30.

Nakaminami, K., Hill, K., Perry, S.E., Sentoku, N., Long, J.A., and Karlson, D.T. (2009) Arabidopsis cold shock domain proteins: relationships to floral and silique development. Journal of Experimental Botany 60: 1047-1062.

Pan, J., Dong, L., Lin, L., Ochoa, W.F., Sinkovits, R.S., Havens, W.M., Nibert, M.L., Baker, T.S., Ghabrial, S.A., and Tao, Y.J. (2009) Atomic structure reveals the unique capsid organization of a dsRNA virus. Proceedings of the National Academy of Science of the United States of America 106: 4225-4230.

Parthasarathy, R., and Palli, S.R. (2009) Molecular analysis of juvenile hormone analog action in controlling the metamorphosis of the red flour beetle, Tribolium castaneum. Archives of Insect Biochemistry and Physiology 70: 57-70.

Parthasarathy, R., Tan, A., Sun, Z., Chen, J., Rainkin, M., and Palli, S.R. (2009) Juvenile hormone regulation of male accessory gland activity in the red flour beetle, Tribolium castaneum Mechanisms of Development 126: 563-579.

Rao, S., Dinkins, R.D., and Hunt, A.G. (2009) Distinctive interactions of the Arabidopsis homolog of the 30 kD subunit of the cleavage and polyadenylation specificity factor (AtCPSF30) with other polyadenylation factor subunits. BMC Cell Biology 10: 51.

Rehmeyer, C., Kusaba, M., and Farman, M. (2009) The telomere-linked helicase (TLH) gene family in Magnaporthe oryzae: revised gene structure reveals a novel TLH-specific protein motif. Current Genetics 55: 2153-2162.

Sharkey, M.J., Yu, D.S., van Noort, S., Seltmann, K., Penev, L. (2009) DELTA data matrix, images, and other files to the key of the Oriental genera of Agathidinae (Hymenoptera, Braconidae). Zookeys 21: 19-54. doi:10.3897/zookeys 21: 271.

Smith, J.J., Putta, S., Zhu, W., Pao, G.M., Verma, I.M., Hunter, T., Bryant, S.V., Gardiner, D.M., Harkins, T.T., and Voss, S.R. (2009) Genic regions of a large salamander genome contain long introns and novel genes. BMC Genomics 10: 19.

Smith, J.J., and Voss, S.R. (2009) Amphibian sex determination: segregation and linkage analysis using members of the tiger salamander species complex (Ambystoma mexicanum and A. tigrinum). Heredity 102: 542-548.

Venugopal, S.C., Chanda, B., Vaillancourt, L., Kachroo, A., and Kachroo, P. (2009) The common metabolite glycerol-3-phosphate is a novel regulator of plant defense signaling. Plant Signaling and Behavior 4: 746-749.

Venugopal, S.C., Jeong, R.-D., Zhu, S., Chandra-Shekara, A.C., Navarre, D., Kachroo, A., and Kachroo, P. (2009) Enhanced disease susceptibility 1 and salicylic acid act redundantly to regulate resistance gene expression and low oleate-induced defense signaling. PLOS Genetics 5: e1000545.

Vincelli, P., and Seebold, K. (2009) Report of a Watermelon mosaic potyvirus strain in Kentucky undetected by ELISA. Online. Plant Health Progress: doi:10.1094/PHP-2009-0313-01-BR.

Wang, E., and Cambi, F. (2009) Heterogeneous nuclear ribonucleoproteins H and F regulate the proteolipid protein/DM20 ratio by recruiting U1 small nuclear ribonucleoprotein through a complex array of G runs. Journal of Biological Chemistry 284: 11194-11204.

Wang, S., Kurepa, J., and Smalle, J. (2009) Arabidopsis RPN1a is a non-essential 26S proteasome subunit isoform required for optimal plant growth and stress responses. Plant and Cell Physiology 50: 1721-1725.

Wu, C., Kim, Y.-S., Smith, K., Li, W., Hood, H., Staben, C., Selker, E., Sachs, M., and Farman, M.L. (2009) Characterization of chromosome ends in the filamentous fungus Neurospora crassa. Genetics 181: 1129-1145.

Xia, Y., Gao, Q.-M., Navarre, D., Hildebrand, D., Kachroo, A., and Kachroo, P. (2009) An intact cuticle in distal tissues is essential for the induction of systemic acquired resistance in plants. Cell Host and Microbe 5: 151-165.

Young, C.A., Tapper, B.A., May, K., Moon, C.D., Schardl, C.L., and Scott, B. ( 2009) Indole-diterpene biosynthetic capability of epichloe endophytes as predicted by ltm gene analysis., Applied and Environmental Microbiology 75: 2200-2211.

Zhang, D.X., Nagabhyru, P., and Schardl, C.L. (2009) Regulation of a chemical defense against herbivory produced by symbiotic fungi in grass plants. Plant Physiology 150: 1072-1082.

Zhang, D.X., Stromberg, A.J., Spiering, M.J., and Schardl, C.L. (2009) Coregulated expression of loline alkaloid-biosynthesis genes in Neotyphodium uncinatum cultures. Fungal Genetics and Biology 46: 517-530.

Zhang, Z., and Palli, S.R. (2009) Identification of a cis-regulatory element required for 20-hydroxyecdysone enhancement of antimicrobial peptide gene expression in Drosophila melanogaster. Journal of Molecular Entomology 18: 595-605.