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Advanced Genetic Technologies, KY
Department of Plant Pathology
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.
2011 Project Description
The AGTC provided regular, high-quality, high-throughput, and timely data to researchers at the University of Kentucky and elsewhere in the Commonwealth. Computer Science students upgraded and supported the laboratory information management system (LIMS), and assisted clients in data analysis. Five seed-grants were awarded for pilot projects in the AGTC, and an undergraduate student, a high-school student and two graduate students were trained in high-throughput DNA sequencing and bioinformatics.
The results have generated extensive genome and transcriptome sequence databases that are essential for the design and interpretation of experiments to test organism functions in the field, in ecosystems, and in their agricultural or industrial uses.
The results contributed to leveraging numerous grants, with an estimated total of $4-million. Among these was a $0.5-million grant for sequencing the genome of Sarcocystis neurona, an apicomplexan parasite of horses and marine mammals, for which the lab work was exclusively conducted in the AGTC.
Furthermore, because AGTC was a pioneer in use of pyrosequencing, and AGTC staff participated in the Roche/454 users meetings, significant contributions were made to refining genome sequencing strategies and technologies.
Armstrong PR, Tallada JG, Hurburgh C, Hildebrand DF, Specht JE (2011) Development of single-seed near-infrared spectroscopic predictions of corn and soybean constituents using bulk reference values and mean spectra. Transactions of the ASABE 54: 1529-1535.
Arnaoudova E, Haws DC, Huggins P, Jaromczyk JW, Moore N, Schardl CL, Yoshida R (2010) Statistical phylogenetic tree analysis using differences of means. Frontiers in Neuroscience 4: 47. doi: 10.3389/fnins.2010.00047. doi: 10.3389/fnins.2010.00047
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Eskelson MJ, Chapman EG, Archbold DD, Obrycki JJ, Harwood JD (2011) Molecular identification of predation by carabid beetles on exotic and native slugs in a strawberry agroecosystem. Biological Control 56: 245-253. doi: 10.1016/j.biocontrol.2010.11.004
Jaag HM, Lu QS, Schmitt ME, Nagy PD (2011) Role of RNase MRP in viral RNA degradation and RNA recombination. Journal of Virology 85: 243-253. doi: 10.1128/jvi.01749-10
Kang J, Clark A, Van Sanford D, Griffey C, Brown-Guedira G, Dong YH, Murphy JP, Costa J (2011) Exotic scab resistance quantitative trait loci effects on soft red winter wheat. Crop Science 51: 924-933. doi: 10.2135/cropsci2010.06.0313
Raudsepp T, Durkin K, Lear TL, Das PJ, Avila F, Kachroo P, Chowdhary BP (2010) Molecular heterogeneity of XY sex reversal in horses. Animal Genetics 41: 41-52. doi: 10.1111/j.1365-2052.2010.02101.x
Voth DE, Beare PA, Howe D, Sharma UM, Samoilis G, Cockrell DC, Omsland A, Heinzen RA (2011) The Coxiella burnetii cryptic plasmid is enriched in genes encoding type IV secretion system substrates. Journal of Bacteriology 193: 1493-1503. doi: 10.1128/jb.01359-10
Zhang D-X, Nagabhyru P, Blankenship JD, Schardl CL (2010) Are loline alkaloid levels regulated in grass endophytes by gene expression or substrate availability Plant Signaling & Behavior 5: 1419-1422. doi: 10.1104/pp.109.138222