Source: UNIVERSITY OF KENTUCKY submitted to NRP
ADVANCED GENETIC TECHNOLOGIES, KY
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
SPECIAL GRANT
Reporting Frequency
Annual
Accession No.
0214172
Grant No.
2008-34457-19176
Cumulative Award Amt.
$448,178.00
Proposal No.
2008-03192
Multistate No.
(N/A)
Project Start Date
Sep 1, 2008
Project End Date
Aug 31, 2011
Grant Year
2008
Program Code
[RO]- Advanced Genetic Technologies, KY
Recipient Organization
UNIVERSITY OF KENTUCKY
500 S LIMESTONE 109 KINKEAD HALL
LEXINGTON,KY 40526-0001
Performing Department
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.
Animal Health Component
33%
Research Effort Categories
Basic
33%
Applied
33%
Developmental
34%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2017299104050%
3137299104050%
Knowledge Area
313 - Internal Parasites in Animals; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
7299 - Research equipment and methods, general/other;

Field Of Science
1040 - Molecular biology;
Goals / Objectives
The aim of this proposal is 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. The vehicle to support these aims is the core facility called the Advanced Genetic Technologies Center (AGTC). Objective 1: Train and provide expert support for high-throughput molecular genetic analysis methods and bioinformatics. Objective 2: Develop reagents and preliminary data for genome sequencing projects on microorganisms of relevance to Kentucky and U.S. agriculture. Objective 3: Conduct internal competitions for seed-grants to utilize technologies available in the UK-AGTC. Objective 4: Provide undergraduate internships to introduce students to modern high-throughput genetic analyses.
Project Methods
A postdoctoral scholar (postdoc) will prepare clone libraries, oversee sequencing of the clones, and participate in the assembly and annotation of the sequences. A graduate research assistant (RA) in Computer Sciences, will administer the UK-AGTC computers, administer and update the laboratory information management system, and interact with the postdoc and other clients and install, modify or write the necessary computer programs for bioinformatic analyses. Clones of genomic DNA will be generated and sequences determined from selected clones for Neotyphodium coenophialum and Sarcocystis neurona. The N. coenophialum fungus is a symbiont that a natural bioprotectant of the forage grass, tall fescue, and S. neurona is a parasitic microbe that is the primary cause of equine protozoal myeloencephalitis. An internally competitive program of short-term seed grants will also be funded to obtain preliminary data for nationally competitive grants. Finally, six undergraduate internships will be established to introduce students to modern high-throughput genetic analyses.

Progress 09/01/08 to 08/31/11

Outputs
OUTPUTS: 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. PARTICIPANTS: Schardl, Christopher L. Professor, University of Kentucky. Co-PI: Daniel K. Howe, Associate Professor, University of Kentucky. Genome and unigene assembly, gene model construction, genome annotation. Bullock, Charles Thomas, Masters Student, University of Kentucky. Laboratory Information Management Systems. Calder, James O., Postbaccalaureate, University of Kentucky. DNA sequence analysis. Gay, Emily, University of Kentucky. DNA sequence analysis. Kesterson, Abbe, Senior Facilities Manager, University of Kentucky, Next generation sequencing. Webb, Jennifer, Research Analyst, University of Kentucky, Robotic programming, DNA sequence analysis, DNA fragment analysis, laboratory management. TRAINING AND PROFESSIONAL DEVELOPMENT: Kesterson, A., and Webb, J.S. attended training for the new pyrosequencing instrument and technology, and two staff attended a Roche/454 users meeting. Training was also provided to AGTC technical staff programming and using the robotics in the facility. TARGET AUDIENCES: Farmers, livestock producers, plant biotechnology and biofuels companies, homeowners. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
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.

Publications

  • 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
  • Chanda B, Xia Y, Mandal MK, Yu KS, Sekine KT, Gao QM, Selote D, Hu YL, Stromberg A, Navarre D, Kachroo A, Kachroo P (2011) Glycerol-3-phosphate is a critical mobile inducer of systemic immunity in plants. Nature Genetics 43: 421-+. doi: 10.1038/ng.798
  • 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


Progress 09/01/09 to 08/31/10

Outputs
OUTPUTS: The Advanced Genetic Technologies Center at the University of Kentucky College of Agriculture conducted deep-sequence analysis of the transcriptomes of the woody plants, magnolia and acacia, the transcriptome of the oil-producing alga, Botryococcus braunii, and the transcriptomes of two insect species, Cimex lectularius (bedbug) and Leptinotarsa decemlineata (Colorado potato beetle). In addition, the genome was sequenced for the fungus Claviceps purpurea, the ergot pathogen of rye (Secale cereale). Bioinformatic analysis was conducted on the transcriptome and genome sequences. Sequencing was also conducted on thousands of individual cloned or amplified DNA molecules for 13 research groups in the college. Results contributed to 50 published research papers. PARTICIPANTS: PI: Schardl, Christopher L. Professor, University of Kentucky. Co-PI: Daniel K. Howe, Associate Professor, University of Kentucky. Genome and unigene assembly, gene model construction, genome annotation. Bullock, Charles Thomas, Masters Student, University of Kentucky. Laboratory Information Management Systems. Calder, James O., Postbaccalaureate, University of Kentucky. DNA sequence analysis. Gay, Emily, University of Kentucky. DNA sequence analysis. Kesterson, Abbe, Senior Facilities Manager, University of Kentucky, Next generation sequencing. Webb, Jennifer, Research Analyst, University of Kentucky, Robotic programming, DNA sequence analysis, DNA fragment analysis, laboratory management. TRAINING AND PROFESSIONAL DEVELOPMENT: Kesterson, A., and Webb, J. received training on sequencing with the Roche/454 high-throughput genome and transcriptome sequencer, and subsequently attended a Roche/454 users workshop. TARGET AUDIENCES: Farmers and homeowners. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
DNA and RNA sequencing, and bioinformatic analysis supported on this project contributed to new knowledge of plant, insect, and fungal biology. For example, genes were identified for protective metabolites in magnolia and Claviceps, and the genetic basis for insecticide resistance was elucidated in several insect pests.

Publications

  • Stajich JE, Wilke SK, Ahren D, Au CH, Birren BW, Borodovsky M, Burns C, Canback B, Casselton LA, Cheng CK, Deng JX, Dietrich FS, Fargo DC, Farman ML, Gathman AC, Goldberg J, Guigo R, Hoegger PJ, Hooker JB, Huggins A, James TY, Kamada T, Kilaru S, Kodira C, Kues U, Kupfert D, Kwan HS, Lomsadze A, Li WX, Lilly WW, Ma LJ, Mackey AJ, Manning G, Martin F, Muraguchi H, Natvig DO, Palmerini H, Ramesh MA, Rehmeyer CJ, Roe BA, Shenoy N, Stanke M, Ter-Hovhannisyan V, Tunlid A, Velagapudi R, Vision TJ, Zeng QD, Zolan ME, Pukkila PJ (2010) Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proceedings of the National Academy of Sciences of the United States of America 107: 11889-11894.
  • Tang JH, Ochoa WF, Li H, Havens WM, Nibert ML, Ghabrial SA, Baker TS (2010) Structure of Fusarium poae virus 1 shows conserved and variable elements of partitivirus capsids and evolutionary relationships to picobirnavirus. Journal of Structural Biology 172: 363-371.
  • Tang JH, Pan JH, Havens WM, Ochoa WF, Guu TSY, Ghabrial SA, Nibert ML, Tao YZJ, Baker TS (2010) Backbone trace of Partitivirus capsid protein from electron cryomicroscopy and homology modeling. Biophysical Journal 99: 685-694.
  • Tzertzinis G, Egana AL, Palli SR, Robinson-Rechavi M, Gissendanner CR, Liu CH, Unnasch TR, Maina CV (2010) Molecular evidence for a functional ecdysone signaling system in Brugia malayi. PLoS Neglected Tropical Diseases 4: e625.
  • Wei SJ, Shi M, Chen XX, Sharkey MJ, van Achterberg C, Ye GY, He JH (2010) New views on strand asymmetry in insect mitochondrial genomes. PLoS One 5: e12708.
  • Wei SJ, Shi M, He JH, Sharkey M, Chen XX (2009) The complete mitochondrial genome of Diadegma semiclausum (Hymenoptera: Ichneumonidae) indicates extensive independent evolutionary events. Genome 52: 308-319.
  • Wei SJ, Shi M, Sharkey MJ, van Achterberg C, Chen XX (2010) Comparative mitogenomics of Braconidae (Insecta: Hymenoptera) and the phylogenetic utility of mitochondrial genomes with special reference to Holometabolous insects. BMC Genomics 11: 37.
  • Weiss TL, Johnston JS, Fujisawa K, Sumimoto K, Okada S, Chappell J, Devarenne TP (2010) Phylogenetic placement, genome size, and GC content of the liquid-hydrocarbon-producing green microalga Botryococcus braunii strain Berkeley (showa) (Chlorophyta). Journal of Phycology 46: 534-540.
  • Wu MD, Zhang L, Li GQ, Jiang DH, Ghabrial SA (2010) Genome characterization of a debilitation-associated mitovirus infecting the phytopathogenic fungus Botrytis cinerea. Virology 406: 117-126.
  • Xia Y, Yu KS, Navarre D, Seebold K, Kachroo A, Kachroo P (2010) The glabra1 mutation affects cuticle formation and plant responses to microbes. Plant Physiology 154: 833-846.
  • Sharanowski BJ, Robbertse B, Walker J, Voss SR, Yoder R, Spatafora J, Sharkey MJ (2010) Expressed sequence tags reveal Proctotrupomorpha (minus Chalcidoidea) as sister to Aculeata (Hymenoptera: Insecta). Molecular Phylogenetics and Evolution 57: 101-112.
  • Singh AK, Tavva VS, Collins GB, Palli SR (2010) Improvement of ecdysone receptor gene switch for applications in plants: Locusta migratoria retinoid X receptor (LmRXR) mutagenesis and optimization of translation start site. Febs Journal 277: 4640-4650.
  • Xu JJ, Tan AJ, Palli SR (2010) The function of nuclear receptors in regulation of female reproduction and embryogenesis in the red flour beetle, Tribolium castaneum. Journal of Insect Physiology 56: 1471-1480.
  • Yu X, Li B, Fu YP, Jiang DH, Ghabrial SA, Li GQ, Peng YL, Xie JT, Cheng JS, Huang JB, Yi XH (2010) A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. Proceedings of the National Academy of Sciences of the United States of America 107: 8387-8392.
  • Chen TS, Nayak N, Majee SM, Lowenson J, Schafermeyer KR, Eliopoulos AC, Lloyd TD, Dinkins R, Perry SE, Forsthoefel NR, Clarke SG, Vernon DM, Zhou ZS, Rejtar T, Downie AB (2010) Substrates of the Arabidopsis thaliana protein isoaspartyl methyltransferase 1 identified using phage display and biopanning. Journal of Biological Chemistry 285: 37281-37292.
  • Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J, Schmutz J, Taga M, White GJ, Zhou SG, Schwartz DC, Freitag M, Ma LJ, Danchin EGJ, Henrissat B, Coutinho PM, Nelson DR, Straney D, Napoli CA, Barker BM, Gribskov M, Rep M, Kroken S, Molnar I, Rensing C, Kennell JC, Zamora J, Farman ML, Selker EU, Salamov A, Shapiro H, Pangilinan J, Lindquist E, Lamers C, Grigoriev IV, Geiser DM, Covert SF, Temporini E, VanEtten HD (2009) The genome of Nectria haematococca: Contribution of supernumerary chromosomes to gene expansion. PLoS Genetics 5: e1000618.
  • de Sa PB, Havens WM, Ghabrial SA (2010) Characterization of a novel broad-spectrum antifungal protein from virus-infected Helminthosporium (Cochliobolus) victoriae. Phytopathology 100: 880-889.
  • de Sa PB, Li H, Havens WM, Farman ML, Ghabrial SA (2010) Overexpression of the victoriocin gene in Helminthosporium (Cochliobolus) victoriae enhances the antifungal activity of culture filtrates. Phytopathology 100: 890-896.
  • Denlinger DL, Palli SR (2010) A tribute to Judy Willis insect molecular physiology: Basic science to applications. Journal of Insect Physiology 56: 1363-1365.
  • Faraldos JA, Wu SQ, Chappell J, Coates RM (2010) Doubly deuterium-labeled patchouli alcohol from cyclization of singly labeled 2-H-2(1) farnesyl diphosphate catalyzed by recombinant patchoulol synthase. Journal of the American Chemical Society 132: 2998-3008.
  • Ghabrial SA, Suzuki N (2009) Viruses of plant pathogenic fungi. Annual Review of Phytopathology 47: 353-384.
  • Huang B, Troese MJ, Howe D, Ye SJ, Sims JT, Heinzen RA, Borjesson DL, Carlyon JA (2010) Anaplasma phagocytophilum APH_0032 is expressed late during infection and localizes to the pathogen-occupied vacuolar membrane. Microbial Pathogenesis 49: 273-284.
  • Jeong RD, Chandra-Shekara AC, Barman SR, Navarre D, Klessig DF, Kachroo A, Kachroo P (2010) Cryptochrome 2 and phototropin 2 regulate resistance protein-mediated viral defense by negatively regulating an E3 ubiquitin ligase. Proceedings of the National Academy of Sciences of the United States of America 107: 13538-13543.
  • Johansen KJ, Sharkey MJ, Fisher JR (2010) Molecular evidence from a parasitoid wasp, Schlettererius cinctipes (Hymenoptera: Stephanidae), for a North American west-to-east transcontinental conduit for wood-boring insects. Annals of the Entomological Society of America 103: 548-554.
  • Kachroo A, Kachroo P (2009) Fatty acid-derived signals in plant defense. Annual Review of Phytopathology 47: 153-176.
  • Kang HG, Oh CS, Sato M, Katagiri F, Glazebrook J, Takahashi H, Kachroo P, Martin GB, Klessig DF (2010) Endosome-associated CRT1 functions early in resistance gene-mediated defense signaling in Arabidopsis and tobacco. Plant Cell 22: 918-936.
  • Li RZ, Yu KS, Hatanaka T, Hildebrand DF (2010) Vernonia DGATs increase accumulation of epoxy fatty acids in oil. Plant Biotechnology Journal 8: 184-195.
  • Li RZ, Yu KS, Hildebrand DF (2010) DGAT1, DGAT2 and PDAT expression in seeds and other tissues of epoxy and hydroxy fatty acid accumulating plants. Lipids 45: 145-157.
  • Liu HQ, Fu YP, Jiang DH, Li GQ, Xie JT, Cheng JS, Peng YL, Ghabrial SA, Yi XH (2010) Widespread horizontal gene transfer from double-stranded RNA viruses to eukaryotic nuclear genomes. Journal of Virology 84: 11876-11887.
  • Zhang Z, Palli SR (2009) Identification of a cis-regulatory element required for 20-hydroxyecdysone enhancement of antimicrobial peptide gene expression in Drosophila melanogaster. Insect Molecular Biology 18: 595-605.
  • Zhu F, Parthasarathy R, Bai H, Woithe K, Kaussmann M, Nauen R, Harrison DA, Palli SR (2010) A brain-specific cytochrome P450 responsible for the majority of deltamethrin resistance in the QTC279 strain of Tribolium castaneum. Proceedings of the National Academy of Sciences of the United States of America 107: 8557-8562.
  • Zhu F, Wigginton J, Romero A, Moore A, Ferguson K, Palli R, Potter MF, Haynes KF, Palli SR (2010) Widespread distribution of knockdown resistance mutations in the bed bug, Cimex lectularius (Hemiptera: Cimicidae), populations in the United States. Archives of Insect Biochemistry and Physiology 73: 245-257.
  • Addepalli B, Limbach PA, Hunt AG (2010) A disulfide linkage in a CCCH zinc finger motif of an Arabidopsis CPSF30 ortholog. FEBS Letters 584: 4408-4412.
  • Bai H, Gelman DB, Palli SR (2010) Mode of action of methoprene in affecting female reproduction in the African malaria mosquito, Anopheles gambiae. Pest Management Science 66: 936-943.
  • Bai H, Palli SR (2010) Functional characterization of bursicon receptor and genome-wide analysis for identification of genes affected by bursicon receptor RNAi. Developmental Biology 344: 248-258.
  • Bell SA, Hunt AG (2010) The Arabidopsis ortholog of the 77 kDa subunit of the cleavage stimulatory factor (AtCstF-77) involved in mRNA polyadenylation is an RNA-binding protein. FEBS Letters 584: 1449-1454.
  • Bitra K, Palli SR (2010) The members of bHLH transcription factor superfamily are required for female reproduction in the red flour beetle, Tribolium castaneum. Journal of Insect Physiology 56: 1481-1489.
  • Bitra K, Tan AJ, Dowling A, Palli SR (2009) Functional characterization of PAS and HES family bHLH transcription factors during the metamorphosis of the red flour beetle, Tribolium castaneum. Gene 448: 74-87.
  • Chanda B, Venugopal SC, Kulshrestha S, Navarre DA, Downie B, Vaillancourt L, Kachroo A, Kachroo P (2008) Glycerol-3-phosphate levels are associated with basal resistance to the hemibiotrophic fungus Colletotrichum higginsianum in Arabidopsis. Plant Physiology 147: 2017-2029.
  • Luque D, Gonzalez JM, Garriga D, Ghabrial SA, Havens WM, Trus B, Verdaguer N, Carrascosa JL, Caston JR (2010) The T=1 capsid protein of Penicillium chrysogenum virus Is formed by a repeated helix-rich core indicative of gene duplication. Journal of Virology 84: 7256-7266.
  • McDonald M, Kendall A, Bian W, McCullough I, Lio E, Havens WM, Ghabrial SA, Stubbs G (2010) Architecture of the potyviruses. Virology 405: 309-313.
  • Nibert ML, Woods KM, Upton SJ, Ghabrial SA (2009) Cryspovirus: a new genus of protozoan viruses in the family Partitiviridae. Archives of Virology 154: 1959-1965.
  • Parthasarathy R, Sheng ZT, Sun ZY, Palli SR (2010) Ecdysteroid regulation of ovarian growth and oocyte maturation in the red flour beetle, Tribolium castaneum. Insect Biochemistry and Molecular Biology 40: 429-439.
  • Parthasarathy R, Sun ZY, Bai H, Palli SR (2010) Juvenile hormone regulation of vitellogenin synthesis in the red flour beetle, Tribolium castaneum. Insect Biochemistry and Molecular Biology 40: 405-414.
  • Rao SS, Hildebrand D (2009) Changes in oil content of transgenic soybeans expressing the yeast SLC1 gene. Lipids 44: 945-951.
  • Rao SS, Mamadou L, McConnell M, Polisetty R, Kwanyuen P, Hildebrand D (2009) Non-antibiotic selection systems for soybean somatic embryos: the lysine analog aminoethyl-cysteine as a selection agent. BMC Biotechnology 9: 1186.
  • Schwartz SL, Farman ML (2010) Systematic overrepresentation of DNA termini and underrepresentation of subterminal regions among sequencing templates prepared from hydrodynamically sheared linear DNA molecules. BMC Genomics 11: 87.
  • Selote D, Kachroo A (2010) RPG1-B-derived resistance to AvrB-expressing Pseudomonas syringae requires RIN4-like proteins in soybean. Plant Physiology 153: 1199-1211.
  • Soria-Guerra RE, Rosales-Mendoza S, Chang S, Haudenshield JS, Zheng DM, Rao SS, Hartman GL, Ghabrial SA, Korban SS (2010) Identifying differentially expressed genes in leaves of Glycine tomentella in the presence of the fungal pathogen Phakopsora pachyrhizi. Planta 232: 1181-1189.
  • Soria-Guerra RE, Rosales-Mendoza S, Chang SY, Haudenshield JS, Padmanaban A, Rodriguez-Zas S, Hartman GL, Ghabrial SA, Korban SS (2010) Transcriptome analysis of resistant and susceptible genotypes of Glycine tomentella during Phakopsora pachyrhizi infection reveals novel rust resistance genes. Theoretical and Applied Genetics 120: 1315-1333.


Progress 09/01/08 to 08/31/09

Outputs
OUTPUTS: 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. PARTICIPANTS: PI: Schardl, Christopher L. Professor, University of Kentucky. Co-PI: Daniel K. Howe, Associate Professor, University of Kentucky Arnaoudova, Elissaveta, PhD Student, University of Kentucky. Genome and unigene assembly, gene model construction, genome annotation. Bullock, Charles Thomas, Undergraduate Student, University of Kentucky. Laboratory Information Management Systems. Calder, James O., Postbaccalaureate, University of Kentucky. DNA sequence analysis. Davis, Kelley A., Technician, University of Kentucky. DNA sequence analysis. Kaser, Joseph, PhD Student, Oregon State University, Sequence analysis and phylogenetics. Kesterson, Abbe, Senior Facilities Manager, University of Kentucky, Next generation sequencing. Mann, Lesley J., Undergraduate Student, University of Kentucky. Quantitative reverse-transcription polymerase chain reactions. DNA cloning. Gene expression studies. Ms Mann received a Beckman scholarship for her project. Sugawara, Koya, Visiting scholar from NARO, Japan, Polymerase chain reactions, DNA sequence analysis. Webb, Jennifer, Research Analyst, University of Kentucky, Robotic programming, DNA sequence analysis, DNA fragment analysis. Laboratory management. TARGET AUDIENCES: Farmers and livestock producers. Agricultural biotechnology companies. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
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.

Publications

  • 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.
  • 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.
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