Davis Lab

BIOGRAPHICAL SKETCH
NAME Davis, John M.		POSITION TITLE Associate Professor, Molecular Biology
Jmdavis@ufl.edu
365 Newins-Zielger, 846-0879
INSTITUTION AND LOCATION	DEGREE (if applicable)		YEAR(s)	FIELD OF STUDY
University of Washington, Seattle, WA	Postdoc		1989-91	Biochemistry, Mol. Biology
Michigan State University, East Lansing, MI	PhD		1989	Plant Breeding & Genetics
Illinois State University, Normal, IL	BS		1983	Biological Sciences

 

 

Synergistic Activities
1. Co-Director, Forest Biology Research Cooperative, a UF-, industry-, and state agency-supported research program to understand mechanisms of forest productivity. I provide genetics and molecular biology expertise, assist in design of experiments, guide staff work priorities and flow, and help chart overall research direction. The FBRC has installed >20 field trials of clonal loblolly pine for mapping and association studies since its creation in 1996. Current research is on understanding adaptive trait variation and bioenergy applications.

2. Co-Leader (with George Casella), Statistical Genomics Discussion Group, weekly sessions since 2001.  Averaging 10 faculty and 5 students per semester, we discuss recent papers that involve both genetics and statistics. Sessions involve discussion of methods, re-analysis of datasets, exploration of alternative approaches, and biological interpretation of complex data.

3. Instructor (with Andrew Hanson, Gary Peter and Fredy Altpeter), Plant Molecular and Cellular Biology, held every Fall semester.  A core course in the Plant Molecular and Cellular Biology Program, I lecture on genomics, transcriptomics, and forward and reverse genetics.

4. Graduate student education and training program participant. Serve as Director of the interdepartmental and intercollegiate Graduate Program in Plant Molecular and Cellular Biology (currently ~35 students enrolled). Founding and continuing member of the Curriculum Committee for the university-wide Graduate Program in Genetics (currently 15 students).

Graduate Students and Postdoctoral Researchers Advised
Chair, PhD Committees: T. Quesada (continuing), G. Ramirez (2008), P. Bocock (2007), G. Kayihan (2006), H. Wu (1998), Y. Qian (1993), M. Popp (1993)
Chair, MS Committees: J. Reed (2005), B. Crane (2002), S. Luce (2000), M. Mason (1997)
Postdoctoral. C. Anderson (2007-), C. Benedict (2007-2008), A. Morse (2004-2008), J. Cooke (2002-2004), D. Wang (1998), M. Tignor (1998), S. Lawrence (1996-1997), J. Greenwood (sabbatical, 1995)

Selected peer-reviewed publications
Refereed Journal Articles (last 5 yrs)

Morse AM, Peterson DG, Islam-Faridi MN, Smith KE, Magbanua Z, Garcia SA, Kubisiak TL, Amerson HV, Carlson JE, Nelson CD, Davis JM. 2009. Evolution of genome size and complexity in Pinus. PLoS ONE 4: e4332. doi:10.1371/journal.pone.0004332.

Baltunis BS, Martin TA, Huber DA, Davis JM. 2008. Inheritance of foliar stable carbon isotope discrimination and third-year height in Pinus taeda clones on contrasting sites in Florida and Georgia. Tree Genetics and Genomes 4: 797-807.

Quesada T, Li Z, Dervinis C, Li Y, Bocock PN, Tuskan GA, Casella G, Davis JM, Kirst M. 2008. Comparative analysis of the transcriptomes of Populus trichocarpa and Arabidopsis thaliana suggests extensive evolution of gene expression regulation in angiosperms. New Phytologist 180: 408-420.

Frost CJ, Mescher MC, Dervinis C, Davis JM, Carlson JE, De Moraes CM. 2008. Priming defense genes and metabolites in hybrid poplar by the green leaf volatile cis-3-hexenyl acetate. New Phytologist 180: 722-734.

Quesada T, Li Z, Dervinis C, Li Y, Bocock PN, Tuskan GA, Casella G, Davis JM, Kirst M. 2008. Comparative analysis of the transcriptome of Populus trichocarpa and Arabidopsis thaliana suggests extensive evolution of gene expression regulation in angiosperms. New Phytologist (in press).

Frost CJ, Carlson JE, Mescher MC, Dervinis C*, Davis JM, De Moraes CM. 2008. Priming defense genes and metabolites in hybrid poplar by the green leaf volatile cis-3-hexenyl acetate. New Phytologist (in press).

Baltunis BS, Martin TA, Huber DA, Davis JM. 2008. Inheritance of foliar stable carbon isotope discrimination and third-year height in Pinus taeda on contrasting sites in Florida and Georgia. Tree Genetics and Genomes (Online First DOI 10.1007/s11295-008-0152-2).

 Gonzalez-Martinez SC, Huber D, Ersoz E, Davis JM, Neale DB. 2008. Association genetics in Pinus taeda L. II. Carbon isotope discrimination. Heredity 101: 19-26.

Bocock PN, Morse AM, Dervinis C, Davis JM. 2008. Evolution and diversity of invertase genes in Populus trichocarpa. Planta 227: 565-576.

Ramirez-Carvajal G, Morse AM, Davis JM. 2008. Transcript profiles of the cytokinin response regulator gene family in Populus imply diverse roles in plant development. New Phytologist 177: 77-89.

Morse AM, Tschaplinksi TJ, Dervinis C, Pijut PM, Schmelz EA, Day W, Davis JM. 2007. Salicylate and catechol levels are maintained in nahG transgenic poplar. Phytochemistry 68: 2043-2052.

Filichkin SA, DiFazio SP, Brunner AM, Davis JM, Yang ZK, Kalluri UC, Arias RS, Etherington E, Tuskan GA, Strauss SH. 2007. Efficiency of gene silencing in Arabidopsis: direct inverted repeats vs. transitive RNAi vectors. Plant Biotechnology Journal 5: 615-626.

Huang L-F, Bocock PN, Davis JM, Koch KE. 2007. Regulation of invertase: a ‘suite’ of transcriptional and post-transcriptional mechanisms. Functional Plant Biology 34: 499-507.
                                                                                             
Myburg H, Morse AM, Amerson HV, Kubisiak TL, Huber D, Osborne JA, Garcia SA, Nelson CD, Davis JM, Covert SF, van Zyl LM. 2006. Differential gene expression in loblolly pine (Pinus taeda L.) challenged with the fusiform rust fungus, Cronartium quercuum f.sp. fusiforme. Physiological and Molecular Plant Pathology 68: 79-91.

Tuskan GA, DiFazio SP, Hellsten U, Jansson S, Rombauts S, Putnam N, Sterck L, Bohlmann J, Schein J, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen G, Cooper D, Coutinho PM, Couturier J, Covert SF, Cunningham R, Davis J, Degroeve S, dePamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grigoriev I, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Islam-Faridi N, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé JC, Déjardin A, Pilate G, Locascio P, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson CD, Nieminen KM, Nilsson O, Peter G, Philippe R, Poliakov A, Ralph S, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Salamov A, Schrader J, Segerman B, Sterky F, Souza C, Tsai C, Unneberg P, Wall K, Wessler S, Yang G, Yin T, Douglas C, Sandberg G, Van de Peer Y, Rokhsar D. 2006. The genome of western black cottonwood, Populus trichocarpa. Science 313: 1596-1604.

Lawrence SD, Dervinis C, Novak N, Davis JM. 2006. Wound and insect herbivory responsive genes in poplar. Biotechnology Letters 28: 1493-1501.
                                                      
Kayihan GC, Huber DA, Morse AM, White TL, Davis JM. 2005. Genetic dissection of fusiform rust and pitch canker disease traits in loblolly pine. Theoretical and Applied Genetics 110: 948-958.

Cooke JEK, Martin TA, Davis JM. 2005. Short-term physiological and developmental responses to nitrogen availability in hybrid poplar. New Phytologist 167: 41-52.

Morse AM, Nelson CD, Covert SF, Holliday AG, Smith KE, Davis JM.  2004.  Pine genes regulated by the necrotrophic pathogen Fusarium circinatum.  Theoretical and Applied Genetics 109: 922-932.

Book and Book Chapters
Davis JM. 2008. Genetic improvement of poplar (Populus spp.) as a bioenergy crop. In: Genetic Improvement of Bioenergy Crops, Vermerris W (Ed.), Springer-Verlag New York LLC (in press).

Davis JM, Becwar MR. 2007. Developments in Tree Cloning. Developments in Fibres and Fibre Treatment Series, PIRA International Ltd, Surrey, UK, 69 pp.

Morse AM, Cooke JEK, Davis JM. 2004. Functional genomics in forest trees. In: Kumar S, Fladung M (eds) Molecular Genetics and Breeding of Forest Trees, Haworth Press, Binghamton, NY, pp.3-18.

Cooke JEK, Morse AM, Davis JM. 2004. Forestry. IN: Christou P, Klee H (eds), Handbook of Plant Biotechnology, John Wiley & Sons, West Sussex, UK, pp.881-904.