John E. Carlson, Ph.D.

  • Professor of Molecular Genetics
  • Director of The Schatz Center for Tree Molecular Genetics
John E. Carlson, Ph.D.
323 Forest Resources Building
University Park, PA 16802
Work Phone: 814-863-9164
Fax: 814-863-3725

Areas of Expertise

  • Genomics
  • Conservation Genetics
  • Renewable Energy
  • Biotechnology


  1. B.S., University of Pittsburgh (1974)
  2. M.Sc., University of Illinois (1978)
  3. Ph.D., University of Illinois (1983)

Responsibilities and Interests

Research, education and technology transfer in forest genetics, genomics and plant biotechnology.

Courses Taught

  • FOR430 "Conservation Biology"
  • FOR496 "Honors/Independent Research"
  • FOR530 "Conservation Genetics"
  • FOR880 "Bioenergy Feedstocks"
  • PLBIO512 "Plant Resource Acquisition and Utilization"
  • PLBIO513 "Plant Communication and Growth Regulation"

Recent Research/Educational Projects

Dr. Carlson's group conducts research in the areas of Genomics, Conservation Genetics, and Biotechnology. Current projects in The Schatz Center cover a wide range of topics from sequencing the chestnut genome to soil metagenomics of short rotation biomass crops.


The organization of genes and genomes are studied through transcriptomics, genome sequencing, genetic linkage mapping, and metagenomics. This research identifies genes, DNA markers and quantitative trait loci governing growth, stress resistance, and plant-microbe interactions in hardwood tree species.

Conservation genetics

Genetic diversity is the foundation for biodiversity. DNA markers in the nuclear, mitochondrial and chloroplast genomes are used to study genetic diversity in forest trees and associated organisms.

Environmental tree biotechnology

Research is being conducted on the molecular basis of lignin synthesis and the response of trees to environmental stresses such as introduced pests and diseases, climate change, and pollutants. The goal for this research is environmentally friendly bioenergy production and ecosystem restoration.

Selected Publications:

Wu D, Koch J, Coggeshall M, Carlson J. 2019. The first genetic linkage map for Fraxinus pennsylvanica and syntenic relationships with four related species, Plant Molecular Biology, 99 (3):251–264.

Tuskan GA, Groover AT, Schmutz J, DiFazio SP, Myburg A, Grattapaglia D, Smart LB, Yin T, Aury JM, Kremer A, Leroy T, Le Provost G, Plomion C, Carlson JE, Randall, J, Westbrook J, Grimwood J, Muchero W, Jacobson D, Michener JK. 2018. Hardwood tree genomics: Unlocking woody plant biology. Frontiers in Plant Science, 9, p.1799, 9 pages.

Weathers TC, Kazyak DC, Stauffer JR, Jr., Kulp MA, Moore SE, King TL, Carlson JE. 2018. Neutral Genetic and Phenotypic Variation Within and Among Isolated Headwater Brook Trout Populations, Transactions of the American Fisheries Society, 148(1) 58-72.

Scully E., Geib SM, Mason CJ, Carlson JE, Tien M, Chen H-Y, Harding S, Tsai C-J, Hoover K. 2018. Host-plant induced changes in microbial community structure and midgut gene expression in an invasive polyphage (Anoplophora glabripennis)” Scientific Reports, 8(1), p.9620, 16 pages.

Ćalić I, Koch J, Carey D, Addo-Quaye C, Carlson JE, Neale DB, 2017. Genome-wide association study identifies a major gene for beech bark disease resistance in American beech (Fagus grandifolia Ehrh.). BMC Genomics, 18(1), p.547, 14 pp.

Staton ME, Best TO, Khodwekar SD, Owusu SA, Xu T, Yu Y, Jennings TN, Knaus BJ, Cronn RC, Arumuganathan AK, Coggeshall MV, Gailing O, Liang H, Romero-Severson J, Schlarbaum SE, Carlson JE. 2015. Preliminary genomic characterization of ten hardwood tree species from multiplexed low coverage whole genome sequencing. PLoS ONE, 10(12): e0145031, 13 pages.

Staton M, Zhebentyayeva T, Olukolu B, Fang GC, Nelson D, Carlson JE, Abbott AG. 2015. Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes. BMC Genomics, 16:744, 14 pages.

Diningrat DS, Widiyanto SM, Pancoro1 A, Iriawati, Shim D, Panchangam B, Zembower N, Carlson JE. 2014. Transcriptomes of Teak (Tectona grandis, L.f) in Vegetative to Generative Transition Stage Development. International Journal of Innovation and Applied Studies, 9(3): 1416-1427. 

Scully E; Geib SM; Carlson JE; Tien M; Hoover K. 2014. Functional genomics and microbiome profiling of the Asian longhorned beetle (Anoplophora glabripennis) reveal insights into the digestive physiology and nutritional ecology of wood feeding beetles. BMC Genomics, 15:1096, 21 pp.  

Meinhardt LW, Thomazella DPT, Teixeira PJPL, Costa GGL, Carazzolle MF, Schuster SC, Carlson JE, Guiltinan MJ, Mieczkowski P, Farmer A, Ramaraj T, Crozier J, Davis RE, Shao J, Melnick RL, Pereira GAG, Bailey BA.  2014.  Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: Mechanisms of the biotrophic and necrotrophic phases. BMC Genomics, 15(1): 164, 25 pages.

Sha T, Liang H, Yan D, Zhao Y, Han X, Carlson JE, Xia X, Yin W. 2013. Populus euphratica: the transcriptomic response to drought stress. Plant Molecular Biology 83(6): 539-557.

Xu Y, Chen C-F, Thomas TP, Azadi P, Diehl B, Tsai C-J, Brown N, Carlson JE, Tien M, Liang H.  2013.  Wood chemistry analysis and expression profiling of a poplar clone expressing a tyrosine-rich peptide. Plant Cell Reports, 32 (12), 1827-1841.

Scully ED, Geib SM, Hoover K, Tien M, Tringe SG, Barry KW, Glavina del Rio T, Chovitia M, Herr JR, Carlson JE. 2013. Metagenomic Profiling Reveals Lignocellulose Degrading System in a Microbial Community Associated with a Wood-Feeding Beetle. PLoS ONE 8(9): e73827.

Fang GC, Blackmon BP, Staton ME, Nelson CD, Kubisiak TL, Olukolu BA, Henry D, Zhebentyayeva Y, Saski CA, Cheng CH, Monsanto M, Ficklin S, Atkins M, Georgi LL, Barakat A, Wheeler N, Carlson JE, Sederoff R, Abbott AG. 2013. A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map. Tree Genetics & Genomes, 9(2): 525-537.

Petit RJ, Carlson J, Curtu AL, Loustau ML, Plomion C, González-Rodríguez A, Sork V, Ducousso A. 2012. Fagaceae trees as models to integrate ecology, evolution and genomics. New Phytologist, 197: 369 – 371.

Costa GGL, et al. 2012. The mitochondrial genome of Moniliophthora roreri, the frosty pod rot pathogen of cacao. Fungal Biology, 116 (5): 551-562. 

Kremer K, Abbott AG, Carlson JS, Manos PS, Plomion C, Sisco P, Staton ME, Ueno S, Vendramin GG. 2012. Genomics of Fagaceae (Review). Tree Genetics & Genomes, 8(3): 583-610.

Barakat A, Staton M, Cheng C-H, Park J, Buang N, Yassin M, Ficklin S, Yeh C-C, Hebard F, Baier K, Powell W, Schuster S, Wheeler N, Abbott A, Carlson J, Sederoff R. 2012. Chestnut resistance to the blight disease: insights from transcriptome analysis. BMC Plant Biology, 12:38, 14 pp. 

Zuccolo A, et al. 2011. A Physical Map for the Amborella Genome Sheds Light on the Evolution of Angiosperm Genome Structure. Genome Biology, 12:R48, 14 pp.

Argout, et al. 2011. The genome of Theobroma cacao L. Nature Genetics 43: 101–109.

Tuskan, et al. 2006, The Genome of Western Black Cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw).  Science 313: 1596-1604.