John E. Carlson, Ph.D.

John E. Carlson, Ph.D.

  • Professor of Molecular Genetics
  • Director of The Schatz Center for Tree Molecular Genetics
323 Forest Resources Building
University Park, PA 16802

Areas of Expertise

  • Genomics
  • Conservation Genetics
  • Renewable Energy
  • Biotechnology


  • B.S., University of Pittsburgh (1974)
  • M.Sc., University of Illinois (1978)
  • 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 Recent Publications

Stanton et al. 2020. Inter-Specific Hybridization of Alnus rubra and Alnus rhombifolia: Preliminary Report of a New Taxon and DNA Marker Resources for Bioenergy Feedstock Production. Tree Genetics & Genomes 16:70, 13 pages

Wang W, Carlson CH, Smart LB, Carlson JE. 2020. Transcriptome analysis of contrasting resistance to herbivory by Empoasca fabae in two shrub willow species and their hybrid progeny. PLOS ONE 15(7): e0236586, 25 pages.

Staton, et al. 2020. A reference genome assembly and adaptive trait analysis of Castanea mollissima 'Vanuxem', a source of resistance to chestnut blight in restoration breeding. Tree Genetics and Genomes, 16:57, 23 pages.

Tchatchoua TD, Poethig RS, Doody E, Weathers TC, Swartz K, Mathieson I, Zembower N, Zhebentyayeva T, Carlson JE. 2020. Genetic diversity of Faidherbia albida populations in the Sudano Sahelian region of Cameroon, using SSR (Simple Sequence Repeat) markers. African Journal of Biotechnology, 19(7): 415-425.

Soltani N, Best T, Grace D, Nelms C, Shumaker K, Romero-Severson J, Moses D, Schuster S, Staton M, Carlson J, Gwinn K. 2020. Transcriptome profiles of Quercus rubra responding to increased O3 stress. BMC Genomics, 21(1): 1-18.

Guo L, Guo S, Xu J, He L, Carlson JE, Hou X. 2020. Phylogenetic analysis based on chloroplast genome uncover evolutionary relationship of all the nine species and six cultivars of tree peony. Industrial Crops and Products, 153: p.112567, 10 pages.

Bell TH, Kaminsky LM, Gugino BK, Carlson JE, Malik RJ, Hockett KL, Trexler RV. 2019. Factoring Ecological, Societal, and Economic Considerations into Inoculant Development. Trends in Biotechnology, 37(2): 140-151.

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 pages.

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.

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 pages.