John E. Carlson, Ph.D.

John E. Carlson, Ph.D.

  • Academy Professor and Professor Emeritus of Molecular Genetics
  • Past Director of The Schatz Center for Tree Molecular Genetics
326 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.

Recent Research/Educational Projects


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

Abbott AG, Staton ME, Lohtka JM, DeWald LE, Zhebentyayeva T, Kapoor B, Thomas AM, Larson DA, Hadziabdic D, DeBolt S, Nelson CD, Carlson JE. 2024. Will “Tall Oaks from Little Acorns Grow”? White Oak (Quercus alba) Biology in the Anthropocene. Forests, 15(2), 269.

Kapoor B, Jenkins J, Schmutz J, Zhebentyayeva T, Kuelheim C, Coggeshall M, Heim C, Lasky J, Leites L, Islam-Faridi N, Romero-Severson J, DeLeo V, Lucas S,  Lazic D, Gailing O, Carlson J, Staton M. 2023. A haplotype-resolved chromosome-scale genome for Quercus rubra L. provides insights into the genetics of adaptive traits for red oak species. G3: Genes|Genomes|Genetics, 13(11).

Chatwin W, Shirley D, Lopez J, Sarro J, Carlson J, Devault A, Pfrender M, Revord R, Coggeshall M, Romero-Severson J. 2023. Female flowers first: QTL mapping in eastern black walnut (Juglans nigra L.) identifies a dominant locus for heterodichogamy syntenic with that in Persian walnut (J. regia L.). Tree Genetics & Genomes, 19(1), p.4.

Li Y, Guo L, Wang Z, Zhao D, Guo D, Carlson JE, Yin W, Hou X. 2022. Genome-wide association study of twenty-three flowering phenology traits and four floral agronomic traits in tree peony (Paeonia section Moutan DC.) reveals five genes known to regulate flowering time. Horticulture Research, 10(2):uhac263.

Sutherland J, Bell T, Trexler RV, Carlson JE, Lasky JR. 2022. Host genomic influence on bacterial composition in the switchgrass rhizosphere. Molecular Ecology, 31(14): 3934-3950.

Huff M, Wu D, Seaman J, Zhebentyayeva T, Kelly L, Islam-Faridi N, Nelson CD, Cooper E, Best T, Steiner K, Koch J, Romero-Severson J, Carlson J, Buggs R, Staton M. 2022. A high quality reference genome for Fraxinus pennsylvanica for ash species restoration and research. Molecular Ecology Resources, 22(4): 1284-1302.

Lei BJ, Frost C, Xu T, Herr JR, Carlson JE, Liang H. 2021. Poplar Allene Oxide Synthase 1 Gene Promoter Drives Rapid and Localized Expression by Wounding. Biotechnology Journal International, 25(5):16-28.

Lazic D, Hipp AL, Carlson JE, Gailing O. 2021. Use of genomic resources to assess adaptive divergence and introgression in oaks. Forests 12:690, 18 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 ME, Addo-Quaye C, Cannon N, Yu J, Zhebentyayeva T, Huff M, Islam-Faridi N, Fan S, Georgi LL, Nelson CD, Bellis E, Fitzsimmons S, Henry N, Drautz-Moses D, Noorai RE, Ficklin S, Saski C, Mandal M, Wagner T, Zembower N, Bodénès C, Holliday J, Westbrook J, Lasky J, Hebard FV, Schuster SC, Abbott AG, Carlson JE. 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. 

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

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

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