Matthew Zinkgraf

Assistant Professor

Research Interests

My research is focused on the ecological and evolutionary genetics of plants. To accomplish this research, my lab applies an interdisciplinary approach that utilizes methods from computational biology, molecular biology, genetics/genomics and forest ecology. Ongoing research in the lab is concentrated around three main themes: 1) dissecting how genetic variation of populations is structured across the landscape, 2) identifying process that have influenced the adaptation and evolution of populations and 3) understanding the genetic regulation of important ecologically and economically traits such as wood formation, response to abiotic stress and resistance to insects. These studies are primarily focused on undomesticated forest trees because forests are the foundation of many natural systems in the world, which society relies heavily upon for ecosystem services, forest products, and recreation. 

Educational & Professional Experience


  • B.S. in Biology and Natural Resource Management from the University of Wisconsin at Stevens Point, 2001
  • M.S. in Natural Resources from the University of Wisconsin at Stevens Point, 2004 
  • Ph.D. in Biology from Northern Arizona University, 2012

Professional Preparation

  • Postdoctoral Fellow - US-Forest Service, 2013-2014
  • Postdoctoral Fellow - NSF-Plant Genome Research Program, 2015-2017

Recent Publications

  1. Body, M.; M.S. Zinkgraf; T.G. Whitham; C.-H. Lin; R.A. Richardson; H.M. Appel; and J.C. Schultz. Accepted. Heritable phytohormone profiles of poplar genotypes vary in resistance to a galling aphid. Molecular Plant-Microbe Interactions doi:10.1094/MPMI- 11-18-0301-R
  2. Zinkgraf, M.S.; A.T. Groover and V. Filkov. 2018. Reconstructing gene networks of forest trees from gene expression data: Toward higher-resolution approaches. ICT Innovations 2018. Engineering and Life Sciences. Cham: Springer International Publishing, Switzerland. pp. 3-12. 
  3. Zinkgraf, M.S.; S. Gerttula; S. Zhao; V. Filkov and A.T. Groover. 2018. Transcriptional and temporal response of Populus stems to gravi-stimulation. Journal Integrated Plant Biology 60(7): 578-590. 
  4. Woolbright, S.A.; B.J. Rehill, R.L. Lindroth, S.P. DiFazio, G.D. Martinsen, M.S. Zinkgraf, G.J. Allan, P. Keim and T.G. Whitham. 2018. Large effect quantitative trait loci for salicinoid phenolic glycosides in Populus: Implications for gene discovery. Ecology and Evolution 8(7): 3726-3737. 
  5. Zinkgraf, M.S.; S. Gerttula and A.T. Groover. 2017. Transcript profiling of a novel plant meristem, the monocot cambium. Journal Integrated Plant Biology 59:436-449.
  6. Zinkgraf, M.S.; L. Liu; A. Groover and V. Filkov. 2017. Identifying gene co-expression networks underlying the dynamic regulation of wood-forming tissues in Populus under diverse environmental conditions. New Phytologist 214:1464-1478.
  7. Zinkgraf, M.S.; K. Haiby; M. Lieberman; L. Comai, I. Henry and A. Groover. 2016. Creation and analysis of irradiation hybrids in Populus. Current Protocols in Plant Biology 1:431-450.
  8. Zinkgraf, M.S.; N. Meneses; T.G. Whitham and G. Allan. 2016. Genetic variation in NIN1 and C/VIF1 genes is significantly associated with Populus angustifolia resistance to a galling herbivore, Pemphigus betae. Journal of Insect Physiology 84:50-59.
  9. Gerttula, S.; M.S. Zinkgraf; G.K. Muday; D.R. Lewis; F.M. Ibatullin; H. Brumer; F. Hart; S.D. Mansfield; V. Filkov and A.T. Groover 2015. Transcriptional and hormonal regulation of gravitropism of woody stems in Populus. Plant Cell 27:2800-2813.
  10. Henry, I.M.; M.S. Zinkgraf; A.T. Groover and L. Comai. 2015. A system for dosage-based functional genomics in Poplar. Plant Cell 27:2370-2383.
  11. Lamit, L.J.; P.E. Busby; M.K. Lau; Z.G. Compson; T. Wojtowicz; A.R. Keith; M.S. Zinkgraf; J.A. Schweitzer; S.M. Shuster; C.A. Gehring and T.G. Whitham. 2015. Tree genotype mediates covariance among communities from microbes to lichens and arthropods. Journal of Ecology. 103:840-850.
  12. Liu, L.; T. Ramsay; M. Zinkgraf; D. Sundell; N.R. Street; V. Filkov and A. Groover. 2015. A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus. Plant Journal 82:887-898.
  13. Liu, L.; M. Zinkgraf; H.E. Petzold; E.P. Beers; V. Filkov and A. Groover. 2015. The Populus ARBORKNOX1 homeobox transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function. New Phytologist 205:68-694
  14. Liu, L.; V. Missirian; M. Zinkgraf; A. Groover and V. Filkov. 2014. Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees. BMC Genomics 15:S3