John I. Yoder

John Yoder

Position Title

Department of Plant Sciences, College of Agricultural and Environmental Sciences

101 Asmundson Hall

Profile Introduction

My lab investigates molecular genetic mechanisms governing plant-plant interactions. We are specifically interested in understanding how molecules released by the roots of some plants effect the growth and development of nearby plants and intend to translate these findings into developing crops that are “self-weeding”. Probably the most robust model for investigating chemical signaling between plants are parasitic plants in the Orobanchaceae because there root parasites use molecules released into the rhizosphere by host roots as chemical cues to initiate the development of invasive haustoria. Haustorium development can be monitored in vitro by adding host-derived chemicals to aseptically grown parasite seedlings and visualizing haustorium development under a dissecting microscope within hours of treatment. Our lab uses a combination of genomics, biochemistry, and plant biology approaches to identify bioactive molecules in host root exudates, learn how their release into the rhizosphere is regulated, and understand how the parasite recognizes and responds to molecular signals from other plants.

Research Interests

Genomics and molecular biology of subterranian plant-plant interactions

Grad Group Affiliations

  • Horticulture and Agronomy Graduate Group
  • Integrative Genetics and Genomics
  • Plant Biology

Specialties / Focus

  • Cell and Developmental Biology
  • Developmental Genetics
  • Environmental and Integrative Biology
  • Integrated Genetics and Genomics
  • Model Plants
  • Molecular Biology, Biochemistry and Genomics


  • BIT 001 Introduction to biotechnology, spring
  • BIT 171 Professionalism and ethics in biotechnology, Fall, spring
  • GGG 296 Professionalism and integrity in life sciences, Fall


  • Yoder Lab

Professional Societies

  • American Association Plant Biologists
  • International Society of Parasitic Plants


  • 1977 BS Microbiology University of Michigan
  • 1982 PhD Genetics Stanford University


Liu, Siming and Yoder, John I. (2016) Chemical induction of hairpin RNAi molecules to silence vital genes in plant roots, Scientific Reports 6: 37711

Yang, Zhenzhen, Yeting Zhang, Eric Wafula, Loren A. Honaas, Paula E. Ralph, Sam Jones, Christopher R. Clarke, Siming Liu, Chun Su, Huiting Zhang, Naomi S. Altman, Stephan C. Schuster, Michael P. Timko, John I. Yoder, James H. Westwood, Claude W. dePamphilis (2016) You are what you eat: Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation, PNAS 113 (45): 7010-7019

Yang, Z., E. K. Wafula, L. A. Honaas, H. Zhang, M. Das, M. Fernandez-Aparicio, K. Huang, P. C. G. Bandaranayake, B. Wu, J. P. Der, C. R. Clarke, P. E. Ralph, L. Landherr, N. S. Altman, M. P. Timko, J. I. Yoder, J. H. Westwood and C. W. dePamphilis (2015). "Comparative Transcriptome Analyses Reveal Core Parasitism Genes and Suggest Gene Duplication and Repurposing as Sources of Structural Novelty." Molecular Biology and Evolution 32(3): 767-790.

Bandaranayake, P.C.G. and Yoder, J.I. (2013) Trans-specific gene silencing of acetyl-CoA carboxylase in a root parasitic plant. Mol Plant Microb Interact. 26: 575-584

Pradeepa C.G. Bandaranayake and John I. (2013) Haustorium Initiation and Early Development in Joel, DM, Musselman LJ, Gressel J (Eds.) Parasitic Orobanchaceae ‒ parasitic mechanisms and control strategies. Springer 

Zhang, Y., Fernandez-Aparicios, M., Wafula, E.K., Das, M., Jiao, Y., Wickett, N.J., Honaas, L.A., Ralph, P.E., Wojciechowski, M.F., Timko, M.P., Yoder, J.I., Westwood, J.H., and dePamphilis, C.W. (2013). Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species. BMC Evol Biol. 13, 10.1186/1471-2148-13-48

Honaas, L.A., Wafula, E.K., Yang, Z., Der, J.P., Wickett, N.J., Altman, N.S., Taylor, C.G., Yoder, J.I., Timko, M.P., Westwood, J.H., and dePamphilis, C.W. (2013). Functional genomics of a generalist parasitic plant:  Laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression. BMC Plant Biol. 13 (9), DOI.10.1186/1471-2229-13-9

Bandaranayake, P.C., Tomilov, A., Tomilova, N.B., Ngo, Q.A., Wickett, N., dePamphilis, C.W., and Yoder, J.I. (2012). The TvPirin gene is necessary for haustorium development in the parasitic plant Triphysaria versicolor. Plant Physiol. 158: 1-8.

Wickett, Norman J., Honaas, Loren A., Wafula, Eric K., Das, M., Huang, K., Wu, B., Landherr, L., Timko, Michael P., Yoder, J., Westwood, James H., and dePamphilis, Claude W. (2011). Transcriptomes of the Parasitic Plant Family Orobanchaceae Reveal Surprising Conservation of Chlorophyll Synthesis. Curr. Biol. 21, 2098-2104.

Bandaranayake, P.C.G., Filappova, T., Tomilov, A., Tomilova, N.B., Jamison-McClung, D., Ngo, Q., Inoue, K., and Yoder, J.I. (2010) A single-electron reducing quinone oxidoreductase is necessary to induce haustorium development in the root parasitic plant Triphysaria. Plant Cell, 22(4): 1404-1419.

Yoder, JI and Scholes, JD. (2010) Host plant resistance to parasitic weeds; recent progress and bottlenecks. Curr. Opin. Plant Biol. 13(4): 478-484