Dan Kliebenstein

image of Dan Kliebenstein



Population Biology
UC Davis Genome Center
Plant Sciences

Offices and Labs

129 Asmundson Hall


1999 PhD Genetics Cornell University
1993 BS Genetics Iowa State University

Research Contribution

The linkage between genotype and phenotype is central to all areas of biology from crop productivity to cancer susceptibility. However this is only understood at the most rudimentary of levels. We are attemptign to develop a new theoretical framework within which to linkg genotype and phenotype that should help to better understand any biological system.

Research Interests

Quantitative Systems Biology

We focus on two major questions using plant natural chemistry as our model system. Plant natural chemistry generates compounds that provide the taste, flavor, color and medicinal activities that people associate with specific plants. However, their primary role appears to be helping the plant cope with its environment by attracting pollinators, repelling attackers and protecting the plant from sunlight. These aspects make these compounds easy to measure and key tools in understanding modern systems biology and genomics. The first question that we use these chemicals for is to understand how thousands of genes coordinate within a system to control the proper functioning of the system. This involved modern quantitative genomics and tools such as genome wide association mapping and QTL analysis. We are at the forefront of developing network analysis approaches and theory to help with the modern synthesis of the gene-to-phenotype linkage. The second question we focus on is why plants make these chemicals. They have broad activities and plants make an amazing diversity of chemicals, each potentially with its own function and evolutionary history. We are primarily using the model plant, Arabidopsis thaliana, to study how its secondary metabolites control interactions with both insects and fungi. As a part of this we are using a mixture of functional genetics, quantitative genetics, plant biology, evolutionary biology and metabolite profiling to develop as in depth and broad a picture as possible. To broaden this picture, we are expanding into rice, tomato, Lycopersicon, and grapes, Vitis. An additional avenue that we are pursuing is the fact that fungi also make secondary metabolites. For instance, Botrytis cinerea produces a suite of secondary metabolites whose main role appears to be killing plant cells. Thus by studying how Arabidopsis and Botrytis interact, we hope to analyze how organisms can combat each other through metabolism. We are expanding our quantitative systems approaches to study genetic variation in both the host and pathogen of this system simultaneously.

Department and Center Affiliations

Department of Plant Sciences
Genome Center

CBS Grad Group Affiliations

Integrated Genetics and Genomics
Plant Biology
Population Biology

Specialties / Focus

Plant Biology
  • Molecular Biology, Biochemistry, and Genomics
  • Environmental and Integrative Biology
Integrated Genetics and Genomics
  • Model Plants
  • Plant Breeding


Kliebenstein website

Teaching Interests

Natural variation and secondary metabolites.


BIS 101 Genes and Gene Regulation (Winter)


1/8/2018 2:34:08 PM
  • Zhang, W., Corwin, J.A., Eshbaugh, R., Copeland, D., Feusier, J., Chen, F., Atwell, S. and D.J. Kliebenstein (2017) Plastic transcriptomes stabilize immunity to pathogen diversity: The jasmonic acid and salicylic acid networks within the Arabidopsis/Botrytis pathosystem. Plant Cell 29(11)2727-2752.

  • Kerwin, R.E., Feusier, J., Rubin, M., Corwin, J.A., Lin, C., Muok, A., Larson, B., Li, B., Joseph, B., Francisco, M., Copeland, D., Weinig, C. and D.J. Kliebenstein. (2017) Epistatic by Environment Interactions Among Arabidopsis thaliana Glucosinolate Genes Impact Complex Traits and Fitness in the Field. New Phytologist 215(3)1249-1263.

  • Malinovsky, F.G., Thomsen, M-L.F., Nintemann, S.J., Jagd, L.M., Bourgine, B., Burow, M. and D.J. Kliebenstein. (Online) An evolutionarily young defense metabolite, 3-hydroxypropyl glucosinolate, influences the root growth of plants via the ancient TOR signaling pathway. eLife 6:e29353.

  • Wisecaver, J.H., Borowsky, A.T., Tzin, V., Jander, G., Kliebenstein, D.J. and A. Rokas (2017) A global co-expression network approach for connecting genes to specialized metabolic pathways in plants. Plant Cell 29(5)944-959.

  • Corwin, J.A., Copeland, D., Feusier, J., Subedy, A., Eshbaugh, R., Palmer, C., Maloof, J. and D.J. Kliebenstein (2016) The Quantitative Basis of the Arabidopsis Innate Immune System to Endemic Pathogens Depends on Pathogen Genetics. PLoS Genetics 12(2):e1005789.

  • Chan, E.K.F., Rowe, H.C., Corwin, J.A. Joseph, B. and D.J. Kliebenstein. (2011) “Combining genome-wide association mapping and transcriptional networks to identify novel genes controlling glucosinolates in Arabidopsis thaliana”. PLoS Biology 9(8)e1001125
  • Chan, E.K.F., Rowe, H.C., Hansen, B.G, and Kliebenstein, D.J. (2010) “The complex genetic architecture of the metabolome”. PLoS Genetics 6(11)e1001198
  • Osbourn, AE and D.J. Kliebenstein (2012) “Making new molecules – evolution of pathways for novel metabolites in plants” Current Opinion in Plant Biology 15(4)415-23.
  • Hageman Blair, R. Kliebenstein, D.J. and G.A. Churchill. (2012) “What can causal networks tell us about metabolic pathways” PLoS Computational Biology 8(4)e1002458
  • Jimenez-Gomez, J.M., Corwin, J.A., Joseph, B., Maloof, J.N. and Kliebenstein, D.J. (2011) “Genomic analysis of QTLs and genes altering natural variation in stochastic noise” PLoS Genetics 7(9)e1002295
  • Züst, T., Shimizu, K., Joseph, B., Kliebenstein, D.J. and L.A. Turnbull. (2011). “Using knockout mutants to reveal the costs of defensive plant secondary metabolites”. Proceedings of the Royal Society B: Biological Sciences 278(1718)2598-2603
  • Bidart-Bouzat, M.G. and D.J. Kliebenstein. (2011) “An ecological genomic approach challenging the paradigm of differential plant responses to specialist versus generalist insect herbivores”. Oceologia 167(3)677-89
  • Chan, E.K.F., Rowe, H.C. and Kliebenstein, D.J. (2010) “Understanding the evolution of defense metabolites in Arabidopsis thaliana using genome-wide association mapping” Genetics 185(3)991-1007
  • Kliebenstein, D.J., West, M.A.L, van Leeuwen, H., Kim, K., Doerge, R.W., and D.A. St. Clair. (2006) Identification of QTL Controlling Gene Expression Networks Defined A Prioiri. BMC Bioinformatics 7(1):308.
  • Brown, B.A., Cloix, C., Jiang, G.H., Kaiserli, E., Herzyk, P., Kliebenstein, D.J. and G.I. Jenkins. (2005) A UV-B-specific signaling component orchestrates plant UV-protection. (In press) Proc. Natl. Acad. Sci. USA