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Department of Plant Pathology

Christopher Toomajian

Toomajian, Christopher

 Associate Professor
 1712 Claflin Rd
 4018C Throckmorton Ctr.
 Manhattan, KS 66506
 Phone: 785-532-0879
 Fax: 785-532-5692
 Laboratory Website
 View My Curriculum Vitae

Area of Specialization

Population genetics, molecular evolution, evolutionary genomics; plant and fungal genetics/genomics; bioinformatics. 

Biography and Education


Dr. Chris Toomajian was born and raised in the suburbs of Cleveland, Ohio. After finishing high school, he was accepted into Northwestern University's Integrated Science Program. He had several research experiences as an undergrad, but the one with the biggest impact was his human genetics research work with Dr. Anna Di Rienzo, then a member of Northwestern's Anthropology Department. He graduated from Northwestern with a double major in Biological Sciences and Integrated Science, with a minor in Anthropology. Inspired by his undergrad genetics research and interested in exploring the topic of evolution further, he enrolled in the University of Chicago's Committee on Genetics PhD program. He studied genetic variation linked to human disease loci and asked what patterns of variation could tell us about the evolutionary history of the disease mutations. His PhD advisor was Dr. Martin Kreitman, of Chicago's Department of Ecology and Evolution. As a postdoc, he switched his focus in population genetics from humans to the model plant Arabidopsis thaliana. Working in the lab of Dr. Magnus Nordborg, then at the University of Southern California, he helped catalog natural genetic variation in Arabidopsis, infer the consequences of natural selection on this genetic variation, and develop resources for performing genome-wide association mapping studies in this species.

He began at K-State in 2008, accepting a 90% Research and 10% Teaching appointment. In addition to continued studies of Arabidopsis, Chris has expanded his work to include the population genetics and comparative genomics of various Fusarium species. In addition to his active participation in the Department of Plant Pathology, he is a graduate faculty member of the Interdepartmental Genetics Program and helps with the admissions of new graduate students in this program.


Ph.D. Genetics, University of Chicago, 2002
B.A. Biology & Integrated Science, Northwestern University, 1995

Staff and Students

Wei Yue - PhD student (GRA).




Interests include:

  • the study of model and non-model organisms, fungi and plants, and both natural and domesticated species
  • the natural genetic variation found in different species, the connection this variation has to important traits and adaptation, and the molecular and population-level forces that contribute to the levels and patterns of this variation (i.e. mutation, recombination, genetic drift, demography, and natural selection)
  • the application of next-generation sequencing technology (Illumina, 454) to questions in population genetics, transcriptomics, comparative genomics, functional genomics and QTL mapping
  • using natural genetic variation for QTL or association mapping of important plant and fungal traits
  • the characterization of natural populations, including quantifying their similarity at the genetic level and identifying divergent genome regions that may contribute to adaptation to the environment

Current or recently funded projects:

  • Genotyping by sequencing for footprints of selection in Fusarium graminearumUS Wheat and Barley Scab Initiative, USDA. PI, with co-PI John Leslie, 2014-2016, Objective - genotype 570 F. graminearum isolates at genotyping by sequencing markers, investigate the genetic structure of US populations, the haplotype structure of this variation along chromosomes, and scan for footprints of recent selection that may explain documented shifts in different classes of isolates.
  • Arabidopsis 2010: Transcriptomes for functional and evolutionary studies, NSF IOS-0929262. co-PI, with PI Richard Clark, 2009-2013, Objective - use RNA-Seq to identify the global complement of expressed genes in 19 sequenced Arabidopsis strains and describe how sequence variation affects variation in gene expression.


PLPTH 820 - Population Genetics. 3 credits. Taught Spring semester of ODD years.

Population Genetics is a required course for graduate students in the Interdepartmental Genetics Program, and is an alternative requirement for graduate students in Plant Pathology (1 of 3 alternative courses for MS students, 1 of 2 alternative options for PhD students).

The course introduces students to the growing and modern field of population genetics and the major questions that it can address in the era of genomics. Lectures cover the theoretical and quantitative foundation of the field and include the application of population genetic principles to natural populations of model and nonmodel species and managed populations of domesticated species. 

The class is usually a mix of graduate students from Genetics, Plant Pathology, Agronomy, and Biology with some representation from additional students in the natural and agricultural sciences. Students with a strong background in the basics of genetics and who have familiarity with various quantitative fields (algebra, basic probability theory, statistics) are generally well prepared for this course.

In addition to teaching this graduate course, Chris serves on the advisory committees of about 10 graduate students from 4 different graduate programs, and is happy to provide population genetics advice and interpretation to additional students and faculty.


Full publication list can be found on NCBI's MyBibliography  

Selected publications:

Jordan, KW, S Wang, Y Lun, L-J Gardiner, R MacLachlan, P Hucl, K Wiebe, D Wong, KL Forrest, IWGSC, AG Sharpe, CHD Sidebottom, N Hall, C Toomajian, T Close, J Dubcovsky, A Akhunov, L Talbert, UK Bansal, HS Bariana, MJ Hayden, C Pozniak, JA Jeddeloh, A Hall & E Akhunov. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biology 16:48 (2015) (doi: 10.1186/s13059-015-0606-4).

Carlson, AL, H Gong, C Toomajian, RJ Swanson. Parental genetic distance and patterns in nonrandom mating and seed yield in predominantly selfing Arabidopsis thalianaPlant Reproduction 26: 317-328 (2013) (doi:10.1007/s00497-013-0228-5). 

Garrett, KA, A Jumpponen, C Toomajian, L Gomez-Montano. Climate change and plant health: Designing research spillover from plant genomics for understanding the role of microbial communities. Canadian Journal of Plant Pathology 34:349-361 (2012) (doi:10.1080/07060661.2012.706832). 

Studt, L, C Troncoso, F Gong, P Hedden, C Toomajian, JF Leslie, H-U Humpf, MC Rojas, B Tudzynski. Segregation of secondary metabolite biosynthesis in hybrids of Fusarium fujikuroi and Fusarium proliferatumFungal Genetics and Biology 49: 567-577 (2012) (doi:10.1016/j.fgb.2012.05.005). 

Horton, MW, AM Hancock, YS Huang, C Toomajian, S Atwell, A Auton, NW Muliyati, A Platt, FG Sperone, BJ Vilhjálmsson, M Nordborg, JO Borevitz, J Bergelson. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel.Nature Genetics 44:212-216 (2012) (doi:10.1038/ng.1042). 

Hancock, AM, B Brachi, N Faure, MW Horton, LB Jarymowycz, FG Sperone, C Toomajian, F Roux & J Bergelson. Adaptation to climate across the Arabidopsis thaliana genome. Science 334: 83-86 (2011) (doi:10.1126/science.1209244). 

Gan, X, O Stegle, J Behr, JG Steffen, P Drewe, KL Hildebrand, R Lyngsoe, SJ Schultheiss, EJ Osborne, VT Sreedharan, A Kahles, R Bohnert, G Jean, P Derwent, P Kersey, EJ Belfield, NP Harberd, E Kemen, C Toomajian, PX Kover, RM Clark, G Rätsch & R Mott. Multiple reference genomes and transcriptomes for Arabidopsis thalianaNature 477: 419-423 (2011); published online 28 August 2011 (doi:10.1038/nature10414).

Kim*, S, V Plagnol*, TT Hu*, C Toomajian*, RM Clark, S Ossowski, JR Ecker, D Weigel & M Nordborg. Recombination and linkage disequilibrium in Arabidopsis thalianaNat Genet 39: 1151-1155 (2007); published online 5 August 2007 (doi:10.1038/ng2115). (*these authors contributed equally to this work)

Tang, C, C Toomajian, S Sherman-Broyles, V Plagnol,YL Guo, TT Hu, RM Clark, JB Nasrallah, D Weigel, & M Nordborg. The evolution of selfing in Arabidopsis thalianaScience 317: 1070-1072(2007);published online 26 July 2007 (doi:10.1126/science.1143153).

Clark, RM, G Schweikert*, C Toomajian*, S Ossowski*, G Zeller*, P Shinn, N Warthmann, TT Hu, G Fu, DA Hinds, H Chen, KA Frazer, DH Huson, B Schölkopf, M Nordborg, G Rätsch, JR Ecker & D Weigel. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thalianaScience 317: 338-342 (2007)(doi:10.1126/science.1138632). (*these authors contributed equally to this work)

Toomajian C, TT Hu, MJ Aranzana, C Lister, C Tang, H Zheng, K Zhao, P Calabrese, C Dean & M Nordborg. A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome. PLoS Biol 4: e137 (2006); published online 25 April 2006 (doi:10.1371/journal.pbio.0040137).

Nordborg, M, TT Hu, Y Ishino, J Jhaveri, C Toomajian et al. The pattern of polymorphism in Arabidopsis thalianaPLoS Biol 3: e196 (2005); published online, 24 May 2005 (doi:10.1371/ journal.pbio.0030196).