Charkowski, Amy - Current Faculty Profile
Amy Charkowski

682 Russell Laboratories
1630 Linden Dr
Madison, WI 53706

Faculty Profile Tab

Education and Training

Ph.D. Cornell University, Plant Pathology

B.S. Univ. Wisconsin-Madison, Biochemistry/Plant Pathology


Professional Appointments

1998 - 2001  Research Microbiologist, Food Safety and Health Research Unit, Albany California Agricultural

Research Service, United States Dept. Agriculture (ARS, USDA)

2001 - 2008  Assistant Professor, Dept. Plant Pathology, University of Wisconsin-Madison

2008 - 2013 Associate Professor, Dept. Plant Pathology, University of Wisconsin-Madison

2013-present Professor, Dept. Plant Pathology, University of Wisconsin-Madison



2005-present   UW-Madison Middle East Studies Program

2007-present   UW-Madison Microbiology Doctoral Training Program

2012-present   UW-Madison Agroecology Program


Administrative Responsibilities

2001-present Administrative Director, Wisconsin Seed Potato Certification Program (WSPCP)

The WSPCP is an approximately $1,000,000/yr program that includes management of a tissue culture laboratory and an early generation seed potato farm that produces 2,000,000 lbs of potatoes of over 20 varieties annually, and an inspection program that is responsible for certification of approximately 400 lots of potatoes on 27 farms, annually. Approximately $240 million in yearly national potato production can be traced back to this program.


Recent Honors and Awards

2005    Wisconsin Potato and Vegetable Grower Research of the Year

2011    American Phytopathological Society Syngenta Award


Former Graduate Students

Mee-Ngan Yap, Ph.D., degree awarded 2007, assistant professor in the Dept. Biochem and Mol. Biology at Saint Louis University School of Medicine

Courtney Jahn, Ph.D., degree awarded 2008, assistant professor in the Dept. of Bioagricultural Sciences and Pest Management at Colorado State

Daniel Gerhardt, M.S., degree awarded 2009, researcher at Nimblegen

Hye-Sook Kim, Ph.D. degree awarded 2010, postdoc at the University of Chicago

Maria del Pilar Marquez Villavincencio, Ph.D. degree awarded 2010, family leave

Jeff Olsen, M.S. 2008-2010, employed at EpiCentre

Chakradhur Mattupalli, Ph.D. degree awarded 2013, researcher at PhylloTech  

Cliff Hogan, Ph.D. degree awarded 2013, USDA-ARS postdoc


Former Postdoctoral trainees

Jeri Barak 2000-2001, assistant professor at University of Wisconsin-Madison

Ralph Reedy 2004-2007, Wisconsin Crime Lab, deceased

Mark Nakhla 2004-2006, USDA-APHIS scientist

Mafmudije Selimi 2006-2009, pre-health majors advisor, UW-Madison

Ruth Genger 2007-2009, academic staff, UW-Madison


Visiting international students/scholars

Kasia Janczur – visiting student from Poland (Jan-June 2004)

Eva Haenssler – visiting student from Germany (Oct-Nov 2004)

Iris Yeddidia – visiting scientist from Israel (July 2005)

Ahmed Gomaa – visiting scientists from Egypt (Nov-Dec 2005)

Ali Mohamed Zaid – visiting scientists from Egypt (Nov-Dec 2005)

Fernando de la Calle – visiting scientist from Peru (Jan-July 2006)

Jiraphan Sopee – visiting student from Thailand (June-Aug 2008)

Adil El-Aouad – visiting student from Morocco (Sept-Nov 2008)

Ebtisam Mohammed Al Ali – visiting scientist from Kuwait (Feb 2010; Feb 2012)

Jose Caram de Souza Dias - visiting scientist from Brazil (April-Aug 2012)

Jeffry Dorgans - visiting student from France (June-Aug 2012)


Recent Scientific Service

2010-2012       Senior Editor for Plant Disease

2007-2013       Biology Chair for American Phytopathological Society Annual Meeting Board

2013-present  Director, American Phytopathological Society Annual Meeting Board

I am the administrative director of the Wisconsin Seed Potato Certification Program, which has been part of the Department of Plant Pathology, College of Agricultural and Life Sciences, University of Wisconsin - Madison since 1913. The seed potato program includes a certification program and an early generation seed potato farm, known as the Lelah Starks Elite Foundation Seed Potato Farm. Approximately 7.5% of the potatoes produced in the United States can be traced back to this program. Potato (Solanum tuberosum) is an exciting and important crop to work with since it is the fourth largest food crop in the world and the leading vegetable crop in the United States.

My lab group's research has close ties to seed potato certification and production. Photos of our work are here and our current projects are described below:

Control of soft rot diseases. These two genera cause soft rot, wilt and blackleg diseases in numerous crops, ranging from potatoes to corn to African violets. These diseases are characterized by water soaked lesions and decayed plant tissue that may turn brown or black. Dickeya and Pectobacterium have long served as models for plant-bacterial interactions and much is known about the plant cell wall degrading enzymes that these pathogens use to cause symptoms in plants. In contrast, relatively little is known about how they survive and spread in the environment, what genes contribute to host specificity in these genera, and how plants resist these pathogens. In the past, my lab group studied the diversity and virulence of these pathogens. Currently, PhD student Isael Rubio is focusing on bacterial volatiles that contribute to virulence and MS student Jenna Lind is mapping genes in potato that provide resistance to Pectobacterium. MS student Eric Bietila is working on a related project to better understand volatile molecules produced by soil-borne bacteria. Their work is funded by a USDA Hatch grant, by the WPVGA, and by an NSF graduate fellowship.

Control of Potato viruses Y. This virus is the main cause of rejection of seed potato lots in North America. It causes a wide range of symptoms that depend on the virus strain, potato variety, and environment, including mosaic, leaf drop, and tuber necrosis symptoms. PhD student Ana Cristina Fulladolsa is studying practical methods to control this virus, including novel seed potato production and virus detection methods. She is also working with the UW-Madison potato breeding program to aid in adoption of marker assisted selection for PVY resistance in potato. Her work is funded by a USDA-SCRI grant and by the WPVGA.

Control of Common Scab. This disease is the most common reason for culling potatoes on organic farms in Wisconsin and farmers have few control options. In collaboration with the Jansky Lab, PhD student Christina Allen is developing markers for common scab resistance genes in potato and studying mechanisms of resistance to common scab. 

Organic potato production. There are about 250 organic farms growing potatoes in Midwest, with about 130 of these farms located in Wisconsin. Healthy seed potatoes for specialty and heirloom varieties favored by these farmers and their customers are difficult to obtain. Since 2007, in a project led by scientist Ruth Genger, we have been trialing organically-approved control methods for pests and pathogens important in seed potato production on organic farmers. We have found that seed potatoes can be effectively grown on organic farms in the Midwest. In order to better trial heirloom and speciatly varieties, we have placed nearly 100 high priority lines into tissue culture and produced disease-free minitubers of these lines for field trials on local organic farms. Our goal is to identify varieties that are robust on organic farms and resistant to or tolerant of pests and pathogens common on organic farms. This work was initiated with funding from the Organic Farms Research Foundation and Organic Valley and is now supported by funding from USDA-OREI, the CERES Trust, and USDA-SARE. Yield trial reports or variety lists from this work are available upon request. 

  • Pl Path 375/875 Organic and Urban Agriculture (Summer 2011; Spring 2013)
  • Co-taught Pl Path 558 Biology of Plant Pathogens (Spring 2011; Spring 2013)
  • Pl Path 923 Plant Pathology Seminar Series (Fall 2013; Spring 2014)
  • Co-taught MMI 810 Topics in Microbiology (Fall 2013)


Guenthner, J. F., A. Charkowski, R. Genger, and G. Greenway. 2014. Varietal differences in minituber production costs. Amer. J. Potato Res. In press

Chakradhur, M., J. D. Glasner, and A. O. Charkowski. 2014. A draft genome sequence reveals the Helminthosporium solani arsenal for cell wall degradation. Amer. Potato J. In press. 


Frost, K., R. K. Groves, and A. O. Charkowski. 2013. Integrated control of potato pathogens through seed potato certification and provision of clean seed potatoes. Plant Dis. 97:1268-1280.  

Hogan, C. B. M. Mole, S. R. Grant, D. K. Willis, and A. O. Charkowski. 2013. The type III secreted effector DspE is required early in Solanum tuberosum leaf infection by Pectobacterium carotovorum to elicit cell death, and requires Wx(3-6)D/E motifs. PloS One. 8(6): e65534.

Mattupalli, C., R. K. Genger, A. O. Charkowski. 2013. Evaluating incidence of Helminthosporium solani and Colletotrichum coccodes on asymptomatic organic potatoes and screening potato lines for resistance to silver scurf. Amer. J. Potato Res. 90:369-377 

Fulladolsa, A. C., R. Kota, and A. O. Charkowski. 2013. Optimization of a chemiluminescent dot-blot immunoassay for detection of potato viruses. Amer. J. Potato Res. 90:306-312

Kwan G., A. O. Charkowski and J. D. Barak. 2013. Salmonella enterica suppresses Pectobacterium carotovorum subsp. carotovorum population and soft rot progression by attenuating environmental alkalinization. MBio 4(1):e00557-12


Charkowski, A. O. et al. 2012. The role of secretion systems and small molecules in soft-rot Enterobacteriaceae. Ann. Rev. Phytopathol. 50:425-449.

Charkowski, A. O. “Control of Soft Rot in Potato” 2012. Focus on Potato, Plant Disease Management Network. Recorded July 2012. http://www.plantmanagementnetwork.org/edcenter/seminars/potato/softrot/

Charkowski, A. O. “Early Generation Seed Potato Production” Focus on Potato, Plant Disease Management. Recorded July 2012. http://www.plantmanagementnetwork.org/edcenter/seminars/Potato/EarlyGene...

Babujee, L. J. Apodaca, V. Balakrishnan, P. Liss, P. J. Kiley, A. O. Charkowski, J. D. Glasner and N. T. Perna. 2012. Evolution of the metabolic and regulatory networks associated with oxygen availability in two phytopathogenic enterobacteria. BMC Genomics 13:110.

Verchot-Lubicz, J., D. H. Halterman, and A. O. Charkowski. 2012. Potato, Viruses, and Seed Certification in the USA to Provide Healthy Propagated Tubers. Pest Technology.


Jahn, C. E., D. A. Selimi, J. D. Barak, and A. O. Charkowski. 2011. TheDickeya dadantii biofilm matrix consists of cellulose nanofibers and is an emergent property dependent upon the type III secretion system and the cellulose synthesis operon. Microbiology 157: 2733-2744.

Marquz-Villavincencio, M. P., B. Weber, R. A. Witherell, D. K. Willis, and A. O. Charkowski. 2011. The 3-hydroxy-2-butanone pathway is required for Pectobacterium carotovorum pathogenesis. PLoS ONE 6(8): e22974. doi:10.1371/journal.pone.0022974.

Kim, H.-S, P. Thammarat, P., S. A. Lommel, and A. O. Charkowski. 2011. Pectobacteriumcarotovorum elicits plant cell death with DspE/F, but does not suppress callose or induce expression of plant genes early in plant-microbe interactions. Mol. Plant-Microbe Interact. 24:773-786

Glasner et al. 2011. Genome sequence of the plant pathogenic bacterium Dickeya dadantii 3937. J. Bacteriology. Published ahead of print on 7 Jan 2011

Marquez-Villavincencio, M. P., R. L. Groves, and A. O. Charkowski. 2011. Soft rot disease severity is affected by potato physiology and Pectobacterium taxa. Plant Dis. 95:232-241


Allen, C. Z., A. F. Bent, and A. O. Charkowski. 2009. Underexplored niches in research on plant pathogenic bacteria. Plant Physiology. 150:1631-1637., *chosen to be feature article reprinted as a Feature Article on the APS Net website

Kim, H.-S., B. Ma, N. T. Perna, and A. O. Charkowski. 2009. Prevalence and virulence of natural type III secretion system deficient Pectobacterium strains. Appl. Environ. Microbiol. 75:4339-4349.

Charkowski, A. O. 2009. Decaying Signals: Will understanding bacterial-plant communications lead to control of soft rot? Curr. Opin. Biotechnol. 20:178-184.

Kinscherf, T. G., M.-N. Yap, A. O. Charkowski, and D. K. Willis. 2009. CHEF procedures: a rapid high-temperature method for sample preparation, a high voltage HEPES buffer system, and the use of Nusieve agarose. J. Rapid Meth. Microbiol. Automation. Microbiol. 17:9-16

Li, Y., Q.Peng, D. Selimi, Q. Wang, A. O. Charkowski, X. Chen, and C.-H. Yang. 2009. The plant phenolic compound p-coumaric acid represses the Dickeya dadantii type III secretion system. Appl. Environ. Microbiol. 75:1223-1228.


Copas, M. E., A. J. Bussan, M. J. Drilias, and A. O. Charkowski. 2008. Influence of compaction and subsoil tillage on soil conditions and pink eye. Amer. Potato J.  85:342-352.

Glasner, J. D., M. Marquez-Villavicencio, H.-S. Kim, C. E. Jahn, B. Ma, B. S. Biehl, A. I. Rissman, B. Mole, X. Yi, C.-H. Yang, J. L. Dangl, S. R. Grant, N. T. Perna, A. O. Charkowski. 2008. Niche-specificity and the variable fraction of the Pectobacterium pan-genome. Mol. Plant-Microbe Interact. 12:1549-1560.

Jahn, C. E., D. K. Willis, and A. O. Charkowski. 2008. The flagellar sigma factor FliA is required for Dickeya dadantii virulence. Mol. Plant-Microbe Interact. 21:1431-1442.

Jahn, C. E., A. O. Charkowski, and D. K. Willis. 2008. Evaluation of isolation methods and RNA integrity for bacterial RNA quantitation. J. Microbiol. Meth. 75:318-324.

Yang, S., Q. Zhang, Q. Peng,, X. Yi, C. J. Choi, R. M. Reedy, A. O. Charkowski, and C.-H. Yang. 2008. Dynamic regulation of GacA in type III secretion system, pectinase gene expression, pellicle formation, and pathogenicity of Dickeya dadantii (Erwinia chrysanthemi 3937). Mol. Plant-Microbe Interact. 21:133-142.

Yap, M.-N., C.-H. Yang, and A. O. Charkowski. 2008. The response regulator HrpY of Dickeya dadantii 3937 regulates virulence genes not linked to thehrp cluster. Mol. Plant-Microbe Interact. 21:304-314.