Selecting for Resilience in Low-input Potato Cropping Systems: Connecting Farmers and Breeders with the Genetic Resources of an Underutilized Potato Germplasm Collection

Final Report for LNC12-339

Project Type: Research and Education
Funds awarded in 2012: $190,512.00
Projected End Date: 12/31/2016
Region: North Central
State: Wisconsin
Project Coordinator:
Dr. Amy Charkowski
University of Wisconsin-Madison
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Project Information


The goal of our organic potato research program is an integrated, participatory potato breeding, variety evaluation and seed potato production system that serves the needs of the approximately 220 organic and low-input potato farmers in the Midwest. Modern potato varieties have been bred using conventional practices and may not be suited for organic and low input production systems. We evaluated heirloom potato varieties from the Seed Savers Exchange (SSE)potato collection for their immediate value in low-input and organic potato cropping systems in a participatory trial. The 12 participating farmers evaluated variety performance with guidance from researchers, focusing on traits such as plant vigor, pest and disease resistance, yield, taste and market appeal. Several heirloom potato varieties that exhibited higher yield or other attractive characteristics for marketing were identified. Additionally, we used single nucleotide polymorphism markers to characterize the diversity of a subset of the SSE potato collection and identify potential duplicate accessions.


Organic potato growers are in need of access to a greater diversity of varieties, and to varieties specifically adapted to organic production systems. Modern breeding programs serve high-input conventional farms, and produce varieties that are not well adapted to low input farming systems. In our conversations with Wisconsin organic growers, recurring themes have been their need for varieties suited to organic production with characteristics such as low nitrogen requirement, weed suppression, and resistance to insect pests and diseases. Heirloom varieties released before the advent of chemical fertilizers and pesticides are likely to be more suited to organic production. Characterization of heirloom varieties in organic growing environments is a necessary step to enable organic growers to make informed variety choices and to allow breeders to select suitable parents to breed cultivars suitable for organic farming systems. On-farm characterization by growers, in collaboration with UW researchers, will generate variety performance data that is directly relevant to grower needs.

Most potato breeding programs focus on traits important for the processing industry, since this is the largest market for conventional potatoes. Attributes that are important in low input systems such as organic farms, which are more likely to target local fresh markets, are rarely addressed. Increasing consumer interest in the flavor and nutritional qualities of specialty potatoes, especially pigmented cultivars, gives organic growers who specialize in these varieties a marketing edge. By evaluating potato varieties throughout the growing and storage season, and incorporating taste panels, nutritional analyses, and customer reaction into these evaluations, our farmer-researcher team will generate variety descriptions that are highly relevant to low input organic farms in the Midwest, and that include critical characteristics to assist organic growers in making variety choices and in marketing. An on-farm participatory approach to variety evaluation will generate information relevant to farmers, and is anticipated to increase the rate of adoption of better-performing varieties by farmers.

Germplasm collections are essential resources for continued crop improvement through breeding. Although the large Seed Savers Exchange (SSE) potato collection includes many rare heirloom varieties unavailable from any other source, this resource is underutilized by growers and breeders alike. This underuse is in large part due to the accumulation of yield-limiting levels of viral contamination during field-based vegetative propagation (tuber to tuber). A recent collaboration between SSE and the UW-Madison Charkowski laboratory has focused on eradicating pathogens from a subset of 100 potato varieties as tissue culture plantlets, and training SSE staff to continue pathogen eradication. Our proposal affords the first opportunity to characterize the true varietal potential of this germplasm in a pathogen-free state.

The single nucleotide polymorphism (SNP) marker platform recently developed as part of the Solanaceae Coordinated Agricultural Project (SolCAP) has massively expanded the capacity to evaluate the genetic diversity of variety collections, and to map variety traits such as disease resistance to genetic locations, an essential tool for directed plant breeding. Our genotypic characterization of SSE germplasm will utilize the SNP marker platform, allowing us to tap into the huge database and resources of this cross-disciplinary project. In particular, ongoing research to associate SNP markers with traits of importance in potato production will allow breeders to use the SNP data generated by our project to select for traits beneficial in low input production systems. Twenty varieties in the SSE collection that are suspected to be duplicates have been identified. These varieties will be evaluated with a dense array of SNP in order to confidently determine whether they are identical. This information will allow SSE to reduce redundancy in their potato collection, so that limited resources can be used more efficiently.

Project Objectives:

Our objectives were to (1) evaluate heirloom potato varieties for their immediate value in low-input potato cropping systems, and for the resilience of their performance across multiple environments; and (2) characterize the genetic diversity of heirloom potato varieties to determine the potential for crop improvement through a breeding program for low-input cropping systems.


Click linked name(s) to expand
  • Dr. Ruth Genger
  • Dr. Shelley Jansky
  • Dr. Tim Johnson


Materials and methods:

Potato varieties from the SSE collection were evaluated in on-farm trials involving a network of 12 Wisconsin farmers. A central-satellite model was used, adapting methods used by other participatory research workers. We maintained a central site at one location (West Madison Agricultural Research Station) in which all varieties were grown and evaluated in randomized replicated trials. Other farms acted as satellite sites, evaluating a subset of varieties as single replicates. To maximize the relevance of variety evaluations to farmers, and to sample a wide range of environmental and management conditions, trial plots were planted and managed by participating farmers according to their usual practices.  Farmers evaluated variety performance with guidance from researchers, focusing on traits including plant vigor, pest and disease resistance, yield, taste and market appeal.

DNA for 154 SSE cultivars was isolated from tissue culture plants and submitted to the SolCAP genotyping facility at Michigan State University for genotyping using a single nucleotide polymorphism (SNP) marker platform. Joseph Coombs (MSU) performed initial hierarchical cluster analysis to generate a phylogenetic tree, and pairwise comparisons to identify identical and closely related genotypes.   

Research results and discussion:

Objective 1. Each farmer selected a subset of varieties of interest from 37 varieties in 2013, 60 varieties in 2014, and 41 varieties in 2015, including check varieties that were grown at each farm. All varieties were grown in replicated trials on organic land at the West Madison Agricultural Research Station. Although several farmers submitted observations on plant vigor, pest and disease resistance, and taste, the most consistently submitted data was for total and marketable yield.

Varietal performance for yield varied widely among sites. This observation was confirmed by ANOVA analysis of yield, using a linear mixed model which showed that “farm” had a significant impact on both total and marketable yield. Varieties also differed significantly for both total and marketable yield (Figure 1). Three heirloom varieties performed better than standard check varieties for marketable yield: Candy Stripe and Early Bangor (red, compared to Dark Red Norland) and Purple Chief (blue flesh, compared to Adirondack Blue). Major causes of unmarketability were common scab, averaging 27% yield loss; greening, averaging 28% yield loss; and shape defects, averaging 19% yield loss. Heirloom varieties that yielded as well as check varieties and were mentioned by growers as having marketing appeal included Yellow Rose (red), Charlotte and Epicure Banana (yellow), Purple Valley and Fenton Blue (blue flesh), Abnaki (white), Elmers Blue and Papa Cacho (fingerlings) and Australian Crawlers, Gui Valley, Scotia Blue, Mark Varshaw and Cowhorn (other specialty).

Objective 2. Data was received for 147 cultivars (7 were excluded for high No-Call rates) for 4859 single nucleotide polymorphisms (SNPs). A phylogenetic tree was generated based on hierarchical cluster analysis (Figure 2), giving an indication of the degree of relatedness among cultivars. Varieties that were likely to be duplicates based on observed phenotype or name were compared. Seventeen varieties were found to fall into 6 genotypic groups, indicating that these genotypes are duplicated in the collection. Groups identified include the following varieties: Austrian Crescent III, Fingerling, German Lady Finger, Corahila, Fingerling Salad (group 1); Black Toes, MacIntyre Blue, Seweca Horn (group 2); Black Russian, Purple (group 3), Blue Eye, Fenton Blue (group 4); Bug and Blight Proof, Poorlander, Red Bugless (group 5); and Stefanyshin’s Yellow-Fleshed, Yello Fleshed (Group 6).

The Douches research group at Michigan State University is currently genotyping the remaining 575 potato varieties in the SSE collection. We plan to collaborate on analysis of this genotypic dataset so that information on the full collection can be used. We will use the Shannon index, one of the most widely used diversity measures, to evaluate diversity based on the SNP data set. Genetic similarity among clones will be calculated using Jaccard’s Similarity Index (JSI). If further groups of clones with no genotypic differences are found, this information can be used by SSE to choose which varieties to retain in the collection. While eliminating duplicates will allow more resources to be devoted to preserving the remaining unique varieties, it is important to note that somaclonal variants can have identical SNP profiles but differ phenotypically. Phenotypic data collected in our greenhouse and field experiments will be provided to SSE to help with choices of varieties to retain or eliminate.



Research conclusions:

Feedback from participating farmers indicated an appreciation of the value of variety trials on-farm, and satisfaction with the clarity and organization of evaluation materials. Additionally, farmers showed substantial increases in understanding of ways in which potato varieties differ, and how these differences can be assessed. In particular, many farmers showed a greater awareness of specific potato pests and diseases including potato leafhopper, a damaging pest with symptoms commonly mistaken for environmental stress. Farmers also showed increased comfort identifying tuber defect diseases including common scab, silver scurf and black scurf. Farmers feedback encouraged us to modify our evaluation materials to reduce focus on specific disorders (for which data can be collected at replicated trials on the research station) and increase focus on questions that determine the desirability of a variety for continued production, e.g. tuber attractiveness, marketability, eating quality, storability.

Our genotypic analysis of 154 SSE varieties provided a preliminary snapshot about the full collection of 642 varieties, and allowed SSE to find partners to genotype the remaining varieties so that a full analysis can be performed. This will enable SSE to make final decisions on eliminating duplicate varieties, and, combined with phenotypic data, will allow prioritization of varieties for elimination of viral infections and field evaluation. Potato breeders will be able to access disease-free seed stocks, select varieties with valuable traits, and maximize diversity in their breeding crosses by avoiding combinations of individuals that are highly related.

Undergraduate students with interests in organic agriculture and participatory research participated in in-season variety evaluations and evaluation of harvested tubers at West Madison Agricultural Research Station and several farms. Student feedback indicated that they developed a greater understanding of the diverse markets served by organic farmers, including direct market, CSA, retail, and wholesale markets, and the differing requirements of these markets for tuber quality. In addition, students developed an understanding of the complementarity between data collection by farmers and researchers, and the value of combining varietal assessment through replicated trials with assessment of varietal suitability on working farms.

Economic Analysis

Proposal did not include economic analysis.

Farmer Adoption

All 12 farmers involved in this study have indicated a desire to continue trialing potato varieties, and additional farmers have contacted us wishing to be involved in potato trialing. Farmers differ in their interest in heirloom/specialty varieties versus more standard varieties (white, russet, red, yellow) and these differences are mostly attributable to differences in markets served, with farmers who market primarily through CSAs having the most interest in unusual potato types. Feedback from direct market farmers indicates that a few unusual varieties increase interest at farmers markets, but that demand is mostly for more standard types. Three farmers have conducted public potato tastings by working with local chefs, in addition to their own evaluations of potato taste.

Participation Summary

Educational & Outreach Activities

Participation Summary

Education/outreach description:

Conference presentations

Genger, R.K. Potatoes: Keeping diversity in the field through participatory plant breeding. Workshop at Indigenous Farming Conference, Callaway MN, March 2016.

Genger, R.K. On-farm Conservation of Genetic Diversity and Organic Plant Breeding. Panel presentation at Organic Seed Growers Conference, Corvallis OR, January 2016.

Genger, R.K., R. Groves, S.H. Jansky, D.I. Rouse and A.O. Charkowski. Improving the health and productivity of organic potato crops through participatory research. Talk at American Phytopathological Society annual meeting, Pasadena CA, August 2015.

Genger, R.K., R. Groves, S.H. Jansky, D.I. Rouse and A.O. Charkowski.  Heirloom and specialty potatoes: Selecting varieties for organic production systems. Talk at Wisconsin Potato and Vegetable Growers Association Grower Education Conference, Stevens Point WI, February 2015.

Genger, R.K. Growing potatoes organically. Workshop at “Notes from the Underground: Advanced Workshop on Organic Management of Root & Tuber Crops”, Michael Fields Agricultural Institute, East Troy WI, February 2015.

Genger, R.K., R. Groves, S.H. Jansky, D.I. Rouse and A.O. Charkowski.  Developing a seed potato system for the needs of Midwest organic farmers: a participatory approach. Talk at Organic Agriculture Research Symposium, La Crosse WI, February 2015.

Genger, R.K. On Water, Seeds, and Second Chances: Women’s Roles in Sustainable Agriculture and Seed Systems. Panel presentation at Wisconsin and Midwest Women’s, Gender, and LGBTQ Studies Conference, River Falls WI, October 2014.

Genger, R.K., R. Groves, S.H. Jansky, D.I. Rouse and A.O. Charkowski. Building a healthy organic seed system for potatoes through farmer-researcher partnerships. Organic Agriculture Research Symposium, La Crosse WI, February 2014. Oral presentation.

Genger, R.K. and D.I. Rouse. Organic Potato Production: From Starts to Storage. MOSES Organic Farming Conference, La Crosse WI, February 2014. Workshop presentation.

Genger, R.K., R. Groves, S.H. Jansky, D.I. Rouse and A.O. Charkowski. Participatory evaluation of potato varieties on organic farms: opportunities for education and research. 1006th Annual Meeting of the American Phytopathological Society, Minneapolis MN, August 9-13 2014. Poster presentation.

Genger R.K., R. Groves, S.H. Jansky, D.I. Rouse and A.O. Charkowski. On-farm evaluation of heirloom potato varieties. MOSES Organic Farming Conference, La Crosse WI, February 2014. Poster presentation.

Genger, R.K., K. Becker, J. Dawson. More Trial, Less Error: Picking Suitable Crops for your Farm. Workshop at Growing Power Urban and Small Farms conference, Milwaukee WI, November 2014.

Genger, R.K., Malek, C. and Charkowski, A.O. Growing Great Potatoes: Insights from variety trials on Wisconsin organic farms. Organic Farming Conference, February 21-23 2013. Workshop presentation.

Project Outcomes


Areas needing additional study

A potential limitation of this project’s continuing impact after the funding period is the need for a supply of high quality seed potatoes to meet the demand from growers for SSE varieties that perform well in evaluations. Previous and ongoing research by Dr. Charkowksi and the major participants, Drs. Rouse and Genger, focuses on small scale production systems for on-farm multiplication of high quality seed potatoes. The single Wisconsin organic producer of certified seed potatoes had adopted a scaleable system developed by our research group to produce first year seed potatoes from greenhouse grown minitubers. Continued on-farm research and outreach to increase seed potato production for varieties suited to low input potato production is needed.


Additionally, breeding for resistance to diseases including Potato Virus Y and late blight is needed to produce potato varieties that are more likely to produce high quality disease free tubers under organic management. Once SSE has finalized decisions about eliminating duplicates from their potato collection, additional varieties can be prioritized for virus elimination leading to field evaluation.

Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.