Diversity Prospecting for an Open Source Plant Breeding Framework

Final Report for GNC13-175

Project Type: Graduate Student
Funds awarded in 2013: $9,945.00
Projected End Date: 12/31/2015
Grant Recipient: University of Wisconsin- Madison
Region: North Central
State: Wisconsin
Graduate Student:
Faculty Advisor:
Irwin Goldman
University of Wisconsin- Madison
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Project Information

Summary:

We examined what freedom to operate (FTO) looks like in a single crop: carrot, beginning with a set of 142 commercially available carrot cultivars. Two datasets were collected: (1) phenotypic diversity on root and shoot characteristics of each cultivar and (2) an accounting of any form of legal protection or restrictions associated with each cultivar that may impact future breeding efforts. We found that there were significant differences for many of the phenotypic traits measured between the group of cultivars that had FTO compared to those cultivars that did not have FTO.

Introduction:

Several recent reports have noted the importance of maintaining and utilizing plant genetic resources and the dangers of diversity loss in crop plants (Lauer et al. 2012, Fedoroff et al. 2010, Esquinas-Alcazar 2005, Commission on Genetic Resources for Food and Agriculture 2010). Access to crop germplasm resources is arguably one of our most important public resources. The diversity within crop species is what we as humans depend on to ensure food security and resiliency of our agricultural system. With the increasing uncertainty of weather events due to a changing climate, access to the insurance that genetic diversity provides will be essential to developing new cultivars that are resilient under adverse conditions (Tester and Langridge 2010). However, our germplasm resources have seen a number of important threats in recent decades. Over the past century, crop plant germplasm resources have increasingly moved from a freely available public resource into proprietary structures managed by the private sector. Plant breeding, in its most fundamental form, relies on human directed selection in genetically variable populations of plants. In order to be able to utilize the power of selection, genetic diversity within the population under selection is essential. People have been practicing plant breeding since the domestication of crop plants and selection for increased yields, improved flavor and adaptation to new disease and environmental conditions has resulted in all of the plant-based foods and fibers that we utilize today. With the increase in proprietary protection for crop plants, the exchange of germplasm that will be necessary to develop new cultivars that can feed a growing population, perform under low-input conditions, and are resilient in the face of a changing climate is threatened.

Concerns over difficulties accessing genetic resources have led to the creation of the Open Source Seed Initiative (OSSI) by a working group of plant breeders, farmers, non-profit agencies, seed advocates, and policy makers. OSSI seeks to maintain fair and open access to plant genetic resources worldwide and foster innovative plant breeding to develop productive and resilient cultivars. Critical to supporting these goals is the development of an open source mechanism for crop plant germplasm to be able to move between and among farmers, plant breeders, seed companies and gardeners in a viral fashion without restrictions on further breeding.  

One of the challenges to the development of a useful open source framework will be determining the genetic diversity of germplasm currently in use and what proportion of that diversity is freely available to use in breeding. Using carrot as a model crop, this project seeks to describe the genotypic and phenotypic diversity currently distributed in the United States and to determine what proportion of that diversity is legally protected and what is freely available for future breeding. With farmer input, we will then begin to develop populations that represent this available diversity. We will distribute these cultivars to interested parties under one of the OSSI open source licenses. This project will insure that diversity remains available for everyone to access, as it is this diversity upon which the future of a successful, sustainable agriculture depends.

Historically, farmers used their own seeds saved from previous harvests to produce grain the following year. Farmers decided what seeds to plant, whom to share seeds with, and facilitated the sharing and dissemination of seed over a wide area (Salazar et. al. 2007). Access to a wide pool of germplasm has facilitated the development of new and resilient cultivars and helped maintain genetic diversity within agriculture systems (Kloppenburg 2010). However, the 20th century has seen a dramatic transition in the distribution of plant germplasm development and release from a freely available resource, primarily in the public sector, into proprietary structures managed largely by the private sector (Aoki 2009). Plant breeding as a scientific discipline began in the early 20th century with land grant institutions established plant breeding programs to develop new crop cultivars for farmers in different parts of the country. While public plant breeding departments still exist, the role of these programs has largely shifted from production of new cultivars toward basic genetic research. The invention of hybrid corn in the 1930’s and the application of biotechnology to crop plants in the 1970’s led to increasingly restrictive intellectual property rights utilization and legislation. The accrual of patent protections for biological organisms has resulted in significant changes in the seed industry. Intellectual property legislation passed in the United States over the past eighty years has increased proprietary rights to genetic material, leading to consolidation of the global seed industry and significantly decreasing breeders’ and farmers’ sharing of and access to germplasm (Kloppenburg 2004). These proprietary restrictions threaten the exchange of germplasm necessary to the development of new cultivars capable of feeding a growing world population and that are resilient to more extreme environmental stressors caused by climate change. Several people have called for the development of an open source system for plant germplasm, similar to that developed by software programmers that would provide an alternative path for germplasm release to maintain unrestricted access to seed for farmers as well as for breeding and research enterprises. (Aoki 2009, Bragdon 2005, Jefferson 2006, Kloppenburg 2010, Srinivas 2006). This project will examine questions of available diversity and will determine key issues in the development of an open source framework for plant germplasm.

Literature Cited:

Aoki, K. 2009. “Free seeds, not free beer”: Participatory plant breeding, open source seeds, and acknowledging user innovation in agriculture. Fordham Law Review, 77(5): 2275-2310.

Bragdon, S. 2005. Open source mechanisms: The example of BIOS. Generation Challenge Programme Conference 2005.

Commission on Genetic Resources for Food and Agriculture. 2010. The second report on the state of the world’s plant genetic resources for food and agriculture. FAO, Rome.

Esquinas-Alcazar, J. 2005. Protecting crop genetic diversity for food security: political, ethical and technical challenges. Nature Reviews Genetics 6 (946-953).

Fedoroff, N.V. et al. 2010. Radically rethinking agriculture for the 21st century. Science 327 (833-834).

Jefferson, R. 2006. Science as social enterprise: The CAMBIA BiOS initaitve. Innovations: Technology, Governance, Globalization, 1:11-42.

Kloppenburg, J., 2004. First the Seed: The Political Economy of Plant Biotechnology, 1492–2000. Reissued with a new preface and an additional final chapter, ‘Still the Seed’. Madison, WI: University of Wisconsin Press.

Kloppenburg, J. 2010. Impeding dispossession, enabling repossession: biological open source and the recovery of seed sovereignty. Journal of Agrarian Change 10(3): 367-388.

Lauer, J.G. et al. 2012. The scientific grand challenges of the 21st century for the Crop Science Society of America. Crop Science, 52 (1003-1010).

Salazar, R., N. Louwaars and B. Visser, 2007. ‘Protecting Farmers’ New Varieties: New Approaches to Rights on Collective Innovations in Plant Genetic Resources’. World Development, 35 (9): 1515-28.

Srinivas, K.R. 2006. Intellectual property rights and bio commons: Open source and beyond. International Social Science Journal, 58: 319 -334

Tester, M. and P. Langridge. 2010. Breeding technologies to increase crop production in a changing world. Science, 327 (818-822).

Project Objectives:

There are several distinct outputs that will result from this project including several peer reviewed journal articles, diverse populations of carrot, and data on the phenotypic and genotypic diversity present in commercially available carrot cultivars. We plan to publish on the level of diversity present in commercially available carrot cultivars in the US, specifically focusing on what proportion of that diversity is available to use and what is protected through intellectual property rights. After analyzing this diversity and determining what is available, we will develop several populations based on market class of carrot. These populations will be released under the OSSI Pledge, ensuring that the diversity represented by these populations will remain available for future use. In addition, we will develop protocols for analyzing diversity and intellectual property rights protection that could be applied to other crops. We hope that these outputs will inform the development of OSSI as an organization and increase access to and sharing of plant genetic resources.

Cooperators

Click linked name(s) to expand
  • Eric Elderbrock
  • Irwin Goldman
  • Steve Pincus

Research

Materials and methods:

Through consultation with carrot breeders in the public and private sectors as well as through seed catalogs, we were able to obtain seed of 142 hybrid, open-pollinated and heirloom carrot cultivars that were commercially available in the United States in 2013. Seed of each cultivar was sown in replicated plots on certified organic land at Tipi Organic Produce in Evansville, WI (42.78oN, 89.30oW) and Elderberry Hill Farm in Waunakee, WI (43.18oN, 89.38oW) in the summers of 2013 and 2014.

At Tipi Organic Produce, carrots were planted in 3.7 m rows with three rows to each 1 m bed and 1.2 m alleys between ranges. At Elderberry Hill Farm, carrots were planted in 2.5 m rows with three rows to each 1m bed and 0.6 m alleys between ranges. Carrots were planted using a Planet Junior planter (Planet Junior, Tunkhannock, PA) fitted with a cone seeder attachment. Experimental design was a randomized complete block design with two blocks at Tipi Organic Produce and one block at Elderberry Hill Farm. In 2013, carrots were planted on July 1 and harvested between October 8-11 at Tipi Organic Produce and planted on July 3 and harvested on October 6 at Elderberry Hill Farm. In 2014, carrots were planted on June 26 and harvested between September 23-26 at Tipi Organic Produce and planted on July 10 and harvested between October 7-10 at Elderberry Hill Farm. Carrots were thinned depending on market class. Spacing was approximately 30 plants per meter for dicer types, 60 per meter for cellos and novel colors, and 120 per meter for cut & peel types. In the field, the following characteristics were measured (Table 1): petiole anthocyanin, leaf growth habit, top height, top strength (1-5 scale) and bolting.

Immediately after harvesting, carrots were packed in paper bags with wood shavings. The paper bag was then placed in a plastic bag with several holes. Roots were stored at 4oC in the dark until the time of sampling, within 5 weeks of harvest. At sampling, the following were measured on 10 carrots from each row (Table 1): Red/purple on shoulder, green on shoulder, root length, root diameter, root shape, smoothness, branching, uniformity, tip shape, relative core diameter, outer root color, xylem color, and phloem color. Samples approximately 1cm thick were taken from the bottom third of the root for soluble solids analysis. These samples were stored at -80oC until analysis.

In addition to phenotypic characteristics for each cultivar, we also noted information on IPR, determining the freedom to operate and ability to use the cultivars in breeding. This included noting whether the cultivar was protected by contract, ‘bag tag’ license, MTA, PVP, or utility patent.

After the 2013 harvest, roots from the 87 cultivars with no associated IPR restrictions were selected and advanced for development of the populations during the winter of 2013-2014 (Table 2). Hybrids that were available to use in breeding were included in the composite populations. While sterile plants have been rogued in subsequent cycles of intermating, cytoplasmic male sterility continues to be present within the populations.

Eight open source composite populations were developed based on market class and root color. The market class populations were classified as ‘Nantes’, ‘Danvers’, ‘Chantenay’, and ‘Ball’ (Figure 1), and are meant to represent those root shapes. The root color populations are ‘Red’, ‘Purple’, ‘White’, and ‘Yellow’ (Figure 2). Roots from a sample of plants of each selected cultivar from the Tipi Organic Produce plots were separated from tops, trimmed, and stored at 4oC for 10 weeks. 7-10 roots of each cultivar were planted in pots in the greenhouse in December and grown in a 16hr photoperiod at 20oC. Roots were separated according to market class categories and colors and grouped accordingly. Each group was placed under an insect-proof netted cage. There was a large attrition rate, with many roots rotting or not producing seed. After attrition, each cage contained between 20 and 60 roots and 3 to 19 cultivars depending on the composite. When the primary umbels began to open, house fly (Musca domestica) pupae were placed in each cage at weekly intervals for six weeks. Flowering was not completely synchronous among all plants in each cage. However, since plants exhibit 3-5 umbels, a window of time where cross-pollination could occur was achieved in all cages. At seed maturity, seeds were harvested from each plant separately, and a balanced bulk of seed was produced for each composite population for planting in June 2013. Seeds of each composite population were sown in replicated plots at Tipi Organic Produce in Evansville, WI in 2014. All roots from these plots were harvested in October and stored at 4oC for 24 weeks. Roots were transplanted to cages in the field at Tipi Organic Produce in April 2015. When the primary umbels opened, Blue Bottle Fly (Diptera Calliphoridae) pupae were introduced into each cage at weekly intervals for six weeks. A balanced bulk of seed will be produced for each composite population. The resulting Composite 2 seed of each population is being released through the Open Source Seed Initiative Pledge: “You have the freedom to use these OSSI-Pledged seeds in any way you choose. In return, you pledge not to restrict others’ use of these seeds or their derivatives by patents, licenses or other means, and to include this pledge with any transfer of these seeds or their derivatives (www.osseeds.org).”

 

Research results and discussion:

Analysis of data collected for this project is still on-going.

 

Phenotypic Analysis:

A mixed model ANOVA was used to determine if there was a statistically significant difference for each phenotypic trait measured for cultivars with freedom to operate (FTO) compared to those without FTO. We found that for root length, root diameter, uniformity, smoothness, branching, purple shoulders, green shoulders, and petiole anthocyanins there was a significant difference between the two FTO classes (p<0.01) (Table 3). We also found that there were significant differences (p<0.01) among cultivars for soluble solids, root length, root diameter, uniformity, smoothness, branching, purple shoulders, green shoulders, and petiole anthocyanins (Table 3). Using the phenotypic data (Figure 3), a principal components analysis again shows some clustering of market types, but even though the first two PC explain more of the total variation (46%), we do not see a strong separation of carrot market classes.

 

 

Open Source Population Development:

Over the past several decades, there has been a trend toward increasingly restrictive intellectual property rights (IPR) over plant germplasm including contracts, material transfer agreements (MTA), ‘bag tag’ licenses, plant variety protection certificates (PVP) and utility patents. This has limited the “freedom to operate” for plant breeders wanting to use a diverse array of germplasm in their breeding programs and has complicated the exchange of plant germplasm around the world (Luby et al., 2015). The goal of many plant breeding programs is to develop cultivars or inbred lines that are genetically stable and homogenous. The goal of breeding the eight populations released here was the opposite: take commercially available cultivars that had freedom to operate for breeding and create diverse carrot populations based on market class and root color. These composite populations are meant to represent some of the diversity present in commercially available carrot germplasm that is available to use in breeding. The populations are the Wisconsin Open Source Composite (WI-OSC) collection: ‘WI-OSC Nantes’, ‘WI-OSC Danvers’, ‘WI-OSC Chantenay’, ‘WI-OSC Ball’, ‘WI-OSC Yellow’, ‘WI-OSC White’, ‘WI-OSC Red’, and ‘WI-OSC Purple’.

In order to ensure that the diversity present in these populations will remain available for use in breeding and seed production into the future, the WI-OSC populations are being released under the Open Source Seed Initiative (OSSI) Pledge, a mechanism developed by OSSI in 2014 to enhance plant breeder’s freedom to operate and farmers and gardeners to save and share seed. The OSSI Pledge states: “You have the freedom to use these OSSI-Pledged seeds in any way you choose. In return, you pledge not to restrict others’ use of these seeds or their derivatives by patents, licenses or other means, and to include this pledge with any transfer of these seeds or their derivatives (www.osseeds.org).” This means that these populations will serve as reservoirs of carrot diversity that will remain freely available for anyone to use, for whatever purpose, with the condition that when derivatives are created using any of these populations, they will also remain available for others to use and will not be use-restricted by intellectual property rights. Instead of making germplasm available through a public commons, where resources can be used and appropriated by IPR, the OSSI Pledge creates a ‘protected commons’ around germplasm, ensuring that it remains available to use into the future (Luby et al. 2015).

The populations developed to represent different market classes are ‘Nantes’, ‘Danvers’, ‘Chantenay’, and ‘Ball’ (Table 2, Figure 1). The ‘Nantes’ population has orange roots with the typical narrow shoulders, cylindrical shape, and blunt tip that characterize the ‘nantes’ shape. Tops range in vigor and were generally less strong than the other populations.

The ‘Danvers’ population has orange roots that are characterized by the pronounced shoulders and tapered shape of the ‘Danvers’ type. Tops are very vigorous.

The ‘Chantenay’ population is orange in color. Roots are characterized by large shoulders with a wide diameter at the crown, tapering, shorter roots than the Danvers type and a blunt tip. Tops are very vigorous.

The ‘Ball’ population is orange in color and has generally round, ball shaped roots. Roots vary slightly in shape with some that are truly round and others that were slightly longer.

The populations characterized by color include the ‘Yellow’, ‘White’, ‘Red’, and ‘Purple’ populations (Table 2, Figure 2). Bolting was prevalent in the ‘yellow’, ‘white’ and ‘red’ populations. Bolting plants were rogued during the first cycle of selection.

The ‘Yellow’ population is characterized by variation in the intensity of yellow color, or accumulation of xanthophylls, in the roots with occasional white and orange roots appearing. Some roots have green crowns. Roots vary in shape and are generally ‘Danvers’ or ‘Belgian’, with relatively pronounced shoulders and tapered roots. Tops are very strong and vigorous.

The ‘White’ population is characterized by white colored roots and green shoulders. Roots are generally ‘Belgian’ shaped, with large cylindrical roots and tapered tips. This population has very vigorous tops and large roots.

The ‘Red’ population is characterized by the accumulation of lycopene in the roots, creating an intense red or rose color. Roots are generally ‘Danvers’ or ‘Nantes’ in shape, so there is variation in the definition of the root’s shoulders, as well as the amount of taper in the roots and tips. Some roots are quite tapered while others are more cylindrical. There is variation in smoothness of roots. Some roots are quite smooth but others have very large lenticels or are prone to branching. Additionally, seed production has proved difficult with this population with many roots rotting during storage or producing unviable seed.

The ‘Purple’ population has purple exterior color (anthocyanin accumulation) with a variation of purple, orange, and white interiors. Roots are generally quite large in diameter with a significant taper. Tops are very vigorous.

Participation Summary

Educational & Outreach Activities

Participation Summary

Education/outreach description:

Publications in review:

Luby, C.H., and I.L. Goldman. 2015. Release of Eight Open Source Carrot (Daucus carota L. var. sativa) Composite Populations Developed Under Organic Conditions: ‘WI-OSC Nantes’, ‘WI-OSC Danvers’, ‘WI-OSC Chantenay’, ‘WI-OSC Ball’, ‘WI-OSC Yellow’, ‘WI-OSC White’, ‘WI-OSC Red’, and ‘WI-OSC Purple’. Submitted to HortScience, July 6, 2015.

 

Published proceedings papers and abstracts:

Luby, C.H., and I.L. Goldman. 2015. Abstract: Exploring Phenotypic and Genotypic Diversity and Freedom to Operate in Commercially Available Carrot Cultivars. HortScience Supplement. Accepted. To be published August 2015.

Kloppenburg, J., J. Chappel, M. Colley, I. Goldman, C. Luby, T. Michaels, F. Morton, M. Sligh, and T. Stearns. Free as in Speech, Not as in Beer: The Open Source Seed Initiative. Proceedings of the 7th annual Organic Seed Growers Conference: Innovation in the Field, Corvallis, OR, January 30 – February 1, 2014.

 

Anticipated Publications:

Luby, C.H., and I.L. Goldman. Improving freedom to operate in carrot breeding through the development of open source composite carrot populations.

Luby, C.H., J. Dawson, I.L. Goldman. Examining Genetic and Phenotypic Diversity in US Carrot Cultivars to Determine Freedom to Operate for Plant Breeding.

 

Outreach/Presentations:

Luby, C.H., and I.L. Goldman. Presentation: Examining Genetic and Phenotypic Diversity in US Carrot Cultivars to Determine Freedom to Operate for Plant Breeding. To be presented at the International Carrot Conference, Toronto, ON. September 15-17, 2015.

Luby, C.H., and I.L. Goldman. Presentation: Potential Uses in Organic Systems for Eight Open Source Carrot Populations. To be presented at the Student Organic Seed Symposium, Madison, WI. August 9-13, 2015.

Luby, C.H., and I.L. Goldman. Presentation: Exploring Phenotypic and Genotypic Diversity and Freedom to Operate in Commercially Available Carrot Cultivars. HortScience Supplement. To be presented at the ASHS Conference, New Orleans, LA. August 4-7, 2015.

Luby, C.H. Poster: Developing Freedom to Operate for Plant Breeding through the Development of Eight Open Source Carrot Populations. University of Minnesota Plant Breeding Symposium, Saint Paul, MN. March 27, 2015.

Luby, C.H. Poster: Developing Freedom to Operate for Plant Breeding through the Development of Eight Open Source Carrot Populations. Midwest Organic and Sustainable Education Service (MOSES) Conference, La Crosse, WI. February 26-28, 2015.

Luby, C.H., and I.L. Goldman. Presentation: Development of Eight Open Source Carrot Populations. Student Organic Seed Symposium. Ithaca, NY. August 17-20, 2014.

Jack Kloppenburg, J., J. Chappel, M. Colley, I. Goldman, C. Luby, T. Michaels, Frank Morton, M. Sligh, and T. Stearns. Panel Presentation: Free as in Speech, Not as in Beer: The Open Source Seed Initiative. Paper prepared and presented at the Organic Seed Growers Conference, Corvallis, OR. January 30-February 1, 2014.

 

Project Outcomes

Project outcomes:

This project has had several demonstrable impacts. We have developed eight open source composite populations of carrot based on different market and color classes. In order to ensure that the diversity present in these populations will remain available for use in breeding and seed production into the future, the WI-OSC populations are being released by the University of Wisconsin-Madison carrot breeding program under the Open Source Seed Initiative (OSSI) Pledge, a mechanism developed by OSSI in 2014 to enhance plant breeder’s freedom to operate and farmers and gardeners to save and share seed. These composite populations have proven to be of interest to a variety of constituents. We are working with a seed company to begin selecting phenotypes of interest from within several of the populations. Additionally, the populations will be featured in several ‘Seed to Table’ events this fall (2015). We hope that these populations will serve as reservoirs of diversity that are available to use in breeding and seed saving now and into the future.

            The analysis of phenotypic and genotypic diversity in relation to intellectual property rights (IPR) that was supported by this project is one of the first studies to look at the demonstrable impact of IPR on plant genetic diversity. We found that there were differences in phenotypic diversity for many of the traits measured between the groups that had freedom to operate for plant breeding and those that did not have freedom to operate. The genetic analysis suggested that there was no distinctive population structure among varieties.

Economic Analysis

Not Applicable

Farmer Adoption

We have released eight diverse open source composite populations of carrot. These populations have complete freedom to operate for plant breeding. These populations were developed under organic production conditions and we hope that useful cultivars for farmers will be created from these populations. It is difficult to calculate the number of farmers reached at this time.

Recommendations:

Areas needing additional study

There is significant potential to apply this technique and analysis in other crops to determine the freedom to operate for a variety of different crops. Utilization of diverse genetic material will help to ensure that we have plant cultivars that are suitable for sustainable farming systems. We must also think about how these cultivars will be released to ensure that plant breeders and farmers have freedom to operate for plant breeding and seed saving.

 

 

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.