Status of Gene Editing Use in Public Canadian Crop Breeding

In Spring 2021, Health Canada released proposed new guidance for the Novel Food Regulations, specifically focused on plant breeding, and conducted an open consultation seeking feedback from both industry stakeholders and general Canadian public.  This move reflects the government’s intent to establish a predictable commercialization pathway in preparation for new products that are developed using new plant breeding techniques, more specifically, “gene editing” (GEd) techniques. 

Crop breeders have been using genetic improvement technologies for decades, picking up tools that enhance their ability to effect change as they see a fit in their programme.  Many tools have been developed to assist plant breeders in developing new cultivars that deliver higher yields, are more resistant to biotic and abiotic stresses, and are better adapted to changing environmental conditions.  Most recently, the Clustered Regularly Interspaced Short Palindromic Repeats method (CRISPR/Cas9) of GEd has been touted to have great promise due to its immense versatility and the relative ease with which it can be used.  While policymakers are reviewing laws and regulations to anticipate an “imminent” shift towards the use of these kinds of technologies, our research showed that the CRISPR/Cas9 technology is yet to be widely adopted by public crop breeding programs in Canada. This policy brief explores the reasons behind the slow uptake and presents policy recommendations that could enable breeders to make GEd tools part of their ‘toolbox,’ should they choose to make use of them.

We screened the peer-reviewed and public access publications of public Canadian crop breeders for evidence of GEd use and found only two instances of CRISPR/Cas9 proof-of-concept applications. This finding seems inconsistent with the findings of a recent survey by Gleim et al. 2020 [1], which shows that both public and private Canadian crop breeders are aware of and knowledgeable about CRISPR/Cas9. Therefore, to get a better understanding of the status of GEd use by public breeding programs in Canada, we interviewed crop breeders from six Canadian universities.  Some crop breeders we interviewed reported using CRISPR/Cas9 in their research activities but not in their breeding programs. No other GEd technique was reported as being used among public Canadian crop breeders at this time. CRISPR/Cas9 use remains low for several reasons.  

First, asked directly about the existence of barriers (internal or external) to the use of GEd at their host institution, few could identify any specific barriers. It is noteworthy that a significant number of breeders admitted that they were not knowledgeable about the specific rules of their host institution regarding the use of GEd tools.

Second, a concern of most breeders was that even if they successfully developed a trait through GEd, they might not be able to navigate Canada’s regulatory regime in order to bring the resulting crop to market. This uncertainty makes breeders apprehensive about using GEd in their breeding programmes.

Third, pressed on their lack of use of novel crop breeding technologies, a significant number of breeders noted that consumer perceptions were an important factor in their decision about whether to use a new technology in their breeding program. Many breeders asserted that they would not use GEd technologies yet because consumer opinions about these remain largely unknown. One breeder suggested that given that there is no difference between a trait developed through certain GEd techniques or conventionally derived traits at a whole-genome level, reporting on GEd applications might not be strictly necessary in Canada.  Meanwhile, critics that are against Health Canada’s recent Novel Food Regulations revision proposal are quick to tie GEd with genetically modified food [2].    

Fourth, some respondents asserted that while GEd could be powerful tools, they are not necessarily the appropriate tool for every crop breeding objective. In fact, for some crops (e.g., lentils and sunflower), GEd and CRISPR/Cas9 specifically, are not viable tools because of the biological complexity underpinning their most important traits and additional laboratory steps to which they are recalcitrant. In addition to these concerns, all crop breeders emphasized that to be able to use GEd appropriately a thorough understanding of the plant’s genome is needed. Functional genomics is the field that concerns itself with understanding the relationship between the information contained in an organism’s genome and its physical characteristics [3]. This field was born 20 years ago when the human genome was first sequenced; it then became clear that the next step in biology was to understand the function of genes [4]. Twenty years on, moving from phenotype (traits) to genotype (genetic base) remains difficult because the biological mechanism that translates between them has yet to be fully understood, especially for crops with more complex genomes – for example, lentils and sunflower.

Beyond these issues, the use and application of GEd in Canada trips over questions of intellectual property. Specifically, ownership of CRISPR/Cas9 technology has not yet been established in Canada [5]. While over 3,400 patents and pending patent applications refer to CRISPR/Cas9, there are three competing claims over the foundational technology open in Canada (Table 1). To commercialize technologies that use CRISPR/Cas9 in Canada, licenses to the foundational patents and particular applications would be needed [6]. But from whom? While basic research or proof-of-concept studies often proceed without license, if they generate new traits of value they could be subject to retroactive licensing once patents are issued, which could significantly reduce the bargaining power of the inventor. For that reason, many researchers and crop breeders could understandably avoid using the technology.

Table 1. Parties Claiming CRISPR system ownership in Canada

Patent Application	Title	Inventors	Applicant	PCT Filing Date
CA3081937	Type V Crispr/Cas Effector Proteins For Cleaving Ssdnas And Detecting Target Dnas	Doudna, Jennifer A. Chen, Janice S. Harrington, Lucas Benjamin Ma, Enbo	The Regents of the University of California (United States of America)	2018-11-20
CA2930877	CRISPR-CAS System Materials and Methods	Charpentier, Emmanuelle Chylinski, Krzysztof Fonfara, Ines	CRISPR Therapeutics AG	2014-11-17
CA 2932439	CRISPR-CAS Systems and Methods For Altering Expression Of Gene Products, Structural Information And Inducible Modular Cas Enzymes	Zhang, Feng Zetsche, Bernd	The Broad Institute & the Massachusetts Institute of Technology	2014-12-12
Source: CIPO [4] Notes: All three parties have filed a patent claim with the Canadian Intellectual Property Office (CIPO) through the Patent Cooperation Treaty (PCT). As per current regulations, ‘CRISPR Therapeutics AG’ requested their application be ‘examined’ five years after their initial submission on 2019-11-18. It is now up to CIPO to consider the merit of their claim.

The decision of whether or not to use GEd technologies is but one factor in a complex interplay of decisions a crop breeder makes. The decision to use these tools ultimately come down to: (1) whether it is the most appropriate tool for the task at hand (not always a biotechnology tool), (2) whether consumers and the market would accept the product resulting from the application of the tool they choose, followed by (3) whether there is a pathway through regulations to the market. No breeder mentioned the legal aspects surrounding the use of CRISPR/Cas9 specifically, but these are important issues that need clarification if these tools are to be employed to their fullest potential. Conceptually, the order of each aspect, from most important to least as considered by most Canadian public crop breeders can be listed as:

1. Fitness of the technology to the crop and task at hand;
2. Market acceptance;
3. Regulatory hurdles; and
4. Legal issues of GEd applications.

Above all, GEd use comes down to whether they are the right tools (cheapest and fastest) to achieve a crop breeder’s objectives.

How can public policy help?

We recommend the following actions to ensure that GEd can be available to Canadian public crop breeders. 

• First, the legal issues surrounding CRISPR/Cas9 need to be clarified. Doing so could serve as precedent for other GEd techniques and technologies.
• Second, more research (and therefore, more funding) is needed to understand the function of genes in relation to traits (functional genomics). This deficit in knowledge is a serious constraint to using GEd in the public crop breeding sector, particularly because many of the crops under development have complex genomes that are understudied.   
• Lastly, Canadian public crop breeders signal that they would benefit from greater insight into Canadian and foreign buyer’s perceptions and willingness to accept of GEd products. Directed research on preferences in key markets could benefit Canadian public crop breeding programs both specifically and more generally, as this information would help breeders develop new and more accurate research and breeding objectives.

This research was conducted as part of the ‘Enhancing the Value of Lentil Variation for Ecosystem Survival (EVOLVES)' project funded by Genome Canada and managed by Genome Prairie. We are grateful for the matching financial support from the Saskatchewan Pulse Growers, Western Grains Research Foundation, the Government of Saskatchewan, and the University of Saskatchewan. We also acknowledge support from BASF, AGT Foods, Global Institute for Food Security, Palacky University, and Polytechnical University of Marche.

1. Gleim, S., S. Lubieniechi, and S.J. Smyth, CRISPR-Cas9 Application in Canadian Public and Private Plant Breeding. The CRISPR Journal, 2020. 3(1): p. 44-51.
2. Canadian biotechnology Action Network (cban). No Regulatory Exemptions. 2021; Available from: https://cban.ca/take-action/no-exemptions/.
3. National Academies of Sciences, E. and Medicine, Next steps for functional genomics: proceedings of a workshop. 2020: National Academies Press.
4. Function, A focus on function. Nature Genetics, 2000. 25(3): p. 243-244.
5. CIPO. Canadian Patents Database. 2021; Available from: https://www.ic.gc.ca/opic-cipo/cpd/eng/search/basic.html.
6. Lipkus, N. The nascent CRISPR-Cas9 patent landscape in Canada. 2018 [cited 2021; Available from: https://www.osler.com/en/resources/regulations/2018/the-nascent-crispr-cas9-patent-landscape-in-canada.

Dr. Peter W.B. Phillips is the director of the Centre for the Study of Science and Innovation, and a distinguished professor in the Johnson Shoyama Graduate School of Public Policy's University of Saskatchewan campus.

He earned his Ph.D. at the LSE and practiced for 13 years as a professional economist in industry and government. At the University of Saskatchewan, he was the Van Vliet Research Professor, created and held an NSERC SSHRC Chair in Managing Technological Change in Agriculture, and was director of the virtual College of Biotechnology.

He has had appointments at the LSE, OECD, European University Institute in Florence, University of Edinburgh and University of Western Australia. He was a founding member of the Canadian Biotechnology Advisory Committee and was on the boards of Canadian Agri-food Policy Institute, Pharmalytics and Ag-West Bio Inc. He has also held over 15 peer-reviewed grants worth more then $250 million and is author/editor of 15 books, and over 60 journal articles and 55 book chapters.

Diego Macall obtained his undergraduate degree in Agricultural Engineering from the Catholic University of El Salvador. He specialized in coffee production and processing, but also volunteered regularly to help implement rural development projects in impoverished villages and towns throughout the entire country. Seeing up close the socio-economic realities that afflicted a great segment of the Salvadoran population, inspired him to pursue graduate studies in agricultural policy. In 2014, Diego was accepted into the University of Saskatchewan’s Department of Agricultural and Resource Economics master’s programme. Upon obtaining his degree, Diego worked briefly as a market analyst in the USDA’s Foreign Agricultural Service Office in São Paulo, Brazil. Diego returned to USASK in 2017 as Dr. Stuart Smyth’s research assistant, since then, he has co-authored numerous papers and blogs about agricultural biotechnology. Since October 2020, he has been assisting Dr. Peter WB Phillips with certain components of the EVOLVES project.

Dr. Simona Lubieniechi is a Professional Research Associate in the Johnson Shoyama School of Public Policy at the University of Saskatchewan, Saskatoon, Canada. In 2011 she completed her PhD studies in agricultural economics. Her current research interests include behavioural economics, in particular prospect theory and its extension to framing effects and overconfidence. For the past few years Simona has been working on plant breeders’ decision-making processes and innovation adoption.