Purple Tomato Is First Genetically Engineered Plant To Be Deregulated Through USDA’S New Regulatory Status Review Process

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On September 7, 2022, the United States Department of Agriculture’s Animal and Plant Health Inspection Service (USDA-APHIS) announced the completion of the first Regulatory Status Review (RSR) of a genetically engineered plant under the SECURE rule. APHIS concluded that a new genetically engineered tomato produced by Norfolk Plant Sciences is unlikely to pose an increased plant pest risk compared to a conventional tomato, and is therefore not subject to regulation under the SECURE rule. This means that these tomato plants, which have been engineered to produce deep purple tomatoes with enhanced nutritional quality, may be legally imported, moved interstate, or “released” into the environment (including, for example, in a field trial) in the United States without a permit from APHIS.

Notably, this finding also means that subsequent genetic transformation events involving the same combination of plant species, trait, and mechanism of action (“PTMOA”) as Norfolk Plant Sciences’ purple tomatoes are also no longer regulated under the SECURE rule. Thus, other subspecies and varieties of Solanum lycopersicum that have been modified to produce the same trait by the same mechanism of action—even if by different transgenic events—are now exempt under § 340.1(c) of the SECURE rule. More information on this so-called PTMOA exemption is available in APHIS’s “Guide for Requesting a Confirmation of Exemption from Regulations under 7 CFR part 340” (published August 31, 2022; document ID BRS-GD-2020-0001). This approach is different from the “event-by-event” regulation that was previously required, and represents the first time that APHIS has made an RSR determination under its new rules.

Additional information about the contours of the SECURE rule and the genetic engineering that Norfolk Plant Sciences used to produce their purple tomato is provided below.

About the SECURE Rule

The SECURE rule (7 CFR part 340) governs how APHIS regulates certain organisms developed using genetic engineering, with the goal of protecting U.S. agriculture from plant pest risks under the Plant Protection Act of 2000 (7 U.S.C. §§ 7701 et seq.). It replaced the previous version of 7 CFR part 340, which had been in place largely unchanged since APHIS’s biotechnology regulations were established in 1987, in phases between May 18, 2020 and October 1, 2021.

The new regulations completely overhauled and streamlined the regulatory process for assessing the plant pest risk of organisms developed using genetic engineering, taking into account advances in scientific understanding, and focusing more on the properties of the engineered organism and less on the method(s) used to produce it.

The revised regulations exempt certain types of modifications from regulation; such exemptions are self-determined, though developers may voluntarily request confirmation from APHIS that a given exemption applies. This exemption/confirmation process replaced the previous “Am I Regulated?” process on June 17, 2020, and APHIS has since issued 15 confirmation letters as of this writing, with the earliest in April 2021.

However, no plant had made it through the new RSR process until now. The RSR process is an option for instances in which no SECURE rule exemptions apply to a given engineered plant, but the developer feels that the plant nonetheless does not pose an increased plant pest risk and should therefore not be regulated by the SECURE rule. The RSR process replaced the previous “petition” process for requesting deregulation from 7 CFR part 340 due to low likelihood of posing a plant pest risk.

The RSR process became available for corn, soybean, cotton, potato, tomato, and alfalfa on April 5, 2021, and for all other plant species on October 1, 2021. APHIS received Norfolk Plant Sciences’ RSR request on August 4, 2021 and responded on September 6, 2022 (both the request and the response documents are available here, under RSR number 21-166-01rsr). As of this writing, Norfolk Plant Sciences’ tomato is the only RSR request publicly available on APHIS’s website.

Under the RSR process, APHIS reviews “the biological properties of the plant; and the trait (or new characteristic); and the mechanism of action (or how the genetic modification causes the new trait to occur)” in order to evaluate plant pest risk. There are two potential steps to this process, depending on what APHIS determines during the first step. In Step 1, APHIS identifies whether the engineered plant poses a plausible pathway to increased plant pest risk compared to a “comparator” plant. If APHIS finds no such pathway, the RSR process concludes, and APHIS notifies the requestor that the plant in question is not subject to regulation under the SECURE rule. This was the outcome for Norfolk Plant Sciences’ tomato.

On the other hand, if APHIS does determine that the engineered plant may plausibly pose an increased plant pest risk, there are several potential next steps. First, the developer may accept that the plant is regulated under the SECURE rule, and then either request a permit before moving or releasing the plant, or take no further action and not move or release the plant. Alternatively or additionally, the developer may request that APHIS proceed to Step 2 of the RSR process, which entails a more involved review, subsequent publication in the Federal Register, and solicitation and review of public comments before a final determination. As of this writing, no plant has gone through this second step of the RSR process.

About the Purple Tomato

As described in its RSR request, Norfolk Plant Sciences created its purple tomato plant by Agrobacterium-mediated insertional mutagenesis of the “MicroTom” tomato variety, and subsequent crossing into other tomato varieties. The plants are engineered to increase expression of their natural anthocyanin pigments, which is what causes the fruits to have a deep purple color and also enhances their nutritional value.

Specifically, the inserted DNA contains two transcription factors from the snapdragon plant (Antirrhinum majus), which serve to activate production of the tomato’s native anthocyanin biosynthesis pathway, causing increased anthocyanin production. Each of these two transcription factor genes, called Del and Ros1, is expressed from the T-DNA under a native tomato promotor that causes fruit-specific expression. The T-DNA also includes the nptII selectable marker with a promotor and terminator from Agrobacterium tumefaciens, which have a decades-long history of safe use and consumption.

Complete genome sequencing revealed that the T-DNA was inserted at a single site in chromosome 4, accompanied by several small deletions. Phenotypic evaluation of the transformed plants revealed that they grew effectively the same as non-transgenic tomatoes, except that they produce deep purple fruit with significantly higher anthocyanin content. Photos of the plants and fruit are available in the published RSR request.

APHIS considered the information disclosed in Norfolk Plant Sciences’ RSR request, alongside “publicly available resources, and APHIS’ familiarity with tomato and knowledge of the trait, phenotype, and mechanism of action” and “did not identify any plausible pathway by which [the] modified tomato, or any of its sexually compatible relatives, would pose an increased plant pest risk relative to a comparator tomato” (21-116-01 RSR Response, page 1). As such, APHIS concluded that these purple tomatoes are not subject to regulation under the SECURE rule.

Other Regulatory Agencies

It is important to note that deregulation from APHIS’s SECURE rule does not mean that the plant is wholly removed from U.S. federal regulatory oversight. For example, regulations implemented by the Food and Drug Administration (FDA), Environmental Protection Agency (EPA), and/or other arms of USDA (such as Plant Protection and Quarantine (PPQ) import and export regulations, and/or Agricultural Marketing Service (AMS) labeling requirements) may still apply. Along those lines, Norfolk Plant Sciences’ RSR request states that Norfolk Plant Sciences submitted a food and feed safety and nutritional assessment of the Purple Tomato to FDA under the voluntary Biotechnology Notification Consultation program, which was received as BNF number 178. As of this writing, FDA has not yet published a completed consultation for Norfolk Plant Sciences’ purple tomato.

Conclusion

This regulatory review is an important milestone for regulation of genetically engineered plants in the United States. It is the first public test of the SECURE rule’s RSR process since its implementation more than a year ago, when it became one of the most scientifically progressive such review processes in the world, at least on paper. The deregulation of Norfolk Plant Sciences’ purple tomatoes shows that USDA-APHIS is embracing its new product-focused regulations. Although the review took more than a year—significantly longer than the 180 days promised by APHIS for Step 1—the process will likely become more efficient as the agency and developers become more familiar and comfortable with the new system. It will be interesting to see how the exemption and review processes grow and possibly become more streamlined with additional use.

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DISCLAIMER: Because of the generality of this update, the information provided herein may not be applicable in all situations and should not be acted upon without specific legal advice based on particular situations.

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