An InSECURE Future: Court Ruling Guts USDA Regs on Genetically Engineered Plants

In a decision that raises significant questions about the future oversight of genetically engineered (GE) plants in the United States, the U.S. District Court for the Northern District of California on Monday, December 2, 2024, struck down the 2020 USDA Animal and Plant Health Inspection Service (APHIS) rule codified at 7 C.F.R. § 340 regarding GE plants. The court vacated APHIS's 2020 rule, formerly known as the SECURE (Sustainable, Ecological, Consistent, Uniform, Responsible, Efficient) rule, which had been adopted to streamline USDA oversight of plants developed using genetic engineering.

Summary judgment ruling on December 2, 2024

On December 2, 2024, Judge James Donato issued a summary judgment ruling in National Family Farm Coalition et al. v. Tom Vilsack et al., vacating a 2020 update to APHIS's biotechnology regulations (7 C.F.R. § 340), which had exempted many GE plants from USDA regulation and streamlined the deregulation process for others. The three main exemptions under the now vacated 2020 rule are codified at 7 CFR § 340.1(b)(1)-(3) and relate to a genetic change caused by cellular repair of a targeted, single double-stranded break; a targeted single base pair substitution; and the introduction of certain types of known sequences from the plant's gene pool, respectively.

The November 2024 updates to the 2020 rule are not explicitly included in the vacatur

In late 2023, APHIS proposed five additional exemptions to be incorporated into the 2020 rule. After a review of public comments, two new exemptions were finalized, effective November 13, 2024, and APHIS immediately began to inform developers about their function and effects, including at a November 14, 2024, stakeholder meeting. However, following the December 2 ruling, the new exemptions, which APHIS termed "Additional Modification 1" (AM1) and "Additional Modification 2" (AM2), are now in jeopardy.

The November 2024 exemptions are defined as follows:

• AM1: An indel or contiguous deletion of any size, made at a targeted location, with or without insertion of DNA if generated without using a repair template, or without insertion of DNA if generated using a repair template.
• AM2: A plant with up to twelve (12) modifications, made simultaneously or sequentially, if each modification individually qualifies for exemption and occurs in a different gene.

The parties briefed the court regarding these new exemptions prior to the summary judgment ruling. However, the court did not rule on the 2024 updates, and addressed only the 2020 final rule in its December 2 opinion. The parties have been ordered to brief the court by January 13, 2025, as to the impact of the vacatur on the November 2024 exemptions.

Thus, as of December 2, the 2020 rule and its exemptions have been vacated. The new exemptions under the 2024 revisions, however, appear to remain in place, at least for now, though it is unclear whether or how APHIS can process requests related to these new exemptions given the status of the 2020 rule.

What happens to plants that were approved or exempted under the 2020 rule?

APHIS confirmed in a December 4, 2024, announcement that "Regulatory Status Review responses, Confirmation Request responses, and active permits that USDA issued prior to December 2, 2024, remain valid." However, it is uncertain how the ruling will impact both developers who did not engage in a voluntary confirmation of exemption or Regulatory Status Review (RSR) and were proceeding with development under a self-determined exempt status, and developers with pending confirmation or RSR requests.

The ruling does not affect applicable parallel regulatory oversight by the FDA, EPA, or other (e.g., non-APHIS) branches within the USDA.

How did this happen?

Judge Donato granted partial summary judgment in favor of the plaintiffs, a group of 29 farming and organic non-profit and public-interest groups, finding that APHIS's adoption of the rule was arbitrary and capricious under the Administrative Procedure Act (APA). The plaintiffs argued in a lawsuit filed on July 6, 2021, that the 2020 rule failed to comply with federal statutes, including the Plant Protection Act (PPA).

APHIS adopted the now-vacated rule after nearly 15 years of attempts to update its regulations under part 340 of the PPA for better efficiency in regulation and better reflection of the advances made in gene editing and crop breeding. The 2020 rule introduced regulatory exemptions for certain GE plant modifications, including targeted DNA breaks repaired without a template (part 340(b)(1)), targeted single base pair substitutions (part 340(b)(2)), and insertion of a gene from the plant's gene pool (part 340(b)(3)). The effect of the rule was to remove certain categories of GE crops from oversight by USDA-APHIS's Biotechnology Regulatory Services, including some types of GE plants that could be created by conventional breeding techniques and those that the agency determined do not pose a plant pest risk. This change decreased the regulatory burden and facilitated entry for smaller developers.

One issue in the December 2 ruling was how APHIS dealt with "noxious weeds" in the 2020 rule. The 2020 rule did not incorporate APHIS's authority to regulate noxious weeds into its regulation of GE crops, despite previous proposed rules by APHIS that sought to evaluate GE plants for noxious-weed risk. Citing Transportation Division of the International Association of Sheet Metal, Air, Rail, & Transportation Workers v. Federal Railroad Administration (Transp. Workers), 988 F.3d 1170 (9th Cir. 2021), Judge Donato held that APHIS's failure to explain the agency's reversal of its position on additional risk assessments for noxious weeds was arbitrary and capricious.

Judge Donato also took issue with the categorical exemptions, which treat the risk of conventionally bred plants as the baseline in determining the scope of regulatory oversight. His reasoning relied heavily on a 2002 National Academy of Sciences publication that concluded that risks associated with crop cultivars that could have been developed through conventional breeding "should not be assumed to be acceptable." Despite APHIS' position in the briefing that it had carefully assessed the risks of conventionally-bred plants over the past 30 years, Judge Donato categorized the 2020 rule as being in direct conflict with APHIS's own experts.

What's next?

The case may not be immediately appealable as the summary judgment order did not rule on all the plaintiffs' claims. Plaintiffs also challenged the rule under the Endangered Species Act and the National Environmental Policy Act. The court asked the parties to jointly propose a status conference date to address the remaining claims. USDA could immediately appeal if the district court certifies the summary judgment ruling under Federal Rule of Civil Procedure 54(b), which allows a district court to certify for appeal an order granting summary judgment on an issue that is separate and distinct from other claims in the case. Even if such certification were to occur, expedited review by the Ninth Circuit would not be guaranteed.

In the meantime, the vacatur of the 2020 rule reverts the core USDA biotechnology regulations to their pre-2020 framework. Under the pre-2020 system, APHIS regulated GE organisms based on the use of plant pests in the genetic engineering process, rather than the plant pest risks of the final edited products, to which the 2020 rule had shifted focus. Developers could petition APHIS under the old rule for a determination that a GE organism was unlikely to pose a plant pest risk, a process known as a petition for non-regulated status, or obtain an indication of non-regulated status under the legacy "Am I Regulated" (AIR) procedures.

APHIS has acknowledged the court ruling and plans to provide more detailed guidance to stakeholders in the coming days, but as of this writing, the USDA has not announced any intent or capacity to enforce the old framework.

Of note, in March 2018, then-Secretary of Agriculture Sonny Perdue stated that the USDA had no plans to regulate plants that could be developed through conventional breeding techniques, provided they were not plant pests or created using plant pests. The incoming Trump administration may seek to retain this approach. However, the vacatur of the 2020 rule's categorical exemptions undoes much of the groundwork to automatically exempt many such plants from USDA review, assuming the legacy regulations are back in place in the interim.

If APHIS moves to propose a new rule to address the court's ruling, the process would likely be subject to customary procedural requirements, including notice and comment procedures, before finalization.

This is a developing story.

We are closely monitoring developments in this case and USDA's forthcoming guidance, and will continue to share updates.

Alice Carli, a law clerk in our Los Angeles office, contributed significantly to the drafting of this post. Caressa Tsai, a law clerk in our San Francisco office, also contributed to the drafting of this post.

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