Federal District Judge Vacates Key Provisions of U.S. Department of Agriculture Regulations Governing Path to Market for Gene-Edited Plants

Background

The U.S. Department of Agriculture’s (USDA) Animal and Plant Health Inspection Service (APHIS or the agency) is charged with protecting U.S. agriculture from pests and diseases, in part through authority conferred by the Plant Protection Act of 2000 (PPA).  The PPA defines a plant pest as an organism that “can directly or indirectly injure, cause damage to, or cause disease in any plant or plant product.”¹ The PPA prohibits the movement of a plant pest without a permit from APHIS but allows APHIS to suspend permitting requirements for “specified plant pests . . . if the [agency] finds that a permit . . . is not necessary.”² The PPA also defines “noxious weed” and authorizes APHIS to “prohibit or restrict . . . the movement in interstate commerce of any . . . noxious weed” as “necessary.”³ Historically, APHIS treated all plants created through the use of genetic engineering (GE plants) as plant pests under its regulations at 7 CFR Part 340 because the genetic engineering techniques in use at the time (the 1990s) typically used genetic material from plant pests to alter the genetic characteristics of the target plants. As a result, the plants had to be reviewed and approved by APHIS prior to commercialization.     

The current APHIS regulations governing the permitting of GE plants (including gene edited plants modified through the use gene editing tools like CRISPR) are the product of a complicated, nearly fifteen-year long rulemaking process.⁴ Promulgated in 2020, the final rule streamlines the procedures for issuing a permit, where required, and categorically exempts from the permitting requirement, inter alia, GE plants that incorporate modifications that APHIS determines could have been developed through conventional breeding techniques (7 CFR § 340.1(b)(1)-(4);  the conventional breeding exemption) as well as plant-trait mechanism of action combinations APHIS has previously determined do not pose plant-pest risks (7 CFR §340.1(c); the plant-trait MOA exemption). As a result, newly developed GE plants that qualify for one or more of these exemptions may move in commerce without prior APHIS review, although proponents of new GE plants routinely seek confirmation of their determination that a plant is exempt under a voluntary public process established by APHIS.  The final rule also maintains the historic separation between APHIS’ regulation of noxious weeds and GE plants.  APHIS’ authority over noxious weeds under the PPA is not integrated into the regulations at Part 340.  Rather, the risks posed by noxious weeds are addressed through permitting and pre-market authorization requirements at 7 C.F.R. Part 360, which define noxious weeds by taxon.  Thus, a GE plant is not regulated as a noxious weed unless its non-GE counterpart is also a noxious weed. 

Litigation

Led by the National Family Farm Coalition, a group of NGOs challenged the APHIS final rule in 2021 under the Administrative Procedure Act (APA).⁶ The plaintiffs alleged the final rule was arbitrary and capricious and in violation of law because APHIS had ignored procedural requirements under the Endangered Species Act (ESA) and National Environmental Policy Act (NEPA), failed to follow specific Congressional directives including provisions of the PPA, and, by establishing the categorical exemptions, unconstitutionally delegated statutory authority to private parties. According to the plaintiffs, as a result of the final rule:

GE organisms will no longer be subject to USDA oversight and approval before open-air experiments and before commercial sale and planting. Since there will no longer be a USDA final agency approval action under the Administrative Procedure Act (APA), there will not be any analysis or transparency under NEPA or the ESA of GE crops’ agricultural or environmental risks.  In effect, USDA has attempted to get out of the regulation business entirely in this area.⁷

The plaintiffs moved for summary judgment in December 2022, and the court issued its decision on the motion on December 2, 2024.⁸

The Court’s Decision

The court rejected plaintiff’s claims that APHIS exceeded its statutory authority and violated the PPA by failing to incorporate the agency’s authority over noxious weeds into the final Part 340 rule.  The court sided with APHIS that the text of the PPA gives the agency discretion as to how it discharges its authority over the movement of noxious weeds, citing the Supreme Court’s recent decision in Loper Bright. However, the court found APHIS’ explanation as to why it decided not to incorporate noxious weeds as a trigger for regulation under the final rule at Part 340 wanting.  The court noted that at the time of the rulemaking the record included recommendations to incorporate the expanded definition of noxious weeds into the Part 340 regulation and, in the years leading up to issuance of the final rule, APHIS itself had acknowledged certain drawbacks to not doing so.  According to the court, the “final rule does not address a single one of these issues” and, as a result, it does not satisfy the APA’s requirement that an agency engage in “reasoned decision making” and articulate the bases of its decisions.⁹

The court turned next to the plaintiffs’ challenge to the categorical exemptions established by the final rule.  The plaintiffs argued the exemptions are not grounded on “sound science” and, for that reason, are arbitrary and capricious.  With respect to the conventional breeding exemption, the court again found APHIS’ explanation of why it did what it did wanting.  The court cited evidence in the record, specifically a 2002 study by the National Academy of Sciences, that conflicts with APHIS’ position that the conventional breeding exemption is justified because conventional techniques have not introduced plant pest risk concerns.  According to the court, the conventional breeding exemption amounts to “[a]n agency conclusion that is in ‘direct conflict with the conclusion of its own experts’” observing that “[n]owhere in the final rule does APHIS acknowledge the conflicting evidence concerning the basis on which the exemption is premised. . . . That is arbitrary and capricious.”¹⁰  The court acknowledges that APHIS can take the position the conventional breeding exemption is appropriate “after reasoned consideration of other evidence or its own expertise, but it must provide an ‘adequate explanation and support for its determinations.’”¹¹ In contrast, the court upheld the agency’s explanation as to the basis for creating the plant-trait MOA exemption, concluding “the record indicates that APHIS supported its view with scientific evidence, and plaintiffs make no argument that the rule conflicts with, or is unsupported by, the evidence on which the agency purported to rely or that there was other evidence undermining the conclusion the agency drew from its expertise.” ¹²

Remedy

Calling APHIS’ errors under the APA “significant,” the court vacated the final rule in its entirety but did so only on a prospective basis.  The judge declined to apply vacatur retroactively, finding that to do so would be an “invitation to chaos” and said he is “mindful that the rule took effect in 2020 and that this area of our national agricultural economy is rapidly developing.”¹³ For newly developed GE plants, however, the applicable permitting requirements and procedures revert to those in place prior to promulgation of the 2020 final rule, essentially requiring APHIS to assess the plant-pest risk of every new GE plant variety separately.¹⁴ APHIS acknowledged the court’s ruling and its impact on agency procedures on its website and, as of this writing, says it is determining next steps and will provide additional guidance to stakeholders.

Why It Matters 

The court’s decision represents a setback in efforts over multiple administrations to adopt a more risk-based approach to the regulation of GE plants that focuses on the characteristics of the plants themselves rather than the process used to develop them.  Close to 100 new GE plants, including numerous gene-edited plants, have received confirmation of exemption determinations since the final rule was promulgated in 2020.  Although those exemptions will stand under the court’s decision, newly developed GE plants now confront a more uncertain and potentially more onerous regulatory path to market, with obvious implications for innovation in the agriculture and food sectors, until APHIS is able to address the court’s concerns, whether through appeal or by reissuing the final rule in a manner that passes muster under the APA.  

In the meantime, the court’s decision is also an important reminder of agencies’ ongoing obligation under the APA to provide a reasoned basis for their decisions in exercising authority granted to them by Congress.  Failure to explain agency reasoning for adopting one approach versus another, particularly if the record includes expert evidence or prior statements by the agency that are at odds with the agency’s chosen path, remains vulnerable to challenge. Thus, even when the heightened standard of review established by Loper Bright does not apply because an agency is not interpreting an ambiguous statute, courts will not merely rubber stamp an agency action.  The agency must adequately explain its decision.  At the same time, however, the timing of the decision—nearly four and a half years after APHIS promulgated its final rule—illustrates that APA litigation can move slowly, which can limit its effectiveness as a tool to shape or impact regulatory policy in the short term.

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Please contact us if you have questions about the court’s decision or its implications for commercializing new GE plants moving forward. 

Authored by Brian Eyink and Andrea Bruce.