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Meeting Agricultural Sustainability Goals by Increasing Federal Funding for Research on Genetically Engineered Organisms

03.24.23 | 10 min read | Text by Vivian Zhong


Ensuring the sustainability and resiliency of American food systems is an urgent priority, especially in the face of challenges presented by climate change and international geopolitical conflicts. To address these issues, increased federal investment in new, sustainability-oriented agricultural technology is necessary in order to bring greater resource conservation and stress tolerance to American farms and fields. Ongoing advances in bioengineering research and development (R&D) offer a diverse suite of genetically engineered organisms, including crops, animals, and microbes. Given the paramount importance of a secure food supply for national well-being, federal actors should promote the development of genetically engineered organisms for agricultural applications. 

Two crucial opportunities are imminent. First, directives in the Biden Administration’s bioeconomy executive order provide the U.S. Department of Agriculture (USDA) a channel through which to request funding for sustainability-oriented R&D in genetically engineered organisms. Second, renewal of the Farm Bill in 2023 provides a venue for congressional legislators to highlight genetic engineering as a funding focus area of existing research grant programs. Direct beneficiaries of the proposed federal funding will predominantly be nonprofit research organizations such as land grant universities; innovations resulting from the funded research will provide a public good that benefits producers and consumers alike. 

Challenge and Opportunity

The resiliency of American agriculture faces undeniable challenges in the coming decades. The first is resource availability, which includes scarcities of fertile land due to soil degradation and of water due to overuse and drought. Resource availability is also vulnerable to acute challenges, as revealed by the impact of the COVID-19 pandemic and the Russian-Ukraine war on the supply of vital inputs such as fertilizer and gas. The second set of challenges are environmental stressors, many of which are exacerbated by climate change. Flooding can wipe out an entire harvest, while the spread of pathogens poses existential risks not only to individual livelihoods but also to the global market of crops like citrus, chocolate, and banana. Such losses would be devastating for both consumers and producers, especially those in the global south. 

Ongoing advances in bioengineering R&D provide technological solutions in the form of a diverse suite of genetically engineered organisms. These have the potential to address many of the aforementioned challenges, including increasing yield and/or minimizing inputs and boosting resilience to drought, flood, and pathogens. Indeed, existing transgenic crops, such as virus-resistant papaya and flood-tolerant rice, demonstrate the ability of genetically engineered organisms to address agricultural challenges. They can also address other national priorities such as climate change and nutrition by enhancing carbon sequestration and improving the nutritional profile of food. 

Recent breakthroughs in modifying and sequencing DNA have greatly enhanced the speed of developing new, commercializable bioengineered varieties, as well as the spectrum of traits and plants that can be engineered. This process has been especially expedited by the use of CRISPR gene-editing technology; the European Sustainable Agriculture Through Genome Editing (EU-SAGE)’s database documents more than 500 instances of gene-edited crops developed in research laboratories to target traits for sustainable, climate-resilient agriculture. There is thus vast potential for genetically engineered organisms to contribute to sustainable agriculture. 

More broadly, this moment can be leveraged to bring about a turning point in the public perception of genetically engineered organisms. Past generations of genetically engineered organisms have been met with significant public backlash, despite the pervasiveness of inter-organism gene transfer throughout the history of life on earth (see FAQ). Reasons for negative public perception are complex but include the association of genetically engineered organisms with industry profit, as well as an embrace of the precautionary principle to a degree that far exceeds its application to other products, such as pharmaceuticals and artificial intelligence. Furthermore, persistent misinformation and antagonistic activism have engendered entrenched consumer distrust. The prior industry focus on herbicide resistance traits also contributed to the misconception that the technology is only used to increase the use of harmful chemicals in the environment. 

Now, however, a new generation of genetically engineered organisms feature traits beyond herbicide resistance that address sustainability issues such as reduced spoilage. Breakthroughs in DNA sequencing, as well as other analytical tools, have increased our understanding of the properties of newly developed organisms. There is pervasive buy-in for agricultural sustainability goals across many stakeholder sectors, including individual producers, companies, consumers, and legislators on both sides of the aisle. There is great potential for genetically engineered organisms to be accepted by the public as a solution to a widely recognized problem. Dedicated federal funding will be vital in seeing that this potential is realized.

Plan of Action

Recommendation 1: Fund genetically engineered organisms pursuant to the Executive Order on the bioeconomy.

Despite the importance of agriculture for the nation’s basic survival and the clear impact of agricultural innovation, USDA’s R&D spending pales in comparison to other agencies and other expenditures. In 2022, for example, USDA’s R&D budget was a mere 6% of the National Institutes of Health’s R&D budget, and R&D comprised only 9.6% of USDA’s overall discretionary budget. The Biden Administration’s September 2022 executive order provides an opportunity to amend this funding shortfall, especially for genetically engineered organisms.  

The Executive Order on Advancing Biotechnology and Biomanufacturing Innovation for a Sustainable, Safe, and Secure American Bioeconomy explicitly embraces an increased role for biotechnology in agriculture. Among the policy objectives outlined is the call to “boost sustainable biomass production and create climate-smart incentives for American agricultural producers and forest landowners.” 

Pursuant to this objective, the EO directs the USDA to submit a plan comprising programs and budget proposals to “support the resilience of the United States biomass supply chain [and] encourage climate-smart production” by September 2023. This plan provides the chance for the USDA to secure funding for agricultural R&D in a number of areas. Here, we recommend (1) USDA collaboration in Department of Energy (DoE) research programs amended under the CHIPS and Science Act and (2) funding for startup seed grants. 

CHIPS and Science Act

The 2022 CHIPS and Science Act aims to accelerate American innovation in a number of technology focus areas, including engineering biology. To support this goal, the Act established a new National Engineering Biology Research and Development Initiative (Section 10402). As part of this initiative, the USDA was tasked with supporting “research and development in engineering biology through the Agricultural Research Service, the National Institute of Food and Agriculture programs and grants, and the Office of the Chief Scientist.” Many of the initiative’s priorities are sustainability-oriented and could benefit from genetic engineering contributions. 

A highlight is the designation of an interagency committee to coordinate activities. To leverage and fulfill this mandate, we recommend that the USDA better coordinate with the DoE on bioengineering research. Specifically, the USDA should be involved in the decision-making process for awarding research grants relating to two DoE programs amended by the Act.

The first program is the Biological and Environmental Research Program, which includes carbon sequestration, gene editing, and bioenergy. (See the Appendix for a table summarizing examples of how genetic engineering can contribute sustainability-oriented technologies to these key focus areas.)

The second program is the Basic Energy Sciences Program, which has authorized funding for a Carbon Sequestration Research and Geologic Computational Science Initiative under the DoE. Carbon sequestration via agriculture is not explicitly mentioned in this section, but this initiative presents another opportunity for the USDA to collaborate with the DoE and secure funding for agricultural climate solutions. Congress should make appropriating funding for this program a priority.

Seed Grants

The USDA should pilot a seed grant program to accelerate technology transfer, a step that often poses a bottleneck. The inherent risk of R&D and entrepreneurship in a cutting-edge field may pose a barrier to entry for academic researchers as well as small agricultural biotech companies. Funding decreases the barrier of entry, thus increasing the diversity of players in the field. This can take the form of zero-equity seed grants. Similar to the National Science Foundation (NSF)’s seed grant program, which awards $200+ million R&D funding to about 400 startups, this would provide startups with funding without the risks attached to venture capital funding (such as being ousted from company leadership). The NSF’s funding is spread across numerous disciplines, so a separate agricultural initiative from the USDA dedicated to supporting small agricultural biotech companies would be beneficial. These seed grants would meet a need unmet by USDA’s existing small business grant programs, which are only awarded to established companies.

Together, the funding areas outlined above would greatly empower the USDA to execute the EO’s objective of promoting climate-smart American agriculture.

Recommendation 2: Allocate funding through the 2023 Farm Bill.

The Farm Bill, the primary tool by which the federal government sets agricultural policy, will be renewed in 2023. Several existing mandates for USDA research programs, administered through the National Institute of Food and Agriculture as competitive grants, have been allocated federal funding. Congressional legislators should introduce amendments in the mandates for these programs such that the language explicitly highlights R&D of genetically engineered organisms for sustainable agriculture applications. Such programs include the Agriculture and Food Research Initiative, a major competitive grant program, as well as the Specialty Crop Research Initiative and the Agricultural Genome to Phenome Initiative. Suggested legislative text for these amendments are provided in the Appendix. Promoting R&D of genetically engineered organisms via existing programs circumvents the difficulty of securing appropriations for new initiatives while also presenting genetically engineered organisms as a critically important category of agricultural innovation.

Additionally, Congress should appropriate funding for the Agriculture Advanced Research and Development Authority (AgARDA) at its full $50 million authorization. Similar to its counterparts in other agencies such as ARPA-E and DARPA, AgARDA would enable “moonshot” R&D projects that are high-reward but high-risk or have a long timeline—such as genetically engineered organisms with genetically complex traits. This can be especially valuable for promoting the development of sustainability-oriented crops traits: though they are a clear public good, they may be less profitable and/or marketable than crops with consumer-targeted traits such as sweetness or color, and as such profit-driven companies may be dissuaded from investing in their development. The USDA just published its implementation strategy for AgARDA. Congress must now fully fund AgARDA such that it can execute its strategy and fuel much-needed innovation in agricultural biotechnology. 


Current federal funding for genetically engineered organism R&D does not reflect their substantial impact in ensuring a sustainable, climate-smart future for American agriculture, with applications ranging from increasing resource-use efficiency in bioproduction to enhancing the resilience of food systems to environmental and manmade crises. Recent technology breakthroughs have opened many frontiers in engineering biology, but free market dynamics alone are not sufficient to guarantee that these breakthroughs are applied in the service of the public good in a timely manner. The USDA and Congress should therefore take advantage of upcoming opportunities to secure funding for genetic engineering research projects.


Biological and Environmental Research Program Examples 

Research focus area added in CHIPS and Science ActExample of genetic engineering contribution
Bioenergy and biofuelOptimizing biomass composition of bioenergy crops
Non-food bioproductsLab-grown cotton; engineering plants and microbes to produce medicines
Carbon sequestrationImproving photosynthetic efficiency; enhancing carbon storage in plant roots
Plant and microbe interactionsEngineering microbes to counter plant pathogens; engineering microbes to make nutrients more accessible to plants
BioremediationEngineering plants and microbes to sequester and/or breakdown contaminants in soil and groundwater
Gene editing Engineering plants for increased nutrient content, disease-resistance, storage performance
New characterization toolsCreating molecular reporters of plant response to abiotic and biotic environmental dynamics 

Farm Bill Amendments 

Agriculture and Food Research Initiative

One of the Agriculture and Food Research Initiative (AFRI)’s focus areas is Sustainable Agricultural Systems, with topics including “advanced technology,” which supports “cutting-edge research to help farmers produce higher quantities of safer and better quality food, fiber, and fuel to meet the needs of a growing population.” Furthermore, AFRI’s Foundational and Applied Science Program supports grants in priority areas including plant health, bioenergy, natural resources, and environment. The 2023 Farm Bill could amend the Competitive, Special, and Facilities Research Grant Act (7 U.S.C. 3157) to highlight the potential of genetic engineering in the pursuit of AFRI’s goals. 

Example text: 

Subsection (b)(2) of the Competitive, Special, and Facilities Research Grant Act (7 U.S.C. 3157(b)(2)) is amended—

(1) in subparagraph (A)—

(A) in clause (ii), by striking the semicolon at the end and inserting “including genetic engineering methods to make modifications (deletions and/or insertions of DNA) to plant genomes for improved food quality, improved yield under diverse growth conditions, and improved conservation of resource inputs such as water, nitrogen, and carbon;”;

(B) in clause (vi), by striking the “and”;

(C) in clause (vii), by striking the period at the end and inserting “; and”; and

(D) by adding at the end the following: 

“(viii) plant-microbe interactions, including the identification and/or genetic engineering of microbes beneficial for plant health”

(2) in subparagraph (C), clause (iii), by inserting “production and” at the beginning;

(3) in subparagraph (D)– 

(A) in clause (vii), by striking “and”;

(B) in clause (vii), by striking the period at the end and inserting “; and”; and

(C) by adding at the end the following: 

“(ix) carbon sequestration”.

Agricultural Genome to Phenome Initiative

The goal of this initiative is to understand the function of plant genes, which is critical to crop genetic engineering for sustainability. The ability to efficiently insert and edit genes, as well as to precisely control gene expression (a core tenet of synthetic biology), would facilitate this goal.

Example text:

Section 1671(a) of the Food, Agriculture, Conservation, and Trade Act of 1990 (7 U.S.C. 5924(a)) is amended—

  1. In subparagraph (4), by inserting “and environmental” after “achieve advances in crops and animals that generate societal”; and
  2. In subparagraph (5), by inserting “genetic engineering, synthetic biology,” after “to combine fields such as genetics, genomics,”

Specialty Crop Research Initiative

Specialty crops can be a particularly fertile ground for research. There is a paucity of genetic engineering tools for specialty crops as compared to major crops (e.g. wheat, corn, etc.). At the same time, specialty crops such as fruit trees offer the opportunity to effect larger sustainability impacts: as perennials, they remain in the soil for many years, with particular implications for water conservation and carbon sequestration. Finally, economically important specialty crops such as oranges are under extreme disease threat, as identified by the Emergency Citrus Disease Research and Extension Program. Genetic engineering offers potential solutions that could be accelerated with funding. 

Example text:

Section 412(b) of the Agricultural Research, Extension, and Education Reform Act of 1998 (7 U.S.C. 7632(b)) is amended—

  1. In paragraph (1), by inserting “transgenics, gene editing, synthetic biology” after “research in plant breeding, genetics,” and—
    1. In subparagraph (B), by inserting “and enhanced carbon sequestration capacity” after “size-controlling rootstock systems”; and
    2. In subparagraph (C), by striking the semi-colon at the end and inserting “, including water-use efficiency;”
Frequently Asked Questions
What is the definition of a genetically engineered organism? What is the difference between genetically engineered, genetically modified, transgenic, gene-edited, and bioengineered?

Scientists usually use the term “genetic engineering” as a catch-all phrase for the myriad methods of changing an organism’s DNA outside of traditional breeding, but this is not necessarily reflected in usage by regulatory agencies. The USDA’s glossary, which is not regulatorily binding, defines “genetic engineering” as “​​manipulation of an organism’s genes by introducing, eliminating or rearranging specific genes using the methods of modern molecular biology, particularly those techniques referred to as recombinant DNA techniques.” Meanwhile, the USDA’s Animal and Plant Health Inspection Service (APHIS)’s 2020 SECURE rule defines “genetic engineering” as “techniques that use recombinant, synthesized, or amplified nucleic acids to modify or create a genome.” The USDA’s glossary defines “genetic modification” as “the production of heritable improvements in plants or animals for specific uses, via either genetic engineering or other more traditional methods”; however, the USDA National Organic Program has used “genetic engineering” and “genetic modification” interchangeably. 

“Transgenic” organisms can be considered a subset of genetically engineered organisms and result from the insertion of genetic material from another organism using recombinant DNA techniques. “Gene editing” or “genome editing” refers to biotechnology techniques like CRISPR that make changes in a specific location in an organism’s DNA. 

The term “bioengineered” does carry regulatory weight. The USDA-AMS’s National Bioengineered Food Disclosure Standard (NBFDS), published in 2018 and effective as of 2019, defines “bioengineered” as “contains genetic material that has been modified through in vitro recombinant deoxyribonucleic acid (DNA) techniques; and for which the modification could not otherwise be obtained through conventional breeding or found in nature.” Most gene-edited crops currently in development, such as those where the introduced gene is known to occur in the species naturally, are exempt from regulation under both the AMS’s NBFDS and APHIS’s SECURE acts.

What are some examples of genetic engineering methods?

Though “genetic engineering” has only entered the popular lexicon in the last several decades, humans have modified the genomes of plants for millennia, in many different ways. Through genetic changes introduced via traditional breeding, teosinte became maize 10,000 years ago in Mesoamerica, and hybrid rice was developed in 20th-century China. Irradiation has been used to generate random mutations in crops for decades, and the resulting varieties have never been subject to any special regulation.

In fact, transfer of genes between organisms occurs all the time in nature. Bacteria often transfer DNA to other bacteria, and some bacteria can insert genes into plants. Indeed, one of the most common “genetic engineering” approaches used today, Agrobacterium-mediated gene insertion, was inspired by that natural phenomenon. Other methods of DNA delivery including biolistics (“gene gun”) and viral vectors. Each method for gene transfer has many variations, and each method varies greatly in its mode of action and capabilities. This is key for the future of plant engineering: there is a spectrum—not a binary division—of methods, and evaluations of engineered plants should focus on the end product.

How are genetically engineered organisms regulated in the United States?

Genetically engineered organisms are chiefly regulated by USDA-APHIS, the EPA, and the FDA as established by the 1986 Coordinated Framework for the Regulation of Biotechnology. They oversee experimental testing, approval, and commercial release. The Framework’s regulatory approach is grounded in the judgment that the potential risks associated with genetically engineered organisms can be evaluated the same way as those associated with traditionally bred organisms. This is in line with its focus on “the characteristics of the product and the environment into which it is being introduced, not the process by which the product is created.”

USDA-APHIS regulates the distribution of regulated organisms that are products of biotechnology to ensure that they do not pose a plant pest risk. Developers can petition for individual organisms, including transgenics, to be deregulated via Regulatory Status Review.

The EPA regulates the distribution, sale, use, and testing of all pesticidal substances produced in plants and microbes, regardless of method of production or mode of action. Products must be registered before distribution. 

The FDA applies the same safety standards to foods derived from genetically engineered organisms as it does to all foods under the Federal Food, Drug, and Cosmetic Act. The agency provides a voluntary consultation process to help developers ensure that all safety and regulatory concerns, such as toxicity, allergenicity, and nutrient content, are resolved prior to marketing.

How do genetically engineered crops work?

Mechanisms of action vary depending on the specific trait. Here, we explain the science behind two types of transgenic crops that have been widespread in the U.S. market for decades. 

Bt crops: Three of the major crops grown in the United States have transgenic Bt varieties: cotton, corn, and soybean. Bt crops are genetically engineered such that their genome contains a gene from the bacteria Bacillus thuringiensis. This enables Bt crops to produce a protein, normally only produced by the Bt bacteria, that is toxic to a few specific plant pests but harmless for humans, other mammals, birds, and beneficial insects. In fact, the bacteria itself is approved for use as an organic insecticide. However, organic applications of Bt insecticides are limited in efficacy: since the bacteria must be topically applied to the crop, the protein it produces is ineffective against insects that have penetrated the plant or are attacking the roots; in addition, the bacteria can die or be washed away by rain. 

Engineering the crop itself to produce the insecticidal protein more reliably reduces crop loss due to pest damage, which also minimizes the need for other, often more broadly toxic systemic pesticides. Increased yield allows for more efficient use of existing agricultural land. In addition, decreased use of pesticides reduces the energy cost associated with their production and application while also preserving wildlife biodiversity. With regards to concerns surrounding insecticide resistance, the EPA requires farmers who employ Bt, both as a transgenic crop and as an organic spray, to also plant a refuge field of non-Bt crops, which prevents pests from developing resistance to the Bt protein.

The only substantive difference between Bt crops and non-Bt crops is that the former produces an insecticide already permitted by USDA organic regulations. 

Ringspot-resistant rainbow papaya: The transgenic rainbow papaya is another example of the benefits of genetic engineering in agriculture. Papaya plantations were ravaged by the papaya ringspot virus in the late 1900s, forcing many farmers to abandon their lands and careers. In response, scientists developed the rainbow papaya, which contains a gene from the virus itself that allows it to express a protein that counters viral infection. This transgenic papaya was determined to be equivalent in nutrition and all other aspects to the original papaya. The rainbow papaya, with its single gene insertion, is widely considered to have saved Hawaii’s papaya industry, which in 2013 accounted for nearly 25% of Hawaii’s food exports. Transgenic papaya now makes up about 80% of the Hawaiian papaya acreage. The remaining comprise non-GMO varieties, which would have gone locally extinct had it not been for transgenic papayas preventing the spread of the virus. The rainbow papaya’s success has clearly demonstrated that transgenic crops can preserve the genetic diversity of American crops and preserve yield without spraying synthetic pesticides, both of which are stated goals of the USDA Organic Program. However, the National Organic Program’s regulations currently forbid organic farmers from growing virus-resistant transgenic papaya.

How have recent biotechnology breakthroughs accelerated the development of new crops?

With the advent of CRISPR gene-editing technology, which allows scientists to make precise, targeted changes in an organism’s DNA, new genetically engineered crops are being developed at an unprecedented pace. These new varieties will encompass a wider variety of qualities than previously seen in the field of crop biotechnology. Many varieties are directly aimed at shoring up agricultural resilience in the face of climate change, with traits including tolerance to heat, cold, and drought. At the same time, the cost of sequencing an organism’s DNA continues to decrease. This makes it easier to confirm the insertion of multiple transgenes into a plant, as would be necessary to engineer crops to produce a natural herbicide. Such a crop, similar to Bt crops but targeting weeds instead of insects, would reduce reliance on synthetic herbicides while enabling no-till practices that promote soil health. Furthermore, cheap DNA sequencing facilitates access to information about the genomes of many wild relatives of modern crops. Scientists can then use genetic engineering to make wild relatives more productive or introduce wild traits like drought resilience into domesticated varieties. This would increase the genetic diversity of crops available to farmers and help avoid issues inherent to monocultures, most notably the uncontrollable spread of plant diseases. 

At present, most crops engineered with CRISPR technology do not contain genes from a different organism (i.e., not transgenic), and thus do not have to face the additional regulatory hurdles that transgenics like Bt crops did. However, crops developed via CRISPR are still excluded from organic farming.

What are examples of genetically engineered organisms currently on the market or in active development that address sustainability issues?

  • Improving sustainability and land conservation: potatoes that are slower to spoil, wheat with enhanced carbon sequestration capacity 

  • Increasing food quality and nutrition: vegetables with elevated micronutrient content 

  • Increasing and protecting agricultural yields: higher-yield fish, flood-tolerant rice

  • Protecting against plant and animal pests and diseases: blight-resistant chestnut, HLB-resistant citrus

  • Cultivating alternative food sources: bacteria for animal-free production of protein

Which agricultural stakeholders are engaged in genetic engineering R&D and will benefit from federal funding?

The pool of producers of genetically engineered crops is increasingly diverse. In fact, of the 37 new crops evaluated by APHIS’s Biotechnology Regulatory Service under the updated guidelines since 2021, only three were produced by large (>300 employees) for-profit corporations. Many were produced by startups and/or not-for-profit research institutions. USDA NIFA research grants predominantly fund land-grant universities; other awardees include private nonprofit organizations, private universities, and, in select cases (such as small business grants), private for-profit companies.

Why are GMOs so often vilified?

Historically, the concept of GMOs has been associated with giant multinational corporations, the so-called Big Ag. The most prevalent GMOs in the last several decades have indeed been produced by industry giants such as Dow, Bayer, and Monsanto. This association has fueled the negative public perception of GMOs in several ways, including: 

  • Some companies, such as Dow, were responsible for producing the notorious chemical Agent Orange, used to devastating effect in the Vietnam War. While this is an unfortunate shadow on the company, it is unrelated to the properties of genetically engineered crops.

  • Companies have been accused of financially disadvantaging farmers by upholding patents on GMO seeds, which prevents farmers from saving seeds from one year’s crop to plant the next season. Companies have indeed enforced seed patents (which generally last about 20 years), but it is important to note that (1) seed-saving has not been standard practice on many American farms for many decades, since the advent of (nonbioengineered) hybrid crops, from which saved seeds will produce an inferior crop, and (2) bioengineered seeds are not the only seeds that can be and are patented.