Proceedings of a Workshop—in Brief

The State of Knowledge and Research Needs Regarding Heritable Genomic Modification in Food Animals

Proceedings of a Workshop—in Brief

On February 27–28, 2024, the National Academies of Sciences, Engineering and Medicine’s (National Academies) Board on Agriculture and Natural Resources held a hybrid workshop entitled State of Knowledge and Research Needs Regarding Heritable Genomic Modification in Food Animals.¹ The workshop was associated with a National Academies project established through the Consolidated Appropriations Act, 2023 (P.L. 117-328) and Explanatory Statement. The Explanatory Statement required the National Institutes of Health (NIH) to contract with the National Academies to conduct a study to identify genetic and other molecular mechanisms that could present risks to human health based on heritable genetic modification (GM) (natural, induced, intended, or designed) in food animal species.

This workshop, executed under the auspices of the study, aimed to examine the state of the science of the development of food animals with heritable GMs and their potential health risks, identify knowledge gaps in the ability to assess health risks, and explore potential approaches to address them.

This workshop was followed by another entitled Oversight and Food Safety Concerns Posed by Heritable Genetic Modification in Food Animals² where regulatory and risk challenges were presented.

This workshop began with opening remarks from committee chair Eric Hallerman of Virginia Polytechnic Institute and State University. The two-day workshop featured a combination of presentations by, and panel discussions featuring, experts in animal genetics and agriculture.

This Proceedings of a Workshop—in Brief has been prepared by the workshop rapporteurs as a factual summary of what occurred at the workshop, highlights the presentations and discussions, and is not intended to provide a comprehensive summary of all complex topics considered and information shared during the workshop. The information summarized here reflects the knowledge and opinions of individual workshop participants and should not be seen as a consensus of the workshop participants; the Board on Agriculture and Natural Resources; or the National Academies of Sciences, Engineering, and Medicine.

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METHODS FOR GENERATING HERITABLE GENETIC MODIFICATIONS IN FOOD ANIMALS

The first session of the workshop, moderated by committee member Elizabeth Maga of the University of California, Davis, focused on animal genomic modification technologies. Jonathan Gootenberg of Harvard University introduced the topic of novel molecular tools for genome editing and delivery, with a focus on clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (Cas9), which uses a guide ribonucleic acid to target and alter a specific gene. Gootenberg provided background on genome editing, stating that it has been over 20 years since scientists first sequenced a complete human genome. Improvements in science and technology since then have led to a better understanding of telomeres, how genetic diversity drives trait expression, and how targeted gene alterations can lead to cures for genetic diseases. Gootenberg described how tools such as CRISPR allow for a “search and replace” method of gene editing, and noted that newer methods like “prime editing” allow for even greater precision. He stated that his research focuses on phages—viruses that infect bacterial cells. When using a phage, researchers can combine two molecules and insert deoxyribonucleic acid (DNA) into a host genome. This process is called the programmable addition via site-specific targeting elements (PASTE) system and uses CRISPR technology to target the specific site within the host genome.

Omar Abudayyeh, also with Harvard University, continued Gootenberg’s presentation and spoke in depth about PASTE. He noted that the system can be packaged into adenoviruses and injected into animals for in vivo delivery of gene editing technology. He also spoke about this technology’s applications for human health, stating that with support from the Cystic Fibrosis Foundation, he and colleagues are attempting to edit the gene responsible for cystic fibrosis to eliminate the disease.

Jon Oatley of Washington State University provided an overview of the tools for editing genes in livestock, how they are used, and the novel animals they create. He began by describing the benefits of modifying the genomes of farm animals, including how these edits may help address food insecurity. Oatley noted how the growing global population increases the demand for dietary protein, requiring 60 percent more agricultural output, while the land and resources needed to produce such products are shrinking (OECD iLibrary, 2023). This combination of increased demand and reduced resources makes genetic engineering (GE) an important tool, “as it can reduce water and feed needed to grow the same amount of animal protein, making the process more efficient. Oatley said that improving the efficiency of animal protein production increases food security and may reduce the negative environmental impacts of raising animals for food. He noted that although selective breeding can produce similar effects, it takes much longer—more than 10 years to establish a new trait in mammalian systems. Using gene editing, Oatley said, allows scientists to produce trait changes in just one or two generations.

Oatley acknowledged that gene editing technologies like PASTE hold promise for the future but have not been tested on animals yet. He provided examples of successful genetically engineered animal projects, including the use of CRISPR/Cas9 and transcription activator-like effector nucleases (TALENs) to create pigs that are resistant to porcine reproductive and respiratory syndrome, hornless dairy cattle, and cows that are resistant to bovine viral diarrhea virus (BVDV). He stated that the next generation of editing will focus on germline transmission, stemming from a best practice of producing edited embryos that transmit edited germlines to create heritable traits. Oatley noted some potential hazards, such as off-target edits, foreign DNA integration, and high levels of mosaicism, which gives rise to multiple different alleles in founder animals. However, he said that these off-target edits are not known to pose a risk to animal health or food safety. Oatley closed by stating that improving food security will partially depend on livestock genome editing and that this editing should aim to improve farm animal efficiency and resiliency.

HORIZON SCAN: WHAT TRAITS MIGHT BE PURSUED WITHIN THE NEXT TWO YEARS?

The workshop’s second session included a horizon scan of traits that could be introduced in the near future and was introduced and moderated by Thomas Spencer of the University of Missouri. Speakers discussed the future of animal genomics, including challenges and opportunities related to GM of poultry, ruminants, pigs, and fish.

Speakers addressed how GE can help meet the global food landscape’s growing protein demands and how existing species can be mined for beneficial traits to be integrated into cultivated species.

Mike McGrew of the Roslin Institute opened with the concept of scanning the horizon of genome editing. McGrew focused on genome editing in chickens and associated applications for the poultry industry. He stated that gene editing in poultry primarily seeks to support food production, as chickens are an important source of dietary protein for consumers around the globe. Each year, 70 billion chickens are slaughtered for food worldwide, a number expected to grow 50 percent by 2050 to accommodate anticipated population growth and economic development, particularly in low- and middle-income countries (LMICs) (OECD iLibrary, 2023). McGrew highlighted the role that large-scale farming plays in preventing hunger and malnutrition and satisfying the growing demand for protein in LMICs. He also noted that significant progress has already been made by using selective breeding in poultry production. Specifically, there has been an 80 percent increase in meat production efficiency since the 1950s (Ritchie and Roser, 2024). McGrew described the additional potential improvements gene editing technologies can provide, including reducing the burden of pandemic poultry diseases and the need for antibiotics, mitigating the adverse environmental effects of poultry farming, enhancing animal welfare, and conserving poultry genetic diversity.

McGrew discussed technologies used to edit poultry genomes, including CRISPR, TALENs, and zinc finger nucleases. He said that these technologies allow for precise changes to the genome and operate on the reproductive cells of chickens, which are already present in early embryos. These technologies mediate changes to the early embryo and ultimately modify germ cells to create genetically modified offspring. This specific technique works for chickens, McGrew noted, because they have primordial germ cells that can be cultured in vitro. Using sterile male chickens and female chimeras in these processes allows for the creation of homozygous gene edited chickens.

Gene editing technologies, McGrew said, can also improve the efficiency and animal welfare of the egg-production industry. Only female egg-producing chickens are useful to the industry, resulting in the culling of five billion male chicks globally each year. The European Union recently enacted a law against this practice, requiring male layer chicks to be raised for meat, but since these chickens were not bred for meat production, they are not feed-efficient, and raising them has a large carbon footprint. Genome editing could allow the egg industry to identify male-producing eggs at point-of-lay, allowing those eggs to be used for other products while retaining female-producing eggs for hatching—preventing the culling of newly hatched males and improving resource efficiency.

Finally, McGrew noted the potential for gene editing to reduce disease susceptibility in chickens. He described this method as more efficient and feasible than mass vaccination, especially because wild birds often transmit disease to industry flocks, and wild birds cannot be systematically captured and vaccinated. Therefore, McGrew said that altering the genes of commercial poultry stocks to make them more resilient against viral infection could benefit the industry overall.

Dan Carlson of Recombinetics focused on the traits of ruminants and using GE to pursue optimized trait expression. He stated that desired traits are governed by several factors, including the regional needs of producers, changing environments, and consumer demand. Carlson divided the types of traits that producers might pursue into three categories: quality, resilience, and efficiency. He noted some overlap in the categories—for example, a resilience trait may also make an animal more adaptable to their environment, increasing their efficiency.

Carlson also spoke about existing market forces on deploying these trait improvements. Although industry had focused on single trait alterations in the past, he said that producers may now want to explore multiple simultaneous gene alterations that lead to optimized phenotypes. He provided examples of existing and past projects, including the Thamani dairy cattle project funded by the Bill & Melinda Gates Foundation, which

is working to generate dairy animals that contribute to sustainable production gains for African dairy production systems. The project seeks to deploy novel sequence variants through multiplex gene editing and develop a breeding system to propagate gene edited animals. The cattle breeds in the project were chosen for their efficiency and edits were designed to adapt the animals to the target region. The resulting cow, the “Girlando”, is a cross between a breed with high milk production and a breed that is well adapted to hot climates. The Girlando shows, on average, increased milk production and a lower, less stressful body temperature than its unmodified counterparts.

In closing, Carlson said that producers may attempt to replicate naturally occurring variants to facilitate regulatory approval, as variants in existing cattle breeds can improve efficiency, quality, and resilience. However, he reiterated that “multiplexing” gene edits may support more efficient trait deployment and phenotype optimization. In response to audience questions about business and economic considerations, including how traits might be deployed in different markets and the technology’s affordability for smallholder farmers in Africa, Carlson suggested that an initial market adoption focus could be to distribute gene edited semen to regions where the species could thrive, then establish breeding nucleus herds to more broadly deploy the animals. He also noted that creating government-funded breeding hubs could be an effective approach.

Kevin Wells of the University of Missouri provided a horizon scan of optimal heritable traits in pigs over the next five years. As with poultry and ruminants, swine gene alterations are targeted toward improving animal welfare, reducing the carbon footprint of animal production, and increasing disease resistance. Wells described how producers want to make pigs resistant to influenza, diarrheal disease, and classic swine fever viruses. The carbon footprint of swine production could also be decreased by altering the pig’s metabolism to improve thermoregulation, Wells suggested. Additionally, he spoke about potential feed efficiency and animal welfare improvements by altering digestive enzyme production to allow pigs to digest a wider variety of materials and neutralize common mycotoxins, such as aflatoxin, in their feed.

With respect to future considerations, Wells stated that his main concern is regulation, as there is no clear regulatory path for genetically modified animals entering the food supply. He described the lack of a rational, biological basis for determining which mutations are regulated and called for both establishing a biological hypothesis of risk and reducing barriers to producing livestock with expressed genetic alterations. To this end, Wells suggested that the U.S. Department of Agriculture (USDA), rather than the U.S. Food and Drug Administration (FDA), should oversee food-safety considerations related to genetically engineered animals in the food supply, noting that the focus on food, rather than on biomedical research, makes USDA the most appropriate federal regulatory authority.

In response to questions from the audience about international regulation of swine gene editing technology, Wells noted that other countries are ahead of the United States. In the current U.S. regulatory environment, Wells said there is little potential for return on investment in modified animal genomes—especially for venture capital investors. Meanwhile, China is advancing its use of gene editing technology, Wells said, due to their interest in approaches to feed their growing population.

An audience member asked about the potential impact of genome editing on animal welfare and how phenotype can be used to assess the success and health of a genetically modified animal. Wells asserted that an unhealthy animal is not economically or commercially viable.

Ross Houston of BMK Genetics focused on genome editing’s potential benefits for the aquaculture industry. He addressed how selective breeding and genome editing can be combined to improve the health and resiliency of fish in commercial settings within the next 25 years. Houston said gene editing will play a key role in disease prevention and resilience, noting that globally, only 1 percent of fish are vaccinated—in stark contrast to high vaccination rates for terrestrial animals. As a result, gene editing may be an ideal disease prevention tool for the aquaculture industry. Houston noted that genetic marker genotyping has already had a major impact on commercial breed-

ing programs and highlighted that since fish are earlier in their domestication process than terrestrial livestock, there have been fewer genetic bottlenecks and there is great potential to make rapid advancements using these technologies.

Houston noted that the current focus of research and development in aquaculture genome editing is scalable gene editing methods, which can be effectively integrated into commercial breeding programs. He acknowledged that mosaicism is likely to remain a concern and highlighted the importance of edits that are both accurate and scalable. He suggested that introducing sterility into genetically engineered lines of fish may expedite regulatory approval while protecting intellectual property for commercial interests. He also spoke about the benefits of GE technology to commercial breeders—most notably that gene editing allows for less time between generations, providing a major benefit to breeders who focus on fish with lengthy generational intervals.

Houston concluded by emphasizing the benefits of genomics to commercial aquaculture, including the importance of focusing on scalable methods and traits that confer disease resistance. He pointed out that existing species can be mined for preferable traits—for example, coho salmon are naturally resistant to sea lice. In response to an audience member’s question about the potential risks of inbreeding when using gene editing technologies, Houston stated that inbreeding is heavily monitored and not considered a problem. He also said that targeted gene editing may be more effective than other methods for sourcing gene alterations like mutagenesis, which has a much higher likelihood of producing random off-target and potentially detrimental mutations compared to conventional breeding.

Martin Lema of the National University of Quilmes, Argentina, addressed the future of heritable genomic traits in livestock through the lens of researchers and producers in Argentina. Lema spoke about how GE is mostly used in non-food animals—like polo horses and racing camels—in Argentina. He also spoke about genome editing for human health research applications, including studying human deafness in sheep animal models and creating potential human kidney and heart xenografts. He introduced the concept of molecular “pharming”, in which animal genomes are modified to produce potential therapeutic compounds for human health applications. One example of pharming is expressing therapeutic compounds into bovine mammary glands, which would then secrete them into milk expressed by the gland.

Lema spoke about potential commercial gains due to GE in farm animals in Argentina, including how researchers are using GE to reduce the allergenicity of milk protein and “humanize” the proteins for optimized human digestion, as well as “knock out” myostatin expression in sheep to produce meat more efficiently. Researchers have also engineered sheep so they can be fed a wider variety of carbohydrates and created a rotavirus-resistant cattle line. Lema also noted that GE is being used to improve production and increase commercial output in the silk industry.

Lema added to Wells’ prior comments about regulatory challenges, noting the complex regulatory landscape around introducing animals engineered for non-food uses into the food production system. Lema described the different regulatory structures for animals used for food compared with animals used as research subjects and noted that genetically engineered animals could fall under either of these categories. Lema asked if these animals should be held to both standards or if they require a new standard tailored to their unique case. Lema noted questions about whether the meat from the same cow would also be perceived as “humanized”, and thus perhaps inappropriate for human consumption. Broadly, Lema said that consumer confusion about genetically engineered animals limits acceptance. In closing, Lema spoke about the importance of risk management, especially when using gene editing to reduce disease susceptibility, as these edits may also alter other important gene functions that could increase susceptibility to other diseases.

VIEWS OF STAKEHOLDERS: INDUSTRY, PUBLIC HEALTH, AND CONSUMERS

The workshop’s third session featured two panel discussions on the views of stakeholders involved in the GM of food animals, including the private sector, public agencies, and consumers. The first panel of industry

stakeholders included Tad Sonstegard of Acceligen, Elena Rice of Genus, and Bo Harstine of Select Sires, and was moderated by Jon Oatley of Washington State University.

Oatley began by asking the panelists about leading global regulatory challenges. Sonstegard described a lack of venture capital investment due to uncertainty about how the product will reach the market. While there are profitable investments in genetically modified plants and crops, no such profits currently exist for genetically modified animals. Harstine added that potential investors want clarification regarding long-term federal regulation of the industry. Rice explained that a genetically engineered animal is currently regulated by the FDA as a drug because the changes to the animal genome may be transmitted to the next generation. Rice noted the lack of clarity in this reasoning and expressed her view that a living animal should not be regulated as a drug. She said that bridging the gap between regulatory expectation and reality is a major challenge.

Oatley asked the panelists about challenges with consumer perception and acceptance of genetically modified animal products. Sonstegard said that because gene editing is not consumer-facing, wholesaler and producer adoption is a more significant challenge. Harstine agreed with this point. Rice added that interest and acceptance differ widely across countries and highlighted the importance of global marketplace acceptance. She noted that the United States is a cultural leader and that other countries may base their decisions on American acceptance and regulation. Even in countries where laws and regulations are more favorable towards genetically modified animals, Rice said, until America accepts the technology, cultural barriers to acceptance will remain.

The panel discussed the importance of genetically engineering farm animals for sustainability and adaptation to climate change. Rice pointed out that consumers care deeply about these issues, and that framing GE as a sustainability measure could help increase understanding and acceptance. For example, Rice said, it is possible to show consumers the exact amount of carbon production that is reduced by gene editing pigs. Harstine concurred and discussed the use of life cycle analyses for illustrating potential environmental footprint reductions that can be achieved through GE.

Rice and Harstine both pointed to regulatory considerations as the most significant industry concerns. Sonstegard said that his greatest concerns are about profitability, describing the importance of quality control and reducing risks of product adoption by the market.

The second panel focused on public agencies, consumers, and the public, and was moderated by Bernadette Dunham of George Washington University. The panelists included Steven Moeller of USDA Agriculture Research Service (ARS) Food Animal Production Program, Adam Moyer of FDA, and Jennifer Kuzma of North Carolina State University.

Moeller addressed USDA’s perception of the current state of animal biotechnology and existing research gaps. He described a 2023 USDA report titled, “Genome to Phenome: Improving Animal Health, Production, and Well-Being—A New USDA Blueprint for Animal Genome Research 2018–2027”, that outlined a research strategy and priorities for animal genomics research (Rexroad et al., 2019). The report points to the impact of genetically modified animals, including benefits such as animals that are more efficient and adapted to a changing climate. Moeller noted that genome editing is a priority within the government and public funds have been allocated for research and technological improvements.

Moeller then described USDA’s focus on translating research into action to benefit farmers and producers. He highlighted locations across the United States where USDA funding is used to advance animal genomic research. He echoed some earlier speakers, including Abudayyeh and Houston, in stating that natural mutations can serve as the basis for designing precision edits; that existing species can be mined for traits; and that GE technology can be harnessed to add these desirable traits to other lines, breeds, and species. In closing, Moeller noted that the purpose of GE technology is to improve the safety of the food supply, lower the burden of infectious disease, and reduce antibiotic use. He highlighted challenges, such as the time and cost that effective research requires, and remarked on the importance of public-private partnerships in overcoming these barriers.

Moyer defined FDA’s approach to GE as “risk-based” and said that their view of the hazards of GE in animals can be divided into three broad categories: unintended consequences of intended gene alterations, unintended alterations at the target site, and unintended alterations elsewhere in the genome. However, he noted that the presence of unintended consequences or alterations does not inherently present a safety concern, and risks should be addressed on a case-by-case basis, considering all relevant factors.

Moyer established the importance of addressing potential hazards in genetically engineered animals, stating that unintended consequences can have negative impacts, especially when they are quickly adopted into the production population and transmitted across generations. He then described FDA’s review process to assess risk and address safety concerns.

Moyer closed by noting that FDA is interested in further exploration of any potential harms to human and environmental health, the potential risk of horizontal gene transfer to gut organisms, and any downstream hazards. He also described the Veterinary Innovation Program, which can provide a path to regulatory approval for a genetically engineered animal product that shows potential benefit to animal or human health and well-being.

Kuzma presented the perspectives of consumers and the public, describing uncertainty and confusion. She addressed discrepancies between the perspectives of scientists and regulators compared to the public. For example, Kuzma said that public perception is often values-based instead of science-based—a distinction that scientists and policy makers should consider. She also noted that the public does not understand who the decision makers are regarding the safety of genetically modified animals or how risk assessments are conducted. She reminded scientists to consider their role in educating the public.

To illustrate the complex views of the public and the role that scientists and policy makers can play in education, Kuzma gave an example of a policy development process for genetically modified salmon in Canada. Studies were conducted to determine whether genetically modified salmon were more allergenic than traditional salmon, with inconclusive results (Smith et al., 2010). The data from these studies can be interpreted differently depending on previously held thoughts. Kuzma explained that while scientists may interpret uncertain data as the absence of risk, this interpretation does not align with the views and values of the public.

Looking to the future, Kuzma said that current regulatory assessments do not sufficiently consider the public’s most important concerns. She proposed an approach that considers the values of all stakeholders, describing the way forward as “post-normal science,” which could help to minimize blind spots, engage outside experts and the public, and bring alternative perspectives into policy making and regulation. She supported the life-cycle analyses mentioned by Rice and Harstine and said that she was encouraged that their use represented a future in which scientists address consumer values.

ANIMAL WELFARE

The workshop’s fourth session, focused on animal welfare, was moderated by Bill Muir of Purdue University and featured a presentation by Mark Tizard of the Commonwealth Scientific and Industrial Research Organisation (CSIRO), an Australian government agency responsible for scientific research. Tizard discussed animal welfare from an Australian perspective through the lens of the egg-layer industry. As McGrew previously described, about 5 billion male layer chicks are culled annually since they are not useful to the industry. Males of layer lines that are not culled provide an outsized carbon footprint, having been bred for egg-laying rather than efficient meat production. Tizard reiterated that GE can be used to sex-segregate eggs at time-of-lay, selecting for female chickens, and reducing the need to either cull or raise inefficient animals, providing benefits for the entire supply chain and improving animal welfare. He noted that gene editing technology would need to be integrated into the chicken breeding pyramid to integrate it into the commercial egg industry.

Regarding consumer perception, Tizard said that GE technology is highly accepted by Australian consumers, who recognize the widespread benefits. He also said that eggs produced by creating null segregants are not officially considered a genetically modified organism (GMO), making market adoption easier. Tizard noted the challenges and inconsistencies in the global regulatory

landscape and closed by stating that the future of GE research will depend on public-private partnerships and investment from commercial partners.

GENOME ANNOTATION AND RELATION TO FOOD SAFETY OF GENETICALLY MODIFIED ANIMALS

The workshop’s fifth session focused on genome annotation and relation to food safety of genetically modified animals, was moderated by Penny Riggs of Texas A&M University, and featured presentations from Fiona McCarthy of the University of Arizona and Terence Murphy of the National Center for Biotechnology Information (NCBI).

McCarthy provided an overview of the current state of farm animal reference genomes. She said that good reference genomes exist for most farm animals, including cows, pigs, sheep, and chickens. Although there are many reference genomes for aquaculture, it is a challenging sector due to the large number of species under production. McCarthy stated that genome annotation is essential for supporting genome editing, but is poorly defined. She posited that “normal” gene expression is unknown, and there is no single annotation set for farmed animals. Many edits are made in non-coding regions of farm animal genes, but uncertainty remains about which regions are truly non-coding. The industry is moving towards “functional annotation” of the genome, when information about the function of a gene product is identified and which supports the prediction of phenotypic effects of any edits. McCarthy emphasized that a standardized gene nomenclature, or a common language for describing the functions that might follow from gene changes, may be beneficial. Establishing a standardized gene nomenclature and database of high-quality annotations may allow science and industry to improve the assessment of gene edits.

McCarthy closed by stating her desire to incorporate animal welfare into the functional assessment of gene edits. She noted that the complexity of aquaculture genomes makes improving annotation and assessment even more important. Finally, she suggested that food safety assessments should be based on phenotypic and physiological changes, echoing remarks previously made by Wells and Rice.

Murphy spoke about the NIH Comparative Genome Resource (CGR). The CGR includes more than 36,000 genomes from more than 15,000 species. Murphy said that there has been a recent shift in the CGR to genomes constructed with large contigs, or long contiguous sequences, meaning there are fewer gaps in the reference genome. This is an important marker of quality because genomes containing large contigs are more accurate and thus more useful as a reference.

Murphy described a CGR toolkit for researchers, which includes an interface to access genomic data, tutorials, and a comparative genome viewer that allows researchers to compare genomes through assembly alignments. It also includes a foreign containment screening process, given the persistent concern of bacterial genomes contaminating animal genomes. Almost 3 million proteins in the database are currently identified as contamination. The NCBI is working with submitters to improve the quality and usefulness of the database by ensuring that future entries do not contain bacterial genomes and that contaminated entries are edited out, resulting in more accurate representations of the target animal’s genomic information.

Murphy ended his remarks by looking ahead to the future of genome reference tools. He said that the CGR and related resources should be useful to researchers conducting animal genomic research. He noted that NCBI is working to make it easier for researchers to submit information into the database and to distribute the database more broadly, making the tools more useful and accessible.

The session ended with a discussion about the value of assessing genomic data compared to phenotype. Murphy, McCarthy, Wells, and Rice agreed that phenotype should be considered the most useful measurement.

BIOLOGICAL MECHANISMS THAT MAY PRESENT NOVEL HAZARDS

The workshop’s sixth session focused on biological mechanisms that may present novel hazards, was moderated by Lyda Garcia of Ohio State University, and featured presentations from Allison Van Eenennaam of the University of California, Davis, and Fred Gould of North Carolina State University.

Van Eenennaam began by sharing a case study of assessing animal health and food safety in products from genetically engineered polled calves. The polled trait is a naturally occurring variant and gene editing was used to mimic it, making the trait both dominant and stably inherited. Van Eenennaam’s research group conducted a full genome analysis of the genetically engineered calves, which showed that the edit was successful and did not produce any unintended modifications that could impact animal well-being or food safety. The average rate of mutation of conventionally-bred calves and gene edited calves was approximately equal, showing that gene editing did not impact the cows beyond typical levels of mutation. Van Eenennaam also described a food safety analysis of the meat and milk from genetically engineered cows, noting that neither differed significantly from those of conventionally-bred cows.

Van Eenennaam concluded by saying that traditional animal breeding, despite the high level of variation produced, has an excellent history of safety. There are no regulations for bringing a new breed to market using traditional breeding methods, but there are limitations for genetically engineered animals, creating high barriers to entry. She urged progress toward using a biological risk hypothesis in future assessments.

Gould opened a conversation about the multi-omics assessment of crop plants and lessons learned during the approval process. He noted that transgenic crops face the most regulatory scrutiny of any crop type and that updates to plant breeding technology have outpaced consumer understanding and regulatory action. Gould described the global fragmentation of genetically engineered crop labeling and inconsistencies in labeling requirements, neither of which reflect the current science. He emphasized the illogical approach to regulating genetically engineered crop foods compared to those that have been altered using conventional breeding and processes for inducing mutations. He suggested avoiding these inconsistencies in the regulatory approach for genetically engineered animals.

Gould ended his remarks by saying that the public’s perspective should be considered in scientific, regulatory, and industry decisions about genetically engineered farm animals. He emphasized that the most important question about a genetically engineered cow is not whether it appears different from the cow it came from, but whether it is meaningfully different from other cows on the market.

NOVEL RESISTANCE TO DISEASE

The workshop’s seventh session focused on novel resistance to disease; was moderated by Aspen Workman of USDA-ARS; and featured presentations from Darrell Kapczynski of USDA-ARS, Julianna Lenoch of USDA Animal and Plant Health Inspection Service, Shayan Sharif of the University of Guelph, Canada; and Wendy Barclay of Imperial College London. The presentations were followed by a panel discussion moderated by Workman that included speaker responses to audience questions.

Kapczynski spoke about how GM of poultry could play a role in improving disease resistance, preventing avian influenza virus (AIV) pandemics, and reducing related industry losses. Kapczynski offered background on AIV, stating that there are 144 subtypes of the virus that are subdivided into high- or low-pathogenicity pathotypes. High-pathogenicity AIV kills 75 percent of infected birds, representing a massive industry loss during an outbreak (Rexroad et al., 2019). AIV is maintained in wild migratory birds and spillover from these birds impacts domesticated birds and other animals, such as cattle and swine. These spillover events can infect millions of birds, leading to depopulation efforts to control the spread. Importantly, Kapczynski mentioned, viruses can mutate from low- to high-pathogenicity during mutation and replication.

Kapczynski discussed the history of Highly Pathogenic Avian Influenza Virus (HPAIV) H5, which emerged in China in 1996. From 2011 to 2013, only 20 countries reported its presence, but from 2014 to 2015, the virus adapted and spread widely. Between 2020 and 2023, it was introduced to the United States, traveled down the Eastern seaboard, moved to the Western seaboard, and entered South America. HPAIV H5 is a global problem and has spilled over into mammals, including marine animals. Kapczynski discussed control methods for AIV, the first of which is biosecurity, or keeping the virus out of a population. Vaccination also plays a role but is difficult to apply due to poultry industry regulations and the inability to capture and vaccinate wild birds. For these rea-

sons, Kapczynski stated, it would be useful to engineer HPAIV-resistant poultry.

Kapczynski concluded by addressing the future of research on genetically engineered disease resistance, noting that genetically engineered poultry will likely represent a major opportunity and path forward for the industry. For example, GE could be used to enhance innate immunity or inhibit viral replication. Targeting cell receptors could be key, he said, but the receptors may be unique to each virus. Kapczynski also warned of the potential for a genetically engineered disease-resistant animal to act as a novel reservoir in which more virulent or transmissible viruses might evolve.

Lenoch began by addressing whether genetically engineering disease resistance in animals might drive pathogen evolution. She presented a case study in which her team used surveillance data to understand how disease spreads from wild to domesticated birds. Lenoch said that HPAIV is usually asymptomatic in wild birds, making surveillance and testing critical to understanding disease spread and associated mutations. She stressed the importance of private-public partnerships for gathering, analyzing, and utilizing these data. She concluded by focusing specifically on the 2022 outbreak of H5N1 AIV and its implications for the poultry industry. She reported losses of nearly 80 million birds, noting that the ongoing threat of this virus extends beyond the poultry industry, as it could spill over into farm animals, aquaculture species, and humans.

Sharif described the function of chicken immune systems and how they respond to viral infection. He highlighted the importance of private-public partnerships and international collaboration given the global nature of viral disease spread. Sharif detailed potential interventions for reducing viral spread, including vaccination’s mixed successes. He described how labor-intensive and costly widespread poultry vaccination campaigns in France and Canada have been. He offered some suggestions for an ideal vaccine, noting that it should be inexpensive, developed quickly to outpace viral mutation, effective in a single dose, implementable through a mass campaign, effective across multiple species, and result in long-term immunity. He emphasized the importance of a vaccine that would reduce viral transmission rather than improve resilience against infection, as increased resilience could potentially create asymptomatic carriers of disease. Sharif closed by positing that future viral disease reduction in chickens might benefit from a multi-pronged approach that combines GE and mass vaccination.

Barclay spoke about the potential for GE to improve viral disease resistance in chickens. Earlier in her career, Barclay discovered a host factor in chickens that viruses rely on for replication. This protein, ANP32A, is different in poultry than mammals and is a potential target for engineering viral resistance in chickens. Barclay described research on altering the ANP32A protein that was conducted by her team using CRISPR. They produced chickens that appeared healthy and exhibited resilience against viral infection—but not immunity. In an additional series of experiments, birds with the novel ANP32A protein exhibited half the viral load of unedited birds after being inoculated, were less likely to catch the virus from other birds, and showed unique viral mutations. Barclay described concerns stemming from research findings that genetically engineered animals could result in novel viral mutations and potentially lead to a human pandemic but noted that this risk has not yet materialized with the ANP32A protein alteration and that the risk of viral mutation and spread is possible with any imperfectly vaccinated population. Barclay reiterated a comment from Sharif that a combination of GE and vaccination, which simultaneously target both viral susceptibility and spread, may be an ideal solution.

GENOMICS

The final workshop session, on genomics, was moderated by Fiona McCarthy of the University of Arizona and featured presentations by Michel Georges of the University of Liege, Belgium; Elena Rice of Genus; and Rachel Hawken of Cobb-Vantress. Georges presented an overview of genomics, discussing genetic mutations that may occur in humans, cattle, and pigs. He said that while there is significant genetic diversity in human populations, pig populations are even more diverse, despite being bred in a highly selective manner. Humans are more likely than cows to carry potentially deleterious mutations at the rate of up to 5 genetic mutations per generation, compared with an average of 0.5 mutations

per generation in cows (Robinson et al., 2023). Georges examined de novo mutations in cattle germ lines, noting that cattle sperm cells carry an average of 41 de novo mutations uniformly distributed across the genome. Georges stated that 1 in every 16 cattle births has a structural variant. The variants primarily occur in early development and more frequently on paternally derived chromosomes. Interestingly, the use of in vitro fertilization increased rates of structural mutations fivefold, with 1 in every 3 births showing structural changes.

Georges concluded by stating that the cattle mutations he described do not impact food safety, animal health, or consumer safety. He said that these genetic changes can occur using classical breeding methods and none of the GE-derived mutations are functionally different from natural de novo mutation. However, he noted the importance of tracking these changes to assess potential impacts on food safety, animal welfare, and the environment.

Rice spoke about gene editing in the context of genomic variation. She discussed the genomic information that is available in public databases, highlighting the natural variation that occurs across breeds. She described research conducted by Genus to identify and address off-target mutations in the porcine genome. She noted that incomplete reference genomes can lead to misidentified de novo or off-target mutations, which is a challenge. Genus’ research traced the genome from F1 founder animals and showed that most mutations were inherited from the prior generation. While some de novo mutations were identified in gene edited pigs, none of the de novo mutations were found in the targeted regions of genes and, there was no significant difference in the frequency of off-target mutations in genetically engineered pigs compared with conventionally-bred pigs. The use of GE facilitated the identification of off-target mutations due to its highly focused approach. Rice concluded by calling for more precise and comprehensive annotation of farm animal genomes to support improved identification of off-target and de novo mutations.

Hawken spoke about genomic variation in chickens. She noted that more than 1,400 heritage chicken breeds and more than 100 commercial breeds exist worldwide. Analyzing this natural diversity could help identify potential genetic improvements that could be integrated into the poultry industry using GE. Hawken noted challenges with sequencing chicken genomes due to factors including their variety and the presence of micro-chromosomes, which are difficult to sequence reliably. She emphasized the importance of understanding the wide variety of genetic variation in chickens as breeders use GE to incorporate new traits. Hawken described her research examining the genes that give rise to specific traits in chickens and reiterated comments made by Rice and McCarthy about the importance of moving toward functional annotation to improve understanding of breed differences. In closing, Hawken stated that rare and indigenous breeds provide particularly valuable traits for future gene editing, including genes that promote disease resistance and longevity.

REFERENCES

DISCLAIMER This Proceedings of a Workshop—in Brief was prepared by Melissa Maitin-Shepard and Marian Flaxman as a factual summary of what occurred at the workshop. The statements made are those of the rapporteur(s) or individual workshop participants and do not necessarily represent the views of all workshop participants; the planning committee; or the National Academies of Sciences, Engineering, and Medicine.

*The National Academies of Sciences, Engineering, and Medicine’s planning committees are solely responsible for organizing the workshop, identifying topics, and choosing speakers. The responsibility for the published Proceedings of a Workshop—in Brief rests with the institution. The planning committee comprises Eric M. Hallerman (Chair), Bernadette M. Dunham, Virginia A Stallings, Lyda G. Garcia, Fred Gould, Darrell R. Kapczynski, Elizabeth Maga, Fiona M. McCarthy, Mike J. McGrew, William (Bill) M. Muir, James (Jim) D. Murray, Jon M. Oatley, Penny K. Riggs, Thomas E. Spencer, and Aspen M. Workman.

REVIEWERS To ensure that it meets institutional standards for quality and objectivity, this Proceedings of a Workshop—in Brief was reviewed by: Shane Burgess, University of Arizona; and John McNamara, Washington State University.

SPONSORS This workshop was supported by the Office of Science Policy, National Institutes of Health.

STAFF Albaraa Sarsour, Mitchell Hebner, Robin Schoen, and Samantha Sisanachandeng from the Board on Agriculture and Natural Resources and Ann Yaktine from the Health and Medicine Division of the National Academies of Sciences, Engineering, and Medicine supported this work.

For additional information about this workshop, visit https://www.nationalacademies.org/event/41706_02-2024_state-ofknowledge-and-research-needs-regarding-heritable-genomic-modification-in-food-animals-a-workshop.

Suggested citation: National Academies of Sciences, Engineering, and Medicine. 2024. The State of Knowledge and Research Needs Regarding Heritable Genomic Modification in Food Animals: Proceedings of a Workshop—in Brief. Washington, DC: The National Academies Press. https://doi.org/10.17226/27591.

Division on Earth and Life Studies Copyright 2024 by the National Academy of Sciences. All rights reserved.