Genetic Engineering of Livestock: The Opportunity Cost of Regulatory Delay

Global status of gene edited animals for agricultural applications

Gene editing (GnEd) involves using a site-directed nuclease to introduce a double-strand break (DSB) at a targeted location in the genome. A literature search was performed on the use of GnEd in animals for agricultural applications. Data was extracted from 212 peer-reviewed articles that described the production of at least one living animal employing GnEd technologies for agricultural purposes. The most common GnEd system reported was CRISPR/Cas9, and the most frequent type of edit was the unguided insertion or deletion resulting from the repair of the targeted DSB leading to a knock-out (KO) mutation. Animal groups included in the reviewed papers were ruminants (cattle, sheep, goats, n=63); monogastrics (pigs and rabbits, n=60); avian (chicken, duck, quail, n=17); aquatic (many species, n=65), and insects (honeybee, silkworm, n=7). Yield (32%), followed by reproduction (21%) and disease resistance (17%) were the most commonly targeted traits. Over half of the reviewed papers had Chinese first-authorship. Several countries, including Argentina, Australia, Brazil, Colombia and Japan, have adopted a regulatory policy that considers KO mutations introduced following GnEd DSB repair as akin to natural genetic variation, and therefore treat these GnEd animals analogously to those produced using conventional breeding. This approach has resulted in a non-GMO determination for a small number of GnEd food animal applications, including three species of GnEd KO fast-growing fish, (red sea bream, olive flounder and tiger pufferfish in Japan), KO fish and cattle in Argentina and Brazil, and porcine reproductive and respiratory syndrome (PRRS) virus disease-resistant KO pigs in Colombia.

Genome editing: An insight into disease resistance, production efficiency, and biomedical applications in livestock

One of the primary concerns for the survival of the human species is the growing demand for food brought on by an increasing global population. New developments in genome-editing technology present promising opportunities for the growth of wholesome and prolific farm animals. Genome editing in large animals is used for a variety of purposes, including biotechnology to improve food production, animal health, and pest management, as well as the development of animal models for fundamental research and biomedicine. Genome editing entails modifying genetic material by removing, adding, or manipulating particular DNA sequences from a particular locus in a way that does not happen naturally. The three primary genome editors are CRISPR/Cas 9, TALENs, and ZFNs. Each of these enzymes is capable of precisely severing nuclear DNA at a predetermined location. One of the most effective inventions is base editing, which enables single base conversions without the requirement for a DNA double-strand break (DSB). As reliable methods for precise genome editing in studies involving animals, cytosine and adenine base editing are now well-established. Effective zygote editing with both cytosine and adenine base editors (ABE) has resulted in the production of animal models. Both base editors produced comparable outcomes for the precise editing of point mutations in somatic cells, advancing the field of gene therapy. This review focused on the principles, methods, recent developments, outstanding applications, the advantages and disadvantages of ZFNs, TALENs, and CRISPR/Cas9 base editors, and prime editing in diverse lab and farm animals. Additionally, we address the methodologies that can be used for gene regulation, base editing, and epigenetic alterations, as well as the significance of genome editing in animal models to better reflect real disease. We also look at methods designed to increase the effectiveness and precision of gene editing tools. Genome editing in large animals is used for a variety of purposes, including biotechnology to improve food production, animal health, and pest management, as well as the development of animal models for fundamental research and biomedicine. This review is an overview of the existing knowledge of the principles, methods, recent developments, outstanding applications, the advantages and disadvantages of zinc finger nucleases (ZFNs), transcription-activator-like endonucleases (TALENs), and clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR/Cas 9), base editors and prime editing in diverse lab and farm animals, which will offer better and healthier products for the entire human race.

Asexual reproduction for improved livestock breeding

As natural environments deteriorate, genetic improvements to agricultural animals will be required to ensure global food security. Improving livestock production by introducing asexual reproduction (AR) into mainstream animal husbandry can help meet the challenge, but its advantages must be accompanied by social, commercial, and governmental acceptance.

Simulation of dual-purpose chicken breeding programs implementing gene editing

BACKGROUND

In spite of being controversial and raising ethical concerns, the application of gene editing is more likely to be accepted when it contributes to improving animal welfare. One of the animal welfare and ethical issues in chicken breeding is chick culling, the killing of the male layer chicks after hatching due to the poor fattening performance. Although establishing dual-purpose chicken lines could solve this problem, unfavorable genetic correlations between egg and meat production traits hindered their competitiveness. Although it is also controversial in ethical terms, gene editing may accelerate genetic progress in dual-purpose chicken and alleviate the ethical concerns from chick culling.

RESULTS

The simulation compared the utility improvement in dual-purpose use under two breeding schemes: one consisting in the improvement of the laying hens, and the second in the improvement of a synthetic line obtained from a layer broiler cross. In each breeding scheme, the breeding programs were simulated with and without gene editing. Polygenic breeding values and 500 simulated quantitative trait loci (QTL) with different levels of pleiotropy caused negative correlations between egg production, meat production, and overall health. The results of the simulation demonstrated that genetic gain could be accelerated by at most 81% for several generations if gene editing was used. The actual increase in genetic gain depended on the number of single nucleotide polymorphisms (SNPs) being edited per animal. The rate of genetic improvement became equal in scenarios with and without gene editing after 20 generations. This is because the remaining segregating QTL had small effects and their edition would have negative overall health effects from potential off-target edits. Although gene editing can improve genetic gain in quantitative traits, it can only be recommended as long as QTL with reasonable effect sizes are segregating and detectable.

CONCLUSIONS

This simulation demonstrates the potential of gene editing to accelerate the simultaneous improvement of negatively correlated traits. When the risk of negative consequences from gene editing persists, the number of SNPs to be edited should be chosen carefully to obtain the optimal genetic gain.

Stem cell-based strategies and challenges for production of cultivated meat

Cultivated meat scale-up and industrial production will require multiple stable cell lines from different species to recreate the organoleptic and nutritional properties of meat from livestock. In this Review, we explore the potential of stem cells to create the major cellular components of cultivated meat. By using developments in the fields of tissue engineering and biomedicine, we explore the advantages and disadvantages of strategies involving primary adult and pluripotent stem cells for generating cell sources that can be grown at scale. These myogenic, adipogenic or extracellular matrix-producing adult stem cells as well as embryonic or inducible pluripotent stem cells are discussed for their proliferative and differentiation capacity, necessary for cultivated meat. We examine the challenges for industrial scale-up, including differentiation and culture protocols, as well as genetic modification options for stem cell immortalization and controlled differentiation. Finally, we discuss stem cell-related safety and regulatory challenges for bringing cultivated meat to the marketplace.

Perspectives in Genome-Editing Techniques for Livestock

Genome editing of farm animals has undeniable practical applications. It helps to improve production traits, enhances the economic value of livestock, and increases disease resistance. Gene-modified animals are also used for biomedical research and drug production and demonstrate the potential to be used as xenograft donors for humans. The recent discovery of site-specific nucleases that allow precision genome editing of a single-cell embryo (or embryonic stem cells) and the development of new embryological delivery manipulations have revolutionized the transgenesis field. These relatively new approaches have already proven to be efficient and reliable for genome engineering and have wide potential for use in agriculture. A number of advanced methodologies have been tested in laboratory models and might be considered for application in livestock animals. At the same time, these methods must meet the requirements of safety, efficiency and availability of their application for a wide range of farm animals. This review aims at covering a brief history of livestock animal genome engineering and outlines possible future directions to design optimal and cost-effective tools for transgenesis in farm species.

Genetic engineering and genome editing in plants, animals and humans: Facts and myths

Human history is inextricably linked to the introduction of desirable heritable traits in plants and animals. Selective breeding (SB) predates our historical period and has been practiced since the advent of agriculture and farming more than ten thousand years ago. Since the 1970s, methods of direct plant and animal genome manipulation are constantly being developed. These are collectively described as "genetic engineering" (GE). Plant GE aims to improve nutritional value, insect resistance and weed control. Animal GE has focused on livestock improvement and disease control. GE applications also involve medical improvements intended to treat human disease. The scientific consensus built around marketed products of GE organisms (GEOs) is usually well established, noting significant benefits and low risks. GEOs are exhaustively scrutinized in the EU and many non-EU countries for their effects on human health and the environment, but scrutiny should be equally applied to all previously untested organisms derived directly from nature or through selective breeding. In fact, there is no evidence to suggest that natural or selectively bred plants and animals are in principle safer to humans than GEOs. Natural and selectively bred strains evolve over time via genetic mutations that can be as risky to humans and the environment as the mutations found in GEOs. Thus, previously untested plant and animal strains aimed for marketing should be proven useful or harmful to humans only upon comparative testing, regardless of their origin. Highlighting the scientific consensus declaring significant benefits and rather manageable risks provided by equitably accessed GEOs, can mitigate negative predispositions by policy makers and the public. Accordingly, we provide an overview of the underlying technologies and the scientific consensus to help resolve popular myths about the safety and usefulness of GEOs.

Perspectives of gene editing for cattle farming in tropical and subtropical regions

Cattle productivity in tropical and subtropical regions can be severely affected by the environment. Reproductive performance, milk and meat production are compromised by the heat stress imposed by the elevated temperature and humidity. The resulting low productivity contributes to reduce the farmer's income and to increase the methane emissions per unit of animal protein produced and the pressure on land usage. The introduction of highly productive European cattle breeds as well as crossbreeding with local breeds have been adopted as strategies to increase productivity but the positive effects have been limited by the low adaptation of European animals to hot climates and by the reduction of the heterosis effect in the following generations. Gene editing tools allow precise modifications in the animal genome and can be an ally to the cattle industry in tropical and subtropical regions. Alleles associated with production or heat tolerance can be shifted between breeds without the need of crossbreeding. Alongside assisted reproductive biotechnologies and genome selection, gene editing can accelerate the genetic gain of indigenous breeds such as zebu cattle. This review focuses on some of the potential applications of gene editing for cattle farming in tropical and subtropical regions, bringing aspects related to heat stress, milk yield, bull reproduction and methane emissions.

Progress and opportunities through use of genomics in animal production

The rearing of farmed animals is a vital component of global food production systems, but its impact on the environment, human health, animal welfare, and biodiversity is being increasingly challenged. Developments in genetic and genomic technologies have had a key role in improving the productivity of farmed animals for decades. Advances in genome sequencing, annotation, and editing offer a means not only to continue that trend, but also, when combined with advanced data collection, analytics, cloud computing, appropriate infrastructure, and regulation, to take precision livestock farming (PLF) and conservation to an advanced level. Such an approach could generate substantial additional benefits in terms of reducing use of resources, health treatments, and environmental impact, while also improving animal health and welfare.

Antimicrobials in Animal Agriculture in the United States: A Multidisciplinary Overview of Regulation and Utilization to Foster Collaboration: On Behalf Of the Society of Infectious Diseases Pharmacists

Given the complexity of antimicrobial resistance and the dire implications of misusing antimicrobials, it is imperative to identify accurate and meaningful ways to understand and communicate the realities, challenges, and opportunities associated with antimicrobial utilization and measurement in all sectors, including in animal agriculture. The objectives of this article are to (i) describe how antimicrobials are regulated and used in US animal agriculture and (ii) highlight realities, challenges, and opportunities to foster multidisciplinary understanding of the common goal of responsible antimicrobial use. Recognition of the realities of medicine, practice, and policy in the agricultural setting is critical to identify realistic opportunities for improvement and collaboration.

Somatic embryogenesis and β-glucuronidase transformation in chickpea (Cicer arietinum cv. Bivanich)

BACKGROUND

Chickpea (Cicer arietinum L.) is an important kernel legume in the world. To optimize the plant tissue culture some experiments such as direct regeneration, proliferation, rooting shoots and somatic embryogenesis were done.

METHODS AND RESULTS

In experiments were used direct regeneration and proliferation, various levels of plant growth regulators NAA (0 and 1.0 mg/l), BAP (0, 1, 3 and 5 mg/l) and three explants' types (epicotyl, cotyledon and embryonic axis). The results of both experiments showed that embryonic axis explant was better than other explants. The highest percentage was obtained in MS media containing 1 mg/l BAP and also 3 mg/l BAP and 0.1 mg/l NAA with an average of 72%. The highest average number of branches (4.66) was found in the proliferation of embryonic axis in MS medium containing 3 mg/l BAP. The highest rooting shoot (90%) was found in 1/2MS in B5 medium vitamins with 0.2 mg/l of IBA and 0.5 mg/l NAA. Somatic embryogenesis experiments were compared on the concentration gradient of 2,4-D in fine embryonic axis explants. The results displayed that the concentration gradient of 10 mg/l 2,4-D to 5 mg/l of 2,4-D and then to zero concentration showed the highest number of embryos.

CONCLUSION

The best environment for regeneration embryos was MS medium with 2.5 mg/l of 2,4-D concentration gradient to zero. In this study, the PCR reaction showed the presence of the β-glucuronidase (gus) marker gene in regenerated cotyledons for 20 min in all three strains studied.

Towards progressive regulatory approaches for agricultural applications of animal biotechnology

Traditional breeding techniques, applied incrementally over thousands of years, have yielded huge benefits in the characteristics of agricultural animals. This is a result of significant, measurable changes to the genomes of those animal species and breeds. Genome editing techniques may now be applied to achieve targeted DNA sequence alterations, with the potential to affect traits of interest to production of agricultural animals in just one generation. New opportunities arise to improve characteristics difficult to achieve or not amenable to traditional breeding, including disease resistance, and traits that can improve animal welfare, reduce environmental impact, or mitigate impacts of climate change. Countries and supranational institutions are in the process of defining regulatory approaches for genome edited animals and can benefit from sharing approaches and experiences to institute progressive policies in which regulatory oversight is scaled to the particular level of risk involved. To facilitate information sharing and discussion on animal biotechnology, an international community of researchers, developers, breeders, regulators, and communicators recently held a series of seven virtual workshop sessions on applications of biotechnology for animal agriculture, food and environmental safety assessment, regulatory approaches, and market and consumer acceptance. In this report, we summarize the topics presented in the workshop sessions, as well as discussions coming out of the breakout sessions. This is framed within the context of past and recent scientific and regulatory developments. This is a pivotal moment for determination of regulatory approaches and establishment of trust across the innovation through-chain, from researchers, developers, regulators, breeders, farmers through to consumers.

The application of new breeding technology based on gene editing in pig industry

Genome/gene-editing (GE) techniques, characterized by a low technological barrier, high efficiency, and broad application among organisms, are now being employed not only in medical science but also in agriculture/veterinary science. Different engineered CRISPR/Cas9s have been identified to expand the application of this technology. In pig production, GE is a precise new breeding technology (NBT), and promising outcomes in improving economic traits, such as growth, lean or healthy meat production, animal welfare, and disease resistance, have already been documented and reviewed. These promising achievements in porcine gene editing, including the Myostatin gene knockout (KO) in indigenous breeds to improve lean meat production, the uncoupling protein 1 (UCP1) gene knock-in to enhance piglet thermogenesis and survival under cold stress, the generation of GGTA1 and CMP-N-glycolylneuraminic acid hydroxylase (CMAH) gene double KO (dKO) pigs to produce healthy red meat, and the KO or deletion of exon 7 of the CD163 gene to confer resistance to porcine reproductive and respiratory syndrome virus infection, are described in the present article. Other related approaches for such purposes are also discussed. The current trend of global regulations or legislation for GE organisms is that they are exempted from classification as genetically modified organisms (GMOs) if no exogenes are integrated into the genome, according to product-based and not process-based methods. Moreover, an updated case study in the EU showed that current GMO legislation is not fit for purpose in term of NBTs, which contribute to the objectives of the EU’s Green Deal and biodiversity strategies and even meet the United Nations’ sustainable development goals for a more resilient and sustainable agri-food system. The GE pigs generated via NBT will be exempted from classification as GMOs, and their global valorization and commercialization can be foreseen.

Invited review: Use of assisted reproduction techniques to accelerate genetic gain and increase value of beef production in dairy herds

The contribution of the calf enterprise to the profit of the dairy farm is generally considered small, with beef bull selection on dairy farms often not considered a high priority. However, this is likely to change in the future as the rapid rate of expansion of the dairy herd in some countries is set to plateau and improvements in dairy herd fertility combine to reduce the proportion of dairy breed calves required on dairy farms. This presents the opportunity to increase the proportion of beef breed calves born, increasing both the value of calf sales and the marketability of the calves. Beef embryos could become a new breeding tool for dairies as producers need to reassess their breeding policy as a consequence of welfare concerns and poor calf prices. Assisted reproductive technologies can contribute to accelerated genetic gain by allowing an increased number of offspring to be produced from genetically elite dams. There are the following 3 general classes of donor females of interest to an integrated dairy-beef system: (1) elite dairy dams, from which oocytes are recovered from live females using ovum pick-up and fertilized in vitro with semen from elite dairy bulls; (2) elite beef dams, where the oocytes are recovered from live females using ovum pick-up and fertilized with semen from elite beef bulls; and (3) commercial beef dams (≥50% beef genetics), where ovaries are collected from the abattoir postslaughter, and oocytes are fertilized with semen from elite beef bulls that are suitable for use on dairy cows (resulting embryo with ≥75% beef genetics). The expected benefits of these collective developments include accelerated genetic gain for milk and beef production in addition to transformation of the dairy herd calf crop to a combination of good genetic merit dairy female calves and premium-quality beef calves. The aim of this review is to describe how these technologies can be harnessed to intensively select for genetic improvement in both dairy breed and beef breed bulls suitable for use in the dairy herd.