First gene-edited calf with reduced susceptibility to a major viral pathogen

Application of Genomic Selection in Beef Cattle Disease Prevention

Genomic applications in beef cattle disease prevention have gained traction in recent years, offering new strategies for improving herd health and reducing economic losses in the livestock industry. Advances in genomics, including identification of genetic markers linked to disease resistance, provide powerful tools for early detection, selection, and management of cattle resistant to infectious diseases. By incorporating genomic technologies such as whole-genome sequencing, genotyping, and transcriptomics, researchers can identify specific genetic variants associated with resistance to pathogens like bovine respiratory disease and Johne's disease. These genomic insights allow for more accurate breeding programs aimed at enhancing disease resistance and overall herd resilience. Genomic selection, in particular, enables identification of individuals with superior genetic traits for immune function, reducing the need for antibiotic treatments and improving animal welfare. Moreover, precision medicine, powered by genomic data, supports development of tailored health management strategies, including targeted vaccination plans and antimicrobial stewardship. Incorporation of genomic tools in beef cattle management also offers the potential for early disease detection, facilitating proactive interventions that reduce the spread of infections. Despite challenges like cost, data interpretation and integration into current management systems, the potential advantages of genomic applications in disease prevention are substantial. As these technologies advance, they are anticipated to have crucial roles in improving sustainability (by enhancing herd performance), profitability (by improving overall herd longevity), and biosecurity (by decreasing the likelihood of disease outbreaks) of beef cattle production systems worldwide.

The future of beef production in South America

South American beef production varies due to diverse climates, environmental conditions, animal breeds (Bos indicus, Bos taurus and crossbreeds), management strategies, and nutritional sources. Applying technology in the South American beef production system can significantly enhance efficiency, sustainability, and profitability. Reproductive efficiency is a significant challenge, especially in cow-calf operation systems conducted under adverse conditions. Consequently, implementing effective assisted reproduction technologies (ART) can make a significant contribution. In the last two decades, the development of fixed-time artificial insemination (FTAI) protocols permitted the widespread application of artificial insemination for breeding management and genetic improvement in beef herds in South America. Nowadays, FTAI is being applied in South America in large-scale programs, with around 20 % of heifers and cows receiving this technology every year. This results in a greater calving rate and significant genetic gain occurring in this territory. Also, in vitro embryo production, mainly using sex-selected sperm has been widely applied in this region, leading to significant improvements in herd genetics and productivity. Recently, 94 % of all embryo transfers in South America consist of in vitro-produced embryos (41,429 being in vivo-derived and 650,782 being in vitro-produced embryos), mainly using fixed-time embryo transfer technology (FTET). Genomic selection combined with in vitro embryo production with oocytes from heifer calves provides a powerful technology platform to reduce generation interval and significantly increase the rate of genetic gain in beef cattle. Emerging biotechnologies, such as genome editing via the CRISPR/Cas system, are being developed to enhance productivity, confer resilience to adverse environmental conditions, increase disease resistance, and control pest species that affect livestock. Finally, while all these technologies offer significant potential, further progresses are needed to transform livestock production. The vast geographical scale and diverse climates of South America make regional knowledge crucial for aligning beef production with sustainability goals and supporting global food security.

Commercial perspectives: Genome editing as a breeding tool for health and well-being in dairy cattle

Genome editing is the latest breeding tool capable of accelerating the rate of genetic improvement for health and well-being traits in food animals. It enables the introduction of beneficial alleles within a single generation, including those that are of low frequency or absent in the population, while effectively bypassing linkage drag. For the dairy industry, genome editing can be used to make rapid genetic improvements that are precise, efficient, and transgene-free for functional traits that are not practically addressed without disrupting conventional breeding goals for overall economic merit based on genomic selection. Herein, various case studies for dairy cattle breeding are presented that demonstrate applications of genome editing for enhancing heat stress tolerance, reduced disease susceptibility, and other qualitative traits absent in some breeds. One case highlights the success of simultaneous editing of multiple loci through recent advancements in embryonic stem cell biology. Multiplexed editing is crucial for addressing the polygenic nature inherent to many economically important traits in livestock. However, maximizing the benefits of genome editing depends on the continued discovery of targets for editing that are commercially important. Commercialization also depends on rapidly evolving regulatory statutes for risk assessment, where some countries already permit the commercialization of cattle with non-GMO genome alterations through existing regulations. New breeding technologies such as genome editing are now poised to have significant impact in equipping elite performance cattle to be more resilient to infectious disease and climate change without the loss of production gains obtained from decades of selection.

Advancing Dairy and Beef Genetics Through Genomic Technologies

The US beef and dairy industries have made remarkable advances in sustainability and productivity through technological advancements, including selective breeding. Yet, challenges persist due to the complex nature of quantitative traits. While the beef industry has progressed in adopting genomic technologies, the availability of phenotypic data remains an obstacle. To meet the need for sustainable production systems, novel traits are being targeted for selection. Additionally, emerging approaches such as genome editing and high-throughput phenotyping hold promise for further genetic progress. Future research should address the challenges of translating functional genomic findings into practical applications, while simultaneously harnessing analytical methods.

Future Directions for Ruminant Genomics

The current article is a forward-looking synopsis to provide insights into the current state of the industry and some areas where future work may hold additional promise. The integration of genomics into the dairy and beef industries is multifaceted and will impact production gains, identification and management of genetic diseases, and streamlined breeding and selection approaches. Veterinarians are uniquely poised to educate clients, integrate genomic data with existing metrics, and assist in decision-making that will impact the future shape of the global herd.

Gene editing in livestock: innovations and applications

Gene editing technologies have revolutionized the field of livestock breeding, offering unprecedented opportunities to enhance animal welfare, productivity, and sustainability. This paper provides a comprehensive review of recent innovations and applications of gene editing in livestock, exploring the diverse applications of gene editing in livestock breeding, as well as the regulatory and ethical considerations, and the current challenges and prospects of the technology in the industry. Overall, this review underscores the transformative potential of gene editing in livestock breeding and its pivotal role in shaping the future of agriculture and biomedicine.

Multiplexed CRISPR-Cas system targeting ASFV genes in vivo: solution lies within

The emergence and spread of the African swine fever virus (ASFV) posed a significant threat to the global swine breeding industry, calling for innovative approaches benefiting viral containment and control. A recent study (Z. Zheng, L. Xu, H. Dou, Y. Zhou, X., et al., Microbiol Spectr 12: e02164-23, 2024, https://doi.org/10.1128/spectrum.02164-23) established a multiplexed CRISPR-Cas system targeting the genome of ASFV and tested the consequent antiviral activity both in vitro and in vivo. Application of this system showed a significant reduction of viral replication in vitro, while the germline-edited pigs expressing this system exhibited normal growth with continuous guide RNA expression. Although no survival advantage was observed upon ASFV challenge compared with nonengineered pigs, this marks the first attempt of germline editing to pursue ASFV resistance and paves the way for future disease-resistant animal breeding approaches utilizing CRISPR-Cas technology.

CRISPR-mediated editing of β-lactoglobulin (BLG) gene in buffalo

Milk is a good source of nutrition but is also a source of allergenic proteins such as α-lactalbumin, β-lactoglobulin (BLG), casein, and immunoglobulins. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas technology has the potential to edit any gene, including milk allergens. Previously, CRISPR/Cas has been successfully employed in dairy cows and goats, but buffaloes remain unexplored for any milk trait. In this study, we utilized the CRISPR/Cas9 system to edit the major milk allergen BLG gene in buffaloes. First, the editing efficiency of designed sgRNAs was tested in fibroblast cells using the T7E assay and Sanger sequencing. The most effective sgRNA was selected to generate clonal lines of BLG-edited cells. Analysis of 15 single-cell clones, through TA cloning and Sanger sequencing, revealed that 7 clones exhibited bi-allelic (-/-) heterozygous, bi-allelic (-/-) homozygous, and mono-allelic (-/+) disruptions in BLG. Bioinformatics prediction analysis confirmed that non-multiple-of-3 edited nucleotide cell clones have frame shifts and early truncation of BLG protein, while multiple-of-3 edited nucleotides resulted in slightly disoriented protein structures. Somatic cell nuclear transfer (SCNT) method was used to produce blastocyst-stage embryos that have similar developmental rates and quality with wild-type embryos. This study demonstrated the successful bi-allelic editing (-/-) of BLG in buffalo cells through CRISPR/Cas, followed by the production of BLG-edited blastocyst stage embryos using SCNT. With CRISPR and SCNT methods described herein, our long-term goal is to generate gene-edited buffaloes with BLG-free milk.

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.

Diagnosis of bovine viral diarrhea virus: an overview of currently available methods

Bovine viral diarrhea virus (BVDV) is the causative agent of bovine viral diarrhea (BVD), which results in significant economic losses in the global cattle industry. Fortunately, various diagnostic methods available for BVDV have been established. They include etiological methods, such as virus isolation (VI); serological methods, such as enzyme-linked immunosorbent assay (ELISA), immunofluorescence assay (IFA), and immunohistochemistry (IHC); molecular methods, such as reverse transcription-polymerase chain reaction (RT-PCR), real-time PCR, digital droplet PCR (ddPCR), loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), and CRISPR-Cas system; and biosensors. This review summarizes the current diagnostic methods for BVDV, discussing their advantages and disadvantages, and proposes future perspectives for the diagnosis of BVDV, with the intention of providing valuable guidance for effective diagnosis and control of BVD disease.

Current status and future of gene engineering in livestock

The application of gene engineering in livestock is necessary for various reasons, such as increasing productivity and producing disease resistance and biomedicine models. Overall, gene engineering provides benefits to the agricultural and research aspects, and humans. In particular, productivity can be increased by producing livestock with enhanced growth and improved feed conversion efficiency. In addition, the application of the disease resistance models prevents the spread of infectious diseases, which reduces the need for treatment, such as the use of antibiotics; consequently, it promotes the overall health of the herd and reduces unexpected economic losses. The application of biomedicine could be a valuable tool for understanding specific livestock diseases and improving human welfare through the development and testing of new vaccines, research on human physiology, such as human metabolism or immune response, and research and development of xenotransplantation models. Gene engineering technology has been evolving, from random, time-consuming, and laborious methods to specific, time-saving, convenient, and stable methods. This paper reviews the overall trend of genetic engineering technologies development and their application for efficient production of genetically engineered livestock, and provides examples of technologies approved by the United States (US) Food and Drug Administration (FDA) for application in humans. [BMB Reports 2024; 57(1): 50-59].

Molecular breeding of livestock for disease resistance

Animal infectious diseases pose a significant threat to the global agriculture and biomedicine industries, leading to significant economic losses and public health risks. The emergence and spread of viral infections such as African swine fever virus (ASFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV), and avian influenza virus (AIV) have highlighted the need for innovative approaches to develop resilient and disease-resistant animal populations. Gene editing technologies, such as CRISPR/Cas9, offer a promising avenue for generating animals with enhanced disease resistance. This review summarizes recent advances in molecular breeding strategies for generating disease-resistant animals, focusing on the development of disease-resistant livestock. We also highlight the potential applications of genome-wide CRISPR/Cas9 library screening and base editors in producing precise gene modified livestock for disease resistance in the future. Overall, gene editing technologies have the potential to revolutionize animal breeding and improve animal health and welfare.

Structure of Bovine CD46 Ectodomain

CD46, or membrane cofactor protein, is a type-one transmembrane protein from the complement regulatory protein family. Alongside its role in complement activation, CD46 is involved in many other processes, from T-cell activation to reproduction. It is also referred to as a pathogen magnet, because it is used as a receptor by multiple bacteria and viruses. Bovine CD46 (bovCD46) in particular is involved in bovine viral diarrhoea virus entry, an economically important disease in cattle industries. This study presents the X-ray crystallographic structure of the extracellular region of bovCD46, revealing a four-short-consensus-repeat (SCR) structure similar to that in human CD46. SCR1-3 are arranged linearly, while SCR 4 has a reduced interface angle, resulting in a hockey stick-like appearance. The structure also reveals the bovine viral diarrhoea virus interaction site in SCR1, which is likely to confer pestivirus specificity for their target host, CD46. Insights gained from the structural information on pestivirus receptors, such as CD46, could offer valuable guidance for future control strategies.