CRISPR in livestock: From editing to printing

Whole Genome Sequence Analysis of Listeria monocytogenes Isolates Obtained from the Beef Production Chain in Gauteng Province, South Africa

The study used whole-genome sequencing (WGS) and bioinformatics analysis for the genomic characterization of 60 isolates of Listeria monocytogenes obtained from the beef production chain (cattle farms, abattoirs, and retail outlets) in Gauteng province, South Africa. The sequence types (STs), clonal complexes (CCs), and the lineages of the isolates were determined using in silico multilocus sequence typing (MLST). We used BLAST-based analyses to identify virulence and antimicrobial genes, plasmids, proviruses/prophages, and the CRISPR-Cas system. The study investigated any association of the detected genes to the origin in the beef production chain of the L. monocytogenes isolates. Overall, in 60 isolates of Listeria monocytogenes, there were seven STs, six CCs, forty-four putative virulence factors, two resistance genes, one plasmid with AMR genes, and three with conjugative genes, one CRISPR gene, and all 60 isolates were positive for proviruses/prophages. Among the seven STs detected, ST204 (46.7%) and ST2 (21.7%) were the most prominent, with ST frequency varying significantly (p < 0.001). The predominant CC detected were CC2 (21.7%) and CC204 (46.7%) in lineages I and II, respectively. Of the 44 virulence factors detected, 26 (across Listeria Pathogenicity Islands, LIPIs) were present in all the isolates. The difference in the detection frequency varied significantly (p < 0.001). The two AMR genes (fosX and vga(G)) detected were present in all 60 (100%) isolates of L. monocytogenes. The only plasmid, NF033156, was present in three (5%) isolates. A CRISPR-Cas system was detected in six (10%), and all the isolates carried proviruses/prophages. The source and sample type significantly affected the frequencies of STs and virulence factors in the isolates of L. monocytogenes. The presence of fosX and vga(G) genes in all L. monocytogenes isolates obtained from the three industries of the beef production chain can potentially cause therapeutic implications. Our study, which characterized L. monocytogenes recovered from the three levels in the beef production chain, is the first time genomics was performed on this type of data set in the country, and this provides insights into the health implications of Listeria.

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.

A review of the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle

In the past few decades, genomic selection and other refined strategies have been used to increase the growth rate and lean meat production of beef cattle. Nevertheless, the fast growth rates of cattle breeds are often accompanied by a reduction in intramuscular fat (IMF) deposition, impairing meat quality. Transcription factors play vital roles in regulating adipogenesis and lipogenesis in beef cattle. Meanwhile, understanding the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle has gained significant attention to increase IMF deposition and meat quality. Therefore, the aim of this paper was to provide a comprehensive summary and valuable insight into the complex role of transcription factors in adipogenesis and lipogenesis in beef cattle. This review summarizes the contemporary studies in transcription factors in adipogenesis and lipogenesis, genome-wide analysis of transcription factors, epigenetic regulation of transcription factors, nutritional regulation of transcription factors, metabolic signalling pathways, functional genomics methods, transcriptomic profiling of adipose tissues, transcription factors and meat quality and comparative genomics with other livestock species. In conclusion, transcription factors play a crucial role in promoting adipocyte development and fatty acid biosynthesis in beef cattle. They control adipose tissue formation and metabolism, thereby improving meat quality and maintaining metabolic balance. Understanding the processes by which these transcription factors regulate adipose tissue deposition and lipid metabolism will simplify the development of marbling or IMF composition in beef cattle.

Gene editing in small and large animals for translational medicine: a review

The CRISPR/Cas9 system is a simpler and more versatile method compared to other engineered nucleases such as Zinc Finger Nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs), and since its discovery, the efficiency of CRISPR-based genome editing has increased to the point that multiple and different types of edits can be made simultaneously. These advances in gene editing have revolutionized biotechnology by enabling precise genome editing with greater simplicity and efficacy than ever before. This tool has been successfully applied to a wide range of animal species, including cattle, pigs, dogs, and other small animals. Engineered nucleases cut the genome at specific target positions, triggering the cell's mechanisms to repair the damage and introduce a mutation to a specific genomic site. This review discusses novel genome-based CRISPR/Cas9 editing tools, methods developed to improve efficiency and specificity, the use of gene-editing on animal models and translational medicine, and the main challenges and limitations of CRISPR-based gene-editing approaches.

Optimising Electroporation Condition for CRISPR/Cas-Mediated Knockout in Zona-Intact Buffalo Zygotes

Somatic cell nuclear transfer or cytoplasm microinjection has widely been used to produce genome-edited farm animals; however, these methods have several drawbacks which reduce their efficiency. In the present study, we describe an easy adaptable approach for the introduction of mutations using CRISPR-Cas9 electroporation of zygote (CRISPR-EP) in buffalo. The goal of the study was to determine the optimal conditions for an experimental method in which the CRISPR/Cas9 system is introduced into in vitro-produced buffalo zygotes by electroporation. Electroporation was performed using different combinations of voltage, pulse and time, and we observed that the electroporation in buffalo zygote at 20 V/mm, 5 pulses, 3 msec at 10 h post insemination (hpi) resulted in increased membrane permeability and higher knockout efficiency without altering embryonic developmental potential. Using the above parameters, we targeted buffalo POU5F1 gene as a proof of concept and found no variations in embryonic developmental competence at cleavage or blastocyst formation rate between control, POU5F1-KO, and electroporated control (EC) embryos. To elucidate the effect of POU5F1-KO on other pluripotent genes, we determined the relative expression of SOX2, NANOG, and GATA2 in the control (POU5F1 intact) and POU5F1-KO-confirmed blastocyst. POU5F1-KO significantly (p ≤ 0.05) altered the expression of SOX2, NANOG, and GATA2 in blastocyst stage embryos. In conclusion, we standardized an easy and straightforward protocol CRISPR-EP method that could be served as a useful method for studying the functional genomics of buffalo embryos.

CRISPR/Cas9 Landscape: Current State and Future Perspectives

CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 is a unique genome editing tool that can be easily used in a wide range of applications, including functional genomics, transcriptomics, epigenetics, biotechnology, plant engineering, livestock breeding, gene therapy, diagnostics, and so on. This review is focused on the current CRISPR/Cas9 landscape, e.g., on Cas9 variants with improved properties, on Cas9-derived and fusion proteins, on Cas9 delivery methods, on pre-existing immunity against CRISPR/Cas9 proteins, anti-CRISPR proteins, and their possible roles in CRISPR/Cas9 function improvement. Moreover, this review presents a detailed outline of CRISPR/Cas9-based diagnostics and therapeutic approaches. Finally, the review addresses the future expansion of genome editors' toolbox with Cas9 orthologs and other CRISPR/Cas proteins.

The Past, Present, and Future of Genetically Engineered Mouse Models for Skeletal Biology

The ability to create genetically engineered mouse models (GEMMs) has exponentially increased our understanding of many areas of biology. Musculoskeletal biology is no exception. In this review, we will first discuss the historical development of GEMMs and how these developments have influenced musculoskeletal disease research. This review will also update our 2008 review that appeared in BONEKey, a journal that is no longer readily available online. We will first review the historical development of GEMMs in general, followed by a particular emphasis on the ability to perform tissue-specific (conditional) knockouts focusing on musculoskeletal tissues. We will then discuss how the development of CRISPR/Cas-based technologies during the last decade has revolutionized the generation of GEMMs.

CRISPR in Public Health: The Health Equity Implications and Role of Community in Gene-Editing Research and Applications

CRISPR (clustered regularly interspaced short palindromic repeats) is a Nobel Prize-winning technology that holds significant promise for revolutionizing the prevention and treatment of human disease through gene editing. However, CRISPR's public health implications remain relatively uncertain and underdiscussed because (1) targeting genetic factors alone will have limited influence on population health, and (2) minority populations (racial/ethnic, sexual and gender)-who bear the nation's greatest health burdens-historically suffer unequal benefits from emerging health care innovations and tools. This article introduces CRISPR and its potential public health benefits (e.g., improving virus surveillance, curing genetic diseases that pose public health problems such as sickle cell anemia) while outlining several major ethical and practical threats to health equity. This includes minorities' grave underrepresentation in genomics research, which may lead to less effective and accepted CRISPR tools and therapies for these groups, and their anticipated unequal access to these tools and therapies in health care. Informed by the principles of fairness, justice, and equitable access, ensuring gene editing promotes rather than diminishes health equity will require the meaningful centering and engagement of minority patients and populations in gene-editing research using community-based participatory research approaches. (Am J Public Health. 2023;113(8):874-882. https://doi.org/10.2105/AJPH.2023.307315).

Review: Development, adoption, and impact of assisted reproduction in domestic buffaloes

The domestic buffalo (Bubalus bubalis), also known as water buffalo, comprises two sub-species the River buffalo (B. bubalis ssp. bubalis; 50 chromosomes) and the Swamp buffalo (ssp. carabanensis; 48 chromosomes). Domestic buffaloes are a globally significant livestock species. In South Asia, the River buffalo is a primary source of milk and meat and has a very important role in food security. The River buffalo also supports high-value, differentiated food production in Europe and the Americas. The Swamp buffalo is an important draft animal and a source of food in Southeast Asia and East Asia. The growing importance of buffaloes requires that they undergo an accelerated rate of genetic gain for efficiency of production, product quality, and sustainability. This will involve the increased use of assisted reproduction. The initial application of reproductive technology in buffaloes had variable success as it relied on the adoption of procedures developed for cattle. This included artificial insemination (AI), sperm cryopreservation, and embryo technologies such as cloning and in vitro embryo production (IVEP). Reproductive technology has been progressively refined in buffaloes, and today, the success of AI and IVEP is comparable to cattle. Ovarian follicular superstimulation (superovulation) combined with in vivo embryo production results in low embryo recovery in buffaloes and has limited practical application. The contribution of elite female buffaloes to future genetic improvement will therefore rely mainly on oocyte pickup and IVEP. This will include IVEP from females before puberty to reduce generation intervals. This review provides for the first time a clear chronology on the development, adoption, and impact, of assisted reproduction in domestic buffaloes.

Introduction of the FecGF mutation in GDF9 gene via CRISPR/Cas9 system with single-stranded oligodeoxynucleotide

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) 9 system has been a recent focus of breeders owing to its potential to improve economically significant traits of livestock. The introduction of defined point mutations into the ovine genome via CRISPR/Cas9-mediated homology-directed repair has been reported; however, indel and mosaic events observed in genetically modified animals limit the practical application of this system in sheep breeding. The FecG^F mutation (g. G1111A, p. V371 M) in the growth differentiation factor 9 (GDF9) gene is strongly associated with litter size in Belclare and Norwegian White Sheep. In the present study, we introduced the FecG^F mutation in GDF9 by co-injecting the CRISPR/Cas9 system, single-stranded oligodeoxynucleotide (ssODN), and Scr7 into ovine zygotes. Scr7 at various concentrations (0 μM, 1 μM, and 2 μM) had no adverse effects on embryonic development in vitro. No significant differences in total mutation, point mutation, and indel rates in embryos were observed among groups treated with different concentrations of Scr7. However, the mosaicism rates of embryos from zygotes microinjected with 1 and 2 μM Scr7 were significantly lower than that for 0 μM Scr7 (7.7% and 7.5% vs. 19.7%). We successfully obtained lambs with defined nucleotide substitutions by the coinjection of Cas9 mRNA, sgRNA, ssODN, and 1 μM Scr7 into Altay sheep zygotes. The single nucleotide mutation efficiency was 7.69% (3/39) in newborn lambs, with one mosaic. Our findings provide evidence that Scr7 could improve the specificity of the CRISPR/Cas9 system for the introduction of a defined point mutation in livestock to some extent.

Consumer acceptance of new plant-breeding technologies: An application to the use of gene editing in fresh table grapes

This study estimates consumers' willingness to pay for specific product (quality) and process (agronomic) attributes of table grapes, including taste, texture, external appearance, and the expected number of chemical applications, and for the breeding technology used to develop the plant. Considering varietal traits, on average our survey respondents were willing to pay the highest price premiums for specific offers of improvements in table grape taste and texture, followed by external appearance and expected number of chemical applications. Considering breeding methods, on average our respondents were willing to pay a small premium for table grapes developed using conventional breeding rather than gene editing (e.g., CRISPR). Results from a latent class model identify four different groups of consumers with distinct preferences for grape quality attributes and breeding technologies. The group of consumers most likely to reject gene editing considers both genetic engineering and gene editing to be breeding technologies that produce foods that are morally unacceptable and not safe to eat.

Advances in CRISPR/Cas9

CRISPR/Cas9 technology has become the most examined gene editing technology in recent years due to its simple design, yet low cost, high efficiency, and simple operation, which can also achieve simultaneous editing of multiple loci. It can also be carried out without using plasmids, saving lots of troubles caused by plasmids. CRISPR/Cas9 has shown great potential in the study of genes or genomic functions in microorganisms, plants, animals, and human beings. In this review, we will examine the history, structure, and basic mechanisms of the CRISPR/Cas9 system, describe its great value in precision medicine and sgRNA library screening, and dig its great potential in a new field: DNA information storage.

Melatonin promotes the development of sheep transgenic cloned embryos by protecting donor and recipient cells

The yield efficiency of transgenic animal generation is relatively low[1]. To improve its efficiency has become a priority task for researchers[2]. Melatonin (N-acetyl-5-methoxytryptamine, MT) is a potent-free radical scavenger and antioxidant to protect mitochondria, lipids, protein and DNA from oxidative stress[3]. In this study, we observed that improving the quality of both donor and recipient cells by giving physiological concentration (10^-7 M) of MT significantly increase the sheep transgenic embryo development in the in vitro condition. MT promotes the donor cell viability, proliferation, efficiency of monoclonal formation and the electrotransferring efficiency of fetal fibroblast cells (FFCs). The mechanistic exploration indicates that MT has the capacity for the synchronization of cell division cycle, reduction of cellular oxidative stress, apoptosis, and the increase of mitochondrial number and function. All of these render MT's ability to increase the efficiency of animal transgenic processes such as somatic cell nuclear transfer (SCNT) and electroporation. The outcomes are the increased cleavage rate and blastocyst rate of the transgenic sheep embryos after MT treatment. These beneficial effects of MT on transgenic embryo development are worth to be tested in the in vivo condition in the future.

Knockout of Stearoyl-CoA Desaturase 1 Decreased Milk Fat and Unsaturated Fatty Acid Contents of the Goat Model Generated by CRISPR/Cas9

Goat milk contains a rich source of nutrients, especially unsaturated fatty acids. However, the regulatory mechanism of milk fat and fatty acid synthesis remains unclear. Stearoyl-CoA desaturase 1 (SCD1) is the key enzyme catalyzing monounsaturated fatty acid synthesis and is essential for milk lipid metabolism. To explore milk lipid synthesis mechanism in vivo, SCD1-knockout goats were generated through CRISPR/Cas9 technology for the first time. SCD1 deficiency did not influence goat growth or serum biochemistry. Plasma phosphatidylcholines increased by lipidomics after SCD1 knockout in goats. Whole-blood RNA-seq indicated alterations in biosynthesis of unsaturated fatty acid synthesis, cAMP, ATPase activity, and Wnt signaling pathways. In SCD1-knockout goats, milk fat percentage and unsaturated fatty acid levels were reduced but other milk components were unchanged. Milk lipidomics revealed decreased triacylglycerols and diacylglycerols levels, and the differential abundance of lipids were enriched in glycerolipid, glycerophospholipids, and thermogenesis metabolism pathways. In milk fat globules, the expression levels of genes related to fatty acid and TAG synthesis including SREBP1 were reduced. ATP content and AMPK activity were promoted, and p-p70S6K protein level was suppressed in SCD1-knockout goat mammary epithelial cells, suggesting that SCD1 affected milk lipid metabolism by influencing AMPK-mTORC1/p70S6K-SREBP1 pathway. The integrative analysis of gene expression levels and lipidomics of milk revealed a crucial role of SCD1 in glycerolipids and glycerophospholipids metabolism pathways. Our observations indicated that SCD1 regulated the synthesis of milk fat and unsaturated fatty acid in goat by affecting lipid metabolism gene expression and lipid metabolic pathways. These findings would be essential for improving goat milk nutritional value which is beneficial to human health.

Generation of a Human Deafness Sheep Model Using the CRISPR/Cas System

CRISPR/Cas9 system is a promising method for the generation of human disease models by genome editing in non-conventional experimental animals. Medium/large-sized animals like sheep have several advantages to study human diseases and medicine. Here, we present a protocol that describes the generation of an otoferlin edited sheep model via CRISPR-assisted single-stranded oligodinucleotide-mediated Homology-Directed Repair (HDR), through direct cytoplasmic microinjection in in vitro produced zygotes.Otoferlin is a protein expressed in the cochlear inner hair cells, with different mutations at the OTOF gene being the major cause of nonsyndromic recessive auditory neuropathy spectrum disorder in humans. By using this protocol, we reported for the first time an OTOF KI model in sheep with 17.8% edited lambs showing indel mutations, and 61.5% of them bearing knock-in mutations by HDR . The reported method establishes the bases to produce a deafness model to test novel therapies in human disorders related to OTOF mutations.

Generation of Double-Muscled Sheep and Goats by CRISPR /Cas9-Mediated Knockout of the Myostatin Gene

The myostatin (MSTN) gene has shown to play a critical role in the regulation of skeletal muscle mass, and the translational inhibition of this gene has shown increased muscle mass, generating what is known as "double-muscling phenotype." Disruption of the MSTN gene expression using the CRISPR/Cas9 genome-editing system has shown improved muscle development and growth rates in livestock species, including sheep and goats. Here, we describe procedures for the generation of MSTN knockout sheep and goats using the microinjection approach of the CRISPR/Cas9 system, including the selection of targeting sgRNAs, the construction of CRISPR/Cas9 targeting vector, the in vitro examination of system efficiency, the in vivo targeting to generate MSTN knockout founders, the genomic and phenotypic characterization of the generated offspring, and the assessment of off-target effects in gene-edited founders through targeted validation of predicted off-target sites, as well as genome-wide off-target analysis by whole-genome sequencing. Editing the MSTN gene using the CRISPR/Cas9 system might be a rapid and promising alternative to promote meat production in livestock.

Public Perceptions Regarding Genomic Technologies Applied to Breeding Farm Animals: A Qualitative Study

The societal acceptability of different applications of genomic technologies to animal production systems will determine whether their innovation trajectories will reach the commercialisation stage. Importantly, technological implementation and commercialisation trajectories, regulation, and policy development need to take account of public priorities and attitudes. More effective co-production practices will ensure the application of genomic technologies to animals aligns with public priorities and are acceptable to society. Consumer rejection of, and limited demand for, animal products developed using novel genomic technologies will determine whether they are integration into the food system. However, little is known about whether genomic technologies that accelerate breeding but do not introduce cross-species genetic changes are more acceptable to consumers than those that do. Five focus groups, held in the north east of England, were used to explore the perceptions of, and attitudes towards, the use of genomic technologies in breeding farm animals for the human food supply chain. Overall, study participants were more positive towards genomic technologies applied to promote animal welfare (e.g., improved disease resistance), environmental sustainability, and human health. Animal “disenhancement” was viewed negatively and increased food production alone was not perceived as a potential benefit. In comparison to gene editing, research participants were most negative about genetic modification and the application of gene drives, independent of the benefits delivered.

Impact of oocyte donor age and breed on in vitro embryo production in cattle, and relationship of dairy and beef embryo recipients on pregnancy and the subsequent performance of offspring: A review

Genomic selection combined with in vitro embryo production (IVEP) with oocytes from heifer calves provides a powerful technology platform to reduce generation interval and significantly increase the rate of genetic gain in cattle. The ability to obtain oocytes with developmental competence from calves has been recognised for more than 60years. There is renewed interest in the potential of this reproductive technology as the beef and dairy industries seek to identify and multiply animals that satisfy consumer demand for efficient utilisation of natural resources, with minimal environmental impact and high product quality. Heifer calves show a good follicular response to FSH stimulation and oocytes can be recovered by ovum pick-up (OPU). However, the efficiency of OPU/IVEP remains lower for calves compared with peripubertal heifers and cows, in both indicus (Zebu, Bos indicus ) and taurus (Bos taurus ) breeds. Indicus cattle generally have more follicles, yield a greater number of oocytes, and have a better IVEP outcome, compared with taurus cattle. The treatment of prepubertal heifers with bovine somatotrophin (bST) and propylene glycol before OPU/IVEP has yet to show a major improvement in embryo production. Holstein (taurus) dairy heifers derived from different reproductive technologies (AI, MOET, OPU/IVEP) showed a similar age at puberty and first-lactation milk production. OPU/IVEP Holstein embryos transferred to beef or dairy cows likewise yielded heifers with the same performance. The gains in productivity that can be achieved with strategic use of OPU/IVEP in heifer calves make this a relevant and highly important reproductive technology in cattle breeding. Ongoing optimisation of the technology is needed for the potential of OPU/IVEP in young donors to be fully realised.

Direct and indirect contributions of molecular genetics to farm animal welfare: a review

Since domestication, farm animals have played a key role to increase the prosperity of humankind, while animal welfare (AW) is debated even today. This paper aims to comprehensively review the contributions of developing molecular genetics to farm animal welfare (FAW) and to raise awareness among both scientists and farmers about AW. Welfare is a complex trait affected by genetic structure and environmental factors. Therefore, the best welfare status can be achieved not only to enhance environmental factors such as management and feeding practices, but also the genetic structure of animals must be improved. In this regard, advances in molecular genetics have made great contributions to improve the genetic structure of farm animals, which has increased AW. Today, by sequencing and/or molecular markers, genetic diseases may be detected and eliminated in local herds. Additionally, genes related to diseases or adaptations are investigated by molecular techniques, and the frequencies of desired genotypes are increased in farm animals to keep welfare at an optimized level. Furthermore, stress on animals can be reduced with DNA extraction from stool and feather samples which reduces physical contact between animals and veterinarians. Together with molecular genetics, advances in genome editing tools and biotechnology are promising to improve FAW in the future.

LncRNAs in domesticated animals: from dog to livestock species

Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.

A DREaMR system to simplify combining mutations with rescue transgenes in Aedes aegypti

In most experimental animals, it is challenging to combine mutations and rescue transgenes and to use bipartite systems to assess gene expression. To circumvent the difficulties in combining multiple genetic elements, we developed the DREaMR (Drug-on, REporter, Mutant, Rescue) system. Using Drosophila white as the initial model, we demonstrated that introduction of a single insertion by CRISPR/Cas9 created a null mutation, a tagged rescue construct, which could be induced with doxycycline, and which allowed assessment of protein expression. To create a DREaMR in an organism in which combining multiple genetic elements is more problematic than in Drosophila, we tested the mosquito, Aedes aegypti-the insect vector for dengue, yellow fever, Zika, and other viral diseases. We generated a DREaMR allele in the kh gene, which permitted us to induce expression of the rescue construct, and detect expression of Kh. Thus, this system avoids the need to perform genetic crosses to introduce an inducible rescue transgene in a mutant background, or to combine driver and reporter lines to examine expression of the targeted protein. We propose that DREaMR provides a system that can be applied to additional mosquito vectors as well as other organisms in which CRISPR/Cas9 is effective.

Effects of Diluent pH on Enrichment and Performance of Dairy Goat X/Y Sperm

In this paper, on the basis of the differences in the hydrogen ion concentration (pH) of the diluent dairy goat semen on X/Y sperm motility, an X/Y sperm enrichment study was conducted to establish a simple and effective method for gender control in dairy goats. Dairy goat semen was diluted using different pH dilutions and was incubated. Then, the X/Y sperm ratio in the isolated upper sperm was determined using the double TaqMan qPCR method. The internal pH change pattern of sperm cells at different pH dilutions was measured using BCECF-AM probe, and the functional parameters of the isolated sperm were tested with the corresponding kit. Next, an in vitro fertilization test was conducted using isolated spermatozoa and oocytes to determine their fertilization rates, the percentages of female embryos, and the expression of genes related to developing potentially fertilized embryos. Results showed that the percentages of the X sperm cells in the upper sperm layer were 67.24% ± 2.61% at sperm dilution pH of 6.2 and 30.45% ± 1.03% at sperm dilution pH of 7.4, which was significantly different from 52.35% ± 1.72% of the control group (pH 6.8) (P < 0.01). Results also showed that there is a relationship between the external pHo and internal pHi of sperm cells. Furthermore, the percentages of female embryos after the in vitro fertilization of the isolated upper sperm with mature oocytes at pH 6.2 and 7.4 were 66.67% ± 0.05 and 29.73% ± 0.04%, respectively, compared with 48.57% ± 0.02% in the control group (pH 6.8). Highly significant differences occurred between groups (P < 0.01). Additionally, no significant difference was observed during the expression of genes related to embryonic development between the blastocysts formed from sperm isolated by changing the pH of the diluent and the control sperm (P > 0.05). Therefore, this study successfully established a simple and effective method for enriched X/Y sperms from dairy goats, which is important for regulating the desired sex progeny during dairy goat breeding and for guiding dairy goat production.

CRISPR Genome Editing Technology: A Powerful Tool Applied to Developing Agribusiness

The natural increase of the world's population implies boosting agricultural demand. In the current non-optimistic global scenario, where adverse climate changes come associated with substantial population growth, the main challenge in agribusiness is food security. Recently, the CRISPR/Cas system has emerged as a friendly gene editing biotechnological tool, enabling a precise manipulation of genomes and enhancement of desirable traits in several organisms. This review highlights the CRISPR/Cas system as a paramount tool for the improvement of agribusiness products and brings up-to-date findings showing its potential applications in improving agricultural-related traits in major plant crops and farm animals, all representing economic-relevant commodities responsible for feeding the world. Several applied pieces of research have successfully demonstrated the CRISPR/Cas ability in boosting interesting traits in agribusiness products, including animal productivity and welfare, crop yield growth, and seed quality, reflecting positive impacts in both socioeconomics and human health aspects. Hence, the CRISPR/Cas system has revolutionized bioscience and biotechnology, and its concrete application in agribusiness goods is on the horizon.

Sustainable Food Production: The Contribution of Genome Editing in Livestock

The growing demand for animal source foods to feed people has been pushing the livestock industry to increase productivity, a tendency that will continue throughout this century. The challenge for the coming years is to increase the food supply to ensure equity in access to high quality food, while maintaining global sustainability including combating climate change, avoiding deforestation, and conserving biodiversity, as well as ensuring animal health and welfare. The question is, how do we produce more with less? Classical methods to enhance livestock productivity based on the improvement of animal health, nutrition, genetics, reproductive technologies and management have made important contributions; however, this is not going to be enough and thus disruptive approaches are required. Genome editing with CRISPR may be a powerful contributor to global livestock transformation. This article is focused on the scope and perspectives for the application of this technology, which includes improving production traits, enhancing animal welfare through adaptation and resilience, conferring resistance to infectious diseases, and suppressing pests and invasive species that threaten livestock. The main advantages and concerns that should be overcome by science, policy and people are discussed with the aim that this technology can make a real contribution to our collective future. This review is part of the special issue “Genome Editing in Animal Systems to Support Sustainable Farming and Pest Control”.

Progress of genome editing technology and developmental biology useful for radiation research

Following the development of genome editing technology, it has become more feasible to create genetically modified animals such as knockout (KO), knock-in, and point-mutated animals. The genome-edited animals are useful to investigate the roles of various functional genes in many fields of biological science including radiation research. Nevertheless, some researchers may experience difficulty in generating genome-edited animals, probably due to the requirement for equipment and techniques for embryo manipulation and handling. Furthermore, after obtaining F0 generation, genome-edited animals generally need to be expanded and maintained for analyzing the target gene function. To investigate genes essential for normal birth and growth, the generation of conditional KO (cKO) animals in which a tissue- or stage-specific gene mutation can be introduced is often required. Here, we describe the basic principle and application of genome editing technology including zinc-finger nuclease, transcription-activator-like effector nuclease, and clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR associated protein (Cas) systems. Recently advanced developmental biology methods have enabled application of the technology, especially CRISPR/Cas, to zygotes, leading to the prompt production of genome-edited animals. For pre-implantation embryos, genome editing via oviductal nucleic acid delivery has been developed as an embryo manipulation- or handling-free method. Examining the gene function at F0 generation is becoming possible by employing triple-target CRISPR technology. This technology, in combination with a blastocyst complementation method enables investigation of even birth- and growth-responsible genes without establishing cKO strains. We hope that this review is helpful for understanding and expanding genome editing-related technology and for progressing radiation research.

Gene Editing for Improved Animal Welfare and Production Traits in Cattle: Will This Technology Be Embraced or Rejected by the Public?

Integrating technology into agricultural systems has gained considerable traction, particularly over the last half century. Agricultural systems that incorporate the public’s concerns regarding farm animal welfare are more likely to be socially accepted in the long term, a key but often forgotten component of sustainability. Gene editing is a tool that has received considerable attention in the last five years, given its potential capacity to improve farm animal health, welfare, and production efficiency. This study aimed to explore the attitudes of Brazilian citizens regarding the applications of gene editing in cattle that generate offspring without horns; are more resistant to heat; and have increased muscle tissue. Using a mixed-methods approach, we surveyed participants via face-to-face, using in-depth interviews (Study 1) and an online questionnaire containing closed-ended questions (Study 2). Overall, the acceptability of gene editing was low and in cases where support was given it was highly dependent on the type and purpose of the application proposed. Using gene editing to improve muscle tissue growth was viewed as less acceptable compared to using gene editing to reduce heat stress or to produce hornless cattle. Support declined when the application was perceived to harm animal welfare, to be profit motivated or to reinforce the status quo of intensive livestock systems. The acceptability of gene editing was reduced when perceptions of risks and benefits were viewed as unevenly or unfairly distributed among consumers, corporations, different types of farmers, and the animals. Interviewees did not consider gene editing a “natural” process, citing dissenting reasons such as the high degree of human interference and the acceleration of natural processes. Our findings raised several issues that may need to be addressed for gene editing to comply with the social pillar of sustainable agriculture.

CRISPR-Cas and Its Wide-Ranging Applications: From Human Genome Editing to Environmental Implications, Technical Limitations, Hazards and Bioethical Issues

The CRISPR-Cas system is a powerful tool for in vivo editing the genome of most organisms, including man. During the years this technique has been applied in several fields, such as agriculture for crop upgrade and breeding including the creation of allergy-free foods, for eradicating pests, for the improvement of animal breeds, in the industry of bio-fuels and it can even be used as a basis for a cell-based recording apparatus. Possible applications in human health include the making of new medicines through the creation of genetically modified organisms, the treatment of viral infections, the control of pathogens, applications in clinical diagnostics and the cure of human genetic diseases, either caused by somatic (e.g., cancer) or inherited (mendelian disorders) mutations. One of the most divisive, possible uses of this system is the modification of human embryos, for the purpose of preventing or curing a human being before birth. However, the technology in this field is evolving faster than regulations and several concerns are raised by its enormous yet controversial potential. In this scenario, appropriate laws need to be issued and ethical guidelines must be developed, in order to properly assess advantages as well as risks of this approach. In this review, we summarize the potential of these genome editing techniques and their applications in human embryo treatment. We will analyze CRISPR-Cas limitations and the possible genome damage caused in the treated embryo. Finally, we will discuss how all this impacts the law, ethics and common sense.

Improvements in Gene Editing Technology Boost Its Applications in Livestock

Accelerated development of novel CRISPR/Cas9-based genome editing techniques provides a feasible approach to introduce a variety of precise modifications in the mammalian genome, including introduction of multiple edits simultaneously, efficient insertion of long DNA sequences into specific targeted loci as well as performing nucleotide transitions and transversions. Thus, the CRISPR/Cas9 tool has become the method of choice for introducing genome alterations in livestock species. The list of new CRISPR/Cas9-based genome editing tools is constantly expanding. Here, we discuss the methods developed to improve efficiency and specificity of gene editing tools as well as approaches that can be employed for gene regulation, base editing, and epigenetic modifications. Additionally, advantages and disadvantages of two primary methods used for the production of gene-edited farm animals: somatic cell nuclear transfer (SCNT or cloning) and zygote manipulations will be discussed. Furthermore, we will review agricultural and biomedical applications of gene editing technology.

Comparison of the effects of introducing the CRISPR/Cas9 system by microinjection and electroporation into porcine embryos at different stages

Objective

Cytoplasmic microinjection and electroporation of the CRISPR/Cas9 system into zygotes are used for generating genetically modified pigs. However, these methods create mosaic mutations in embryos. In this study, we evaluated whether the gene editing method and embryonic stage for gene editing affect the gene editing efficiency of porcine embryos.

Results

First, we designed five guide RNAs (gRNAs) targeting the B4GALNT2 gene and evaluated mutation efficiency by introducing each gRNA with Cas9 protein into zygotes by electroporation. Next, the optimized gRNA with Cas9 protein was introduced into 1-cell and 2-cell stage embryos by either microinjection or electroporation. The sequence of gRNA affected the bi-allelic mutation rate and mutation efficiency of blastocysts derived from electroporated embryos. Microinjection significantly decreased the cleavage rates in each embryonic stage and blastocyst formation rates in 2-cell stage embryos compared with electroporation (p < 0.05). However, the bi-allelic mutation rate and mutation efficiency of blastocysts from the 1-cell stage embryos edited using microinjection were significantly higher (p < 0.05) than those of blastocysts from the 2-cell stage embryos edited by both methods. These results indicate that the gene editing method and embryonic stage for gene editing may affect the genotype and mutation efficiency of the resulting embryos.

Introducing reticular chemistry into agrochemistry

For survival and quality of life, human society has sought more productive, precise, and sustainable agriculture. Agrochemistry, which solves farming issues in a chemical manner, is the core engine that drives the evolution of modern agriculture. To date, agrochemistry has utilized chemical technologies in the form of pesticides, fertilizers, veterinary drugs and various functional materials to meet fundamental demands from human society, while increasing the socio-ecological consequences due to inefficient use. Thus, more useful, precise, and designable scaffolding materials are required to support sustainable agrochemistry. Reticular chemistry, which weaves molecular units into frameworks, has been applied in many fields based on two cutting-edge porous framework materials, namely metal-organic frameworks (MOFs) and covalent-organic frameworks (COFs). With flexibility in composition, structure, and pore chemistry, MOFs and COFs have shown increasing functionalities associated with agrochemistry in the last decade, potentially introducing reticular chemistry as a highly accessible chemical toolbox into agrochemical technologies. In this critical review, we will demonstrate how reticular chemistry shapes the future of agrochemistry in the fields of farm sensing, agro-ecological preservation and reutilization, agrochemical formulations, smart indoor farming, agrobiotechnology, and beyond.

Allogeneic Embryos Disregulate Leukemia Inhibitory Factor (LIF) and Its Receptor in the Porcine Endometrium During Implantation

Despite its advantages for pig breeding, embryo transfer (ET) has a major handicap: high embryo mortality during the pre- and implantation period, probably caused by divergent phenomena of tolerance between the immunologically unrelated (i.e., allogeneic) embryos and the recipient sow. Thus, to reach a similar maternal tolerance as in conventional breeding by artificial insemination (AI) would be the key to ET-success. For this reason, we studied the expression of the leukemia inhibitory factor (LIF) cytokine and its receptor in the pig endometrium during the implantation period (days 18 and 24) in sows subjected to ET (AL group) vs. post-cervical-AI controls (Hemi-AL group). Quantification of expression was performed at both mRNA (rt-qPCR) and protein (WB) levels. The expression of endometrial LIF on day 24 was considerably lower in ET than in AI pregnancies. Correlations between endometrial mRNA levels of LIF and LIF-R showed that, contrary to early AI-pregnancies, ET-pregnancies lack an inverse relation between cytokine and receptor levels. In conclusion, ET-pregnancies lack sufficient endometrial levels of LIF to develop adequate immunotolerance mechanisms to prevent the rejection of allogeneic ET-embryos.

On the Road to End Pig Pain: Knowledge and Attitudes of Brazilian Citizens Regarding Castration

We explored the attitudes of Brazilians towards different methods to deal with boar taint in pork (surgical castration without pain control, SC; surgical castration with pain control, SC+PC; immunocastration, IC; raising entire males, EM). Two surveys (Sv1, n = 441 and Sv2, n = 768) containing closed and open questions were conducted. Nearly 70% of Sv1 and Sv2 participants were unaware that meat of entire males may have boar taint and that SC is widely used in pig production in Brazil. In Sv1, acceptability of SC+PC (63%) and IC (53%) was greater than of SC (15%). In Sv2, acceptability of IC (55%) and EM (52%) was greater than of SC (18%). Open-ended responses indicated that participants objected to inflicting pain to pigs to attain a production goal, and were concerned with organoleptic traits and risks of exogenous residues in pork. Participants' views regarding the potential increases in the cost of meat due to adoption of alternative methods varied; some argued that avoiding pain justifies an increase in the price of pork and others that this would impact especially lower income citizens. Our findings indicate that participants opposed surgical castration without pain control, and supported alternative methods. However, the concern with potential risks of presence of residues in meat, expressed by a few participants, may need to be addressed among consumers.

Otoferlin gene editing in sheep via CRISPR-assisted ssODN-mediated Homology Directed Repair

Different mutations of the OTOF gene, encoding for otoferlin protein expressed in the cochlear inner hair cells, induces a form of deafness that is the major cause of nonsyndromic recessive auditory neuropathy spectrum disorder in humans. We report the generation of the first large animal model of OTOF mutations using the CRISPR system associated with different Cas9 components (mRNA or protein) assisted by single strand oligodeoxynucleotides (ssODN) to induce homology-directed repair (HDR). Zygote microinjection was performed with two sgRNA targeting exon 5 and 6 associated to Cas9 mRNA or protein (RNP) at different concentrations in a mix with an ssODN template targeting HDR in exon 5 containing two STOP sequences. A total of 73 lambs were born, 13 showing indel mutations (17.8%), 8 of which (61.5%) had knock-in mutations by HDR. Higher concentrations of Cas9-RNP induced targeted mutations more effectively, but negatively affected embryo survival and pregnancy rate. This study reports by the first time the generation of OTOF disrupted sheep, which may allow better understanding and development of new therapies for human deafness related to genetic disorders. These results support the use of CRISPR/Cas system assisted by ssODN as an effective tool for gene editing in livestock.