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 rabbit, 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.

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.

Animal board invited review: Animal agriculture and alternative meats - learning from past science communication failures

Sustainability discussions bring in multiple competing goals, and the outcomes are often conflicting depending upon which goal is being given credence. The role of livestock in supporting human well-being is especially contentious in discourses around sustainable diets. There is considerable variation in which environmental metrics are measured when describing sustainable diets, although some estimate of the greenhouse gas (GHG) emissions of different diets based on varying assumptions is commonplace. A market for animal-free and manufactured food items to substitute for animal source food (ASF) has emerged, driven by the high GHG emissions of ASF. Ingredients sourced from plants, and animal cells grown in culture are two approaches employed to produce alternative meats. These can be complemented with ingredients produced using synthetic biology. Alternative meat companies promise to reduce GHG, the land and water used for food production, and reduce or eliminate animal agriculture. Some CEOs have even claimed alternative meats will 'end world hunger'. Rarely do such self-proclamations emanate from scientists, but rather from companies in their efforts to attract venture capital investment and market share. Such declarations are reminiscent of the early days of the biotechnology industry. At that time, special interest groups employed fear-based tactics to effectively turn public opinion against the use of genetic engineering to introduce sustainability traits, like disease resistance and nutrient fortification, into global genetic improvement programs. These same groups have recently turned their sights on the 'unnaturalness' and use of synthetic biology in the production of meat alternatives, leaving agriculturists in a quandary. Much of the rationale behind alternative meats invokes a simplistic narrative, with a primary focus on GHG emissions, ignoring the nutritional attributes and dietary importance of ASF, and livelihoods that are supported by grazing ruminant production systems. Diets with low GHG emissions are often described as sustainable, even though the nutritional, social and economic pillars of sustainability are not considered. Nutritionists, geneticists, and veterinarians have been extremely successful at developing new technologies to reduce the environmental footprint of ASF. Further technological developments are going to be requisite to continuously improve the efficiency of animal source, plant source, and cultured meat production. Perhaps there is an opportunity to collectively communicate how innovations are enabling both alternative- and conventional-meat producers to more sustainably meet future demand. This could counteract the possibility that special interest groups who promulgate misinformation, fear and uncertainty, will hinder the adoption of technological innovations to the ultimate detriment of global food security.

A novel risk assessment tool for bovine respiratory disease in preweaned dairy calves

Due to the increased morbidity and mortality of bovine respiratory disease (BRD) in dairy calves, as well as an increasing urgency for the judicious use of antimicrobials in farm animals, a comprehensive risk assessment tool for BRD in preweaned dairy calves has been designed based on a longitudinal and a cross-sectional study. As a multifactorial disease complex in which immune function stressors increase susceptibility to respiratory pathology, risk management programs for environmental and husbandry practices may be an effective approach for BRD control. Practices of known or suspected effect on BRD in preweaned calves have been explored in 2 large studies correlating management factors to BRD prevalence (BRD 100 study) and incidence (BRD 10K study) and forming the scores presented here. Priority was given to results from multivariable over univariable model estimates. However, when used, univariable model estimates were adjusted for confounders or stratified by effect modifiers if necessary. Regression coefficients were translated into scores, which are presented in a field-ready tool consisting of (1) a risk assessment questionnaire, which identifies the herd-specific risk factors and the risk scores associated with each; (2) the California BRD scoring system to estimate the BRD prevalence at the time of risk assessment for future comparison with the prevalence after interventions; and (3) the BRD control and prevention herd management plan, which can be used to plan and track the interventions identified. Scores for 100 dairies across California were used to benchmark a dairy's risk on a spectrum. With the help of the risk assessment tool, dairy producers, calf managers, and veterinarians may be able to adjust management factors that affect BRD risk on a farm and objectively monitor BRD prevalence before and after management interventions. As a result, the BRD risk assessment tool described here is the first comprehensive effort for herd-specific BRD control and prevention.

Preweaning cost of bovine respiratory disease (BRD) and cost-benefit of implementation of preventative measures in calves on California dairies: The BRD 10K study

Bovine respiratory disease (BRD) is a multifactorial disease that is estimated to affect 22% of preweaned dairy calves in the United States and is a leading cause of preweaning mortality in dairy calves. Overall cost of calfhood BRD is reflected in both the immediate cost of treating the disease as well as lifetime decrease in production and increased likelihood of affected cattle leaving the herd before their second calving. The goal of this paper was to develop an estimate of the cost of BRD based on longitudinal treatment data from a study of BRD with a cohort of 11,470 preweaned dairy calves in California. Additionally, a cost-benefit analysis was performed for 2 different preventative measures for BRD, an increase of 0.47 L of milk per day for all calves or vaccination of all dams with a modified live BRD vaccine, using differing assumptions about birth rate and number of calves raised per year. Average short-term cost of BRD per affected calf was $42.15, including the use of anti-inflammatory medications in the treatment protocols across all management conditions. The cost of treating BRD in calves appears to have increased in recent years and is greater than costs presented in previous studies. A cost-benefit analysis examined different herd scenarios for a range of cumulative incidences of BRD from 3 to 25%. Increasing milk fed was financially beneficial in all scenarios above a 3% cumulative incidence of BRD. Use of a modified live vaccine in dams during pregnancy, examining only its value as a form of BRD prevention in the calves raised on the farm, was financially beneficial only if the cumulative incidence of BRD exceeded 10 to 15% depending on the herd size and whether the dairy farm was raising any bull calves. The cost-benefit analysis, under the conditions studied, suggests that producers with high rates of BRD may benefit financially from implementing preventative measures, whereas these preventative measures may not be cost effective to implement on dairy farms with very low cumulative incidences of BRD. The long-term costs of calfhood BRD on lifetime productivity were not factored into these calculations, and the reduction in disease may be associated with additional cost savings and an improvement in calf welfare and herd life.

Management factors associated with bovine respiratory disease in preweaned calves on California dairies: The BRD 100 study

The objective of this cross-sectional study was to determine how management practices on California dairies may be associated with bovine respiratory disease (BRD) in preweaned calves. A convenience sample of 100 dairies throughout California, providing a study population of 4,636 calves, were visited between May 2014 and April 2016. During each farm visit, in-person interviews with the herd manager or calf caretaker were conducted to collect information about herd demographics, maternity pen, colostrum and calf management, herd vaccinations, and dust abatement. A random sample of preweaned calves was identified and evaluated for the presence of BRD using a standardized tool. A survey-adjusted generalized linear mixed model with a logit link function was fitted with calf as the unit of analysis and dairy as the random effect. Mean study herd size (±SE) was 1,718 (±189.9) cows. Survey-adjusted estimates of breed types in the sample were 81.6% (±0.6) Holstein, 13.1% (±0.4) Jersey, and 5.3% (±0.5) crossbred or other purebred breeds, and calf sex proportions were 73.8% (±1.0) female and 26.2% (±1.0) male. Overall survey-adjusted BRD prevalence in the study herds was 6.91% (±0.69). Housing factors positively associated with BRD were metal hutches compared with wood hutches [odds ratio (OR) = 11.19; 95% confidence interval (CI) = 2.80–44.78], calf-to-calf contact in calves >75 d of age (OR = 9.95, 95% CI = 1.50–65.86), feeding Holstein calves <2.84 L of milk or replacer per day (OR = 7.16, 95% CI = 1.23–41.68), and lagoon water used for flushing manure under hutches compared with no flush (OR = 12.06, 95% CI = 1.93–75.47). Providing extra shade over hutches (OR = 0.08; 95% CI = 0.02–0.37), feeding calves at least 90% saleable milk (OR = 0.27, 95% CI = 0.13–0.54) or pasteurized milk (OR = 0.10; 95% CI = 0.03–0.36), and feeding >5.68 L of milk or replacer per day to Jersey calves (OR = 0.04; 95% CI = 0.01–0.28) were negatively associated with BRD. Our study identified management practices on California dairies with variability and that may contribute to differences in BRD prevalence, which will be incorporated into a risk-assessment tool to control and prevent BRD in preweaned dairy calves.

Epidemiology of bovine respiratory disease (BRD) in preweaned calves on California dairies: The BRD 10K study

Bovine respiratory disease (BRD) is one of the leading causes of death in dairy heifers. The objective of this prospective cohort study was to characterize the epidemiology of BRD in preweaned dairy calves and to identify management practices associated with decreased risk of BRD. Dairies were chosen for the study based on management practices, location, size, and willingness to participate. A total of 6 dairies, ranging in size from 700 to 3,200 milking cows, in 6 counties across California's Central Valley, were enrolled in the study for at least 1 year. A total of 11,945 calves were born on the study dairies and followed until weaning. Incidence of BRD was estimated using treatment records. Trained study personnel performed comprehensive calf management surveys and estimated BRD prevalence on every dairy at least once every season. A shared frailty model was used to model the associations between management practices and BRD hazard. The final models included data from complete records of 11,470 calves. The overall BRD study period prevalence across the study herds was 22.8%. The mean BRD incidence density rate on all the study dairies was 0.17 BRD cases [95% confidence interval (CI) = 0.16-1.74] per calf-month at risk. The shared frailty model identified that feeding only waste or saleable milk (compared with use of milk replacer), feeding over 3.8 L of milk per day to calves under 21 d of age, frequent changing of maternity pen bedding, and administration of modified live or killed BRD vaccines to dams before calving significantly reduced the risk of BRD. Risk factors for BRD included housing calves in wooden hutches with metal roofs, compared with all-wood hutches, twin births, and perception of dust occurring "regularly," as reported by calf managers, compared with a perception of "no dust" in the calf-raising area. All 4 seasons were analyzed, and both summer (hazard ratio = 1.15; 95% CI = 1.01 to 1.32) and spring (hazard ratio = 1.26; 95% CI = 1.11 to 1.44) were associated with a higher risk of BRD compared with winter. The current longitudinal study identified specific housing and feeding practices that could be modified to decrease risk of BRD. In addition, season was observed to have a strong effect on calves' risk of developing BRD on California dairies.

Bovine respiratory disease (BRD) cause-specific and overall mortality in preweaned calves on California dairies: The BRD 10K study

Mortality in preweaned dairy calves is a significant source of economic loss for dairy producers. In particular, bovine respiratory disease (BRD) is a leading cause of death in preweaned dairy calves. The objectives of this study were to investigate management practices and their effects on mortality, both that specifically attributed to BRD and overall mortality due to all causes, in preweaned dairy calves. Rates of failure of passive transfer of immunity (FPT) are also reported. The study consisted of a convenience sample of 5 dairies across California, selected based on management practices, calf records, location, and size. Trained study personnel performed comprehensive calf management surveys on every dairy at least once every season. Calves were enrolled in the study at birth and followed until weaning. Mixed-effect logistic regression models were specified for the outcomes all-cause mortality (any death before weaning) and mortality attributed to BRD. The 2 final models included a total of 11,470 calves that were born on the study dairies and followed until weaning. The study cohort's overall crude mortality was 2.8%, with crude mortality of individual dairies ranging from 1.7 to 7.2%. The proportion of mortality attributed to BRD was 19.3%, with a range of 0 to 27.1% on the study dairies. Increasing the frequency of changing maternity pen bedding was associated with a decreased risk of mortality due to BRD. Calves diagnosed with BRD in the spring had an increased risk of mortality compared with calves born in the summer; mortality in calves with fall and winter BRD diagnoses did not different significantly from that in summer. Season of mortality was not significant in either model. Feeding ≥5.7 L of milk per day per calf (vs. ≤3.7 L/d) decreased the risk of mortality in calves over 21 d of age. Twins had a 68% increased risk of all-cause mortality compared with calves born as singletons. Both mortality models showed an association between administration of a modified live vaccine in dams (targeting BRD pathogens) and a decreased risk of mortality in calves. Using a serum total protein cut-off of 5.2 g/dL, 16.8% of calves had FPT, with a mean serum total protein concentration of 5.94 ± 0.06 g/dL across all calves sampled.

Comparison of gene editing versus conventional breeding to introgress the POLLED allele into the US dairy cattle population

Disbudding and dehorning are commonly used cattle management practices to protect animals and humans from injury. They are unpleasant, costly processes subject to increased public scrutiny as an animal welfare issue. Horns are a recessively inherited trait, so one option to eliminate dehorning is to breed for polled (hornlessness). However, due to the low genetic merit and scarcity of polled dairy sires, this approach has not been widely adopted. In March 2018, only 3 Holstein and 0 Jersey active homozygous polled sires were registered with the National Association of Animal Breeders. Alternatively, gene editing to produce high-genetic-merit polled sires has been proposed. To further explore this concept, introgression of the POLLED allele into both the US Holstein and Jersey cattle populations via conventional breeding or gene editing (top 1% of bulls/year) was simulated for 3 polled mating schemes and compared with baseline selection on lifetime net merit (NM$) alone, over the course of 20 yr. Scenarios were replicated 10 times and the changes in HORNED allele frequency, inbreeding, genetic gain (NM$), and number of unique sires used were calculated. Gene editing decreased the frequency of the HORNED allele to <0.1 after 20 yr, which was as fast or faster than conventional breeding for both breeds. In the mating scheme that required the use of only existing homozygous polled sires, inbreeding reached 17% (Holstein) and 14% (Jersey), compared with less than 7% in the baseline scenarios. However, gene editing in the same mating scheme resulted in significantly less inbreeding, 9% (Holstein) and 8% (Jersey). Also, gene editing resulted in significantly higher NM$ after 20 yr compared with conventional breeding for both breeds. Additionally, the gene editing scenarios of both breeds used a significantly greater number of unique sires compared with either the conventional breeding or baseline scenarios. Overall, our simulations show that, given the current genetic merit of horned and polled dairy sires, the use of conventional breeding methods to decrease the frequency of the HORNED allele will increase inbreeding and slow genetic improvement. Furthermore, this study demonstrates how gene editing could be used to rapidly decrease the frequency of the HORNED allele in US dairy cattle populations while maintaining the rate of genetic gain, constraining inbreeding to acceptable levels, and simultaneously addressing an emerging animal welfare concern.

Regional management practices and prevalence of bovine respiratory disease in California's preweaned dairy calves

The objective of this cross-sectional study was to estimate the prevalence of bovine respiratory disease (BRD) in California preweaned dairy calves and identify management practices that are associated with BRD. A convenience sample of 100 dairies in the 3 distinct dairy regions of California was surveyed. Regions evaluated were Northern California (NCA), northern San Joaquin Valley (NSJV), and greater Southern California (GSCA). A questionnaire on calf management practices and demographic information was administered via in-person interviews at each dairy and a random sample of preweaned calves was evaluated using the California BRD scoring system on the same day. Prevalence of BRD varied between the 3 dairy regions: 9.30% in NCA, 4.51% in NSJV, and 7.35% in GSCA. Breed was not associated with BRD prevalence at the statewide level, but differences in prevalence were observed between breeds across the regions with a higher prevalence in NCA for Jerseys and in GSCA for Holsteins, compared with NSJV. Prevalence of BRD was not different between organic and conventional dairies. Colostrum management practices, including heat treatment and feeding colostrum from multiparous cows, varied by region and were associated with lower BRD prevalence. Calves housed in group pens, a practice observed primarily in NCA, had a higher BRD prevalence than those in individual housing. Feeding salable milk was also more common in NCA and was associated with lower BRD prevalence. Ground and road surfaces adjacent to the calf raising area were also variable by region, and paved surfaces were associated with lower BRD prevalence. Management practices associated with BRD varied across the state and may be addressed to inform the adoption and implementation of potentially protective management decisions on California dairies and other regions with similar dairy systems.

The contribution of transgenic and genome-edited animals to agricultural and industrial applications

For centuries, animal breeders have intentionally selected the parents of the next generation based on their concept of the 'ideal' animal. The dramatic differences seen in the appearance and productivity of different breeds show the power of such selection on DNA sequence variations. Unfortunately, the global furore over the use of modern biotechnologies to introduce desired genetic variations into animal breeding programmes, and the regulatory uncertainty associated with these recombinant DNA techniques, has effectively precluded the use of these technologies in food animal breeding programmes. Ironically, many of these early transgenic animal applications targeted traits that favoured sustainability, such as disease resistance and decreased environmental impact. As a consequence, transgenic animals have had little opportunity to affect global agriculture, and only a handful of pharmaceutical applications have been successfully commercialised. New developments in genome editing hold considerable promise for targeting traits that improve both animal health and welfare, and frequently involve no introduction of DNA sequences from other species. Nonetheless, future global regulation and public acceptance of such methods remain uncertain. Proposals to regulate genome-edited animals based solely on the process used to influence DNA sequence variations (i.e. intentional genome editing) and any potential attendant risks, with no counterbalancing consideration of the ensuing benefits or risks associated with conventional selection programmes, will potentially forestall the use of genome editing in animal breeding programmes. No activity can survive a risk-only evaluation, and there are considerable opportunity costs associated with preventing breeders' access to safe technologies in order to achieve genetic improvements in livestock populations.

Gene editing in livestock: promise, prospects and policy

Abstract

Although genetically engineered livestock were first introduced in the 1980s, only three biomedical applications (ATryn®, Ruconest®, Kanuma®) and one food animal application (AquAdvantage® salmon) have been brought to market. The initial promise of this technology was hampered by low efficiency, random site integration, public resistance and regulatory hurdles. Gene editing has made it possible to precisely target changes in livestock genomes, overcoming previous challenges. Livestock and poultry editing applications include disease resistance, animal welfare, production traits, animals as bioreactors, xenotransplantation and the development of models for human diseases. The extent to which any of these applications are utilized beyond research laboratories will depend upon regulatory frameworks, uptake by livestock producers and industry, and public acceptance. The 2017 draft US Food and Drug Administration regulatory guidance for gene edited animals, which proposes to regulate 'intentional' genomic alterations introduced by editing as new animal drugs irrespective of product novelty or risk, is at odds with emerging regulations around gene edited plants. Lengthy process-based regulation triggered by human 'intention' rather than novel product risk may dissuade animal genetics companies and breeders from employing gene editing to introduce beneficial genetic alterations into livestock populations, effectively the same fate encountered by genetic engineering in animals. Goal conflicts will likely continue between genetic innovations to address problems like animal disease and welfare and concerns around the use of modern molecular genetics in food animals. The early applications that successfully navigate regulatory hurdles will influence the public discussion around gene edited animals and impact the trajectory of future applications.

Detection of dietary DNA, protein, and glyphosate in meat, milk, and eggs

Products such as meat, milk, and eggs from animals that have consumed genetically engineered (GE) feed are not currently subject to mandatory GE labeling requirements. Some voluntary "non-genetically modified organism" labeling has been associated with such products, indicating that the animals were not fed GE crops, as there are no commercialized GE food animals. This review summarizes the available scientific literature on the detection of dietary DNA and protein in animal products and briefly discusses the implications of mandatory GE labeling for products from animals that have consumed GE feed. Because glyphosate is used on some GE crops, the available studies on glyphosate residues in animal products are also reviewed. In GE crops, recombinant DNA (rDNA) makes up a small percentage of the plant's total DNA. The final amount of DNA in food/feed depends on many factors including the variable number and density of cells in the edible parts, the DNA-containing matrix, environmental conditions, and the specific transgenic event. Processing treatments and animals' digestive systems degrade DNA into small fragments. Available reports conclude that endogenous DNA and rDNA are processed in exactly the same way in the gastrointestinal tract and that they account for a very small proportion of food intake by weight. Small pieces of high copy number endogenous plant genes have occasionally been detected in meat and milk. Similarly sized pieces of rDNA have also been identified in meat, primarily fish, although detection is inconsistent. Dietary rDNA fragments have not been detected in chicken or quail eggs or in fresh milk from cows or goats. Collectively, studies have failed to identify full-length endogenous or rDNA transcripts or recombinant proteins in meat, milk, or eggs. Similarly, because mammals do not bioaccumulate glyphosate and it is rapidly excreted, negligible levels of glyphosate in cattle, pig and poultry meat, milk, and eggs have been reported. Despite consumer concern about the presence of trace concentrations of glyphosate that might have been applied to feed crops and/or the presence of rDNA or recombinant proteins in meat, milk, and eggs, the available data do not provide evidence to suggest that products from animals that have consumed approved GE feed crops differ in any distinguishable way from those derived from animals fed conventional feed or that products from animals fed GE feedstuffs pose novel health risks.

Survey of management practices related to bovine respiratory disease in preweaned calves on California dairies

In the spring of 2013, a survey of California (CA) dairies was performed to characterize management practices related to bovine respiratory disease in preweaned calves, compare these practices across geographic regions of the state, and determine the principal components that explain the variability in management between herds. The questionnaire consisted of 53 questions divided into 6 sections to assess management practices affecting dairy calves from precalving to weaning. The questionnaire was mailed to 1,523 grade A licensed dairies in CA and 224 responses (14.7%) were collected. Survey response rates were similar over the 3 defined regions of CA: northern CA, northern San Joaquin Valley, and the greater southern CA region. The mean size of respondent herds was 1,423 milking cows. Most dairies reported raising preweaned calves on-site (59.7%). In 93.3% of dairies, preweaned calves were raised in some form of individual housing. Nonsaleable milk was the most frequent liquid diet fed to preweaned heifers (75.2%). Several important differences were identified between calf-raising practices in CA and practices reported in recent nationwide studies, including herd sizes, housing practices, and sources of milk fed to heifers. The differences between the CA and nationwide studies may be explained by differences in herd size. Regional differences within CA were also identified. Compared with the 2 other regions, northern CA dairies were found to have smaller herds, less Holstein cattle, calves remained with dams for longer periods of time after calving, were more likely to be certified organic dairies, and raised their own calves more often. Principal component analysis was performed and identified 11 components composed of 28 variables (questions) that explained 66.5% of the variability in the data. The identified components and questions will contribute to developing a risk assessment tool for bovine respiratory disease in preweaned dairy calves.

Prevalence and impacts of genetically engineered feedstuffs on livestock populations

Globally, food-producing animals consume 70 to 90% of genetically engineered (GE) crop biomass. This review briefly summarizes the scientific literature on performance and health of animals consuming feed containing GE ingredients and composition of products derived from them. It also discusses the field experience of feeding GE feed sources to commercial livestock populations and summarizes the suppliers of GE and non-GE animal feed in global trade. Numerous experimental studies have consistently revealed that the performance and health of GE-fed animals are comparable with those fed isogenic non-GE crop lines. United States animal agriculture produces over 9 billion food-producing animals annually, and more than 95% of these animals consume feed containing GE ingredients. Data on livestock productivity and health were collated from publicly available sources from 1983, before the introduction of GE crops in 1996, and subsequently through 2011, a period with high levels of predominately GE animal feed. These field data sets, representing over 100 billion animals following the introduction of GE crops, did not reveal unfavorable or perturbed trends in livestock health and productivity. No study has revealed any differences in the nutritional profile of animal products derived from GE-fed animals. Because DNA and protein are normal components of the diet that are digested, there are no detectable or reliably quantifiable traces of GE components in milk, meat, and eggs following consumption of GE feed. Globally, countries that are cultivating GE corn and soy are the major livestock feed exporters. Asynchronous regulatory approvals (i.e., cultivation approvals of GE varieties in exporting countries occurring before food and feed approvals in importing countries) have resulted in trade disruptions. This is likely to be increasingly problematic in the future as there are a large number of "second generation" GE crops with altered output traits for improved livestock feed in the developmental and regulatory pipelines. Additionally, advanced techniques to affect targeted genome modifications are emerging, and it is not clear whether these will be encompassed by the current GE process-based trigger for regulatory oversight. There is a pressing need for international harmonization of both regulatory frameworks for GE crops and governance of advanced breeding techniques to prevent widespread disruptions in international trade of livestock feedstuffs in the future.

Evaluation of bull prolificacy on commercial beef cattle ranches using DNA paternity analysis

SNP-based DNA testing was used to assign paternity to 5,052 calves conceived in natural service multisire breeding pastures from 3 commercial ranches in northern California representing 15 calf crops over 3 yr. Bulls present for 60 to 120 d at a 25:1 cow to bull ratio in both fall and spring breeding seasons in ∼40 ha or smaller fenced breeding pastures sired a highly variable (P < 0.001) number of calves (Ncalf), ranging from 0 (4.4% of bulls present in any given breeding season) to 64 calves per bull per breeding season, with an average of 18.9 ± 13.1. There was little variation in Ncalf among ranches (P = 0.90), years (P = 0.96), and seasons (P = 0.94). Bulls varied widely (P < 0.01) in the average individual 205-d adjusted weaning weight (I205) of progeny, and I205 varied between years (P < 0.01) and seasons (P < 0.01) but not ranches (P = 0.29). The pattern for cumulative total 205-d adjusted weaning weight of all progeny sired by a bull (T205) was highly correlated to Ncalf, with small differences between ranches (P = 0.35), years (P = 0.66), and seasons (P = 0.20) but large differences (P < 0.01) between bulls, ranging from an average of 676 to 8,838 kg per bull per calf crop. The peak Ncalf occurred at about 5 yr of age for bulls ranging from 2 to 11 yr of age. Weekly conception rates as assessed by date of calving varied significantly and peaked at wk 3 of the calving season. The distribution of calves born early in the calving season was disproportionately skewed toward the highly prolific bulls. The DNA paternity testing of the subset of those calves born in wk 3 of the calving season was highly predictive of overall bull prolificacy and may offer a reduced-cost DNA-based option for assessing prolificacy. Prolificacy of young bulls in their first breeding season was positively linearly related (P < 0.05) to subsequent breeding seasons, explaining about 20% of the subsequent variation. Prolificacy was also positively linearly related (P < 0.05) to scrotal circumference (SC) EPD for Angus bulls that had SC EPD Beef Improvement Federation accuracies greater than 0.05. Varying prolificacy of herd bulls has implications for the genetic composition of replacement heifers, with the genetics of those bulls siring an increased number of calves being disproportionately represented in the early-born replacement heifer pool.

Genetic parameters for concentrations of minerals in longissimus muscle and their associations with palatability traits in Angus cattle

The objective of this study was to estimate genetic parameters for concentrations of minerals in LM and to evaluate their associations with beef palatability traits. Samples of LM from 2,285 Angus cattle were obtained and fabricated into steaks for analysis of mineral concentrations and for trained sensory panel assessments. Nine minerals, including calcium, copper, iron, magnesium, manganese, phosphorus, potassium, sodium, and zinc, were quantified. Restricted maximum likelihood procedures were used to obtain estimates of variance and covariance components under a multiple-trait animal model. Estimates of heritability for mineral concentrations in LM varied from 0.01 to 0.54. Iron and sodium were highly and moderately heritable, respectively, whereas the other minerals were lowly heritable except for calcium, copper, and manganese, which exhibited no genetic variation. Strong positive genetic correlations existed between iron and zinc (0.49, P < 0.05), between magnesium and phosphorus (0.88, P < 0.05), between magnesium and sodium (0.68, P < 0.05), and between phosphorus and potassium (0.69, P < 0.05). Overall tenderness assessed by trained sensory panelists was positively associated with manganese, potassium, and sodium and negatively associated with phosphorus and zinc concentrations (P < 0.05). Juiciness assessed by trained sensory panelists was negatively associated with magnesium and positively associated with manganese and sodium concentrations (P < 0.05). Livery or metallic flavor was not associated with any of the minerals (P > 0.05). Beefy flavor was positively associated with calcium, iron, and zinc and negatively associated with sodium concentration, whereas a painty or fishy flavor was positively associated with sodium and negatively associated with calcium and potassium concentrations (P < 0.05). Beef is a major contributor of iron and zinc in the human diet, and these results demonstrate sufficient genetic variation for these traits to be improved through marker-assisted selection programs without compromising beef palatability.

Hot topic: performance of bovine high-density genotyping platforms in Holsteins and Jerseys

Two high-density single nucleotide polymorphism (SNP) genotyping arrays have recently become available for bovine genomic analyses, the Illumina High-Density Bovine BeadChip Array (777,962 SNP) and the Affymetrix Axiom Genome-Wide BOS 1 Array (648,874 SNP). These products each have unique design and chemistry attributes, and the extent of marker overlap and their potential utility for quantitative trait loci fine mapping, detection of copy number variation, and multibreed genomic selection are of significant interest to the cattle community. This is the first study to compare the performance of these 2 arrays. Deoxyribonucleic acid samples from 16 dairy cattle (10 Holstein, 6 Jersey) were used for the comparison. An independent set of DNA samples taken from 46 Jersey cattle and 18 Holstein cattle were used to ascertain the amount of SNP variation accounted by the 16 experimental samples. Data were analyzed with SVS7 software (Golden Helix Inc., Bozeman, MT) to remove SNP having a call rate less than 90%, and linkage disequilibrium pruning was used to remove linked SNP (r² ≥ 0.9). Maximum, average, and median gaps were calculated for each analysis based on genomic position of SNP on the bovine UMD3.1 genome assembly. All samples were successfully genotyped (≥ 98% SNP genotyped) with both platforms. The average number of genotyped SNP in the Illumina platform was 775,681 and 637,249 for the Affymetrix platform. Based on genomic position, a total of 107,896 SNP were shared between the 2 platforms; however, based on genotype concordance, only 96,031 SNP had complete concordance at these loci. Both Affymetrix BOS 1 and Illumina BovineHD genotyping platforms are well designed and provide high-quality genotypes and similar coverage of informative SNP. Despite fewer total SNP on BOS 1, 19% more SNP remained after linkage disequilibrium pruning, resulting in a smaller gap size (5.2 vs. 6.9 kb) in Holstein and Jersey samples relative to BovineHD. However, only 224,115 Illumina and 241,038 Affymetrix SNP remained following removal of SNP with a minor allele frequency of zero in Holstein and Jersey samples, resulting in an average gap size of 11,887 bp and 11,018 bp, respectively. Combining the 354,348 informative (r² ≥ 0.9), polymorphic (minor allele frequency ≥ 0), unique SNP data from both platforms decreased the average gap size to 7,560 bp. Genome-wide copy number variant analyses were performed using intensity files from both platforms. The BovineHD platform provided an advantage to the copy number variant data compared with the BOS 1 because of the larger number of SNP, higher intensity signals, and lower background effects. The combined use of both platforms significantly improved coverage over either platform alone and decreased the gap size between SNP, providing a valuable tool for fine mapping quantitative trait loci and multibreed animal evaluation.

Genetic polymorphisms in bovine transferrin receptor 2 (TFR2) and solute carrier family 40 (iron-regulated transporter), member 1 (SLC40A1) genes and their association with beef iron content

Beef is considered to be an excellent source of dietary iron. However, little is known about the genetic control of beef iron content. We hypothesized that genetic polymorphisms in transferrin receptor 2 (TFR2) and solute carrier family 40 (iron-regulated transporter), member 1 (SLC40A1) could influence skeletal muscle iron content. The objective of this study was to use Angus cattle to identify single-nucleotide polymorphisms (SNPs) in the exons and flanking regions of the bovine TFR2 and SLC40A1 genes and to evaluate the extent to which genetic variation in them was associated with bovine longissimus dorsi muscle iron content. Ten novel SNPs were identified in TFR2, of which one SNP tended to be associated (P < 0.013) with skeletal muscle iron content. Nine novel SNPs in SLC40A1, NC007300: rs133108154, rs137140497, rs135205621, rs136600836, rs134388440, rs136347850, rs134186279, rs134621419 and rs137555693, were identified, of which SNPs rs134388440, rs136347850 and rs137555693 were significantly associated (P < 0.007) with skeletal muscle iron content. High linkage disequilibrium was observed among SLC40A1 SNPs rs134388440, rs136347850 and rs137555693 (R(2)  > 0.99), from which two haplotypes, TGC and CAT, were defined. Beef from individuals that were homozygous for the TGC haplotype had significantly (P < 0.001) higher iron content than did beef from CAT homozygous or heterozygous individuals. The estimated size of effect of the identified haplotypes was 0.3% of the phenotypic variance. In conclusion, our study provides evidence for genetic control of beef iron concentration. Moreover, SNPs identified in SLC40A1, rs134388440, rs136347850 and rs137555693 might be useful markers for the selection of Angus cattle for altered iron content.

The value of using DNA markers for beef bull selection in the seedstock sector

The objective of this study was to estimate the value derived from using DNA information to increase the accuracy of beef sire selection in a closed seedstock herd. Breeding objectives for commercial production systems targeting 2 diverse markets were examined using multiple-trait selection indexes developed for the Australian cattle industry. Indexes included those for both maternal (self-replacing) and terminal herds targeting either a domestic market, where steers are finished on pasture, or the export market, where steers are finished on concentrate rations in feedlots and marbling has a large value. Selection index theory was used to predict the response to conventional selection based on phenotypic performance records, and this was compared with including information from 2 hypothetical marker panels. In 1 case the marker panel explained a percentage of additive genetic variance equal to the heritability for all traits in the breeding objective and selection criteria, and in the other case to one-half of this amount. Discounted gene flow methodology was used to calculate the value derived from the use of superior bulls selected using DNA test information and performance recording over that derived from conventional selection using performance recording alone. Results were ultimately calculated as discounted returns per DNA test purchased by the seedstock operator. The DNA testing using these hypothetical marker panels increased the selection response between 29 to 158%. The value of this improvement above that obtained using traditional performance recording ranged from $89 to 565 per commercial bull, and $5,332 to 27,910 per stud bull. Assuming that the entire bull calf crop was tested to achieve these gains, the value of the genetic gain derived from DNA testing ranged from $204 to 1,119 per test. All values assumed that the benefits derived from using superior bulls were efficiently transferred along the production chain to the seedstock producer incurring the costs of genotyping. These results suggest that the development of greater-accuracy DNA tests for beef cattle selection could be beneficial from an industry-wide perspective, but the commercial viability will strongly depend on price signaling throughout the production chain.

DNA-based paternity analysis and genetic evaluation in a large, commercial cattle ranch setting1

Deoxyribonucleic acid-based tests were used to assign paternity to 625 calves from a multiple-sire breeding pasture. There was a large variability in calf output and a large proportion of young bulls that did not sire any offspring. Five of 27 herd sires produced over 50% of the calves, whereas 10 sires produced no progeny and 9 of these were yearling bulls. A comparison was made between the paternity results obtained when using a DNA marker panel with a high (0.999), cumulative parentage exclusion probability (P(E)) and those obtained when using a marker panel with a lower P(E) (0.956). A large percentage (67%) of the calves had multiple qualifying sires when using the lower resolution panel. Assignment of the most probable sire using a likelihood-based method based on genotypic information resolved this problem in approximately 80% of the cases, resulting in 75% agreement between the 2 marker panels. The correlation between weaning weight, on-farm EPD based on pedigrees inferred from the 2 marker panels was 0.94 for the 24 bulls that sired progeny. Partial progeny assignments inferred from the lower resolution panel resulted in the generation of EPD for bulls that actually sired no progeny according to the high-P(E) panel, although the Beef Improvement Federation accuracies of EPD for these bulls were never greater than 0.14. Simulations were performed to model the effect of loci number, minor allele frequency, and the number of offspring per bull on the accuracy of genetic evaluations based on parentage determinations derived from SNP marker panels. The SNP marker panels of 36 and 40 loci produced EPD with accuracies nearly identical to those EPD resulting from use of the true pedigree. However, in field situations where factors including variable calf output per sire, large sire cohorts, relatedness among sires, low minor allele frequencies, and missing data can occur concurrently, the use of marker panels with a larger number of SNP loci will be required to obtain accurate on-farm EPD.

Validation of commercial DNA tests for quantitative beef quality traits

Associations between 3 commercially available genetic marker panels (GeneSTAR Quality Grade, GeneSTAR Tenderness, and Igenity Tender-GENE) and quantitative beef traits were validated by the US National Beef Cattle Evaluation Consortium. Validation was interpreted to be the independent confirmation of the associations between genetic tests and phenotypes, as claimed by the commercial genotyping companies. Validation of the quality grade test (GeneSTAR Quality Grade) was carried out on 400 Charolais x Angus crossbred cattle, and validation of the tenderness tests (GeneSTAR Tenderness and Igenity Tender-GENE) was carried out on over 1,000 Bos taurus and Bos indicus cattle. The GeneSTAR Quality Grade marker panel is composed of 2 markers (TG5, a SNP upstream from the start of the first exon of thyroglobulin, and QG2, an anonymous SNP) and is being marketed as a test associated with marbling and quality grade. In this validation study, the genotype results from this test were not associated with marbling score; however, the association of substituting favorable alleles of the marker panel with increased quality grade (percentage of cattle grading Choice or Prime) approached significance (P < or = 0.06), mainly due to the effect of 1 of the 2 markers. The GeneSTAR Tenderness and Igenity TenderGENE marker panels are being marketed as tests associated with meat tenderness, as assessed by Warner-Bratzler shear force. These marker panels share 2 common mu-calpain SNP, but each has a different calpastatin SNP. In both panels, there were highly significant (P < 0.001) associations of the calpastatin marker and the mu-calpain haplotype with tenderness. The genotypic effects of the 2 tenderness panels were similar to each other, with a 1 kg difference in Warner-Bratzler shear force being observed between the most and least tender genotypes. Unbiased and independent validation studies are important to help build confidence in marker technology and also as a potential source of data required to enable the integration of marker data into genetic evaluations. As DNA tests associated with more beef production traits enter the marketplace, it will become increasingly important, and likely more difficult, to find independent populations with suitable phenotypes for validation studies.

Endogenous production and elevated levels of long-chain n-3 fatty acids in the milk of transgenic mice

N-3 Polyunsaturated fatty acids (n-3 PUFA) are important for the normal development and functioning of all organisms. Mammals lack the n-3 fatty acid desaturase required for the synthesis of alpha-linolenic acid (18:3n-3), and are therefore dependent on dietary sources to obtain this essential fatty acid. Currently, the richest source of dietary long-chain n-3 PUFA, eicosapentaenoic acid (20:5n-3) and docosahexaenoic acid (22:6n-3), are triacylglycerides extracted from rapidly declining marine resources. The nematode Caenorhabditis elegans synthesizes a wide range of PUFA and possesses the only known example of an n-3 fatty acid desaturase enzyme in the animal kingdom. Transgenic mice expressing the C. elegans n-3 desaturase under the control of the lactation-induced goat beta-casein mammary gland promoter were generated via pronuclear microinjection. Significant increases in n-3 PUFA, decreases in n-6 PUFA, and an overall decrease in the n-6:n-3 PUFA ratio were observed in the milk produced by transgenic mice. Neonate mice consuming milk from transgenic females accumulated increased levels of docosahexaenoic acid in their brains. This transgenic model may provide useful information to address some basic questions of neonatal nutrition, and demonstrates one of the steps that would be required to increase the n-3 PUFA content of milk and dairy products endogenously. Increasing the proportion of n-3 PUFA in milk fat would help to improve the nutritional composition of an important component of the North American diet.

Hot Topic: Endogenous Production of n-3 and n-6 Fatty Acids in Mammalian Cells

Polyunsaturated fatty acids (PUFA) are important components of mammalian diets, and the beneficial effects of n-3 PUFA on human development and cardiovascular health have been well documented. Caenorhabditis elegans is one of the few animals known to be able to produce linoleic (LA, 18:2n-6) and alpha-linolenic (ALA, 18:3n-3) essential fatty acids. These essential PUFA are generated by the action of desaturases that successively direct the conversion of monounsaturated fatty acids (MUFA) to PUFA. The cDNA coding sequences of the C. elegans Delta(12) and n-3 fatty acid desaturases were each placed under the control of separate constitutive eukaryotic promoters and simultaneously introduced into HC11 mouse mammary epithelial cells by adenoviral transduction. Phospholipids from transduced cells showed a significant decrease in the ratios of both MUFA:PUFA and n-6:n-3 fatty acids relative to control cultures. The fatty acid profile of transduced cellular phospholipids revealed significant decreases in MUFA and arachidonic acid (20:4n-6), and increases in LA, ALA, and eicosapentaenoic acid (20:5n-3). The fatty acid composition of triacylglycerols derived from transduced cells was similarly, but less dramatically, affected. These results demonstrate the functionality of C. elegans fatty acid desaturase enzymes in mammalian cells. Expression of these desaturases in livestock might act to counterbalance the saturating effect that rumen microbial biohydrogenation has on the fatty acid profile of ruminant products, and allow for the development of novel, land-based dietary sources of n-3 PUFA.

Synaptonemal complex analysis in spermatocytes of white sturgeon, Acipenser transmontanus Richardson (Pisces, Acipenseridae), a fish with a very high chromosome number

The surface-spreading synaptonemal complex (SC) technique was used to visualize the process of chromosome synapsis in white sturgeon spermatocytes. Pachytene nuclei had various numbers of univalents (0-3) and self-paired foldback elements with no obvious centromeric region (1-7) that may represent accessory chromosomes. The total SC length was 482 ( ±56) µm and the average number of SC elements per nucleus was 139 ( ±3.4). This SC number suggests a higher chromosome number than had been reported in previous mitotic studies (2n = 248 ± 8). There was variation in the SC count both within and between animals. A representative SC karyotype is presented and some differences between the mitotic and meiotic karyotypes for this species are discussed. There was no evidence of multivalent formation, suggesting that the process of diploidization has gone to completion in the males of this ancient polyploid species. Each SC had lateral elements of equal length, and no bivalent exhibited the atypical pairing behavior that is often characteristically associated with heteromorphic sex chromosomes, suggesting that the male is not the heterogametic sex in white sturgeon.

Financial analysis of alternative treatments for clinical mastitis associated with environmental pathogens

For two large California dairy herds with twice daily milking, 171 infected quarters of lactating cows with mild clinical mastitis were randomly assigned to one of three treatment groups. Group A (50 cows) was treated with 62.5 mg of intramammary amoxicillin every 12 h for three milkings. Group C (50 cows) was treated with 200 mg of intramammary cephapirin every 12 h for two milkings. Group O (71 cows) was treated with 100 U of intramuscular oxytocin every 12 h for three milkings. Clinical cure rates did not differ among treatment groups. The cost per episode of clinical mastitis was higher ($54.47) for group C than for groups A ($38.53) or O ($34.88). Group O had a higher incidence of relapse (41%), and a greater percentage of group O cows (65%) experienced an additional mastitic event in the enrolled lactation than did cows in groups A and C. Treatment had no effect on the mean number of nonsalable milkings (24.7) associated with mastitis in the lactation interval subsequent to enrollment on the trial. Twenty-two percent of the cows accrued more than 30 nonsalable milkings and produced 55% of the total nonsalable milkings associated with mastitis. There was no treatment effect on total milk production, fat production, or time to removal of the enrolled cows from the herd.

Efficacy of intramammary antibiotic therapy for treatment of clinical mastitis caused by environmental pathogens

For three California dairy herds with bulk tank SCC < 200,000/ml, twice daily milking, and no mastitis vaccine, 254 quarters with mild clinical mastitis were randomly assigned to three groups. Group A (n = 74) was treated with 62.5 mg of intramammary amoxicillin every 12 h for three milkings. Group C (n = 75) was treated with 200 mg of intramammary cephapirin every 12 h for two milkings. Group O (n = 105) was treated with 100 units of intramuscular oxytocin every 12 h for two or three milkings. Aseptic pretreatment quarter samples revealed 94 (37%) coliforms, 65 (26%) environmental streptococci, 34 (13%) other bacteria, and 61 (24%) with no isolate on bovine blood agar plates. Contagious pathogens were not isolated. Clinical cure (return of quarter and milk to normal) and bacterial cure (absence of primary pathogen isolated pretreatment) were assessed at milking 8 and d 20 after initial treatment. No difference existed in clinical (67.6, 67.7, or 66.7%) or bacterial (43.9, 55.0 or 49.1%) cure rate among groups. Clinical cure rates did not differ when quarters were grouped by etiology, but clinical cure rates for quarters with pathogens other than streptococci or coliforms were lower in group O.

Evaluation of milk antibiotic residue screening tests in cattle with naturally occurring clinical mastitis

Milk from 172 commercial cows with mild to moderate clinical mastitis was tested with five antibiotic residue detection assay systems. One hundred cows were treated with one of two intramammary beta-lactam antibiotics, and the remaining 72 cows were treated with intramuscular oxytocin. Milk samples were collected pretreatment, twice after therapy, and again 21 d following the initiation of treatment. Presumptive false-positive assay results were tabulated from all pretreatment and 21-d milk samples and from samples collected following oxytocin therapy. The percentage of false-positive results was 43.6, 37.7, 81.7, 2.6, and 18.8% for the CITE probe (beta-lactam), Delvotest-P, Charm Farm, LacTek (beta-lactam), and Bacillus stearothermophilus var. calidolactis disk assay, respectively. In four of the assay systems, average SCC were significantly higher in samples yielding false-positive results than in those with negative results. Specificity and sensitivity were estimated for each assay system, and, based on these estimates, positive and negative predictive value curves were graphed as the prevalence of milk samples containing detectable concentrations of exogenous antibiotic residues in the sample population was varied from 0 to 100%.