ORCID Profile
0000-0003-1562-162X
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University of California Davis
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Publisher: American Dairy Science Association
Date: 08-2006
Publisher: Springer Science and Business Media LLC
Date: 23-11-2015
Publisher: Frontiers Media SA
Date: 2013
Publisher: Springer Science and Business Media LLC
Date: 29-09-2020
DOI: 10.1038/S41598-020-72902-X
Abstract: Introducing useful traits into livestock breeding programs through gene knock-ins has proven challenging. Typically, targeted insertions have been performed in cell lines, followed by somatic cell nuclear transfer cloning, which can be inefficient. An alternative is to introduce genome editing reagents and a homologous recombination (HR) donor template into embryos to trigger homology directed repair (HDR). However, the HR pathway is primarily restricted to actively iding cells (S/G2-phase) and its efficiency for the introduction of large DNA sequences in zygotes is low. The homology-mediated end joining (HMEJ) approach has been shown to improve knock-in efficiency in non- iding cells and to harness HDR after direct injection of embryos. The knock-in efficiency for a 1.8 kb gene was contrasted when combining microinjection of a gRNA/Cas9 ribonucleoprotein complex with a traditional HR donor template or an HMEJ template in bovine zygotes. The HMEJ template resulted in a significantly higher rate of gene knock-in as compared to the HR template (37.0% and 13.8% P 0.05). Additionally, more than a third of the knock-in embryos (36.9%) were non-mosaic. This approach will facilitate the one-step introduction of gene constructs at a specific location of the bovine genome and contribute to the next generation of elite cattle.
Publisher: American Dairy Science Association
Date: 08-2019
Abstract: 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 s le 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 in idual 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 s led.
Publisher: Oxford University Press (OUP)
Date: 08-2017
Publisher: American Dairy Science Association
Date: 02-2016
Abstract: 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 ided 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 in idual 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.
Publisher: Elsevier BV
Date: 12-1996
Publisher: American Dairy Science Association
Date: 08-2019
Abstract: 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.
Publisher: American Dairy Science Association
Date: 08-2019
Abstract: 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 s le 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 s le 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 in idual 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.
Publisher: American Dairy Science Association
Date: 02-2020
Abstract: 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.
Publisher: American Dairy Science Association
Date: 08-2019
Publisher: Cold Spring Harbor Laboratory
Date: 12-06-2020
DOI: 10.1101/2020.06.09.143115
Abstract: Introducing useful traits into livestock breeding programs through gene knock-ins has proven challenging. Typically, targeted insertions have been performed in cell lines, followed by somatic cell nuclear transfer cloning, which can be inefficient. An alternative is to introduce genome editing reagents and a homologous recombination (HR) donor template into embryos to trigger homology-directed repair (HDR). However, the HR pathway is primarily restricted to actively iding cells (S/G2-phase) and its efficiency is low in zygotes, especially for the introduction of large DNA sequences. The homology-mediated end joining (HMEJ)-based strategy harnesses HDR by direct injection of embryos, and has been shown to have an improved knock-in efficiency in non- iding cells. The knock-in efficiency for a 1.8kb gene was contrasted when combining a gRNA/Cas9 ribonucleoprotein complex with either a traditional HR donor template, or a HMEJ template in bovine zygotes. The HMEJ template resulted in a significantly higher rate of gene knock-in as compared to the HR template (37.0% and 13.8% P 0.05). Additionally, more than a third of the knock-in embryos (36.9%) were non-mosaic. This approach will facilitate the one-step introduction of gene constructs at a specific location of the bovine genome and contribute to the next generation of elite cattle.
Publisher: Springer Science and Business Media LLC
Date: 18-07-2019
DOI: 10.1007/S11248-019-00141-6
Abstract: Milk and meat from cattle and buffaloes contribute 45% of the global animal protein supply, followed by chickens (31%), and pigs (20%). In 2016, the global cattle population of 1.0 billion head produced 6.5 billion tons of cows' milk, and 66 million tons of beef. In the past century, cattle breeding programs have greatly increased the yield per animal with a resultant decrease in the emissions intensity per unit of milk or beef, but this has not been true in all regions. Genome editing research in cattle to date has focused on disease resistance (e.g. tuberculosis), production (e.g. myostatin knockout production of all-male offspring), elimination of allergens (e.g. beta-lactoglobulin knockout) and welfare (e.g. polled or hornlessness) traits. Modeling has revealed how the use of genome editing to introduce beneficial alleles into cattle breeds could maintain or even accelerate the rate of genetic gain accomplished by conventional breeding programs, and is a superior approach to the lengthy process of introgressing those same alleles from distant breeds. Genome editing could be used to precisely introduce useful alleles (e.g. heat tolerance, disease resistance) and haplotypes into native locally-adapted cattle breeds, thereby helping to improve their productivity. As with earlier genetic engineering approaches, whether breeders will be able to employ genome editing in cattle genetic improvement programs will very much depend upon global decisions around the regulatory framework and governance of genome editing for food animals.
Publisher: Oxford University Press (OUP)
Date: 06-2014
Abstract: 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 in idual 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.
Publisher: Oxford University Press (OUP)
Date: 2017
DOI: 10.2527/JAS2016.1346
Publisher: Public Library of Science (PLoS)
Date: 13-09-2010
Publisher: Springer Science and Business Media LLC
Date: 18-12-2020
DOI: 10.1038/S41598-020-78264-8
Abstract: The CRISPR/Cas9 genome editing tool has the potential to improve the livestock breeding industry by allowing for the introduction of desirable traits. Although an efficient and targeted tool, the CRISPR/Cas9 system can have some drawbacks, including off-target mutations and mosaicism, particularly when used in developing embryos. Here, we introduced genome editing reagents into single-cell bovine embryos to compare the effect of Cas9 mRNA and protein on the mutation efficiency, level of mosaicism, and evaluate potential off-target mutations utilizing next generation sequencing. We designed guide-RNAs targeting three loci (POLLED, H11, and ZFX) in the bovine genome and saw a significantly higher rate of mutation in embryos injected with Cas9 protein (84.2%) vs. Cas9 mRNA (68.5%). In addition, the level of mosaicism was higher in embryos injected with Cas9 mRNA (100%) compared to those injected with Cas9 protein (94.2%), with little to no unintended off-target mutations detected. This study demonstrated that the use of gRNA/Cas9 ribonucleoprotein complex resulted in a high editing efficiency at three different loci in bovine embryos and decreased levels of mosaicism relative to Cas9 mRNA. Additional optimization will be required to further reduce mosaicism to levels that make single-step embryo editing in cattle commercially feasible.
Publisher: Springer Science and Business Media LLC
Date: 10-2007
Publisher: Oxford University Press (OUP)
Date: 08-2013
Abstract: The objective of this study was to characterize variation and identify SNP and chromosomal regions associated with mineral concentrations in LM of Angus beef cattle. S les of LM from 2,285 Angus cattle were obtained, and concentrations of 7 minerals, including iron, magnesium, manganese, phosphorus, potassium, sodium, and zinc, were quantified. Genomic DNA extracted from the ground beef s le used for mineral composition was genotyped with the Bovine SNP50 Infinium II BeadChip, and effects of SNP on each trait were estimated using the Bayes-Cπ module of GenSel software. Pedigree-based estimates of heritabilities and corresponding genetic variances indicate iron was the only mineral concentration that could be considered a good candidate for manipulation by genomic selection. The amount of variation that could be accounted for by SNP genotypes was concordant with pedigree-based heritabilities and varied from very low for potassium and sodium (<0.09) to medium high (0.37) for iron. Although significant chromosomal regions were identified for all minerals analyzed in this study, further study focused on iron. Seven regions on 6 chromosomes (1, 2, 7, 10, 15, and 28) were identified to have a major effect on the iron content of LM in Angus cattle. The accuracy of direct genomic values (DGV) for iron concentration was estimated using a 5-fold cross-validation strategy. The accuracy of DGV estimated as the genetic correlation between DGV and the phenotype (iron concentration) adjusted for contemporary groups was 0.59. A bivariate animal model was used to estimate genetic correlations between iron concentrations and a reduced set of economically important carcass traits: HCW, rib eye area, calculated USDA yield grade, percent KPH, and marbling score. The genetic correlations between iron concentration and HCW, percentage KPH, marbling score, and rib eye area were small (-0.19 to 0.15) and nonsignificant. Although still weak (0.22), a positive significant genetic correlation was identified between iron content and USDA calculated yield grade. Beef is a major contributor of iron and zinc in the human diet, and this study found that iron content might be effectively manipulated through marker-assisted selection programs, without compromising other carcass and palatability traits.
Publisher: Springer Science and Business Media LLC
Date: 23-03-2021
DOI: 10.1038/S41467-021-22100-8
Abstract: Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. The Functional Annotation of Animal Genomes consortium was formed to collaboratively annotate the functional elements in animal genomes, starting with domesticated animals. Here we present an expansive collection of datasets from eight erse tissues in three important agricultural species: chicken ( Gallus gallus ), pig ( Sus scrofa ), and cattle ( Bos taurus ). Comparative analysis of these datasets and those from the human and mouse Encyclopedia of DNA Elements projects reveal that a core set of regulatory elements are functionally conserved independent of ergence between species, and that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes are also conserved. These datasets represent a unique opportunity for the emerging field of comparative epigenomics, as well as the agricultural research community, including species that are globally important food resources.
Publisher: Springer International Publishing
Date: 2018
Publisher: American Dairy Science Association
Date: 05-1991
Publisher: Oxford University Press (OUP)
Date: 02-2017
Abstract: Epizootic bovine abortion (EBA), or “foothill abortion,” is the leading cause of beef cattle abortion in California and has also been reported in Nevada and Oregon. In the 1970s, the soft-shelled tick Ornithodoros coriaceus, or “pajaroello tick,” was confirmed as the disease-transmitting vector. In 2005, a novel Deltaproteobacterium was discovered as the etiologic agent of EBA (aoEBA), recently named Pajaroellobacter abortibovis. This organism cannot be grown in culture using traditional microbiological techniques it can only be grown in experimentally-infected severe combined immunodeficient (SCID) mice. The objectives of this study were to perform a de novo genome assembly for P. abortibovis and identify and validate potential antigenic proteins as candidates for future recombinant vaccine development. DNA and RNA were extracted from spleen tissue collected from experimentally-infected SCID mice following exposure to P. abortibovis. This combination of mouse and bacterial DNA was sequenced and aligned to the mouse genome. Mouse sequences were subtracted from the sequence pool and the remaining sequences were de novo assembled at 50x coverage into a 1.82 Mbp complete closed circular Deltaproteobacterial genome containing 2250 putative protein-coding sequences. Phylogenetic analysis of P. abortibovis predicts that this bacterium is most closely related to the organisms of the order Myxococcales, referred to as Myxobacteria. In silico prediction of vaccine candidates was performed using a reverse vaccinology approach resulting in the identification and ranking of the top 10 candidate proteins that are likely to be antigenic. Immunologic testing of these candidate proteins confirmed antigenicity of seven of the nine expressed protein candidates using serum from P. abortibovis immunized mice.
Publisher: Oxford University Press (OUP)
Date: 12-2016
Abstract: Variance components were estimated and relative economic importance of bovine respiratory disease (BRD) was derived from 3 yr of performance, morbidity, and mortality data collected from a single beef cattle finishing operation. One thousand one hundred eighty nine of 12,812 Charolais-sired calves were treated for BRD during the finishing period. Weaning weight (WW), DMI, days to harvest (D2H), HCW, yield grade (YG), and marbling score determined by image analysis (MARB) were collected to quantify the economic impact associated with treatment for BRD. Observed means and (co)variances for carcass and production traits were used to simulate populations of 10,000 healthy and 10,000 BRD treated calves. A bio-economic model was developed to derive the economic value associated with the incidence and number of treatments for BRD during the finishing period. Carcasses from healthy calves were worth $58.28 more on average compared to calves treated at least once for BRD. Heritability estimates for BRD were 0.15 when the trait was measured as number of treatments (0 to 4), and 0.14 when measured as incidence (0 or 1). The model indicated that D2H had the lowest relative economic importance in this system, with a cost of $1.91 per head for each additional day on feed. Furthermore, the relative economic value of BRD morbidity was approximately 10.65 greater than D2H when recording the BRD phenotype as the number of BRD treatments. The economic values of HCW, WW, and DMI were 11.47, 5.15, and 3.61 times more important than D2H, respectively. This indicates BRD morbidity has the second greatest relative economic value in this system, with a one percent increase in morbidity associated with an average loss of $2.08 per head. These results indicate that BRD morbidity can have an equal or greater economic importance when compared to carcass and production traits during the finishing period. Further, this indicates the opportunity exists to increase the genetic merit for profitability during the finishing period by incorporating BRD incidence into terminal-sire selection indexes.
Publisher: American Dairy Science Association
Date: 12-2011
Abstract: 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 s les from 16 dairy cattle (10 Holstein, 6 Jersey) were used for the comparison. An independent set of DNA s les taken from 46 Jersey cattle and 18 Holstein cattle were used to ascertain the amount of SNP variation accounted by the 16 experimental s les. 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 s les 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 s les 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 s les, 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.
Publisher: Oxford University Press (OUP)
Date: 02-2011
Abstract: 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 erse 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.
Publisher: Elsevier BV
Date: 03-2008
Publisher: Oxford University Press (OUP)
Date: 12-2012
Abstract: Several organizations have developed prediction models for molecular breeding values (MBV) for quantitative growth and carcass traits in beef cattle using Bovine SNP50 genotypes and phenotypic or EBV data. Molecular breeding values for Angus cattle have been developed by IGENITY, Pfizer Animal Genetics, and a collaboration between researchers from Iowa State University and the University of Missouri-Columbia (ISU/UMC). The U.S. Meat Animal Research Center (USMARC Clay Center, NE) has also developed MBV for 16 cattle breeds using 2 multibreed populations, the Germplasm Evaluation (GPE) Program and the 2,000 Bull Project (2K(ALL)), and 2 single breed subpopulations of the 2,000 Bull Project, Angus (2K(AN)) and Hereford (2K(HH)). In this study, these MBV were assessed relative to commercial ranch EBV estimated from the progeny phenotypes of Angus bulls naturally mated in multisire breeding pastures to commercial cows: 121 for USMARC MBV, 99 for ISU/UMC MBV, and 29 for IGENITY and Pfizer MBV (selected based on number of progeny carcass records). Five traits were analyzed: weaning weight (WW), HCW, marbling score (MS), rib-eye muscle area (RE), and, for IGENITY and Pfizer only, feedlot ADG. The average accuracies of MBV across traits were 0.38 ± 0.05 for IGENITY, 0.61 ± 0.12 for Pfizer, 0.46 ± 0.12 for ISU/UMC, 0.16 ± 0.04 for GPE, 0.26 ± 0.05 for 2K(ALL), 0.24 ± 0.04 for 2K(AN), and 0.02 ± 0.12 for 2K(HH). Angus-based MBV (IGENITY, Pfizer, ISU/UMC, and 2K(AN)) explained larger proportions of genetic variance in this population than GPE, 2K(ALL), or 2K(HH) MBV for the same traits. In this data set, IGENITY, Pfizer, and ISU/UMC MBV were predictive of realized performance of progeny, and incorporation of that information into national genetic evaluations would be expected to improve EPD accuracy, particularly for young animals.
Publisher: Springer Science and Business Media LLC
Date: 08-02-2016
Publisher: Wiley
Date: 1999
Publisher: Elsevier BV
Date: 04-2017
DOI: 10.1016/J.COPBIO.2016.10.007
Abstract: Animal breeders have used a variety of methods in selective breeding programs to genetically improve food animal species. Recently this has included the use of both genetic engineering and genome editing, particularly for targeting improvement in traits for which there is no within-species or within-breed genetic variation. Both intraspecies and interspecies allele substitutions and gene knock-ins have been accomplished with genome editing tools, targeting a number of important traits. The regulatory status of such animals is unclear as the definition of a regulated article is not consistent among different regulatory agencies and organizations. In the absence of a harmonized global regulatory approach to the genetic improvement of animals, it will be difficult for breeders to effectively achieve sustainable breeding objectives.
Publisher: Public Library of Science (PLoS)
Date: 14-04-2022
Publisher: Wiley
Date: 06-2006
DOI: 10.1007/S11745-006-5003-Z
Abstract: The brain contains high levels of the long-chain n-3 FA DHA (22:6n-3), mainly in the gray matter and synaptosomes. Adequate intake of DHA is crucial for optimal nervous system function, particularly in infants. Supplementation of infant formulas with DHA at levels similar to human breast milk is recommended for biochemical and functional benefits to neonates. We generated transgenic mice that produce elevated levels of n-3 PUFA in their milk by expressing the Caenorhabditis elegans n-3 FA desaturase under the control of a lactation-induced goat beta-casein promoter. To examine the postnatal effects of consuming the n-3-enriched milk, we compared the growth and brain and plasma FA composition of mouse pups raised on milk from transgenic dams with those observed for pups raised on milk from nontransgenic dams. A significant decrease in arachidonic acid (ARA, 20:4n-6) and concomitant increases in n-3 PUFA were observed in the phospholipid fraction of transgenic mouse milk. The n-6:n-3 FA ratios were 4.7 and 34.5 for the transgenic and control milk phospholipid fractions, respectively. DHA and DPA (22:5n-6) comprised 15.1% and 2.8% of brain FA from weanling mice nursed on transgenic dams, as compared with 6.9% and 9.2% for weanling mice nursed on control dams, respectively. This transgenic mouse model offers a unique approach to disassociate the effects and fetal programming resulting from a high n-6:n-3 FA ratio gestational environment from the postnatal nutritional effects of providing milk with differing n-6:n-3 FA ratios.
Publisher: The Company of Biologists
Date: 02-2020
DOI: 10.1242/JEB.207159
Abstract: The prospect of genome editing offers a number of promising opportunities for livestock breeders. Firstly, these tools can be used in functional genomics to elucidate gene function, and identify causal variants underlying monogenic traits. Secondly, they can be used to precisely introduce useful genetic variation into structured livestock breeding programs. Such variation may include repair of genetic defects, the inactivation of undesired genes, and the moving of useful alleles and haplotypes between breeds in the absence of linkage drag. Editing could also be used to accelerate the rate of genetic progress by enabling the replacement of the germ cell lineage of commercial breeding animals with cells derived from genetically elite lines. In the future, editing may also provide a useful complement to evolving approaches to decrease the length of the generation interval through in vitro generation of gametes. For editing to be adopted, it will need to seamlessly integrate with livestock breeding schemes. This will likely involve introducing edits into multiple elite animals to avoid genetic bottlenecks. It will also require editing of different breeds and lines to maintain genetic ersity, and enable structured cross-breeding. This requirement is at odds with the process-based trigger and event-based regulatory approach that has been proposed for the products of genome editing by several countries. In the absence of regulatory harmony, researchers in some countries will have the ability to use genome editing in food animals, while others will not, resulting in disparate access to these tools, and ultimately the potential for global trade disruptions.
Publisher: University of California Agriculture and Natural Resources (UC ANR)
Date: 05-2010
Publisher: Elsevier BV
Date: 04-2004
Publisher: Springer Science and Business Media LLC
Date: 08-06-2011
Publisher: SAGE Publications
Date: 21-01-2016
Abstract: The California (CA) and Wisconsin (WI) clinical scoring systems have been proposed for bovine respiratory disease complex (BRDC) detection in preweaned dairy calves. The screening sensitivity (SSe), for estimating BRDC prevalence in a cohort of calves, diagnostic sensitivity (DSe), for confirming BRDC in ill calves, and specificity (Sp) were estimated for each of the scoring systems, as well as for nasal swab cultures for aerobic bacteria and mycoplasma species. Thoracic ultrasound and auscultation were used as the reference standard tests interpreted in parallel. A total of 536 calves (221 with BRDC and 315 healthy) were s led from 5 premises in California. The SSe of 46.8%, DSe of 72.6%, and Sp of 87.4% was determined for the CA system. The SSe of 46.0%, DSe of 71.1%, and Sp of 91.2% was determined for the WI system. For aerobic culture, the SSe was 43.4%, DSe was 52.6%, and Sp was 71.3% for Mycoplasma spp. culture, the SSe was 57.5%, DSe was 68.9%, and Sp was 59.7%. The screening and diagnostic sensitivities of the scoring systems were not significantly different but the Sp of the WI system was greater by 3.8%. Scoring systems can serve as rapid on-farm tools to determine the burden of BRDC in preweaned dairy calves. However, users may expect the SSe to be less than the DSe when confirming BRDC in an ill calf.
Publisher: Springer Science and Business Media LLC
Date: 25-09-2013
Publisher: Springer Science and Business Media LLC
Date: 2014
Publisher: Oxford University Press (OUP)
Date: 08-2011
Abstract: The term sustainable has many meanings, but in agriculture it generally refers to some balance between environmental, social, and economic goals. The objective of this project was to quantify inputs and outputs to assess the sustainability implications of 2 feedlot cattle management systems: Never Ever 3 (NE3) and a conventional (CON) system using metabolic modifiers. Angus-cross steers (n=104) were stratified by BW (337 kg ± 17) and randomly assigned to 4 pens per treatment group. The NE3 cattle received no feed additives or implants, whereas CON were implanted with 100 mg of trenbolone acetate and 14 mg of estradiol benzoate on d 1 and 70, and were additionally fed monensin [330 mg/(animal·d)] and tylosin phosphate [90 mg/(animal·d)] in their ration throughout the course of the study, and ractopamine hydrochloride at 254 mg/(animal·d) for the last 29 d on feed. Cattle were shipped on a constant average pen weight basis (596 kg ± 32 BW). The CON cattle had greater ADG (1.81 vs. 1.35 kg, P < 0.01) and were on feed fewer days (146 vs. 188 d, P 0.05) however, CON carcasses averaged larger ribeye area (87 vs. 80 cm(2), P < 0.01), greater Warner-Bratzler shear force measurement (WBSF 3.46 vs. 3.19 kg, P < 0.01), and smaller USDA marbling score (5.4 vs. 6.2, P < 0.01), and less backfat thickness (1.64 vs. 1.84 cm, P < 0.05) and yield grade (3.38 vs. 3.95, P < 0.01) than NE3 carcasses. Overall, CON cattle consumed 393 kg less DM in the feedlot (1,250 vs. 1,643 kg P < 0.05). No treatment effects were observed for daily methane (CH(4) P=0.62) or nitrous oxide (N(2)O P=0.7) emissions per steer. Assuming a constant emission rate on a DMI basis throughout the course of the feedlot trial, CON feedlot management resulted in a 31% decrease in emissions per finished steer compared with NE3 management. Expressing CH(4) emissions on a carbon dioxide equivalent (CO(2)-eq) basis revealed a 1.10-kg CO(2)-eq difference per kilogram BW gain (5.02 kg of NE3 vs. 3.92 kg of CON) between the 2 feedlot management systems. Although the metabolic modifiers resulted in additional costs for the CON treatment group, the cost per kilogram of feedlot BW gain was significantly less ($1.12/kg vs. $1.35/kg P < 0.05) than NE3. Both production systems satisfied some sustainability criteria, although neither concurrently fulfilled all of the environmental, social, and economic goals of agricultural sustainability.
Publisher: Cambridge University Press (CUP)
Date: 26-11-2014
DOI: 10.1017/S1466252314000164
Abstract: Clinical scoring systems have been proposed for respiratory disease diagnosis in calves, including the Wisconsin (WI) system (McGuirk in 2008) which uses five clinical signs, each partitioned into four levels of severity. Recently, we developed the California (CA) bovine respiratory disease (BRD) scoring system requiring less calf handling and consisting of six clinical signs, each classified as normal or abnormal. The objective of this study was to estimate the on-farm agreement between the WI and the CA scoring systems. A total of 100 calves were enrolled on a CA dairy and assessed for BRD case status using the two scoring systems simultaneously. The Kappa coefficient of agreement between these two systems was estimated to be 0.85, which indicated excellent agreement beyond chance. The simpler design and reduced calf handling required by the CA BRD scoring system may make it advantageous for on-farm use.
Publisher: Oxford University Press (OUP)
Date: 07-2010
Publisher: Oxford University Press (OUP)
Date: 1999
Publisher: Oxford University Press (OUP)
Date: 20-11-2003
DOI: 10.1105/TPC.015875
Publisher: Elsevier BV
Date: 10-2021
Publisher: Springer Science and Business Media LLC
Date: 05-2016
DOI: 10.1038/NBT.3566
Publisher: American Dairy Science Association
Date: 05-2019
Abstract: 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.
Publisher: Springer Science and Business Media LLC
Date: 08-02-2022
DOI: 10.1038/S41598-022-06118-6
Abstract: Dehorning is a common practice in the dairy industry, but raises animal welfare concerns. A naturally occurring genetic mutation (P C allele) comprised of a 212 bp duplicated DNA sequence replacing a 10-bp sequence at the polled locus is associated with the hornless phenotype (polled) in cattle. To test the hypothesis that the 10 bp deletion alone is sufficient to result in polled, a CRISPR-Cas9 dual guide RNA approach was optimized to delete a 133 bp region including the 10 bp sequence. Timing of ribonucleoprotein complex injections at various hours post insemination (hpi) (6, 8, and 18 hpi) as well as in vitro transcribed (IVT) vs synthetic gRNAs were compared. Embryos injected 6 hpi had a significantly higher deletion rate (53%) compared to those injected 8 (12%) and 18 hpi (7%), and synthetic gRNAs had a significantly higher deletion rate (84%) compared to IVT gRNAs (53%). Embryo transfers were performed, and bovine fetuses were harvested between 3 and 5 months of gestation. All fetuses had mutations at the target site, with two of the seven having biallelic deletions, and yet they displayed horn bud development indicating that the 10 bp deletion alone is not sufficient to result in the polled phenotype.
Publisher: American Society for Microbiology
Date: 15-05-2015
DOI: 10.1128/JVI.00064-15
Abstract: Bovine respiratory disease (BRD) is a common health problem for both dairy and beef cattle, resulting in significant economic loses. In order to identify viruses associated with BRD, we used a metagenomics approach to enrich and sequence viral nucleic acids in the nasal swabs of 50 young dairy cattle with symptoms of BRD. Following deep sequencing, de novo assembly, and translated protein sequence similarity searches, numerous known and previously uncharacterized viruses were identified. Bovine adenovirus 3, bovine adeno-associated virus, bovine influenza D virus, bovine parvovirus 2, bovine herpesvirus 6, bovine rhinitis A virus, and multiple genotypes of bovine rhinitis B virus were identified. The genomes of a previously uncharacterized astrovirus and picobirnaviruses were also partially or fully sequenced. Using real-time PCR, the rates of detection of the eight viruses that generated the most reads were compared for the nasal secretions of 50 animals with BRD versus 50 location-matched healthy control animals. Viruses were detected in 68% of BRD-affected animals versus 16% of healthy control animals. Thirty-eight percent of sick animals versus 8% of controls were infected with multiple respiratory viruses. Significantly associated with BRD were bovine adenovirus 3 ( P 0.0001), bovine rhinitis A virus ( P = 0.005), and the recently described bovine influenza D virus ( P = 0.006), which were detected either alone or in combination in 62% of animals with BRD. A metagenomics and real-time PCR detection approach in carefully matched cases and controls can provide a rapid means to identify viruses associated with a complex disease, paving the way for further confirmatory tests and ultimately to effective intervention strategies. IMPORTANCE Bovine respiratory disease is the most economically important disease affecting the cattle industry, whose complex root causes include environmental, genetics, and infectious factors. Using an unbiased metagenomics approach, we characterized the viruses in respiratory secretions from BRD cases and identified known and previously uncharacterized viruses belonging to seven viral families. Using a case-control format with location-matched animals, we compared the rates of viral detection and identified 3 viruses associated with severe BRD signs. Combining a metagenomics and case-control format can provide candidate pathogens associated with complex infectious diseases and inform further studies aimed at reducing their impact.
Publisher: Oxford University Press (OUP)
Date: 12-2012
Abstract: The objective of this study was to estimate genetic parameters for carnitine, creatine, creatinine, carnosine, and anserine concentration in LM and to evaluate their associations with Warner-Bratzler shear force (WBSF) and beef palatability traits. Longissimus muscle s les from 2,285 Angus cattle were obtained and fabricated into steaks for analysis of carnitine, creatine, creatinine, carnosine, anserine, and other nutrients, and for trained sensory panel and WBSF assessments. Restricted maximum likelihood procedures were used to obtain estimates of variance and covariance components under a multiple-trait animal model. Estimates of heritability for carnitine, creatine, creatinine, carnosine, and anserine concentrations in LM from Angus cattle were 0.015, 0.434, 0.070, 0.383, and 0.531, respectively. Creatine, carnosine, and anserine were found to be moderately heritable, whereas almost no genetic variation was observed in carnitine and creatinine. Moderate positive genetic (0.25, P < 0.05) and phenotypic correlations (0.25, P < 0.05) were identified between carnosine and anserine. Medium negative genetic correlations were identified between creatine and both carnosine (-0.53, P < 0.05) and anserine (-0.46, P 0.10), and carnitine concentrations were not associated (P > 0.10) with any of the meat palatability traits analyzed. Carnosine was negatively associated with overall tenderness as assessed by trained sensory panelists. Similar negative associations with overall tenderness were identified for creatinine and anserine. Painty/fishy was the only flavor significantly and negatively associated with creatinine and carnosine. These results provide information regarding the concentration of these compounds, the amount of genetic variation, and evidence for negligible associations with beef palatability traits in LM of beef cattle.
Publisher: Cambridge University Press
Date: 31-01-2012
Publisher: Frontiers Media SA
Date: 07-09-2020
Publisher: Cold Spring Harbor Laboratory
Date: 04-06-2020
DOI: 10.1101/2020.06.04.134759
Abstract: The CRISPR/Cas9 genome editing tool has the potential to improve the livestock breeding industry by allowing for the introduction of desirable traits. Although an efficient and targeted tool, the CRISPR/Cas9 system can have some drawbacks, including off-target mutations and mosaicism, particularly when used in developing embryos. Here, we introduced genome editing reagents into single-cell bovine embryos to compare the effect of Cas9 mRNA and protein on the mutation efficiency, level of mosaicism, and evaluate potential off-target mutations utilizing next generation sequencing. We designed guide-RNAs targeting three loci (POLLED, H11, and ZFX) in the bovine genome and saw a significantly higher rate of mutation in embryos injected with Cas9 protein (84.2%) vs. Cas9 mRNA (68.5%). In addition, the level of mosaicism was higher in embryos injected with Cas9 mRNA (100%) compared to those injected with Cas9 protein (94.2%), with little to no unintended off-target mutations detected. This study demonstrates that the use of Cas9 protein, rather than Cas9 mRNA, results in a higher editing efficiency in bovine embryos while lowering the level of mosaicism. However, further optimization must be carried out for the CRISPR/Cas9 system to become feasible for single-step embryo editing in a commercial system.
Publisher: Springer Science and Business Media LLC
Date: 10-05-2022
DOI: 10.1038/S41598-022-11669-9
Abstract: A long intergenic non-coding RNA ( lincRNA#1 ) is overexpressed in the horn bud region of polled (hornless) bovine fetuses, suggesting a potential role in horn bud suppression. Genome editing was used to test whether the absence of this sequence was associated with the horned phenotype. Two gRNAs with high mutation efficiencies targeting the 5′ and the 3′ regions flanking the lincRNA#1 sequence were co-injected with Cas9 as ribonucleoprotein complexes into bovine zygotes (n = 121) 6 h post insemination. Of the resulting blastocysts (n = 31), 84% had the expected 3.7 kb deletion of these embryos with the 3.7 kb deletions, 88% were biallelic knockouts. Thirty-nine presumptive edited 7-day blastocysts were transferred to 13 synchronized recipient cows resulting in ten pregnancies, five with embryos heterozygous for the dominant P C POLLED allele at the POLLED locus, and five with the recessive pp genotype. Eight (80%) of the resulting fetuses were biallelic lincRNA#1 knockouts, with the remaining two being mosaic. RT-qPCR analysis was used to confirm the absence of lincRNA#1 expression in knockout fetuses. Phenotypic and histological analysis of the genotypically (P C p) POLLED , lincRNA#1 knockout fetuses revealed similar morphology to non-edited, control polled fetuses, indicating the absence of lincRNA#1 alone does not result in a horned phenotype.
Publisher: Oxford University Press (OUP)
Date: 09-2017
DOI: 10.1534/G3.117.1137
Abstract: Extended laboratory culture and antimicrobial susceptibility testing timelines hinder rapid species identification and susceptibility profiling of bacterial pathogens associated with bovine respiratory disease, the most prevalent cause of cattle mortality in the United States. Whole-genome sequencing offers a culture-independent alternative to current bacterial identification methods, but requires a library of bacterial reference genomes for comparison. To contribute new bacterial genome assemblies and evaluate genetic ersity and variation in antimicrobial resistance genotypes, whole-genome sequencing was performed on bovine respiratory disease–associated bacterial isolates (Histophilus somni, Mycoplasma bovis, Mannheimia haemolytica, and Pasteurella multocida) from dairy and beef cattle. One hundred genomically distinct assemblies were added to the NCBI database, doubling the available genomic sequences for these four species. Computer-based methods identified 11 predicted antimicrobial resistance genes in three species, with none being detected in M. bovis. While computer-based analysis can identify antibiotic resistance genes within whole-genome sequences (genotype), it may not predict the actual antimicrobial resistance observed in a living organism (phenotype). Antimicrobial susceptibility testing on 64 H. somni, M. haemolytica, and P. multocida isolates had an overall concordance rate between genotype and phenotypic resistance to the associated class of antimicrobials of 72.7% (P & 0.001), showing substantial discordance. Concordance rates varied greatly among different antimicrobial, antibiotic resistance gene, and bacterial species combinations. This suggests that antimicrobial susceptibility phenotypes are needed to complement genomically predicted antibiotic resistance gene genotypes to better understand how the presence of antibiotic resistance genes within a given bacterial species could potentially impact optimal bovine respiratory disease treatment and morbidity/mortality outcomes.
Publisher: American Dairy Science Association
Date: 11-1993
Publisher: American Dairy Science Association
Date: 10-2020
Publisher: Oxford University Press (OUP)
Date: 12-2007
Abstract: 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.
Publisher: Public Library of Science (PLoS)
Date: 28-03-2017
Publisher: American Dairy Science Association
Date: 10-1993
Publisher: Mary Ann Liebert Inc
Date: 04-2022
Publisher: Public Library of Science (PLoS)
Date: 29-06-2015
Publisher: Springer Science and Business Media LLC
Date: 07-10-2020
DOI: 10.1186/S12864-020-07078-9
Abstract: Although considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. This lack of functional annotation poses a substantial roadblock to agricultural research and diminishes the value of these species as model organisms. As active regulatory elements are typically characterized by chromatin accessibility, we implemented the Assay for Transposase Accessible Chromatin (ATAC-seq) to annotate and characterize regulatory elements in pigs and cattle, given a set of eight adult tissues. Overall, 306,304 and 273,594 active regulatory elements were identified in pig and cattle, respectively. 71,478 porcine and 47,454 bovine regulatory elements were highly tissue-specific and were correspondingly enriched for binding motifs of known tissue-specific transcription factors. However, in every tissue the most prevalent accessible motif corresponded to the insulator CTCF, suggesting pervasive involvement in 3-D chromatin organization. Taking advantage of a similar dataset in mouse, open chromatin in pig, cattle, and mice were compared, revealing that the conservation of regulatory elements, in terms of sequence identity and accessibility, was consistent with evolutionary distance whereas pig and cattle shared about 20% of accessible sites, mice and ungulates only had about 10% of accessible sites in common. Furthermore, conservation of accessibility was more prevalent at promoters than at intergenic regions. The lack of conserved accessibility at distal elements is consistent with rapid evolution of enhancers, and further emphasizes the need to annotate regulatory elements in in idual species, rather than inferring elements based on homology. This atlas of chromatin accessibility in cattle and pig constitutes a substantial step towards annotating livestock genomes and dissecting the regulatory link between genome and phenome.
Publisher: Public Library of Science (PLoS)
Date: 16-11-2015
Publisher: Oxford University Press (OUP)
Date: 03-2013
Abstract: 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. S les 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). 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.
Publisher: Springer Science and Business Media LLC
Date: 08-2011
DOI: 10.1038/NBT.1938
Publisher: Oxford University Press (OUP)
Date: 09-2016
Publisher: Elsevier BV
Date: 11-2013
DOI: 10.1016/J.CVFA.2013.07.012
Abstract: This article reviews the literature on breed, biological type, and breeding system and their impact on female fertility, especially as they relate to heifer development. The attributes of different breeding systems and their appropriate use is discussed. In addition, the extant and emerging selection tools that are available for replacement heifer selection are reviewed.
Publisher: Canadian Science Publishing
Date: 09-12-2017
Publisher: Oxford University Press (OUP)
Date: 04-2007
DOI: 10.2527/JAS.2006-512
Abstract: 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.
Publisher: Springer Science and Business Media LLC
Date: 20-03-2019
DOI: 10.1038/S41538-019-0035-Y
Abstract: Dietary DNA is generally regarded as safe to consume, and is a routine ingredient of food obtained from any living organism. Millions of naturally-occurring DNA variations are observed when comparing the genomic sequence of any two healthy in iduals of a given species. Breeders routinely select desired traits resulting from this DNA variation to develop new cultivars and varieties of food plants and animals. Regulatory agencies do not evaluate these new varieties prior to commercial release. Gene editing tools now allow plant and animal breeders to precisely introduce useful genetic variation into agricultural breeding programs. The U.S. Department of Agriculture (USDA) announced that it has no plans to place additional regulations on gene-edited plants that could otherwise have been developed through traditional breeding prior to commercialization. However, the U.S. Food and Drug Administration (FDA) has proposed mandatory premarket new animal drug regulatory evaluation for all food animals whose genomes have been intentionally altered using modern molecular technologies including gene editing technologies. This runs counter to U.S. biotechnology policy that regulatory oversight should be triggered by unreasonable risk, and not by the fact that an organism has been modified by a particular process or technique. Breeder intention is not associated with product risk. Harmonizing the regulations associated with gene editing in food species is imperative to allow both plant and animal breeders access to gene editing tools to introduce useful sustainability traits like disease resistance, climate adaptability, and food quality attributes into U.S. agricultural breeding programs.
Publisher: Canadian Science Publishing
Date: 1998
DOI: 10.1139/GEN-41-1-51
Publisher: Springer Science and Business Media LLC
Date: 20-12-2017
DOI: 10.1038/S41598-017-18205-0
Abstract: Bovine respiratory disease (BRD) is the most common infectious disease of beef and dairy cattle and is characterized by a complex infectious etiology that includes a variety of viral and bacterial pathogens. We examined the global changes in mRNA abundance in healthy lung and lung lesions and in the lymphoid tissues bronchial lymph node, retropharyngeal lymph node, nasopharyngeal lymph node and pharyngeal tonsil collected at the peak of clinical disease from beef cattle experimentally challenged with either bovine respiratory syncytial virus, infectious bovine rhinotracheitis, bovine viral diarrhea virus, Mannheimia haemolytica or Mycoplasma bovis . We identified signatures of tissue-specific transcriptional responses indicative of tropism in the coordination of host’s immune tissue responses to infection by viral or bacterial infections. Furthermore, our study shows that this tissue tropism in host transcriptional response to BRD pathogens results in the activation of different networks of response genes. The differential crosstalk among genes expressed in lymphoid tissues was predicted to be orchestrated by specific immune genes that act as ‘key players’ within expression networks. The results of this study serve as a basis for the development of innovative therapeutic strategies and for the selection of cattle with enhanced resistance to BRD.
Publisher: Springer Science and Business Media LLC
Date: 15-06-2010
Publisher: SAGE Publications
Date: 17-10-2018
Abstract: We conducted a nested, case-control study of pre-weaned dairy calves ( n = 477 4 California dairy farms) to assess the association between bovine respiratory disease (BRD) and hematologic biomarkers, including plasma haptoglobin (Hp) and plasma bactericide (PB). At each location, heifer or bull dairy calves were observed 2–4 times per week until confirmed as BRD-positive using parallel interpretation of thoracic ultrasound examination and auscultation. In addition, control calves were enrolled after being confirmed as BRD-negative using ultrasound and auscultation. Complete blood counts (CBC), PB, and Hp concentrations were measured. Hp values were higher in calves with confirmed BRD than in controls ( p 0.01). The area under the curve (AUC) for the various biomarkers was obtained from the corresponding receiver operating characteristic curves. The AUC for Hp was 0.68, a value greater than those for PB or the remaining CBC parameters, indicating that Hp may be the most useful biomarker of BRD in pre-weaned dairy calves. The cutoff value for Hp was 0.195 g/L.
Publisher: Annual Reviews
Date: 16-02-2021
DOI: 10.1146/ANNUREV-ANIMAL-061220-023052
Abstract: Genetically engineered (GE) livestock were first reported in 1985, and yet only a single GE food animal, the fast-growing AquAdvantage salmon, has been commercialized. There are myriad interconnected reasons for the slow progress in this once-promising field, including technical issues, the structure of livestock industries, lack of public research funding and investment, regulatory obstacles, and concern about public opinion. This review focuses on GE livestock that have been produced and documents the difficulties that researchers and developers have encountered en route. Additionally, the costs associated with delayed commercialization of GE livestock were modeled using three case studies: GE mastitis-resistant dairy cattle, genome-edited porcine reproductive and respiratory syndrome virus–resistant pigs, and the AquAdvantage salmon. Delays of 5 or 10 years in the commercialization of GE livestock beyond the normative 10-year GE product evaluation period were associated with billions of dollars in opportunity costs and reduced global food security.
Publisher: Hindawi Limited
Date: 09-1999
Publisher: Elsevier BV
Date: 12-2021
Publisher: Annual Reviews
Date: 02-2014
DOI: 10.1146/ANNUREV-ANIMAL-022513-114119
Abstract: Genomic selection (GS) is the use of statistical methods to estimate the genetic merit of a genotyped animal based on prediction equations derived from large ancestral populations with both phenotypes and genotypes. It has revolutionized the dairy cattle breeding industry and has been implemented with varying degrees of success in other animal breeding programs, including swine, poultry, and beef cattle. The findings of empirical field studies applying GS to the breeding sectors of these main animal protein industries are reviewed. Several translational considerations must be addressed before implementing GS in genetic improvement programs. These include determining and obtaining economically relevant phenotypes and determining the optimal size of the training population, cost-effective genotyping strategies, the practicality of field implementation, and the relative costs versus the benefits of the realized rate of genetic gain. GS may additionally change the optimal breeding scheme design, and studies that address this consideration are also reviewed briefly.
Publisher: Springer Science and Business Media LLC
Date: 04-03-2022
DOI: 10.1186/S43170-022-00080-Z
Abstract: Genetic improvement of cattle around the globe has been, and will continue to be, an important driver of animal agriculture sustainability. There are several reproductive and molecular biotechnologies that are used in genetic improvement of cattle, and their impact on the rate of genetic progress is maximized when combined synergistically in a structured breeding program with a clear breeding objective. One of the most recently developed and increasingly popular tools, gene editing, allows animal breeders to precisely add, delete, or replace letters in the genetic code so as to influence a specific trait of interest (e.g., disease resistance), in as little as one generation. However, for gene editing to be an important factor for genetic improvement, it must integrate smoothly into conventional cattle breeding programs to maintain or accelerate rates of genetic gain. This review first summarizes the current state of key reproductive and molecular biotechnologies available for the genetic improvement of cattle, and then discusses potential strategies for effectively incorporating gene editing into cattle genetic improvement programs and methods for disseminating traits improved via gene editing. Moreover, it examines how genetic improvement strategies, including the use of gene editing, will differ depending on the cattle industry sector (i.e., dairy or beef), and the region of the world in which they are being deployed.
Publisher: American Dairy Science Association
Date: 09-1995
Publisher: Cambridge University Press (CUP)
Date: 11-11-2014
DOI: 10.1017/S1466252314000231
Abstract: The Bovine Respiratory Disease Coordinated Agricultural Project (BRD CAP) is a 5-year project funded by the United States Department of Agriculture (USDA), with an overriding objective to use the tools of modern genomics to identify cattle that are less susceptible to BRD. To do this, two large genome wide association studies (GWAS) were conducted using a case:control design on preweaned Holstein dairy heifers and beef feedlot cattle. A health scoring system was used to identify BRD cases and controls. Heritability estimates for BRD susceptibility ranged from 19 to 21% in dairy calves to 29.2% in beef cattle when using numerical scores as a semi-quantitative definition of BRD. A GWAS analysis conducted on the dairy calf data showed that single nucleotide polymorphism (SNP) effects explained 20% of the variation in BRD incidence and 17–20% of the variation in clinical signs. These results represent a preliminary analysis of ongoing work to identify loci associated with BRD. Future work includes validation of the chromosomal regions and SNPs that have been identified as important for BRD susceptibility, fine mapping of chromosomes to identify causal SNPs, and integration of predictive markers for BRD susceptibility into genetic tests and national cattle genetic evaluations.
Publisher: Oxford University Press (OUP)
Date: 09-2018
DOI: 10.1093/TAS/TXY054
Publisher: Mary Ann Liebert Inc
Date: 12-2004
Abstract: Fish offer some advantages for the study of vertebrate reproductive physiology. Only a few of the genes encoding the components of the hypothalamic-pituitary-gonadal axis have been identified from model teleosts. This study describes a combination of database searching and molecular approaches to identify the FSH and LH gonadotropin beta-subunits (fshb and lhb, respectively), and the LH receptor (lhr) from two model teleost species: zebrafish (Danio rerio) and Fugu (Takifugu rubripes). Sequence and phylogenetic analyses were used to examine the relationships that exist between gonadotropins and their receptors from species representing several piscine orders. The gonadotropin alpha-subunit (Cga) is highly conserved among teleosts and tetrapods. The presence of a genomic pseudogene (cgap) was also noted in zebrafish. Generally, teleostean FSHbeta protein sequences share less identity with each other than do LHbeta protein sequences, supporting the hypothesis that FSHbeta erged more rapidly during teleost evolution. Interestingly, and uniquely, zebrafish Fshb lacked two highly conserved cysteine residues in the "determinant loop" which is thought to contribute towards receptor binding and specificity. Teleost gonadotropin receptor sequences clearly erged into two distinct groups, FSHR and LHR. As has been seen with mammalian gonadotropin receptor transcripts, splice variants of zebrafish lhr were also observed.
Publisher: Springer Science and Business Media LLC
Date: 07-10-2019
DOI: 10.1038/S41587-019-0266-0
Abstract: Genome editing followed by reproductive cloning was previously used to produce two hornless dairy bulls. We crossed one genome-edited dairy bull, homozygous for the dominant P C Celtic POLLED allele, with horned cows (pp) and obtained six heterozygous (P C p) polled calves. The calves had no horns and were otherwise healthy and phenotypically unremarkable. We conducted whole-genome sequencing of all animals using an Illumina HiSeq4000 to achieve ~20× coverage. Bioinformatics analyses revealed the bull was a compound heterozygote, carrying one naturally occurring P C Celtic POLLED allele and an allele containing an additional introgression of the homology-directed repair donor plasmid along with the P C Celtic allele. These alleles segregated in the offspring of this bull, and inheritance of either allele produced polled calves. No other unintended genomic alterations were observed. These data can be used to inform conversations in the scientific community, with regulatory authorities and with the public around ‘intentional genomic alterations’ and future regulatory actions regarding genome-edited animals.
Publisher: Springer Science and Business Media LLC
Date: 28-01-2020
DOI: 10.1038/S41587-020-0423-5
Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Publisher: American Dairy Science Association
Date: 05-1991
Publisher: CSIRO Publishing
Date: 2012
DOI: 10.1071/AN11060
Abstract: DNA information has the potential to generate value for each sector of the beef-cattle industry. The value distribution among sectors (breeding, commercial, feedlot, processing) will differ depending on marketing. The more descendants an animal produces, the more valuable each unit of genetic improvement becomes. Therefore, the value of using DNA testing to increase the accuracy of selection and accelerate the rate of genetic gain is highest in the breeding sector, particularly for replacement stud animals. There is a lesser value associated with increasing the accuracy of yearling commercial bulls. The cost to DNA test commercial sires will likely be incurred by breeders before sale, and must be recouped through higher bull sale prices or increased market share. Commercial farmers could also use DNA tests to improve the accuracy of replacement female selection. This assumes the development of DNA tests that perform well for the low-heritability traits that directly affect maternal performance (e.g. days to calving) in commercial cattle populations. DNA tests may provide the sole source of information for traits that are not routinely measured on commercial farms. In that case, DNA test information will provide new selection criteria to allow for genetic improvement in those traits. As DNA test offerings mature to have improved accuracy for traits of great value to the feedlot (e.g. feed conversion, disease resistance) and processing (e.g. meat quality) sectors, the added value derived from DNA-enabled selection for these traits will need to be efficiently transferred up the beef production chain to incentivise continued investment. The widespread adoption of DNA testing to enhance the accuracy of selection will likely require an approach to share the value realised by downstream sectors of the beef-cattle industry with those upstream sectors incurring DNA collection and testing expenses.
Publisher: Springer Science and Business Media LLC
Date: 12-02-2021
DOI: 10.1186/S12864-021-07418-3
Abstract: The homologous recombination (HR) pathway is largely inactive in early embryos prior to the first cell ision, making it difficult to achieve targeted gene knock-ins. The homology-mediated end joining (HMEJ)-based strategy has been shown to increase knock-in efficiency relative to HR, non-homologous end joining (NHEJ), and microhomology-mediated end joining (MMEJ) strategies in non- iding cells. By introducing gRNA/Cas9 ribonucleoprotein complex and a HMEJ-based donor template with 1 kb homology arms flanked by the H11 safe harbor locus gRNA target site, knock-in rates of 40% of a 5.1 kb bovine sex-determining region Y ( SRY )-green fluorescent protein ( GFP ) template were achieved in Bos taurus zygotes. Embryos that developed to the blastocyst stage were screened for GFP, and nine were transferred to recipient cows resulting in a live phenotypically normal bull calf. Genomic analyses revealed no wildtype sequence at the H11 target site, but rather a 26 bp insertion allele, and a complex 38 kb knock-in allele with seven copies of the SRY-GFP template and a single copy of the donor plasmid backbone. An additional minor 18 kb allele was detected that looks to be a derivative of the 38 kb allele resulting from the deletion of an inverted repeat of four copies of the SRY-GFP template. The allelic heterogeneity in this biallelic knock-in calf appears to have resulted from a combination of homology directed repair, homology independent targeted insertion by blunt-end ligation, NHEJ, and rearrangement following editing of the gRNA target site in the donor template. This study illustrates the potential to produce targeted gene knock-in animals by direct cytoplasmic injection of bovine embryos with gRNA/Cas9, although further optimization is required to ensure a precise single-copy gene integration event.
Publisher: Springer Science and Business Media LLC
Date: 18-09-2018
Publisher: CABI Publishing
Date: 2018
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 h ered 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.
Publisher: American Dairy Science Association
Date: 03-2005
DOI: 10.3168/JDS.S0022-0302(05)72780-6
Abstract: 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.
Publisher: Mary Ann Liebert Inc
Date: 04-2018
Abstract: A 2017 draft Food and Drug Administration guidance proposes mandatory, multigenerational premarket new animal drug evaluation of all "intentional genomic alterations" induced by site-directed nucleases such as CRISPR in food animal genomes, irrespective of the novelty of the alteration or the existence of any hazards in the resulting product. Such a regulatory approach will effectively introduce additional layers of regulatory scrutiny on products produced using gene editing that are no different from those that could have been obtained using conventional breeding. Although this guidance may not directly impact the basic research community, due to Food and Drug Administration regulatory discretion around genetic modifications in model species, the potential opportunity cost of placing high regulatory costs on gene-edited food animals based solely on the use of modern molecular methods to introduce genomic alterations has potential global implications in terms of sustainability of food animal production.
Publisher: Mary Ann Liebert Inc
Date: 04-2023
Publisher: Wiley
Date: 07-07-2011
DOI: 10.1111/J.1365-2052.2011.02224.X
Abstract: 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 0.99), from which two haplotypes, TGC and CAT, were defined. Beef from in iduals that were homozygous for the TGC haplotype had significantly (P < 0.001) higher iron content than did beef from CAT homozygous or heterozygous in iduals. 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.
Publisher: Springer Science and Business Media LLC
Date: 06-08-2019
Publisher: National Academies Press
Date: 21-03-2019
DOI: 10.17226/25059
Publisher: Oxford University Press (OUP)
Date: 07-1994
Abstract: The 10-point Milk and Dairy Beef Quality Assurance Program was developed collaboratively by the National Milk Producers Federation and the American Veterinary Medical Association and is designed to promote and document the responsible use of antibiotics in the dairy industry. One area of emphasis in this program is testing of in idual animals for antibiotic residues after a specified post-treatment withdrawal time. We examined the performance of various assay systems on milk s les from in idual cows. These assays are used at present on bulk tank milk s les by regulatory agencies, processing plants, producers, and veterinarians to detect the presence of β-lactam antibiotics. A high proportion of false-positive results was obtained for both the pretreatment milk s les from cows with clinical mastitis and the milk s les obtained 21 days after initial therapy (nonantibiotic and antibiotic) for the treatment of mastitis. A high proportion of false-positive outcomes was obtained from the milk of clinically normal cows that had not received any medication for at least 30 days prior to evaluation. The results indicate a serious problem in the use of some assays that were designed to evaluate residues bulk tank milk s les to analyze s les from in idual cows. This error in assay specificity results in the unjustifiable discarding of milk that meets regulatory standards and may be misused to accuse the producer or veterinarian of not adhering to regulatory guidelines. Maintaining a safe, high-quality milk supply is a constant goal of the dairy industry, which must be provided the appropriate tools and techniques to meet this challenge.
Publisher: PeerJ
Date: 02-01-2014
DOI: 10.7717/PEERJ.238
Publisher: Frontiers Media SA
Date: 11-02-2021
DOI: 10.3389/FGENE.2021.593154
Abstract: Dehorning is the process of physically removing horns to protect animals and humans from injury, but the process is costly, unpleasant, and faces increasing public scrutiny. Genetic selection for polled (hornless), which is genetically dominant to horned, is a long-term solution to eliminate the need for dehorning. However, due to the limited number of polled Australian Brahman bulls, the northern Australian beef cattle population remains predominantly horned. The potential to use gene editing to produce high-genetic-merit polled cattle was recently demonstrated. To further explore the concept, this study simulated introgression of the POLLED allele into a tropically adapted Australian beef cattle population via conventional breeding or gene editing (top 1% or 10% of seedstock bulls/year) for 3 polled mating schemes and compared results to baseline selection on genetic merit (Japan Ox selection index, $JapOx) alone, over the course of 20 years. The baseline scenario did not significantly decrease the 20-year HORNED allele frequency (80%), but resulted in one of the fastest rates of genetic gain ($8.00/year). Compared to the baseline, the conventional breeding scenarios where polled bulls were preferentially used for breeding, regardless of their genetic merit, significantly decreased the 20-year HORNED allele frequency (30%), but resulted in a significantly slower rate of genetic gain ($6.70/year, P ≤ 0.05). The mating scheme that required the exclusive use of homozygous polled bulls, resulted in the lowest 20-year HORNED allele frequency (8%), but this conventional breeding scenario resulted in the slowest rate of genetic gain ($5.50/year). The addition of gene editing the top 1% or 10% of seedstock bull calves/year to each conventional breeding scenario resulted in significantly faster rates of genetic gain (up to $8.10/year, P ≤ 0.05). Overall, our study demonstrates that, due to the limited number of polled Australian Brahman bulls, strong selection pressure on polled will be necessary to meaningfully increase the number of polled animals in this population. Moreover, these scenarios illustrate how gene editing could be a tool for accelerating the development of high-genetic-merit homozygous polled sires to mitigate the current trade-off of slower genetic gain associated with decreasing HORNED allele frequency in the Australian Brahman population.
Publisher: Frontiers Media SA
Date: 13-04-2021
DOI: 10.3389/FGENE.2021.648482
Abstract: The introduction of genome editing reagents into mammalian zygotes has traditionally been accomplished by cytoplasmic or pronuclear microinjection. This time-consuming procedure requires expensive equipment and a high level of skill. Electroporation of zygotes offers a simplified and more streamlined approach to transfect mammalian zygotes. There are a number of studies examining the parameters used in electroporation of mouse and rat zygotes. Here, we review the electroporation conditions, timing, and success rates that have been reported for mice and rats, in addition to the few reports about livestock zygotes, specifically pigs and cattle. The introduction of editing reagents at, or soon after, fertilization can help reduce the rate of mosaicism, the presence of two of more genotypes in the cells of an in idual as can the introduction of nuclease proteins rather than mRNA encoding nucleases. Mosaicism is particularly problematic in large livestock species with long generation intervals as it can take years to obtain non-mosaic, homozygous offspring through breeding. Gene knockouts accomplished via the non-homologous end joining pathway have been more widely reported and successfully accomplished using electroporation than have gene knock-ins. Delivering large DNA plasmids into the zygote is hindered by the zona pellucida (ZP), and the majority of gene knock-ins accomplished by electroporation have been using short single stranded DNA (ssDNA) repair templates, typically less than 1 kb. The most promising approach to deliver larger donor repair templates of up to 4.9 kb along with genome editing reagents into zygotes, without using cytoplasmic injection, is to use recombinant adeno-associated viruses (rAAVs) in combination with electroporation. However, similar to other methods used to deliver clustered regularly interspaced palindromic repeat (CRISPR) genome-editing reagents, this approach is also associated with high levels of mosaicism. Recent developments complementing germline ablated in iduals with edited germline-competent cells offer an approach to avoid mosaicism in the germline of genome edited founder lines. Even with electroporation-mediated delivery of genome editing reagents to mammalian zygotes, there remain additional chokepoints in the genome editing pipeline that currently hinder the scalable production of non-mosaic genome edited livestock.
Publisher: O.I.E (World Organisation for Animal Health)
Date: 04-2018
Abstract: 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.
Publisher: Oxford University Press (OUP)
Date: 09-2016
Publisher: Oxford University Press (OUP)
Date: 20-07-2018
DOI: 10.1093/JAS/SKY286
Publisher: Springer New York
Date: 2008
Publisher: Elsevier
Date: 2018
Publisher: Oxford University Press (OUP)
Date: 03-2017
Publisher: Cold Spring Harbor Laboratory
Date: 14-08-2020
DOI: 10.1101/2020.08.13.249870
Abstract: Although considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. This lack of functional annotation poses a substantial roadblock to agricultural research and diminishes the value of these species as model organisms. As active regulatory elements are typically characterized by chromatin accessibility, we implemented the Assay for Transposase Accessible Chromatin (ATAC-seq) to annotate and characterize regulatory elements in pigs and cattle, given a set of eight adult tissues. Overall, 306,304 and 273,594 active regulatory elements were identified in pig and cattle, respectively. 71,478 porcine and 47,454 bovine regulatory elements were highly tissue-specific and were correspondingly enriched for binding motifs of known tissue-specific transcription factors. However, in every tissue the most prevalent accessible motif corresponded to the insulator CTCF, suggesting pervasive involvement in 3-D chromatin organization. Taking advantage of a similar dataset in mouse, open chromatin in pig, cattle, and mice were compared, revealing that the conservation of regulatory elements, in terms of sequence identity and accessibility, was consistent with evolutionary distance whereas pig and cattle shared about 20% of accessible sites, mice and ungulates only had about 10% of accessible sites in common. Furthermore, conservation of accessibility was more prevalent at promoters than at intergenic regions. The lack of conserved accessibility at distal elements is consistent with rapid evolution of enhancers, and further emphasizes the need to annotate regulatory elements in in idual species, rather than inferring elements based on homology. This atlas of chromatin accessibility in cattle and pig constitutes a substantial step towards annotating livestock genomes and dissecting the regulatory link between genome and phenome.
Publisher: Oxford University Press (OUP)
Date: 12-2012
Abstract: Genomic selection involves the assessment of genetic merit through prediction equations that allocate genetic variation with dense marker genotypes. It has the potential to provide accurate breeding values for selection candidates at an early age and facilitate selection for expensive or difficult to measure traits. Accurate across-breed prediction would allow genomic selection to be applied on a larger scale in the beef industry, but the limited availability of large populations for the development of prediction equations has delayed researchers from providing genomic predictions that are accurate across multiple beef breeds. In this study, the accuracy of genomic predictions for 6 growth and carcass traits were derived and evaluated using 2 multibreed beef cattle populations: 3,358 crossbred cattle of the U.S. Meat Animal Research Center Germplasm Evaluation Program (USMARC_GPE) and 1,834 high accuracy bull sires of the 2,000 Bull Project (2000_BULL) representing influential breeds in the U.S. beef cattle industry. The 2000_BULL EPD were deregressed, scaled, and weighted to adjust for between- and within-breed heterogeneous variance before use in training and validation. Molecular breeding values (MBV) trained in each multibreed population and in Angus and Hereford purebred sires of 2000_BULL were derived using the GenSel BayesCπ function (Fernando and Garrick, 2009) and cross-validated. Less than 10% of large effect loci were shared between prediction equations trained on (USMARC_GPE) relative to 2000_BULL although locus effects were moderately to highly correlated for most traits and the traits themselves were highly correlated between populations. Prediction of MBV accuracy was low and variable between populations. For growth traits, MBV accounted for up to 18% of genetic variation in a pooled, multibreed analysis and up to 28% in single breeds. For carcass traits, MBV explained up to 8% of genetic variation in a pooled, multibreed analysis and up to 42% in single breeds. Prediction equations trained in multibreed populations were more accurate for Angus and Hereford subpopulations because those were the breeds most highly represented in the training populations. Accuracies were less for prediction equations trained in a single breed due to the smaller number of records derived from a single breed in the training populations.
Publisher: Springer Science and Business Media LLC
Date: 16-10-2023
Publisher: Canadian Science Publishing
Date: 04-1998
DOI: 10.1139/G98-018
Abstract: The average chromosome number of the North American white sturgeon, Acipenser transmontanus Richardson, was found to be 271 ± 2.5 (ranging from 265 to 276). This number is significantly higher than previous estimates for this species. A representative karyotype was found to consist of 132 meta- and submeta-centric chromosomes, 44 acrocentric chromosomes, and 98 microchromosomes. An improved C-banding technique revealed variation (2-7) between animals in the number of entirely heterochromatic metacentric chromosomes. These heterochromatic chromosomes may represent supernumerary chromosomes. There was no cytogenetic evidence of a heteromorphic sex chromosome pair or any sex-related chromosomal polymorphism in either sex of this species.Key words: C-banding, fish, karyotype, supernumerary chromosomes, white sturgeon.
Publisher: Frontiers Media SA
Date: 16-05-2019
Start Date: 2004
End Date: 2007
Funder: National Institute of Child Health and Human Development
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