bluuebunny/crossref_metadata_2025 huggingface dataset:
7 Mixing aggression and floor type during gestation have implications for sow reproductive performance
Authors: Lagoda Martyna E , Boyle Laura A , Marchewka Joanna , Calderón Díaz Julia A
Published: November 2020

Aggressive behavior resulting from mixing to establish a dominance hierarchy is a welfare concern for group-housed sows. The associated stress could negatively impact reproductive performance (RP). Objectives of this study were to investigate associations between 1) mixing aggression intensity and RP within and between parities one (P1) and two (P2), and 2) aggression intensity, floor type and RP. A total of 164 gilts were followed through two parities. Gilts were mixed into stable groups of eight unfamiliar individuals four days after insemination, and housed on fully-slatted floors, either uncovered (CON; n = 84) or covered (RUB; n = 80) by a rubber slat-mat until farrowing (for both parities). Skin lesion scores (SLS) (proxy for mixing aggression intensity), were recorded 24–72 hrs post-mixing (0 = no lesions to 5 = severe lesions) on five body regions on left and right sides, and on the tail, in both parities. Total SLS was calculated for each sow. RP data were retrospectively acquired from farm records for both parities. Data were analyzed using GLMM in PROC GLIMMIX of SAS (v9.4) where 1) each parity analyzed separately, and 2) SLS in P1 used to predict RP in P2. Gilts with higher SLS in P2 had higher piglet mortality (P = 0.021) and longer cycle length (P = 0.003) in P2. Gilts with higher SLS in P1 had more non-productive days (P < 0.001) in P2. CON gilts had higher SLS than RUB gilts (P = 0.017) in P1, but not in P2 (P > 0.05). CON gilts also had more piglets born dead (P = 0.004) and tended to crush more piglets (P = 0.097) in P2. Our results confirm that mixing aggression impacts RP in the current parity negatively. They also suggest that mixing aggression experienced by gilts may have long-term negative carry-over effects on performance in subsequent parities. Use of rubber flooring appears to mitigate detrimental effects of mixing aggression, perhaps through improved sow comfort.
47 Distortion of Mendelian segregation across Angus cattle genome reveal novel lethal haplotype affecting reproduction
Authors: Lahoucine Samir Id , Casellas Joaquim , Lu Duc , Sargolzaei Mehdi , Miller Stephen P , Canovas Angela
Published: November 2020

The rapid development of DNA technologies, together with the adoption and daily routine use of commercial SNP arrays in livestock industries, provided a valuable resource of large and powerful data that can be explored for innovative applications for animal breeding purposes. Thus, the current availability of trios (i.e., sire-dam-offspring) of genotyped families enables the implementation of the transmission ratio distortion (TRD) approach to discover lethal alleles. Lethal alleles, which are crucial genetic determinants for reproduction, do not follow Mendelian principles but deviate from inheritance expectations, displaying signals of TRD. In this research, TRD was characterized using allelic (specific- and unspecific-parent TRD) and genotypic parameterizations (additive- and dominance-TRD) using both SNP- and haplotype-based methods. The analyses were performed using 258,140 Angus animals with 92,942 autosomal SNP genotypes, including 7,486 sires, 72,688 dams and 205,966 offspring. Across the whole genome, 852 regions displaying TRD were identified with different statistical significance. Among these findings, 19 haplotypes with recessive patterns (potential lethality for homozygote individuals) and 52 genomic regions with allelic patterns exhibiting complete or quasi-complete absence for homozygous individuals in addition to under-representation (potentially reduced viability) of heterozygous offspring were found. The average number of under-represented offspring (i.e., expected but not observed) across 52 allelic TRD regions ranged from 5,000 to 41,008. In contrast, the number of non-observed homozygous offspring for the 19 regions with recessive pattern ranges from 10 to 564. In addition, 64 and 20 genomic regions with TRD showed significant effects on the trait heifer pregnancy P < 0.05 and P < 0.01, respectively, reducing the progeny rate up to 15%. These novel findings in Angus present new candidate genomic regions putatively carrying lethal and semi-lethal alleles providing opportunities to reduce the rates of embryonic losses or death of offspring which could improve fertility and fitness in beef cattle populations.
22 Accuracy of indirect predictions for large datasets based on prediction error covariance of SNP effects from single-step GBLUP
Authors: Garcia Andre , Aguilar Ignacio , Legarra Andres , Miller Stephen P , Tsuruta Shogo , Misztal Ignacy , Lourenco Daniela
Published: November 2020

With an ever-increasing number of genotyped animals, there is a question of whether to include all genotypes into single-step GBLUP (ssGBLUP) evaluations or to include only genotyped animals with phenotypes and use indirect predictions (IP) for the remaining young genotyped animals. Under ssGBLUP, SNP effects can be backsolved from GEBV, and IP can be calculated as the sum of SNP effects weighted by the gene content. To publish IP, a measure of accuracy that reflects the standard error of prediction, and that is comparable to GEBV accuracy, is needed. Our first objective was to test formulas to compute accuracy of IP by backsolving prediction error covariance (PEC) of GEBV into PEC of SNP effects. The second objective was to investigate the number of genotyped animals needed to obtain robust IP accuracy. Data were provided by the American Angus Association, with 38,000 post-weaning gain phenotypes and 60,000 genotyped animals. Correlations between GEBV and IP were ≥0.99. When all genotyped animals were used for PEC computations, accuracy correlations were also ≥0.99. Additionally, GEBV and IP accuracies were compatible, with both direct inversion of the genomic relationship matrix (G) or using the algorithm for proven and young (APY) to obtain G inverse. As the number of genotyped animals in PEC computations decreased to 15,000, accuracy correlations were still high (≥0.96), but IP accuracies were biased downwards. Indirect prediction accuracy can be successfully obtained from ssGBLUP without running an extra SNP-BLUP evaluation to compute SNP PEC. It is possible to reduce the number of genotyped animals in PEC computations, but accuracies may be slightly underestimated. When the amount of genomic and phenotypic data is large, the polygenic part of GEBV becomes small and IP can be very accurate. Further research is needed to approximate SNP PEC with a large number of genotyped animals.
21 President Oral Presentation Pick: Using Deep Neural Networks to determine birth weight data quality for genetic evaluations in beef cattle
Authors: Ribeiro Andre , Golden Bruce L , Spangler Matthew L
Published: November 2020

The objective of this work was to evaluate the use of deep neural networks (DNN) for classifying contemporary groups based on the method used to generate birth weight (BWT) phenotypes. Contemporary groups (CG; n = 120,000) ranging between 10 and 500 animals were simulated assuming 12 data collection and CG formation scenarios that could impact CG phenotypic variance, including weights recorded with a digital scale (REAL), hoof tape (TAPE), and those that were fabricated (FAB). The performance of 6 activation functions (AF; ReLu, sigmoid, exponential, ReLu6, Softmax, Softplus) were evaluated. Four hidden layers were used with 7 different scenarios relative to the number of neurons. The training procedure was implemented in Python 3 with TensorFlow 1.14 and the ADAM optimization. Simulated CG were divided into training (80%) and testing (20%). The correlation between the observed and predicted CG types, averaged across 10 replicates, was used to assess accuracy and the correlations of predictions between replicates were used to measure the consistency of the model. In general, accuracy across AF and numbers of neurons were similar, with mean correlations ranging between 0.91 and 0.99. The AF ReLu, Sigmoid, Exponential and ReLu6 had the greatest consistency between the replicates, with an average correlation greater than 0.90. Independent of the number of neurons used, the sigmoid function produced the highest accuracy (0.99) and consistency (0.96). The DNN was retrained using 10-fold the number of CG and mimicking the CG size distribution observed in real data obtained from the American Hereford Association (n = 46,177 CG). In the real data, the lowest phenotypic variance was for FAB CG (2.98 kg2), REAL CG had the largest (18.33 kg2) and TAPE CG was intermediate (8.64 kg2). Results suggest that a well-trained DNN can be effectively used to classify data based on quality metrics prior to inclusion in routine genetic evaluation.
31 Changes in genomic predictions when new data is included
Authors: Hidalgo Jorge , Lourenco Daniela , Tsuruta Shogo , Miller Stephen P , Garcia Andre , Masuda Yutaka , Misztal Ignacy
Published: November 2020

Persistence of genomic evaluations depends on the amount of data and population parameters. When the data are large enough to estimate nearly all chromosome segments (about 10,000 in Angus), the persistence can be high. Subsequently, the regular evaluations can be run less often, and indirect predictions based on backsolved SNP effects may be accurate over an extended period as full predictions. The objective of this study was to investigate changes in GEBV across monthly genomic evaluations in a large genotyped population. A dataset from American Angus that contained 8,186,503 records for birth weight, 8,881,124 for weaning weight, and 4,386,184 for post-weaning gain was used. A total of 10,129,980 animals born up to December of 2017 had pedigree information, of which 484,074 were genotyped. A truncated dataset kept animals that were born up to December of 2016 (Dec2016). To mimic a scenario where evaluations are run every 30 days, the 2017 data was added month by month and new GEBV were computed using ssGBLUP. Genomic predictions from the Dec2016 evaluation were contrasted to the monthly evaluations for all genotyped animals, genotyped animals with or without phenotypes, genotyped animals with or without new phenotypes after Dec2016 and for young genotyped animals (born in 2016, with no phenotypes or progeny). The average number of animals added by month was 26,225, with a larger concentration from January to April. The correlations between GEBV from Dec2016 and all the 12 consecutive evaluations were greater or equal than 0.99 in all cases. The average (maximum) changes for young animals from Dec2016 to January and December of 2017 ranged from 0.05 (0.25) to 0.10 (0.53) additive standard deviations. The same changes for animals with records past Dec2016 were from 0.05 (0.11) to 0.88 (1.59). Genomic evaluations have high persistence over a year; however, outliers show larger changes.
10 Can single-step genome-wide association analysis (ssGWAA) account for population structure?
Authors: Mancin Enrico
Published: November 2020

Several methods are available for genome-wide association analysis, including the classical GWAA (cGWAA) based on fixed, single-SNP regression; efficient mixed-model association expedited (EMMAX) that fits single-SNP regressions together with a relationship matrix to account for population structure; and single-step GWAA (ssGWAA) where all data, including non-genotyped animals, are used. The objectives of this study were to: 1) investigate the ability of ssGWAA to account for population structure and correctly identify quantitative trait nucleotides (QTN); and 2) compare ssGWAA with cGWAA and EMMAX. Three simulated datasets were used, which mimic fish, beef cattle, and dairy cattle populations. The fish population was composed of 2,040 fish, out of which 1,040 were genotyped and had phenotypes for a trait with heritability of 0.25. The beef cattle population had 6,010 animals in the pedigree, but only 1,500 with phenotypes (h2 = 0.35) and genotypes. Lastly, the dairy cattle population had 40,800 pedigreed animals, of which 20,000 females had phenotypes (h2 = 0.32) and 2,400 males were genotyped. All phenotypes, pedigree, and genotypes were used in ssGWAA, whereas only genotypes and phenotypes were used in cGWAA and EMMAX for the fish and beef cattle analyses. For the dairy cattle analysis using the last two methods, deregressed proofs had to be used instead of phenotypes. The ability to correctly identify QTN and the number of statistically significant SNP (P < 0.05/number of SNP) was assessed among methods. In all populations, cGWAA was able to identify some of the strongest QTN but showed a large number of false positives. EMMAX and ssGWAA did not show false associations and correctly identified the top QTN, with more signals observed in ssGWAA. The ssGWAA accounts for population structure and is a proper association method, especially for livestock populations where sparse genotyping is a reality and phenotypes may not be recorded in genotyped animals.
28 Genomic prediction for marbling score in Hanwoo cattle using sequence data
Authors: Jang Sungbong , Garcia Andre , Lee Seunghwan , Tsuruta Shogo , Lourenco Daniela
Published: November 2020

As sequence information becomes available for some livestock species, there is a question on the amount of non-redundant information that may be embedded in the extra millions of SNPs or in causative variants within sequence. The objective of this study was to assess the gain in accuracy by using imputed whole-genome and selected SNP from sequence data in a beef cattle population. The dataset consisted of marbling score phenotypes for 545K Hanwoo cattle and pedigree information for 1.3M, of which 1,160 were genotyped for 50K SNPs. Imputation was done first to 777K and then to whole-genome sequence (WGS), which comprised 11,146,536 SNPs. Additionally, differentially expressed genes (DEG) and their 321,614 harboring SNPs were identified based on RNA-seq analysis of animals with high and low marbling score. An extra scenario combined 50K with DEG SNPs. Genomic predictions were obtained using GBLUP and single-step GBLUP (ssGBLUP) with and without weights, and BayesR. The last method could not be used for the WGS data because of the large number of SNPs. Predictive ability was calculated as the correlation between phenotypes adjusted for fixed effects and GEBV for 169 young animals. For all the methods, WGS and DEG had a slightly negative impact on predictive ability. Both GBLUP and BayesR had similar performances when using 50K, DEG, and 50K+ DEG, with predictive abilities equal to 0.19, 0.16, and 0.18, respectively. Predictive ability for ssGBLUP was 0.27, 0.26, and 0.27, in the aforementioned order. Using WGS, predictive ability for GBLUP was 0.17 and for ssGBLUP was 0.26. Weighting SNP differently did not improve predictions. As ssGBLUP uses all data available, not only genotyped animals with phenotypes as the other methods, it is more robust for genomic predictions. No gain in accuracy was observed, possibly because the selected sequence variants were not causative.
34 Search for the association of polymorphisms in inhibin alpha and prolactin genes with sperm quality in Russian Holstein bulls
Authors: Nikitkina Elena , Krutikova Anna , Musidray Artem , Anipchenko Polina
Published: November 2020

The formation and functioning of the animal reproductive system occurs as a result of the coordinated interaction of a wide range of genes. The hormone inhibin (INHA) is a marker of Sertoli cell function and exocrine testicular function (spermatogenesis state). The hormone prolactin (PRL) is a regulatory factor in the male reproductive system and affects gametogenesis. The aim of the work was to search for associations of inhibin alpha (INHA) and prolactin (PRL) gens polymorphism in the population of Russian Holstein bulls. Sperm traits (doublet ejaculate volume, concentration, progressive motility) were evaluated over three years of bull use and the highest rates for each trait were selected. 32 bulls had contrasting traits. DNA was isolated from semen samples. Samples were sequenced using the Applied Biosystems 3500 Genetic Analyzer using the BigDye® Terminator v3.1 Sequencing Standard Kit according to the protocol. Genotyping was then performed by PCR-RFLP. Data was analyzed using ANOVA. All pairwise multiple comparison between means were conducted by t-test. No polymorphism was detected in two regions of the PRL gene. The frequency of genotype AA in INHA gene was 0.813, the genotype AG -0.187. The GG genotype has not been identified. Bulls with the genotype AG had a higher concentration of cells (1.64 ± 0.093 billion/ml) than bulls with the genotype AA (1.35 ± 0.058) (P˂0.05). No significant differences were found in the volume of ejaculate and motility. But bulls with the AG genotype had greater ejaculate volume and motility than bulls with the AA genotype. The study of polymorphism in the genes that determine the formation and functioning of the reproductive system will help to understand the basics of these processes, as well as use them as molecular genetic markers for culling young bulls according to sperm quality. Project № АААА-А18-118021990006-9.
23 Current progress in the Agricultural Research Service Beef Grand Challenge: A large-scale genetics by environment by management evaluation project
Authors: Kuehn Larry A , Casperson Shanon L , Derner Justin D , Gunter Stacey A , Hay El Hamidi , Moffet Corey A , Neel James P , Picklo Matthew J , Petersen Mark K , Roemmich James N , Turner Kenneth E , Waterman Richard C , Wheeler Tommy L , Boggess Mark V
Published: November 2020

The Agricultural Research Service (ARS) Beef Grand Challenge is a cooperative, multidisciplinary effort evaluating differences in performance of genetic lines across production environments representative of different geographical regions. Weaned spring-born calves (n = 120 per location), representing natural service matings to Angus, Hereford, Simmental, Charolais, or indicus-composite (Beefmaster or Brangus) bulls from the U.S. Meat Animal Research Center Germplasm Evaluation program in south central Nebraska, are sent to wheat pasture (central Oklahoma) and winter range (eastern Montana), and weaned fall-born calves (n=40 per location) are sent to summer grazing on shortgrass prairie (northeastern Colorado) and southern mixed-grass rangeland (western Oklahoma). All cattle are fed a finishing ration representative of the region that approximately matches energy content across locations. Each calving season has a matching counterpart of calves that remain in Nebraska on a calf-fed drylot program (receiving ration followed by longer finishing ration). Breeds and sires are represented equally, to the extent possible, at each location. To detect differences in breed effects at each location and average over yearly variation, the study is being replicated for 4 years. Weights, stress measures, carcass composition (marbling, yield grade, quality grade, etc.), steak tenderness and steak fatty acid composition are collected from each location. Additionally, rumen metagenomic composition, metagenomic samples, preharvest food safety samples, and feed intake measures are collected at some locations. Grazing impacts and supplemental range feeding are also being evaluated. One year of sampling has been completed, with numeric differences observed for marbling and tenderness as well as growth performance among locations. Statistical differences will be evaluated when replicate years are collected. The USDA is an equal opportunity provider and employer.
11 Genome-wide association study using repeated measures model for stillbirth in Holstein dairy cattle
Authors: Fonseca Pablo Augusto S , Lahoucine Samir Id , Schenkel Flavio , Canovas Angela
Published: November 2020

Reduced fertility is one of the main causes of economic losses in dairy farms. The financial losses are estimated in US$938 per stillbirth case in Holstein herds. The identification of genomic regions associated with stillbirth could help to develop better management and breeding strategies aiming to reduce the frequency of undesirable gestation outcomes. The same cow may show different outcomes in different gestations. Therefore, evaluation of a single time-point may provide a biased indication of the genetic causes of stillbirth. A weighted single-step genomic best linear unbiased prediction (WssGBLUP) was performed using the BLUPF90 software. A total of 14,145 cows (with three or more delivery records) were genotyped for 42,909 SNP markers mapped against the ARS-UCD1.2 bovine reference genome. Three rounds of WssGBLUP were performed using 50,541 stillbirth records (4.8±1.3 records per animal). In total, 5,796 stillbirth cases were observed out of the 50,541 records (~11%). The statistical model included: calf size, calf sex, and dam age class (< 36, 36–50, 50–63, 63–75, ³75 months) as fixed effects; and herd-year-season, cow additive genetic merit, cow permanent environment, and service sire as random effects. Nine windows explaining more than one percent of the total genetic variance were identified, where the top 3 windows explained 7.86% (BTA13:37558814-38550118), 4.92% (BTA18:59897080-60892357) and 2.17% (BTA12:80568320-81508005). The top candidate window, on BTA13, harbors the OVOL2 gene, which codifies a zinc-finger protein crucial for embryo development during the angiogenesis, heart formation, hematopoietic, endothelial, neural tube and placental development. Additionally, OVOL2 is crucial during the spermatogenesis and was already identified as down-regulated between ectopic and eutopic endometrial tissues in woman with endometriosis. These results pinpoint new genomic candidate regions for stillbirth in Holstein, helping to better understand the genetic mechanisms associated with fertility problems.
303 ASAS-EAAP Talk: On the estimation of genetic parameters from molecular data
Authors: Ibáñez Miguel Toro
Published: November 2020

We deal with several problems that arise when inferring genetic parameters at the level of quantitative trait loci (QTL) from molecular data such as SNP markers. Linkage Disequilibrium (LD) is recognized as a factor creating ambiguity in the partition of genetic variance. Here, using a simple model with three loci (one QTL and two markers), it is shown that the markers generate apparent AxA and DxD epistasis, even if only third order disequilibrium exists and the QTL is dominant. The problem of “phantom epistasis” is not alleviated by larger sample sizes (de los Campos et al., 2019). We also show that markers can give a distorted picture of the genetic correlation between traits: The genomic correlation could be greater, lower or even of opposite sign than the true genetic correlation. Therefore, speculating about genetic correlations and even about their causes (e.g., pleiotropy) using genomic data is often conjectural. Thirdly, we examine the problem of directional selection generating negative linkage disequilibrium (“Bulmer effect”) in the short term from a genomic selection perspective. It seems that the reduction in response due to the Bulmer effect is the same for genomic selection as for selection based on traditional BLUP. However, the reduction in response with genomic selection is greater than when selection is based directly on phenotypes only (Van Grevenhof et al. 2012). It is also expected that directional selection for a polygenic trait should increase recombination rate, provided there is genetic variance for recombination. It is then of relevance to ask whether recombination rates could be manipulated in order to increase selection response (Battagin et al., 2016). Finally, we consider that recombination and epistasis are closely intertwined: Epistasis generate LD and recombination break them up. Then, we should expect genomes to be modular: regions with low recombination containing functionally related genes loosely linked to other regions.
49 Hematological and physiological changes observed in commercial stocker operation during early management
Authors: Akter Mst Afroza , Caldwell Marc , Pighetti Gina , Schneider Liesel G
Published: November 2020

Dynamic physiological parameters’ change in recently received stocker calves may indicate disease onset or further progression. Our objective was to capture changes in rectal temperature and blood chemistry to determine relationships between these responses, castration status, and time after arrival at a commercial farm. Forty newly weaned steers of variable breed and body weight were received from order buyer on February 13, 2020 to a commercial stocker farm in Crossville. Calves were monitored for 4 wks; blood samples and rectal temperature were collected at day 0, 7, 14, and 21. All calves were either freshly (FC) (n = 27) or previously castrated (PC) (n = 13). Complete blood count (CBC) was analyzed on each sampling day using Hematology Analyzer, and the correlation between body temperature and CBC parameters was assessed using CORR procedure in SAS 9.4. To test if FC group differed from PC with CBC value changes, mixed model analysis of variance was performed (Proc GLIMMIX) with day as repeated measure (α = 0.05). Rectal temperature was significantly negatively correlated with red blood cells (RBC) (r = -0.33, P = 0.03) and hemoglobin (HGB) (r = -0.37, P = 0.01) on day 21. A castration by day interaction (P = 0.04) was found for white blood cell (WBC). Significant differences were found in between FC and PC groups for WBC on day 0 (10.59 and 14.23, respectively) and 14 (12.04 and 15.80, respectively). Significantly lower RBC, HGB, and Mean Corpuscle Volume (MCV) were found in FC; however, they had increased Mean Corpuscle Hemoglobin (MCH) and platelet (PLT) counts (P < 0.05). In addition, there were day effects on mean WBC, MCH, PLT, and Mean Corpuscular Hemoglobin Concentration (MCHC) (P < 0.001). While previous health history of stocker cattle remains unknown, there are definite differences in hematology and physiology at arrival and over time, which may increase risk for illness in this stage of production.
55 Novel nanofibrous mats for effective delivery of sodium metabisulfite (SMBS) to the intestinal tract of pigs
Authors: Yu Changning , Lu Peng , Liu Shangxi , Gong Joshua , Yang Chengbo , Liu Song
Published: November 2020

Deoxynivalnol (DON) occurs on many commonly used cereal grains. DON levels as low as 0.6 to 2.0 ppm in complete feed cause a reduction in feed intake and growth rate, damage to the intestinal epithelial cells and increased susceptibility to enteric pathogen challenge. Sodium metabisulfite (SMBS) is a sulfite reducing agent commonly added to animal feeds to improve protein digestibility by cleaving disulfide bonds. SMBS can destroy 70%-100% of DON in processed grains or feeds in vitro with 0.45%-0.9% levels at pH around 6.5 but not at acidic conditions. Therefore, little SMBS will remain intact in the small intestine, where an optimal pH environment exists for SMBS to detoxify DON. Thus, the aim of this study is to encapsulate SMBS into nanofiber mats by an electrospinning technology to deliver intact SMBS to the lower gut such as the small intestine to detoxify DON effectively. Electrospinning was implemented to prepare nanofiberous mats from a suspension of particulate SMBS in the solution of a pH sensitive polymer (Eudragit L100-55). The highest loading capacity and loading efficiency of SMBS achieved in the nanofiberous mats were 32.00% and 80.01%, respectively. In vitro release studies showed that 12.23%-19.48% of encapsulated SMBS was released in the simulated gastric fluid (SGF) in 2 h and 66.01%-95.86% of SMBS release was observed in the simulated intestinal fluid (SIF) within 1 h. Additionally, in an in vitro DON detoxification experiment using IPEC-J2 cells, the ability of DON detoxification was reflected by significantly increasing the cell viability of DON and encapsulated SMBS nanofiber group (82.99%) compared with the cell viability of DON group (62.19%) (P < 0.05). For the first time, we demonstrate successful encapsulation of particulate SMBS in a nano-vehicle (electrospun nanofiber), achieve > 50% release of SMBS in SIF, and effective detoxification of DON in an in vitro cell assay.
66 Intra-articular lipopolysaccharide challenge has no long-term effects on inflammation and cartilage metabolism
Authors: Bradbery Amanda N , Leatherwood Jessica L , Silvers Brittany L , Much Mattea L , Martinez Rafael E , Arnold Carolyn E
Published: November 2020

Intra-articular lipopolysaccharide is a common model to induce acute synovitis to investigate the effects of various therapeutic agents or nutraceuticals. The long-term effects of intra-articular lipopolysaccharide use in skeletally mature and immature horses has yet to be investigated; therefore, the objective of this study was to describe long-term effects of single-administration of intra-articular lipopolysaccharide on joint inflammation and cartilage metabolism. To test this objective, both radial carpal joints from 5 stock-type horses never exposed to lipopolysaccharide (CON; n = 10) were compared to radial carpal joints from 17 similar stock-type horses previously exposed to intra-articular lipopolysaccharide (INFL; n = 34). Joints within INFL were further categorized as the joint which received lipopolysaccharide (LPS; n = 17) and contralateral control which received iso-volumetric lactated Ringer’s solution (CONTRA; n = 17). A single synovial fluid sample from each joint was analyzed for prostaglandin E2 (PGE2), collagenase cleavage neopeptide (C2C), carboxypeptide of type II collagen (CPII), and chondroitin sulfate 846 (CS846). All data were analyzed using PROC MIXED of SAS with main effects of treatment (CON, INFL) and joint (CON, LPS, CONTRA). Time post-administration (1.5, 2, 6 yr) and age-at-administration (1, 3, 5, 7 yr) were included in the model within INFL joints (LPS, CONTRA). There was no influence of treatment on any biomarker (P > 0.40). Similarly, inflammation and cartilage metabolism were not different between CON, CONTRA, and LPS joints (P > 0.50). Within INFL, there was no influence of joint, age, or time post-administration for PGE2, CPII, or CS846 (P > 0.10). A joint x time interaction was observed for catabolic C2C (P < 0.01); however, where LPS was less than CONTRA 2 yr post-lipopolysaccharide administration and similarly when lipopolysaccharide was administered at 5 and 7 yr of age (P < 0.01). These data indicate no long-term negative effects for the use of intra-articular lipopolysaccharide as an acute inflammatory model in skeletally mature and immature horses.
72 Estimating the supply and movement of feed for beef production in Alberta, Canada
Authors: Mengistu Genet , Cordeiro Marcos , Legesse Getahun , Pogue Sarah , Taylor Amanda , Ominski Kim , Beauchemin Karen , McGeough E J , McAllister Tim A
Published: November 2020

This study estimated movement of feed between regions of Alberta to meet the needs of the beef sector in 2001, 2006, 2011 and 2016, and included barley and wheat grain, grass hay and grass-legume hay, which can be cost-effectively transported. Feed demands of beef and other livestock (i.e., dairy cattle, chickens, pigs, sheep, bison, horses, turkeys and other poultry) were estimated using county-level inventories from Alberta Agriculture and Rural Development and Statistics Canada, and aggregated to 7 land-use regions: Lower Athabasca, Upper Athabasca, Lower Peace, Upper Peace, North Saskatchewan, Red Deer and South Saskatchewan. Feed requirements were sourced from literature and expert opinion pertinent to Canadian context, and feed demand estimated using annualized feeding days and dry matter (DM) intake. Feed available for beef production was estimated from crop yields minus other livestock feed use. Average feed demand for beef production across Alberta was (tons of DM) 2.71 M, 0.68 M, 2.21 M, and 1.95 M for barley and wheat grain, grass hay, and grass-legume hay, respectively. North Saskatchewan, Red Deer and South Saskatchewan accounted for 90% of the total demand for barley and wheat grain and 81% of grass hay and grass-legume hay. South Saskatchewan had the largest feed deficit and required feed movement in all years. Across years, barley grain deficits ranged from -94% to -31%, grass hay deficit from -142% to a surplus of 1.6% and grass-legume hay deficits from -167% to -15%. Unmet deficits at provincial level occurred for barley grain (2006), grass hay (2001) and grass-legume hay (2001, 2006). Wheat was surplus in all years, ranging from 17% to 90%. Feed movement is critical to support beef production in Alberta, and is highly variable depending on crop yield in different regions. This analysis enables the beef industry to assess provincial feed sourcing and environmental footprints.
320 Analyses of inter-individual variations of sperm DNA methylation and their potential implications in cattle
Authors: Liu George
Published: November 2020

Background: DNA methylation has been shown to be involved in many biological processes, including X chromosome inactivation in females, paternal genomic imprinting, and others. Results: Based on the correlation patterns of methylation levels of neighboring CpG sites among 28 sperm whole genome bisulfite sequencing (WGBS) data (486×coverage), we obtained 31,272 methylation haplotype blocks (MHBs). Among them, we defined conserved methylated regions (CMRs), variably methylated regions (VMRs) and highly variably methylated regions (HVMRs) among individuals, and showed that HVMRs might play roles in transcriptional regulation and function in complex traits variation and adaptive evolution by integrating evidence from traditional and molecular quantitative trait loci (QTL), and selection signatures. Using a weighted correlation network analysis (WGCNA), we also detected a co-regulated module of HVMRs that was significantly associated with reproduction traits, and enriched for glycosyltransferase genes, which play critical roles in spermatogenesis and fertilization. Additionally, we identified 46 VMRs significantly associated with reproduction traits, nine of which were regulated by cis-SNPs, implying the possible intrinsic relationships among genomic variations, DNA methylation, and phenotypes. These significant VMRs were co-localized (± 10kb) with genes related to sperm motility and reproduction, including ZFP36L1, CRISP2 and HGF. We provided further evidence that rs109326022 within a predominant QTL on BTA18 might influence the reproduction traits through regulating the methylation level of nearby genes JOSD2 and ASPDH in sperm. Conclusion: In summary, our results demonstrated associations of sperm DNA methylation with reproduction traits, highlighting the potential of epigenomic information in genomic improvement programs for cattle.
82 The impact of feeding treats containing cannabidiol (CBD) on the daily activity level of dogs
Authors: Morris Elizabeth M , Kitts-Morgan Susanna E , Spangler Dawn M , McLeod Kyle R , Harmon David L
Published: November 2020

Growing public interest in and use of Cannabidiol (CBD) in companion animals has amplified the need to elucidate potential impacts. The purpose of this investigation was to determine the impact of CBD on daily activity of adult dogs. Twenty-four dogs (18.0 ± 3.4 kg) were utilized in a randomized complete block design with treatments consisting of control, 2 mg CBD/kg BW/d, and 4 mg CBD/kg BW/d split between two treats administered after twice-daily exercise (7:00-9:00 and 17:00-19:00). Four hours each day (10:00-12:00, AM and 13:30-15:30, PM), were designated as time when no persons entered the kennels, with 2 h designated as Quiet Time and the other 2 h as Music Time, where calming music played over speakers. Quiet and Music sessions were randomly allotted to daily AM or PM times. Activity monitors were fitted to dogs’ collars for continuous collection of activity parameters. Data were collected over a 2-wk baseline period to block dogs by activity level (high or low) before randomly assigning dogs within each block to treatments. After 1 wk of treatment adaptation, activity parameters were collected for 2 wk. Data were tested for normality using the UNIVARIATE procedure in SAS before examining differences using the MIXED procedure in SAS, including effects of treatment, day, session (Quiet or Music), time of day (AM or PM), and accompanying interactions. CBD did not alter total activity points (P = 0.9971) or activity duration (P = 0.8776). CBD tended (P = 0.0692) to reduce scratching compared to control. Irrespective of treatment, dogs were more active in PM than AM (P < 0.0001). Regardless of session, dogs receiving 4 mg/kg/d tended (P = 0.0914) to be less active in the PM than control. CBD did not affect activity duration during exercise periods (P = 0.1425), but dogs receiving CBD ran more than control (P = 0.0339). These results indicate that when supplemented up to 4 mg/kg/d, CBD does not negatively impact daily activity levels of dogs.
86 Apparent Total Tract Nutrient Digestibility of Human-Grade Dog Foods and Their Effects on Stool Characteristics, Serum Metabolites, and Hematology of Dogs
Authors: Do Sungho , de Godoy Maria R C , Swanson Kelly S
Published: November 2020

Human-grade pet foods are believed to be of higher quality than traditional pet foods, but little research has been conducted on them to date. Therefore, our objective was to determine the apparent total tract digestibility (ATTD) of human-grade pet foods and evaluate their effects on stool characteristics, serum metabolites, and hematology of dogs. Twelve dogs (mean age = 5.5 ± 1.0; BW = 11.6 ± 1.6 kg) were used in a replicated 4×4 Latin square design. The diets included: 1) Chicken and Brown Rice Recipe (extruded; Blue Buffalo); 2) Roasted Meals Tender Chicken Recipe (fresh; Freshpet); 3) Beef & Russet Potato (human-grade; JustFoodForDogs); and 4) Chicken & White Rice (human-grade; JustFoodForDogs). Each period consisted of 28 d, with a 6-d diet transition phase, 16 d of consuming 100% of the diet, a 5-d phase for total and fresh fecal collection, and 1 d for blood collection. All data were analyzed using the Mixed Models procedure of SAS 9.4. Dogs fed the extruded diet had a higher (P < 0.05) daily food intake (dry matter basis; DMB) and fecal output (as-is and DMB) compared with dogs fed fresh or human-grade dog foods. There were no differences in fecal pH or scores across diets, but ATTD of dry matter (DM), organic matter (OM), and acid-hydrolyzed fat (AHF) were greater (P < 0.05) for dogs fed the human-grade diets than those fed the fresh diet. Likewise, DM, OM, and AHF ATTD were greater (P < 0.05) in dogs fed the fresh diet than those fed the extruded diet. The majority of serum metabolites and blood cell counts of dogs fed all diets were within the reference ranges for adult dogs, with few treatment differences. In conclusion, the human-grade foods tested were shown to be highly digestible and maintained stool characteristics, serum chemistry, and complete blood count in adult dogs.
334 Pet food safety: truth in labeling
Authors: Edwards David , Conway Charlotte
Published: November 2020

In the United States, substances intended for use in animal foods are generally considered to be either animal foods or animal drugs. The regulatory classification of a substance relies on its intended use. Claims for substances that are regulated as animal foods are limited to those that can be attributed to the substance’s “food” properties, which the courts in the United States have defined as being related to the provision of nutritive value, taste, or aroma or for a technical effect on the food itself. Any substance intentionally added to an animal food must be either an approved food additive as listed in part 573 in Title 21 of the Code of Federal Regulations (21 CFR 573) or a substance that is generally recognized as safe (GRAS) for an intended use, including those listed in 21 CFR 582 and 584. Also, in coordination with state feed control officials, CVM recognizes ingredients in the Official Publication of the Association of American Feed Control Officials (AAFCO) as being acceptable for use in animal foods. Everything on a pet food label must be truthful, not misleading, and appropriate for a product regulated as food. Federal regulations (21 CFR 501) require that labels include: an appropriate product name, all ingredients in descending order of predominance by weight, a statement of net quantity of contents, and the address of manufacturer or distributor. Most states have additional labeling requirements. Studies conducted for scientific research need to be evaluated to determine if the endpoints and parameters measured are also appropriate as regulatory data. Feeding studies may address target animal safety and/or utility of the substance for its intended use as a food. CVM will provide written feedback on protocols intended to address new feed ingredients.
341 How the IACUC uses the Ag Guide to ensure the best care
Authors: Heath Kelly D
Published: November 2020

All Institutional Animal Care and Use Committees (IACUC) are all subject to the same regulatory requirements. Membership requirements (Scientist, Nonscientist, Attending Veterinarian, Public Members, and Chairperson) are established by the regulatory agencies and appointed by the Institutional Official (IO). Today we will review the basic role of the IACUC: reviewing animal use protocols, inspecting animal facilities and procedure areas, evaluating the program of animal care, investigating allegations of non-compliance, making recommendations to the institutional official about needed changes, and utilizing the Ag Guide as a guidance document. The role of the IACUC at Land Grant Institutions is confounded often by the variety of research that is conducted. At the University of Nebraska, we have traditional food and fiber, biomedical and wildlife research, which requires a diverse set of committee members to adequately review the animal care and use. All IACUC protocols, regardless of the species or funding mechanism, are required to address several common questions. As a principal investigator, you can help yourself tremendously by providing all the required information in a transparent, logical and organized manner. If you can anticipate your audience and provide key information in multiple formats, it will help streamline the review process. Based on membership requirements, most committee members will not come from agriculture backgrounds, so it is imperative you help the committee to understand standard agriculture practices. You can best accomplish this with standard operating procedures, herd management protocols, disaster plans, and veterinary care processes and provide photographs or short video clips of your proposed activities. Additionally, if you are asked to serve on this committee, be willing to proactively educate your peers on what is considered appropriate management, housing, experimental and humane endpoints. By acting as your own advocate, you can ensure good animal care as well as achieve timely approvals.
96 Cover Crop Grazing and Backgrounding on Carcass Quality
Authors: Macaluso Cathryn N , Ehrhardt Richard A , Cassida Kim , Schweihofer Jeannine P , Recktenwald Erin , Makela Barbara
Published: November 2020

Integration of sheep into cropping systems via cover crop grazing leases has potential to benefit sheep producers with a source of inexpensive, high quality forage. We examined this potential by comparing lamb growth and carcass traits of four rearing systems: grain-finished control (GR), cover crop brassica-finished (CCB), cover crop mixture-finished (CCM), and background on brassica and finished on grain (BK-GR). Dorset x Polypay lambs (n = 60; 3 pens or pastures, 5 lambs each) were blocked by body weight and randomly assigned to treatment. All diets were provided to maximize voluntary dry matter intake. Lambs were harvested after 6 wks of feeding for GR and 8 wks for CCB, CCM and BK-GR (BK-GR = 4 wks brassica then 4 wks grain). Grain-fed lambs (GR and BK-GR, 442 g/d) grew faster than pasture-fed lambs (CCB and CCM, 152 g/d) prior to harvest (Table 1, P < 0.01) and attained greater body mass (HCW), muscling (LEA, EMD), fatness (BF, BWF) and yield grade (all P < 0.05). Growth of pasture-fed lambs declined 38% over time (247 wk 1–4 vs. 152 g/d wk5-8; P < 0.05). Pasture-fed lambs were leaner than grain-fed lambs (BF, yield grade; P < 0.01), yet attained a yield grade 2 average. Background lambs (BK-GR) exhibited a 107% increase in growth when fed grain (232 g/d pasture vs. 481 g/d grain, P < 0.01) and were fatter (BF, P < 0.05) yet had reduced eye muscle depth (P < 0.01) at harvest than GR lambs. Lambs did not differ in growth or any carcass measurement according to pasture type (CCB vs. CCM). We conclude that 8 wks of cover crop finishing produced acceptable carcass weight and finish. Backgrounding on cover crops followed by 4 wks of grain finishing results in marked compensatory gain with lambs achieving the same carcass size and similar qualities to lambs fed only grain.
95 Multi-Specie cover crop bale grazing effect after annual forage grazing on yearling steer grazing and feedlot performance, muscling, carcass measurements and carcass value
Authors: Senturklu Songul , Landblom Douglas , Paisley Steve
Published: November 2020

Yearling crossbred steers (n = 144) were randomly assigned to native range (NR) or annual forage (ANN>: native range plus field pea-barley, corn, 13-species cover crop) to evaluate grazing season extension by feeding (“Grazing”) cover crop bales (field pea, forage barley, clover, sorghum sudan 12.8% CP, 54.4% NDF, 31.4% ADF, 59.0% TDN) before feedlot entry to measure the effect on steer grazing and subsequent feedlot performance and economics. Grazing was extended 43.6 days (177.9 to 221.5 days). ANN plus bale grazing ADG was 0.95 kg/day; NR was 0.77 kg/day (P = 0.01). Ending ANN grazing gain was 43.0 kg heavier (P = 0.001). Grazing muscling was measured using ultrasound. The ratio for REA:45.4 kg live weight did not differ (P = 0.53). End grazing ANN steer REA (P = 0.002) and percent intramuscular fat (IMF) were greater (P = 0.05) than NR steers. End grazing marbling score did not differ (489.0 vs. 470.0). In the feedlot, steers were fed 95.7 days. The ANN steer feedlot arrival weight was heavier (P = 0.04), but ending weight did not differ between ANN and NR treatments (717.6 vs. 684.0 kg; P = 0.19). ANN steer hot carcass weight (HCW) was 25.6 kg heavier (P = 0.03). The NR steer dressing percent was greater (P = 0.01) and muscling (REA:HCW) was greater for the NR steers (P = 0.007), resulting in improved USDA yield grade (P = 0.01). Quality grade did not differ (98.6% Choice or better; P = 1.00). ANN steer HCW resulted in $92.26 more per carcass (P = 0.031) than NR. Grazing medium forage quality cover crop bales is an effective method for increasing gain and live animal muscle and intramuscular fat quality before feedlot entry, and ANN steer weight advantage entering the feedlot carried over to greater ending HCW and subsequently, greater carcass value.