bluuebunny/crossref_metadata_2025 huggingface dataset:
25 Gut Microbiome Information Enables Additional Discovery in Genome-wide Association Studies in Swine
Authors: Tiezzi Francesco , Maltecca Christian
Published: October 2021

Several studies have highlighted the relevance of gut microbiome composition in shaping fat deposition in mammals. In contrast, other studies have highlighted how the host genome can control the abundance of individual species in the gut microbiota’s make-up. There is the need to incorporate the different ‘-omics’ data (host genome, gut microbiome, high-throughput phenotyping) in a model that allows to extract information beyond the simple sum of each component’s contribution. We propose a systematic approach to detect host genomic variants that control the gut microbiome, which in turn contributes to the host fat deposition, when this latter is based on multiple phenotypic measures. Using a dataset that included longitudinal records of fat deposition on 1,180 pigs, we implemented a mediation test to describe how fat deposition in swine (Sus scrofa) is affected by the host genotype and the gut microbiome. The phenotypic outcome was described both by measured and latent variables, taking advantage of structural equation modeling. We also implemented a ‘traditional’ genome-wide association analysis, testing the (total) effect of host genomic variants on the phenotype. Results for all models were validated using both bootstrapping and permutation tests. The models identified several host genomic features having microbiome-mediated effects on fat deposition. Our work demonstrates how the host genome can affect the phenotypic trait by inducing a change in gut microbiome composition that leads to a change in the phenotype. The host genomic features identified through the mediation analysis do not entirely overlap the group of features identified by traditional GWAS. Microbiome-mediated analyses can help understand the genetic determination of complex phenotypes. The host genomic features that exert a mediated effect could not be identified by traditional genome-wide association analysis. These can contribute to filling the missing heritability gap and provide further insights into the host genome – gut microbiome interplay.
19 Comparative Evaluation of Human-edible Animal Products Derived from Offspring of Genome Edited and Control Cattle
Authors: Trott Josehine F , Young Amy E , McNabb Bret R , Yang Xiang , Bishop Thomas F , Van Eenennaam Alison L
Published: October 2021

Risk assessments of genetically modified (GM) animals include evaluating whether milk and meat derived from the GM animal is as nutritious to humans and/or animals as traditionally-bred animals. The underlying assumption of this comparative approach is that traditionally-bred animals have a well-established history of safe use. The goal of this project was to provide empirical data on the development and nutritional composition of animal products derived from the offspring of a genome edited dairy bull, homozygous for the dominant PC Celtic POLLED allele. The bull was crossed with horned Hereford (HH) cows (pp) to obtain five male and one female heterozygous hornless (RC) calves. Hereford, Angus and Holstein bulls were also bred to Hereford cows to produce five HH calves, two polled Angus/Hereford (AH) calves, and three horned Holstein/Hereford (HO) calves (with 25% genetic identity to the hornless offspring), respectively as contemporary controls. Weights were recorded at 8 months, 1 year and slaughter (n = 9–16). Following calving, individual quarters of the RC heifer (RC.calf1), one HO heifer (HO.calf2), two horned HH heifers, and one contemporaneous hornless AH cow (3113) were milked at varying timepoints during the first seven weeks of lactation. Meat samples were collected from the 6 hornless RC calves and 3 horned HO comparator offspring after slaughter. Proximate analysis was conducted for meat and milk samples. Cattle that inherited a POLLED allele from the genome-edited bull showed no differences in their overall growth (Figure 1) or meat composition (Figure 2) when compared to contemporary controls. Milk composition varied between animals and by days in milk (DIM), although values were within the normal range reported in peer-reviewed literature (Figure 3). Bovine milk composition is known to be influenced by breed, nutrition, parity, and DIM, making it difficult to obtain appropriate comparators in experiments with a limited number of GM animals.
21 Unravelling Transmission Ratio Distortion Across the Genome of a Crossbreed Beef Cattle Population
Authors: Becker Scalez Daiane C , Id-Lahoucine Samir , Fonseca Pablo A S , Casellas Joaquim , Cánovas Angela
Published: October 2021

Transmission ratio distortion (TRD) is a process when one allele from either parent is preferentially transmitted to the offspring. The identification of genomic regions affected by TRD might help in the detection of lethal alleles or potential genes affecting reproduction. Here, we investigated TRD in crossbreed beef cattle population aiming to identify genomic regions showing altered deviations in segregation that could be affecting reproduction performance. A total of 237 genotyped animals were used including 46 sires, 80 dams, and 111 parent-offspring (trios). The predominant breeds of these animals were Angus (61.83%), Simmental (18.99%), Gelbvieh (6.12%), Charolais (3.65%), Hereford (2.46%) and Limousin (1.57%). After excluding SNPs with minor allele frequency lower than 0.05 and call-rate lower than 0.90, a total of 369,902 autosomal SNPs were retained for further analyses. The SNP-by-SNP analysis was performed within a Bayesian framework using TRDscanv.2.0 software, using 100,000 iterations, with 10,000 iterations being discarded as burn-in. As table 1 shows, 33 SNPs were identified with TRD, considering a Bayes Factor (BF)≥100 and the approximate empirical null distribution of TRD at 0.01% margin error. Among them, 26 SNPs were parent-unspecific and 7 SNPs were parent-specific TRD. For parent-specific TRD, 214 were identified for sire- and 162 for dam-TRD (BF≥100). Among them, 4 SNPs were detected with sire- and dam-TRD in opposite direction of preference of transmission. Preliminary functional and positional analysis was performed using the list of TRD regions with BF≥100 and the approximate empirical null distribution of TRD at 0.01% margin error. For sire-TRD, 14% of the identified QTL (n = 254) were related to non-return rate. For dam-TRD, 21 regions related to conception rate were found (1.5%) and 13 regions related to stillbirth (0.93%). Haplotype analysis is in progress to identify additional candidate regions and alleles with TRD to better understand this phenomenon in a crossbreed beef population.
22 Characterization of tRNA Expression Profiles in Large Offspring Syndrome
Authors: Goldkamp Anna K , Li Yahan , Rivera Rocio M , Hagen Darren
Published: October 2021

Differentially methylated regions (DMRs) have been associated with Large Offspring Syndrome (LOS) in cattle. Some DMRs overlap transfer RNA (tRNA) gene clusters, potentially altering tRNA expression patterns uniquely by treatment group or tissue type. tRNAs are classified as adapter molecules, serving a key role in the translational machinery implementing genetic code. Variation in tRNA expression has been identified in several disease pathways suggesting an important role in the regulation of biological processes. tRNAs also serve as a source of small non-coding RNAs. To better understand the role of tRNA expression in LOS, total RNA was extracted from skeletal muscle and liver of 105-day fetuses and the tRNAs sequenced. Although there are nearly three times the number of tRNA genes in cattle as compared to human (1,659 vs 597), there is a shared occurrence of transcriptionally silent tRNA genes in both species. This study detected expression of 474 and 487 bovine tRNA genes in skeletal muscle and liver, respectively, with the remainder being very lowly expressed or transcriptionally silent. Eleven tRNA isodecoders are transcriptionally silent in both skeletal muscle and liver and another isodecoder is silent in the liver (SerGGA). Further, the highest expressed isodecoders differ by treatment or tissue type with roughly half correlated to codon frequency. While the absence of certain isodecoders may be relieved by wobble base pairing, missing tRNA species could likely increase the likelihood of mistranslation or mRNA degradation. Differential expression of tissue- and treatment-specific tRNA genes may modulate translation during protein homeostasis or cellular stress, altering regulatory products targeting genes associated with overgrowth in skeletal muscle and/or tumor development in the liver of LOS individuals.
30 Calf Performance and Sex Ratios in Second Generation Reciprocal Nellore-angus Crosses
Authors: Mickey Dana , Sanders James , Riley David G , Herring Andy D
Published: October 2021

The objectives of this study were to analyze calf weight and sex distribution differences in reciprocal F2 Nellore-Angus calves (n = 559) born 2010–2015 and calves out of these F2 females through 4 yr age (n = 469) born 2012–2018. The F2 animals were produced by 4 F1 parent type combinations from Nellore-sired (NA) vs. Angus-sired (AN) sires and dams. Weight traits were analyzed using mixed models, and sex distribution was analyzed through PROC GLIMMIX in SAS. Sire type and dam type affected birth weight (P < 0.05) but not weaning weight of the F2 calves. However, the interaction between sire type and dam type accounted for weaning weight differences (P = 0.038). Birth weight averaged 3.5 kg heavier from NA vs. AN sires, and 2.4 kg heavier from NA vs. AN dams. Weaning weight displayed a different pattern than observed in birth weight with the heaviest calves being NAAN (224.5 ± 3.7 kg) and lightest being ANAN (215.9 ± 3.9 kg). Sire type accounted for important variation (P = 0.036) in the calf sex distribution at birth among F2 calves. Percentage males at birth exceeded the expected ratio for NA-sired calves (66.6%, n = 168) but not for AN-sired calves (49.9%, n = 105). The sire and dam type main effects in the F2 females did not influence weight traits or sex distribution in their calves (from predominantly Angus sires). However, the interaction of sire type x dam type x sex showed a trend in birth weight (P = 0.080) and importance for weaning weight (P = 0.010) where only from ANNA and NANA dams were males heavier than females. These results suggest that some of the calf weight reciprocal differences typically observed among F1 Bos indicus-Bos taurus crosses can persist in later generations.
27 Machine Learning Algorithms Based on Haplotype Libraries for Classification of Stillbirth Susceptibility in Holstein Cows
Authors: Fonseca Pablo A S , Tornatore Massimo , Cánovas Angela
Published: October 2021

Reduced fertility is one of the main causes of economic losses in dairy farms. The cost of a stillbirth is estimated in US$ 938 per case in Holstein herds. Machine learning (ML) is gaining popularity in the livestock sector as a mean to identify hidden patterns and due to its potential to address dimensionality problems. Here we investigate the application of ML algorithms for the prediction of cows with higher stillbirth susceptibility in two scenarios: cows with >25% and >33.33% of stillbirths among birth records. These thresholds correspond to percentiles 75 (still_75) and 90 (still_90), respectively. A total of 10,570 cows and 50,541 birth records were collected to perform a haplotype-based genome-wide association study. Five-hundred significant pseudo single nucleotide polymorphisms (pseudo-SNPs) (False-Discovery Rate< 0.05) were used as input features of ML-based predictions to determine if the cow is in the top-75 and top-90 percentiles. Table 1 shows the classification performance of the investigated ML and linear models. The ML models outperformed linear models for both thresholds. In general, still_75 showed higher F1 values compared to still_90, suggesting a lower misclassification ratio when a less stringent threshold is used. We observe that accuracy of the models in our study is higher when compared to ML-based prediction accuracies in other breeds, e.g. compared to the accuracies of 0.46 and 0.67 that were achieved using SNPs for body weight in Brahman and fertility traits in Nellore, respectively. Xgboost algorithm shows the highest balanced accuracy (BA; 0.625), F1-score (0.588) and area under the curve (AUC; 0.688), suggesting that xgboost can achieve the highest predictive performance and the lowest difference in misclassification ratio between classes. The ML applied over haplotype libraries is an interesting approach for the detection of animals with higher susceptibility to stillbirths due to highest predictive accuracy and relatively lower misclassification ratio.
33 Impact of Including the Cause of Missing Records on Genetic Evaluations for Growth in Commercial Pigs
Authors: Hollifield Mary Kate , Lourenco Daniela , Tsuruta Shogo , Bermann Matias , Howard Jeremy T , Misztal Ignacy
Published: October 2021

It is of interest to evaluate crossbred pigs for hot carcass weight (HCW) and birth weight (BW); however, obtaining a HCW record is dependent on livability (LIV) and retained tag (RT). The purpose of this study is to analyze how HCW evaluations are affected when herd removal and missing identification are included in the model and examine if accounting for the reasons for missing traits improves the accuracy of predicting breeding values. Pedigree information was available for 1,965,077 purebred and crossbred animals. Records for 503,716 commercial three-way crossbred terminal animals from 2014 to 2019 were provided by Smithfield Premium Genetics. Two pedigree-based models were compared; model 1 (M1) was a threshold-linear model with all four traits (BW, HCW, RT, and LIV), and model 2 (M2) was a linear model including only BW and HCW. The fixed effects used in the model were contemporary group, sex, age at harvest (for HCW only), and dam parity. The random effects included direct additive genetic and random litter effects. Accuracy, dispersion, bias, and Pearson correlations were estimated using the linear regression method. The heritabilities were 0.11, 0.07, 0.02, and 0.04 for BW, HCW, RT, and LIV, respectively, with standard errors less than 0.01. No difference was observed in heritabilities or accuracies for BW and HCW between M1 and M2. Accuracies were 0.33, 0.37, 0.19, and 0.23 for BW, HCW, RT, and LIV respectively. The genetic correlation between BW and RT was 0.34 ± 0.03, and between BW and LIV was 0.56 ± 0.03. The positive and moderate genetic correlations between BW and other traits imply a heavier BW resulted in a higher probability of surviving to harvest. Despite the heritable and correlated aspects of RT and LIV, results imply no major differences between M1 and M2; hence, it is unnecessary to include these traits in classical models for BW and HCW.
34 Dimensionality of Genomic Information and Its Impact on GWA and Variant Selection: A Simulation Study
Authors: Jang Sungbong , Tsuruta Shogo , Leite Natalia , Misztal Ignacy , Lourenco Daniela
Published: October 2021

The ability to identify true-positive variants increases as more genotyped animals are available. Although thousands of animals can be genotyped, the dimensionality of the genomic information is limited. Therefore, there is a certain number of animals that represent all chromosome segments (Me) segregating in the population. The number of Me can be approximated from the eigenvalue decomposition of the genomic relationship matrix (G). Thus, the limited dimensionality may help to identify the number of animals to be used in genome-wide association (GWA). The first objective of this study was to examine different discovery set sizes for GWA, with set sizes based on the number of largest eigenvalues explaining a certain proportion of variance in G. Additionally, we investigated the impact of incorporating variants selected from different set sizes to regular SNP chip used for genomic prediction. Sequence data were simulated that contained 500k SNP and 2k QTL, where the genetic variance was fully explained by QTL. The GWA was conducted using the number of genotyped animals equal to the number of largest eigenvalues of G (EIG) explaining 50, 60, 70, 80, 90, 95, 98, and 99 percent of the variance in G. Significant SNP had a p-value lower than 0.05 with Bonferroni correction. Further, SNP with the largest effect size (top10, 100, 500, 1k, 2k, and 4k) were also selected to be incorporated into the 50k regular chip. Genomic predictions using the 50k combined with selected SNP were conducted using single-step GBLUP (ssGBLUP). Using the number of animals corresponding to at least EIG98 enabled the identification of the largest effect size QTL. The greatest accuracy of prediction was obtained when the top 2k SNP was combined to the 50k chip. The dimensionality of genomic information should be taken into account for variant selection in GWAS.
39 Combining Different Marker Prioritization Methods in the Analysis of High-density and Sequence Data
Authors: Ling Ashley S , Hay El Hamidi , Aggrey Samuel E , Rekaya Romdhane
Published: October 2021

High-density and sequence genotypes were expected to increase accuracy of genomic predictions through inclusion of markers in high linkage disequilibrium with causal loci, yet the realized increase has been minimal. Marker preselection has been proposed as a strategy to prioritize the most relevant markers to reduce the dimensionality of the association model and potentially increase accuracy. Strength of association statistics (estimated effect, p-value) and population differentiation measurements (FST score) have both been explored as criteria for preselection, but sensitivity to identify relevant markers decreases as random noise exceeds true signal variation. Combining both criteria into an index would leverage the unique contributions of each criterion and potentially increase prediction accuracies. A simulation consisting of 200 QTL, 777k SNP, and 7 generations under selection was generated (10 replicates). Marker preselection was compared across three criteria: only estimated effect (EFF), only FST score (FST), or an index combining the two previous statistics (COMB). In the COMB scenario, markers from genomic regions with high correlation (>0.7) between estimated effect and FST score were selected along with markers whose estimated effect or FST score exceeded a certain threshold. Across replicates, COMB identified additional markers tagging between 1 and 7 QTL not tagged by EFF or FST that explain 0.2–5.4% of the genetic variance. The highest accuracy for EFF and FST was 0.76 and 0.73 when preselecting 2k and 10k markers, respectively. Under the best-case scenario (3,297 preselected markers), COMB improved accuracy by less than 1% and 4% compared to EFF and FST scenarios, respectively. Though an index combining multiple statistics may increase the number of QTL tagged by preselected markers and genetic variance explained relative to single-statistic preselection, this does not necessarily translate to a meaningful increase in accuracy. However, the results are dependent on the indexing method.
37 Single-step Genomic BLUP Fitting Snps or Haplotypes in Genetically-diverse Populations: A Simulation Study
Authors: Araujo Andre C , Carneiro Paulo , Oliveira Hinayah R , Schenkel Flavio S , Brito Luiz F
Published: October 2021

The successful implementation of genomic selection in more genetically diverse populations (e.g., sheep and goats) require larger training populations. Haplotype-based genomic predictions are hypothesized to perform better in comparison to single-SNP methods mainly due to the possibility of better capturing QTL effects in linkage disequilibrium (LD) with the markers. However, most genomic-prediction studies based on haplotypes were performed in populations with low effective population size (Ne < 150). We aimed to investigate alternative approaches for fitting haplotypes using the single-step GBLUP method (ssGBLUP) in a genetically diverse population (Ne = 400). We simulated a composite sheep population, mimicking real populations based on literature parameters, using the QMSim software, with five replicates. We simulated a HD panel (600K) and two traits with different heritabilites (0.10 and 0.30). Pseudo-SNPs from unique haplotype alleles derived from LD blocks with thresholds of 0.1, 0.3, and 0.6 (LD01, LD03, and LD06, respectively) were used in the analyses. The LD-blocks were constructed using a 50K panel designed from the simulated HD. The training population was composed of 60,000 individuals with phenotypes, 8,000 of them also had genotypes, and 2,000 young genotyped individuals were used as the validation set. The genomic relationship (G) in the ssGBLUP was constructed using both independent markers and pseudo-SNPs (haplotypes). A linear mixed effects model was used to test the effect of the G on the accuracies of prediction, followed by the Tukey test with 5% of significance. No blocks were created with LD06. The accuracies with the 50K panel, LD01, and LD03 for the moderate heritability were 0.41(0.00), 0.40(0.01) and 0.41(0.00), respectively, and 0.24(0.01) 0.23(0.01), and 0.24(0.01) for the low heritability scenario. No statistical differences were observed. Based on our findings, haplotype-based predictions did not improve the accuracy of genomic breeding values in genetically diverse populations.
46 Footprints of Selection in Angus and Hanwoo Beef Cattle Using Imputed Whole Genome Sequence Data
Authors: Nawaz Muhammad Yasir , Savegnago Rodrigo Pelicioni , Gondro Cedric
Published: October 2021

In this study, we detected genome wide footprints of selection in Hanwoo and Angus beef cattle using different allele frequency and haplotype-based methods based on imputed whole genome sequence data. Our dataset included 13,202 Angus and 10,437 Hanwoo animals with 10,057,633 and 13,241,550 imputed SNPs, respectively. A subset of data with 6,873,624 common SNPs between the two populations was used to estimate signatures of selection parameters, both within (runs of homozygosity and extended haplotype homozygosity) and between (allele fixation index, extended haplotype homozygosity) the breeds in order to infer evidence of selection. We observed that correlations between various measures of selection ranged between 0.01 to 0.42. Assuming these parameters were complementary to each other, we combined them into a composite selection signal to identify regions under selection in both beef breeds. The composite signal was based on the average of fractional ranks of individual selection measures for every SNP. We identified some selection signatures that were common between the breeds while others were independent. We also observed that more genomic regions were selected in Angus as compared to Hanwoo. Candidate genes within significant genomic regions may help explain mechanisms of adaptation, domestication history and loci for important traits in Angus and Hanwoo cattle. In the future, we will use the top SNPs under selection for genomic prediction of carcass traits in both breeds.
56 Awardee Talk: Genetic Improvement of Disease Resilience
Authors: Dekkers Jack C , Fortin Frederic , Dyck Michael , Harding John , Plastow Graham
Published: October 2021

Infectious disease represents one of the largest cost components to the swine industry, incurring veterinary costs, loss of pigs due to mortality, reduced performance, and reduced animal welfare. Strategies to reduce the incidence and impact of infectious disease include biosecurity, vaccination, veterinary treatment, and selection for genetic resistance. However, biosecurity protocols that keep most infectious pathogens out are not feasible at the commercial level in hog-dense regions, effective vaccines are only available and/or efficacious for some pathogens, and complete genetic resistance is also limited to only a few pathogens (e.g. F18 E.coli) or is only possible to achieve by gene editing (e.g. the PRRS-resistant pig created by editing the CD163 gene). Given these limitations, commercial pigs will continue to be exposed to and infected by pathogens for the foreseeable future. In such a scenario, the ability of an animal to clear the infection while maintaining performance is an important characteristic, which is referred to as disease resilience and is a useful target for inclusion in breeding programs. However, collection of data on disease resilience for genetic improvement requires animals to be exposed to disease, which is not possible in the nucleus herds of breeding programs that most selection is practiced in. To study the genetic basis of disease resilience and develop phenotypes, genetic tests, or indicator traits that could be used to select for disease resilience, a polymicrobial natural disease challenge model was established in grow-finish pigs at the Center de Développement du Porc du Québec, in collaboration with PigGen Canada. The purpose of this presentation is to present results on phenotypes that are relevant to disease resilience, including estimates of genetic parameters, and on potential indicator traits for disease resilience that could be collected in nucleus herds. Funding by Genome Canada, Genome Alberta, PigGen Canada, and USDA NIFA grant #2017-67007-26144.
60 The Effect of Neomycin Inclusion in Milk Replacer on Gut Health and Development in Preweaned Male Holstein Calves
Authors: Buss Lauralise , Yohe Taylor , Cangiano Lautaro Rostoll , Keunen Aaron , Guan Leluo , Renaud David , Steele Michael A
Published: October 2021

Neomycin is commonly used in calf milk replacers (MR) to prevent diarrhea, however, antimicrobial exposure in early life may have consequences to gut development. The objective of this study was to investigate the effects of neomycin inclusion in MR on calf gut health and development. Thirty-six calves were randomly assigned to one of three treatments: control (CON), non-medicated (MR, n = 12), short-term antimicrobial exposure (ST: 20 mg/kg BW neomycin mixed in MR from d 1–14, n = 12), or long-term antimicrobial exposure (LT: 20 mg/kg BW neomycin in MR from d 1–28, n = 12). Fecal samples were collected weekly to measure total bacteria, and gut permeability was measured in week 2 and 4 by comparing serum recovery of orally dosed lactulose and D-mannitol markers. Calves were dissected at week 5 to collect intestinal tissues, which were used to analyze histology, gene expression and total bacteria abundance. Digesta samples were collected to analyze for total bacteria abundance and volatile fatty acid (VFA) concentrations. No treatment effects were found in the amounts of total bacteria in fecal, digesta, or tissue samples. Marker recovery in serum was higher at week 2 compared to week 4 (P < 0.01), suggesting that calves in early life have higher gut permeability. Histomorphological measures were similar, except for villi length in the distal jejunum, which was longest in ST calves (P = 0.05). Tight-junction, mucus, and inflammatory-associated gene expression was similar overall, although the expression of Tight junction protein-1 in the distal jejunum was lowest in CON calves (P = 0.04). Distal jejunum acetic acid, propionic acid, and total VFA tended to be highest in LT calves (P = 0.09; P = 0.06; P = 0.07, respectively). Although this study found few consequences of neomycin to gut health, the lack of benefits supports the argument that antimicrobials should be used prudently.
78 Opportunities and Limitations of Modeling and Data Analytics for Precision Livestock Farming
Authors: Remus Aline , Pomar Candido , Warner Daniel
Published: October 2021

Precision livestock farming (PLF) involves the use of sensors that captures large amounts of real-time information at the building, herd or animal level, which are later processed to control the system. Data processing can be accomplished using mathematical models (MM), artificial intelligence algorithms (AI) or a combination of these and other methods. The choice of the method must be made according to the volume of data to be processed, its nature and the relationship between the available information and the desired control of the system. Several components of PLF such as precision nutrition, early disease detection, animal welfare among others may require sophisticated data processing methods. MM is today the preferred method to estimate nutrient requirements in the precision nutrition component of PLF. Conventional MM estimate average population responses using historical population information. Important limitations of these models are the assumption that all the individuals of the population have the same response to a given nutrient provision and that they have not been developed for real-time estimations using up-to-date available information. Therefore, MM have to be developed specifically for PLF and operate in real-time at individual or small group level, considering the between and within-animal variation. Growth patterns, nutrient utilization and behavior vary among animals and herds. There are opportunities to combine data-driven AI with knowledge-driven MM to control more complex PLF components. AI thrive in large complex datasets, where establishing connections can be otherwise difficult due to data complexity, volume and where flexibility is needed to process real-time data from individuals. In contrast, knowledge-driven MM can simplify complex biological systems based on well-established concepts and information. In both cases, PLF models must be flexible enough to consider changes over time for the same animal or herd, and among animals and herds, acknowledging the method limitation while using its strength.
95 Effects of Three Implant Programs on Growth Performance, Carcass Outcomes, and Weekly Activity Minutes of Finishing Steers Fed Different Days on Feed
Authors: Martinez Socorro , Word Alyssa B , Holland Ben P , Karr Kendall , Hutcheson John P , Walter Lee-Anne J , Richeson John , Lawrence Ty E , Samuelson Kendall L
Published: October 2021

This study evaluated the effects of a single slow-release implant compared to two re-implant programs administered at either 120 days on feed (DOF) or 80 days from harvest on performance, carcass characteristics, and activity of serially harvested feedlot cattle. Using a randomized complete block design, steers (n = 4,680) were randomly assigned to 72 pens and 1 of 12 treatments in a 3 × 4 factorial arrangement. Treatments were either a slow-release implant (SR), an initial slow-release implant followed by re-implant at 120 DOF (SR+RI-120), or an initial slow-release implant followed by re-implant 80 days from harvest (SR+RI-80) administered to cattle harvested at 166, 180, 194, or 208 DOF. A 3-axis accelerometer ear-tag was used in a subset (n =1,080) of animals to quantify rumination time and activity. No interactions (P ≥ 0.09) were observed for implant × DOF. Implant did not affect (P ≥ 0.25) final BW, ADG, or DMI, but re-implanted steers had a greater (P < 0.01) G:F ratio than SR. Re-implanted steers also had greater (P ≤ 0.03) HCW, dressed yield, and ribeye area, but less (P < 0.01) backfat, marbling, and empty body fat (EBF) compared to SR. Re-implanted steers had less (P < 0.01) choice and yield grade 4 and 5 carcasses than SR steers. As DOF increased, HCW, dressed yield, backfat, marbling, and EBF increased linearly (P < 0.01). The percentage of choice and yield grade 4 and 5 carcasses also increased (P < 0.01) linearly with additional DOF. An implant × day effect (P < 0.01) for weekly activity minutes suggests re-implanted steers had greater activity after re-implant administration. Re-implanting within the payout period of a slow-release implant increases feed efficiency, HCW, dressed yield, and activity minutes, but decreases carcass fatness and reduces quality grade regardless of timing of secondary implant administration.
103 The Economics and Role of Beef X Dairy Calves in the Beef Supply Chain
Authors: Smith Jason K , Piñeiro Juan , Benavidez Justin
Published: October 2021

Utilizing beef genetics in dairy herds to produce terminal beef x dairy (BXD) crosses is a growing trend in the U.S. dairy industry. It has been estimated that more than two million U.S. BXD calves were born in 2020, which is a practice that is expected to continue to grow throughout the foreseeable future. While not a new concept, the widespread adoption, scale, and strategies currently being used to produce BXD calves have recently received considerable industry attention. Although the increased duration of feeding exposes BXD feeders to increased price and production risks when compared to straightbred beef cattle, these risks are met with several potential benefits. A prime example of such benefits includes a consistent supply of uniform, traceable feeder cattle that are easily age and source verified, that also serve as ideal candidates for enrollment in or development of other value-added marketing programs. Current demand, as indicated by newborn calf prices, suggests that the industry perceives BXD calves to be superior when compared to their straightbred dairy breed contemporaries, and at times, suggests that they may be overvalued. Sustaining such demand will require BXD calves to meet or exceed the performance and profitability expectations of the various production sectors of the beef industry. Results of a multi-year analysis of the economics of BXD calves as compared to cattle of straightbred beef or dairy breed composition will be presented. Furthermore, specific factors expected to influence value throughout the production supply chain will be outlined and discussed. Calfhood management practices that promote calf health, paired with genetic selection strategies focused on complementary traits that minimize cost of gain and increase cutability, such as feed efficiency, carcass yield, and muscularity, will play key roles in sustaining the value of BXD calves to all aspects of the beef supply chain.
100 Management Strategies to Optimize Health and Performance of Pre-weaned Calves
Authors: Machado Vinicius , Ballou Michael
Published: October 2021

In the United States, 1 in each 10 dairy replacement heifers were raised in a calf raising facility, and that at least half of farms with 500 or more lactating animals raised some of their calves in a specialized calf ranch. Approximately 80% of calves are individually housed, but the type of housing (e.g., outside hutch, inside a barn) varies based on location of calf-raising operations. Generally, the benchmark for optimal growth of calves is to double their birth weight by weaning. Such benchmark can only be achieved with consistent management and nutrition. Hence, it is not surprising that in large operations, up to 90% of facilities receive regular visits of both veterinarians and nutritionists. Milk-replacer is fed in more than 80% of operations, while milk (sealable or non-sealable) is fed in approximately 30% of calf raising facilities. Health challenges such as scours, and bovine respiratory disease (BRD) can hinder the performance of calves and are major causes of mortality in calf ranches. In addition to optimal colostrum management, vaccination and early diagnosis/ treatment can prevent major economic losses caused by these diseases. Compared to calves raised in their original dairies, calves raised in off-site operations are exposed to additional stressors that can lead to impairment of their immune system and weaken their resistance against pathogens. For instance, transportation at a very young age and comingling with animals from other dairies can increase the risk of diseases. Current research efforts are focusing in determining individual factors such as body weight at arrival or biomarkers of inflammation and stress that can be predictive of disease morbidity, mortality, and performance of calves. Such information could be used in the future to optimize management and to develop targeted preventative strategies to reduce incidence of diseases and mortality during the pre-weaned period.
98 What We Think We “know” About Beef X Dairy Crossbred Cattle in the Feedlot
Authors: Felix Tara L
Published: October 2021

To increase profitably, dairy farms across the United States have rapidly adopted breeding a portion of their cows to beef sires, generating crossbred progeny. The resulting progeny have, in some cases, increased the value of the calf to the dairy, due to their perceived potential for improved growth, feed efficiency, and carcass characteristics for beef production. U.S. research is behind our European counterparts in recommending the appropriate beef sires for dairy matings, and U.S. semen trends show Angus sales over many other breeds. However, Kempster et al. (1982) reported that calves sired by British breed bulls were actually at a disadvantage in growth performance compared to even purebred Holstein calves. Finnish researchers agreed, reporting that the resulting crossbreds from Aberdeen Angus and Hereford bulls were extremely variable, making them undesirable for beef production. However, resulting crossbred calves from late maturing breed types (Charolais, Limousine, and Simmental) had better average daily gain and carcass characteristics than their counterparts from early maturing breeds (Huuskonen et al., 2013). A comprehensive review of early crossbred systems similarly suggested that calves sired by Continental breeds, like Charolais, had an advantage in the feedlot and the packing house (Shank, 2003). Going a bit further, another European study examined the used of 3 beef breeds (Belgian Blue, Limousine, and Galacian Blonde) known for heavy muscling, but not common in the United States, for use as crossbreeding sires (Fouz et al., 2012). Holstein cows bred to Belgian Blue sires had the greatest difficulty calving; however, calving difficulties were reduced with increasing dam age (Fouz et al., 2012). Unfortunately, that trial did not go on to evaluate feedlot performance. Thus, there remains a dearth of scientific references for crossbred mating decisions as well as subsequent growth performance and carcass outcomes.
107 Quality Parameters of Pet Treats Generated from Beef Processing Co-products
Authors: Presume Marc R , Soler Rigo F , Sandoval Jorge L , Avila Luis P , Chilenje Moses E , Odom Catherine M , Garner Laura J , Morey Amit U , Mason Robert P , Altom Eric K , Starkey Charles W
Published: October 2021

By-products such as beef liver (BL) and beef heart (BH), while rich in protein, vitamins, and minerals, can be difficult products for incorporation into mixtures. Sodium alginate (SA) and calcium lactate (CL) can be used to improve structure of protein sources. The objective was to determine the quality of restructured BL and BH pet treats using ALGIN as a structure forming agent. Quality parameters assessed were pH, expressible moisture, cooking loss, and water activity of raw and dehydrated pet treats. After grinding, BL and BH, were mixed: 25%BL:75%BH, 50%BL:50%BH, and 75%BL:25%BH. The 3 BL:BH combinations were mixed with 2 dosages of ALGIN (0.5% SA + 0.425% CL, and 1% SA + 0.85% CL) to produce 6 treatments. Each treatment was then extruded into 20-mm-thick jerky slices and refrigerated at 3°C for 48 h. Samples were dehydrated at 93°C for 2.5 h for cooking loss analysis. Ten raw samples (25.4 mm × 25.4 mm) were used to measure expressible moisture, and another ten raw samples were used to measure pH. Water activity was assessed on ten raw and ten dehydrated samples. Data were analyzed with the GLIMMIX procedure of SAS and means were separated at P ≤ 0.05. Cooking loss decreased as ALGIN dosage increased in all BL and BH mixtures (P < 0.0001); however, cooking loss percentage increased as BH proportions increased (P = 0.0001). Water activity of dehydrated samples decreased as BL proportions increased (P < 0.0001), but with increasing ALGIN dosage, water activity of dehydrated treats increased (P = 0.0193). Raw pH was not affected by treatment. Expressible moisture of samples increased with increasing BL proportions (P < 0.0001) but decreased as ALGIN dosage decreased (P < 0.0001). Use of ALGIN allowed for BL and BH to be restructured into an acceptable form for use in pet treats.
113 Owner Dietary and Exercise Regimens Influence Perception of Ideal Body Weight in Dogs
Authors: Banton Sydney , Baynham Andrew , Pezzali Julia Guazzelli , von Massow Michael , Verbrugghe Adronie , Shoveller Anna-Kate
Published: October 2021

The increasing prevalence of canine obesity across the globe has become the number one health concern for dogs. Part of the problem may be the way owner’s perceive their dog’s body weight. The goal of the current survey was to assess what variables, related to both owner and dog’s feeding and exercising practices, were predictive of the owner’s perception of their dog’s body weight across North America (Canada and the United States) and Europe (France, the United Kingdom and Germany). The online survey was distributed by Qualtrics (Qualtrics XM, Utah, USA) in June 2020. A total of 3,298 responses were collected and were equally distributed across country and sex of respondent. Multinomial logistic regression was performed in SPSS Statistics (Version 26, IBM Corp, North Castle, New York, USA). More than 85% of respondents reported that they believe their dog is an ideal body weight. Results from logistic regression suggest that owners of younger dogs (0–2 years) are 5 times more likely to believe their dog is an ideal body weight compared to older dogs (over 11 years; P < 0.0001). Respondents who selected that they perform vigorous exercise, themselves, less often than 4 days per week were less likely to believe that their dog is an ideal body weight compared to those who reported vigorously exercising for more than 5 days per week (P < 0.05). Finally those who reported feeding their dog a fixed amount of food were more likely to believe their dog is an ideal body weight (P = 0.044) while those who reported restricting their dogs food intake to control weight were less likely to believe their dog is an ideal body weight (P < 0.0001). Overall, both human and dog dietary and exercise routines were predictive of a dog owner’s perception of their dogs body weight.
498 Late-Breaking: Identifying Meaningful Measures of Dam and Puppy Welfare in Commercial-breeding (CB) Kennels
Authors: Romaniuk Aynsley , Barnard Shanis , Weller Jennifer , Shreyer Traci , Croney Candace
Published: October 2021

Maternal factors such as fear and stress influence offspring welfare in many species, but this area of research has been underexplored in dogs. As a large proportion of society’s dogs originate from commercial-breeding (CB) kennels, further investigation in this environment is crucial to ensure canine welfare. The current study aimed to refine a set of welfare metrics used to explore associations between maternal factors and litter welfare in CB kennels. Dams (n = 28) from five USDA-licensed CB kennels were tested at 6 and 1-week prepartum, and 4 and 8-weeks postpartum using a stranger approach test, physical health assessment, exposure to novel stimuli, social isolation test, hair cortisol concentration, fecal glucocorticoid metabolites (FGM) and fecal immunoglobulin A (IgA) concentrations. Puppies (n = 138) were tested at 4 (4W) and 8-weeks (8W) old using equivalent measures. Preliminary analyses of the metrics collected during puppy social isolation revealed that locomotion was positively correlated with exploration (4W: rs=0.46, P < 0.001; 8W: rs=0.39, P < 0.001), escape attempt duration (4W: rs=0.26, P = 0.002; 8W: rs=0.31, P < 0.001), frequency of stress behaviors (4W: rs=0.22, P = 0.01; 8W: rs=0.40, P < 0.001), vocalization (4W: rs=0.18, p=0.04; 8W: rs=0.20, P = 0.02), and fecal IgA (4W: rs=0.24, P = 0.05). Stationary behavior was negatively correlated with escape attempt duration (4W: rs=-0.37, P < 0.001; 8W: rs=-0.43, P < 0.001), frequency of stress behaviors (4W: rs=-0.22, P = 0.01; 8W: rs=-0.32, P < 0.001), and physiologic metrics (4W: fecal IgA rs=-0.25, P = 0.04; 8W: FGM rs=-0.23, P = 0.01). Results suggest that, in response to social isolation, 4W and 8W old puppies exhibit one of two coping styles, proactive or passive, and the latter is associated with lower activation of the immune and stress response. The outcomes of this study will inform future research exploring maternal risk factors, including behavioral and physiologic stressors, affecting puppy developmental welfare in CB kennels.
499 Late-Breaking: Impact of a High Calcium Diet in Growing Labrador Retriever Puppies
Authors: Varney Jessica L , Watson Charlene F , Coon Craig N
Published: October 2021

An important function of feeding large breed puppies is providing appropriate amounts of calcium and phosphorus, which is used in skeletal mineralization during growth. National Research Council stated calcium requirements are 0.8–1.2%, and phosphorus 1.0–1.6%. The objective of this study was to compare a high calcium diet (Ca: 5.7%; P: 2.9%) (Nature’s Logic Canine Beef Meal Feast; Nature’s Logic) (HC) to a normal control diet (Ca: 1.6%; P: 1%) (Purina Puppy Chow; Nestle Purina) (CON) in growing Labrador Retriever puppies. Thirty-two puppies (16 HC/16 CON) were used in two 10wk modified AAFCO large breed puppy growth trials. Body weights were measured weekly, feed intake daily, and digestibility, body composition, hematology, chemistry, and bone metabolism biomarkers were measured at 8wks, 13wks, and 18wks of age. All puppies passed all AAFCO large breed puppy growth requirements, including veterinary exams, body weight gain, and bloodwork parameters. Both groups had similar average weight gains from baseline to the end of the trial. No significant differences in bone mineral density were found between HC and CON groups at any timepoint. No significant differences were found between groups after baseline for parathyroid hormone, calcitonin, or tartrate resistant acid phosphatase bone metabolism biomarkers. Total tissue mass, fat mass, and lean mass were lower in the HC group compared to CON group (P < 0.05), likely due to lower caloric content and metabolizable energy in the HC diet than expected. Calcium digestibility was significantly higher in HC diet vs CON diet (P < 0.01). Based on this data, a high calcium diet had no negative impact on major physiological parameters in growing Labrador Retriever puppies.
115 Stability of Thiamine Supplied by Vitamin Premix and Yeast Ingredients in Canned Cat Food
Authors: Dainton Amanda N , Miller Markus F , White Brittany , Lambrakis Leah K , Aldrich Charles G
Published: October 2021

Despite numerous process modifications, thiamine retention of canned cat food has not improved. Yeasts possess a binding protein which may provide a thiamine form able to withstand retort processing. Therefore, the objective was to evaluate dried yeasts as thiamine sources in canned cat food. Treatments were arranged as a 2ｘ4 factorial with 2 levels of vitamin premix (with or without) and 4 sources of yeast (none (NY), LBV, BY, or EA). Inclusion of LBV matched the thiamine contribution from the vitamin premix and BY and EA were capped at 5%. Three replicates were processed in a horizontal still retort to an average total F0 of 79.23 minutes. Thiamine degradation was calculated as the difference between pre- and post-retort thiamine contents. Data were analyzed as a randomized complete block design with pre-retort thiamine content as a covariate and production day as a random effect. The Fisher’s LSD post hoc comparison test was performed with ⍺ = 0.05. On average, experimental formulas retained 33.75% thiamine. Thiamine degradation was not affected by the inclusion of vitamin premix (P = 0.0670), but was affected by the inclusion of yeast (P = 0.0232) and the interaction between vitamin premix and yeast (P = 0.0002). Thiamine loss between NY (-31.3 mg/kg DM) and BY (-33.8 mg/kg DM) were similar (P > 0.05) whereas EA (-40.5 mg/kg DM) and LBV (-55.6 mg/kg DM) lost more (P < 0.05) thiamine than NY. The treatment of EA with vitamin premix (-70.3 mg/kg DM) lost more (P < 0.05) thiamine than no yeast, BY, or EA without vitamin premix (average -17.4 mg/kg DM) and all others (average -57.3 mg/kg DM) were intermediate (P > 0.05). Inclusion of vitamin premix with yeast did not minimize thiamine loss and BY exhibited similar thiamine degradation as intrinsic thiamine in standard ingredients.