bluuebunny/crossref_metadata_2025 huggingface dataset:
29 Effects of Recent and Ancient Inbreeding on Growth in American Angus Cattle
Authors: Lozada-Soto Emmanuel A , Tiezzi Francesco , Lu Duc , Miller Stephen P , Cole John B , Maltecca Christian
Published: October 2021

The accumulation of inbreeding can lead to an unfavorable change in the phenotypic value of individuals for traits related to fitness, also known as inbreeding depression. However, inbreeding accumulated at a more distant past (ancient inbreeding) is expected to have a smaller depressive effect than that accumulated more recently due to the loss of detrimental alleles caused by purifying selection. Therefore, the aim of this study was to quantify the inbreeding depression caused by recent and ancient inbreeding for birth weight, weaning weight, and post-weaning gain. Pedigree and genomic information were obtained from Angus Genetics, Inc. (St. Joseph, MO) for 569,364 individuals from the American Angus breed. Pedigree inbreeding and genomic inbreeding based on runs of homozygosity (ROH) were estimated using the SNP1101 software. Model-based genomic inbreeding based on the probability a marker is part of a homozygous-by-descent segment (HBD) was estimated using the RZooROH in R. The generational cutoffs for designating inbreeding as recent was that acquired 5 generations ago or sooner for pedigree, 6.25 generations ago or sooner for ROH, and 8 generations ago or sooner for HBD inbreeding. The effect of a 1% increase in inbreeding was modeled in males and females using a linear mixed model approach. Recent pedigree inbreeding was found to decrease birth weight by 0.04 and 0.03 kg, decrease weaning weight by 0.50 and 0.48 kg, and decrease post-weaning gain by 0.62 and 0.32 kg, in males and females respectively. Ancient pedigree inbreeding was generally found to have no effect on growth. For genomic inbreeding, when both recent and ancient inbreeding had a detrimental effect on growth, recent inbreeding generally had a larger effect. The results of this study demonstrate that inbreeding accumulated recently should be quantified and managed in beef cattle populations to avoid economic losses.
31 Gametic Incompatibility: Improving the Success of Mate Allocation in Dairy Cattle
Authors: Martin Audrey A A , Id-Lahoucine Samir , Tulpan Dan , Leblanc Stephen J , Cánovas Angela , Baes Christine F , Schenkel Flavio S
Published: October 2021

In the dairy industry, mate allocation is mainly based on the parents’ breeding values and inbreeding coefficients aiming to achieve the producer’s breeding goal. With artificial insemination, the portfolio of sires to choose from is large and the quality of the semen doses is standardized. However, not all sire-dam matings are equally likely to produce a successful pregnancy. Among other reproduction issues, the success of a mating could vary due to the incompatibility of gametes coming from the sire and the dam and could influence the fertilization’s success, additionally to the reproductive capacity of the parents. Considering the gametic incompatibility of the potential parents could be a novel option to improve mating plans. Under the hypothesis that gametic incompatibility has a significant effect on reproduction and reduces the odds of fertilization and pregnancy, this study aimed to determine the genetic background of gametic incompatibility. Transmission ratio distortion (TRD), which detects deviations from Mendelian inheritance expectations, is commonly used to identify deleterious mutations. We adapted the TRD model by including an interaction effect between the gametes leading to the offspring genotype to detect regions with TRD effects and gametic incompatibility. Our dataset contained 436,651 genotyped (50K SNP) Canadian Holstein cattle from 283,817 parents-offspring trios. A total of 482 regions with TRD containing 671 positional genes were found. The functional analysis detected biological pathways associated with uterus development, embryonic skeletal system development, and nervous system development. Additionally, gene ontology terms from the topology-based pathway enrichment analysis were mostly related to the steroid hormones signalling pathway. Although difficult, genes specific to gametic incompatibility could be differentiated from genes underlying other reproduction processes by refining the genetic regions with TRD. With further investigation, we will provide new information to improve mate allocation for the dairy cattle industry.
49 Predicting Breeding Values of Purebred Pigs for Crossbred Performance Using Crossbred Phenotypes and Genotypes
Authors: Leite Natalia , Chen Ching-Yi , Herring Willian O , Tsuruta Shogo , Lourenco Daniela
Published: October 2021

Phenotyping a large number of crossbred progeny for the evaluation of purebred animals can be expensive. As genotyping with low-density panels is becoming cheaper, we aimed to evaluate the tradeoff between having different percentages of genotypes and phenotypes for crossbred progeny of candidate boars. We used the linear regression (LR) method to investigate changes in accuracy, bias, and inflation of breeding values for crossbred traits in purebred boars. A total of 304,582 purebred and 147,474 crossbred animals were phenotyped for average daily gain (ADG) and backfat thickness (BF), out of which 46,691 purebred and 13,117 crossbred animals were genotyped. Genomic information consisted of imputed genotypes for 40,247 SNP markers after quality control. A four-trait animal model under single-step GBLUP was used that included phenotypes recorded in purebred and crossbred animals as correlated traits. The LR statistics were calculated based on breeding values of young purebred sires from complete and partial data. The first complete data included genotypes for purebreds and phenotypes for purebreds and crossbreds, whereas the second included also genotypes for crossbreds. The partial data included phenotypes on 50% or none of the progeny of validation sires, with or without genotypes for crossbred animals. When 50% of the progeny has phenotypes, adding genotypes for crossbred progeny marginally increased accuracy of ADG (0.77 vs 0.78) for 47 boars with more than 150 progeny with phenotypes. No increase was observed for BF. A small increase in bias and inflation by adding crossbred genotypes was observed for ADG but not for BF. When no phenotypes were available for crossbred progeny, accuracy for both traits was lower but improved with crossbred genotypes for ADG (0.61 vs 0.64) for boars with more than 150 progeny. The tradeoff between phenotypes and genotypes should be further investigated in larger datasets with more validation boars.
42 An Improved, High-quality Ovine Reference Genome Assembly
Authors: Davenport Kimberly M , Bickhart Derek M , Worley Kim , Murali Shwetha C , Cockett Noelle , Heaton Michael P , Smith Timothy P L , Murdoch Brenda M , Rosen Benjamin D
Published: October 2021

Sheep are an important agricultural species used for both food and fiber in the United States and globally. A high-quality reference genome enhances the ability to discover genetic and biological mechanisms influencing important traits, such as meat and wool quality. The rapid advances in genome assembly algorithms and emergence of increasingly long sequence read length provide the opportunity for an improved de novo assembly of the sheep reference genome. Tissue was collected postmortem from an adult Rambouillet ewe selected by USDA-ARS for the Ovine Functional Annotation of Animal Genomes project. Short-read (55x coverage), long-read PacBio (75x coverage), and Hi-C data from this ewe were retrieved from public databases. We generated an additional 50x coverage of Oxford Nanopore data and assembled the combined long-read data with canu v1.9. The assembled contigs were polished with Nanopolish v0.12.5 and scaffolded using Hi-C data with Salsa v2.2. Gaps were filled with PBsuite v15.8.24 and polished with Nanopolish v0.12.5 followed by removal of duplicate contigs with PurgeDups v1.0.1. Chromosomes were oriented by identifying centromeres and telomeres with RepeatMasker v4.1.1, indicating a need to reverse the orientation of chromosome 11 relative to Oar_rambouillet_v1.0. Final polishing was performed with two rounds of a pipeline which consisted of freebayes v1.3.1 to call variants, Merfin to validate them, and BCFtools to generate the consensus fasta. The ARS-UI_Ramb_v2.0 assembly has improved continuity (contig N50 of 43.19 Mb) with a 19-fold and 38-fold decrease in the number of scaffolds compared with Oar_rambouillet_v1.0 and Oar_v4.0. ARS-UI_Ramb_v2.0 has greater per-base accuracy and fewer insertions and deletions identified from mapped RNA sequence than previous assemblies. This significantly improved reference assembly, public at NCBI GenBank under accession number GCA_016772045, will optimize the functional annotation of the sheep genome and facilitate improved mapping accuracy of genetic variant and expression data for traits relevant the sheep industry.
47 Genomic Studies of Reproductive Performance in American Mink
Authors: Valipour Shafagh , Karimi Karim , Miar Younes
Published: October 2021

Improving reproductive efficiency is one of the main breeding goals in mink farming. Understanding the genetics of reproductive performance is essential for the development of effective breeding programs in mink. The objectives of this study are to 1) estimate the phenotypic and genetic parameters for litter sizes (LS), mortality rate at birth. (MB) and gestation-length (GL) traits; 2) perform genome-wide association studies (GWAS) for these reproductive traits; 3) implement GWAS results in the selection of mink for reproductive performance; 4) explore the potential for genomic selection in mink. The detailed reproductive performance on 3,500 female mink has been collected at the Canadian Center for Fur Animal Research at Dalhousie University (Truro, NS, Canada), in which, 1,000 of them will be genotyped with Affymetrix 50k SNP panel. A series of univariate and bivariate analyses were implemented in ASREML software to estimate the genetic and phenotypic parameters. Heritability estimates (±SE) were low-to-moderate, ranged from 0.06±0.02 for total number born to 0.23±0.03 for GL. High positive genetic correlations (±SE) were observed between LS traits, ranged from 0.59±0.18 to 0.85±0.11. There was a moderate genetic correlation (±SE) between MB and total number of kits born (0.46±0.15). However, MB had a favorable strong negative genetic correlation (±SE) with the number of weaned kits (–0.75±0.16). These estimated genetic parameters can be incorporated into Canadian mink breeding programs. Considering the low-to-moderate heritability of reproduction traits, the availability of the mink reference genome and genotyping panel will provide opportunities to accelerate mink breeding through genomics. The results of this project will contribute significantly to the current genetic knowledge of reproductive traits and identify the opportunities for genetic improvement through the application of genomics. The overall project aim is to develop a cost-effective, low-density panel of markers for the implementation of genomic selection for reproductive performance in mink.
59 Insights into Complex Traits from Human Genetics
Authors: Kemper Kathryn
Published: October 2021

Genomic selection has been implemented successfully in many livestock industries for genetic improvement. However, genomic selection provides limited insight into the genetic mechanisms underlying variation in complex traits. In contrast, human genetics has a focus on understanding genetic architecture and the origins of quantitative trait variation. This presentation will discuss a number of examples from human genetics which can inform our understanding of the nature of variation in complex traits. So-called ‘monogenic’ conditions, for example, are proving to have more complex genetic architecture than naïve expectations might suggest. Massive data sets of millions of people are also enabling longstanding questions to be addressed. Traits such as height, for example, are affected by a very large but finite number of loci. We can reconcile seemingly disparate heritability estimates from different experimental designs by accounting for assortative mating. The presentation will provide a brief update on current approaches to genomic prediction in human genetics and discuss the implications of these findings for understanding and predicting complex traits in livestock.
58 Integrating Quantitative Genetics and Epidemiology: Why Selection Against Infectious Diseases Is More Promising Than We Think
Authors: Bijma Piter , Bijma Piter
Published: October 2021

Pathogens have profound effects on livestock. The low heritabilities of individual binary disease status suggest limited prospects for genetic improvement. However, a proper quantitative genetic theory for infectious diseases, including transmission dynamics, is currently lacking. Here we present a quantitative genetic theory for endemic infectious diseases, focussing on the genetic factors that determine the prevalence (P; the mean fraction of the population that is infected). We present simple expressions for breeding values and genetic parameters for the prevalence. Without genetic variation in infectiousness, breeding values for prevalence are a factor 1/P greater than the ordinary breeding values for individual binary disease status (0/1). Hence, even though prevalence is the simple average of individual binary disease status, breeding values for prevalence show much greater variation than our ordinary breeding values. This implies that the genetic variance that determines the potential response of prevalence to selection is largely due to indirect genetic effects (IGE), and thus hidden to ordinary genetic analysis and selection. Hence, the genetic variance that determines the potential of livestock populations to respond to selection must be much greater than currently believed, particularly at low prevalence. We evaluated this implication using simulation of endemics following standard methods in epidemiology. Results show that response of prevalence to selection increases very strongly when prevalence decreases, and is much greater than predicted by our ordinary breeding values. These results supports our theoretical findings, and show that selection against infectious diseases is much more promising than currently believed.
57 The Saga of Just One QTL; From Laying Hen Bone Strength to One Carbon Metabolism
Authors: Dunn Ian C , McCormack Heather , de Koning Dirk-Jan , Navarro Alejandro Rodríguez , Schmutz Matthias , Andersson Björn , Cavero David , Fleming Robert , Wilson Peter , Maidin Maisarah
Published: October 2021

Skeletal damage is a challenge for laying hens, as the adaptations for egg laying make them susceptible to osteoporosis. We know that activity, growth and puberty influence skeletal quality genetics. However, in this story, we follow the process of resolving a QTL for skeletal quality to a single gene. Providing both a nutritional and a genetic solution and illustrating another level of complexity. Using divergently selected populations in an F2 cross, a QTL for skeletal quality was described. Utilising a series of experiments in the commercial founder line the QTL was fine mapped on chromosome 1 and the differences in physiology of hens that segregated for markers at the locus defined e.g. tibia breaking strength 200.4 vs 218.1 Newton (p< 0.002). Transcriptome profiling of tibia from the high and low bone strength genotype revealed a highly differentially expressed gene co localising to the QTL, the enzyme cystathionine beta synthase (CBS). CBS is a component of one carbon metabolism. Plasma homocysteine, the substrate of CBS had a higher concentration in the genotype associated with poor bone quality. Homocysteine interferes with crosslinking of the collagen matrix, critical to bone formation. Homocysteine can be re-methylated into methionine, a limiting amino acid in laying hens, using betaine as a methyl donor. Testing the hypothesis that reducing plasma homocysteine by feeding betaine, a widely available feed additive, would improve bone quality in laying hens proved successful.This is just one component of a complex trait and its elucidation took us along unexpected routes. However, I am optimistic that with modern tools and an open mind we can progress more quickly. Alongside understanding the factors that determine skeletal quality genetics, the discovery of the mechanisms behind complex traits, although rarely easy, offer the potential for novel interventions to improve animal health and production.
65 Immunological Changes in Response to Treatment of Bovine Respiratory Disease in Newly Received Commercial Stocker Calves
Authors: Akter Afroza , Shepherd Elizabeth , Caldwell Marc , Pighetti Gina , Schneider Liesel G
Published: October 2021

Immunological changes in stocker calves treated for Bovine Respiratory Disease (BRD) could indicate disease progression or treatment success. Our objective was to determine the changes in immune parameters in stocker calves in response to the number of treatments they received for BRD. Forty newly weaned crossbred beef steers purchased from the auction market were kept at a commercial stocker operation at Crossville during winter 2020. Calves were monitored for 4wks and blood samples were collected on days 0, 7, 14, and 21. All calves were assigned a clinical severity scoring (CSS; 0: normal, 3: moribund) on each sampling day. Antibiotic treatment was assigned when calves were categorized as having BRD based on CSS and rectal temperature. Immune parameters (Haptoglobin, IL-8, IL-1β, and TNFα) were determined using commercial ELISA kits. Calves were categorized based on the cumulative number of treatments received by the end of study period (0x, 1x, and ≥2x). Proc GLIMMIX (SAS 9.4) was used to test the fixed effects of treatment number, day of treatment, and their interaction, accounting for day as a repeated measure. To achieve the normality of residuals, log transformation was performed. Significance was determined at α= 0.05. The incidence of BRD was 40% (16 out of 40). Haptoglobin concentration was higher (P = 0.02) in ≥2x (1.85 ± 0.30 mg/mL) compared to 0x (0.74 ± 0.21 mg/mL). A treatment by day interaction (P = 0.03) was observed for IL-8. On day 14, calves that were treated ≥2x times had higher IL-8 compared to the rest of the statuses; no differences were observed for other days between statuses. The lowest IL-1β (P = 0.04) and TNFα (P = 0.001) concentrations were observed on day 0. Results from this study provide an overview of the immunological changes occurring in BRD-affected stocker calves requiring different treatment numbers.
61 Oral Dosing Loline Alkaloid and Its Effects Against Mixed Infection of L4 Teladorsagia Circumcincta, and Trichostrongylus Colubriformis, and Adult Haemonchus Contortus
Authors: Froehlich Kelly , Greer Andrew
Published: October 2021

Loline, an alkaloid produced by Epichloë endophytes in pastoral grass species, is considered non-toxic with suggested antimicrobial and anthelmintic properties. In vivo metabolism of loline suggests ability to reach the abomasum or intestine, and anthelmintic benefit is indicated in vitro when parasites are in either a developmental stage close to the gastric mucus layers or adult stage consuming blood. Therefore, the objective of this project was to investigate the validation of using a loline seed extract as a natural anthelmintic in parasitized lambs. Sixteen Coopworth lambs were individually penned, offered ad-libitum lucerne pellets and water and randomly assigned to 3 treatment groups; CON; no treatment, or treatment with a Festuca pratensis seed extract with (LOL) or without loline (NIL). Lambs were orally infected with 20,0000 L3 Haemonchus contortus on day 0, and 10,000 L3 Teladorsagia circumcincta, and Trichostrongylus colubriformis on day 14. Parasites then matured to determine lolines efficacy on blood feeding adult Haemonchus contortus and L4 mucosal browsers Teladorsagia circumcincta, and Trichostrongylus colubriformis. Loline was orally dosed at 52.5 mg/kg LW starting on day 13, and every other day until slaughter for worm enumeration on day 28. Feed intake and refusals were recorded daily, and fecal samples were taken prior to infection, on loline dose days and at slaughter. Worm and fecal egg counts were transformed to log10 and all data were analyzed in Genstat (18th edition). Significance was declared at P < 0.05. Worm burdens of T. circumcincta (P = 0.96), T. colubriformis (P = 0.43), and H. contortus (P = 0.15) were not different between treatments. No treatment difference (P = 0.39) was observed in fecal egg counts, weight gain (P = 0.51), or feed intake (P = 0.18). Average growth efficiency (kg LWG/ kg DM intake) was 0.18 in CON which was less (P = 0.01) than LOL (0.24) or NIL (0.23). In conclusion, limited evidence supported an in vivo anti-parasitic effect of loline.
69 Occurrence of Mycotoxins in 2020 US Corn Grain and Corn By-product Feeds
Authors: Gott Paige N , Schwandt Erin , Ramirez Shelby M , Hofstetter Ursula , Murugesan Raj
Published: October 2021

Mycotoxins are fungal metabolites that limit animal health and performance through various negative effects including reduced feed intake, diarrhea, and compromised immune function. These toxic metabolites have been detected in a broad range of feedstuffs worldwide. This study investigated mycotoxin occurrence and contamination levels in U.S. corn grain samples marked as 2020 harvest year and corn by-product feed samples submitted since October 2020. Samples were screened via LC-MS/MS for six major mycotoxin groups including: aflatoxins, type A trichothecenes, type B trichothecenes (B-Trich), fumonisins (FUM), zearalenone (ZEN), and ochratoxin A. Results from samples that were above the limit of detection for each respective mycotoxin group were analyzed using the GLIMMIX procedure (SAS 9.4, Cary, NC) to test the effect of harvest year on mean contamination level. Results are presented in Table 1. Occurrence levels of B-Trich, ZEN, and FUM in 2020 corn grain are numerically lower than those from 2019. Mean B-Trich level (parts per billion, ppb) for corn grain samples harvested in 2020 was similar to 2019 crop year. Contamination levels of FUM and ZEN were similar for 2020 crop as compared to prior harvest years. Mycotoxin occurrence in corn by-product feeds continued to be high at 99, 85, and 95% for B-Trich, ZEN, and FUM, respectively. Mean B-Trich and ZEN levels in 2020 corn by-products were similar to respective contamination levels in 2018, but were lower than 2019 samples. Mean FUM contamination in corn by-products has been similar across reported years. Preliminary results of the 2020 corn grain survey indicate mean mycotoxin contamination levels are similar to those observed the past two crop years while levels of B-Trich and ZEN in corn by-product feeds are reduced from 2019. Corn-based feed ingredients may present challenges to producers due to the presence of mycotoxin contamination, therefore, continued monitoring is warranted.
67 Association of Morbidity and Failure of Transfer of Passive Immunity in Beef-dairy Crossbred Calves
Authors: Pereira Jessica , Marcondes Marcos I , Carvalho Pedro H , Silva Del Rio Noelia , Bittar João , Ferreira Fernanda C
Published: October 2021

The objective of this prospective cohort study was to describe the prevalence of failure of transfer of passive immunity (FTPI) in beef-dairy crossbred calves, and its association with morbidity up to 30 d of life. A total of 393 one d old calves were enrolled upon arrival at a calf facility in Central Valley, California, from Jan-Mar 2021. Farm of origin, breed, sex, and weight were recorded at the day of arrival. Blood was collected at 24 ± 1 h post-arrival to evaluate total serum protein (TSP) and % Brix reading. Calves were classified as having FTPI if TSP < 5.2 g/dL, and brix < 8.2%. Farm personnel performed daily health evaluations and recorded diseases. Descriptive statistics, logistic regression, and survival analysis were conducted using SAS. Calves’ breeds were Angus × Holstein (AN × HO, 58%), Charolais × Jersey (CH × JE, 37%), and Angus × Jersey (AN × JE, 5%). Prevalence of FTPI was 36% (TSP) and 34% (brix). TSP and %Brix readings had a strong correlation (r = 0,99, P < 0.0001). Overall morbidity was 78% (70% had only diarrhea, 7% only respiratory disease and 23% both). The odds of disease up to 30 d was not associated with sex (female vs. male, OR = 0.77, 95% CI = 0.36–1.62), or breed (AN × HO vs. CH × JE, OR = 1.35, CI = 0.63–2.91; AN × JE not included in this analysis). FTPI was associated with greater odds of disease (OR = 2.91, CI = 1.19–7.09, P = 0.01). There was a tendency for association between FTPI and the hazard of disease up to 30 d (HR = 1.43, CI = 0.96–2.10, P = 0.07). Therefore, FTPI may predispose beef-dairy crossbred calves to diarrhea and respiratory disease up to 30 d of life.
73 Antimicrobial Resistance, Agriculture, and the One Health Continuum
Authors: Topp Ed
Published: October 2021

The One Health concept specifies that the microbiomes of humans and animals are connected, both through direct contact, and indirectly through the environment. Managing the flow of microorganisms of human or animal health concern across the One Health continuum requires a transdisciplinary approach to address problems at the intersection of people, animals, and their environments. This presentation will use the management of antimicrobial resistance as an example of how a One Health approach can identify and develop solutions to improve the health and wellness of people, animals, and the environment.
82 Application of Precision Sensor Technologies, Real-time Data Analytics, and Dynamic Models on Extensive Western Rangeland Grazing Systems
Authors: Menendez Hector M , Brennan Jameson
Published: October 2021

Approximately 40% of the land use within the Northern Great Plains is dedicated to livestock production, with much of the 89.9 million head of cattle and calves in the U.S. concentrated in this area. Precision livestock management has ushered in a new era of sensors and technology to monitor individual animal’s health, reproductive, and nutritional status in real-time to improve efficiency. Despite these advances, most of the research has been conducted on dairy operations or within feedlot settings. Incorporation on extensive rangeland production systems remains relatively absent (Brennan et al., 2021). This is primarily due to difficulties in studying animals on rangelands caused by heterogeneity of forage resources, variable environmental conditions, and challenges associated with accessing information across vast distances, often without cellular or internet connection. Advances in communication technology are increasingly connecting remote areas, creating new opportunities to improve livestock production efficiency on extensive rangelands using precision technology. Numerous challenges still exist, including applying and integrating multiple technologies across platforms, effectiveness in a real-world setting, technical skills, and knowledge to utilize real-time data, and achieving economic return for livestock producers. Specifically, we discuss the application of precision technologies and mathematical models for improving ruminant nutrition in rangeland systems (Menendez and Tedeschi, 2020). Opportunities exist to refine or develop the next generation of equations/models that more adequately represent nutrient dynamics such as diet selection, supplementation, movement, behavior, water intake, feed conversion efficiency, heat/cold stress, and gain on an individual animal basis. However, effective adoption and adaptability of new technologies/data analytics merit the consideration of potential intended-and-unintended consequences, such as producer dependency on complex hardware and software systems. Hence, precision capabilities coupled with mathematical models are likely the next step to substantially enhance livestock performance in extensive systems when coupled with feasible and reliable long-term strategies.
94 The Effects of Weather, Body Weight, and Dry Matter Intake on Total Daily Water Intake in Beef Steers
Authors: McDaniel Zach S , Smith Zachary K , Wright Cody , Gonda Michael , Wickremasinghe Himali , Djira Gemechis
Published: October 2021

Weaned angus steers (n = 26; 272.92 + 21.29 kg) were selected to study the effects of weather, predicted daily BW, and DMI on total daily water intake (TDWI) from December 2019 to May 2020 (181 days). Calves were provided with ad libitum access to feed and water, under a monoslope barn, for the duration of the study. In periods of cold stress, cattle were provided with corn stalk bedding within the dry lot, away from the monoslope barn. Measurements of feed and water disappearance were obtained by utilizing an automated feed and water system (Insentec RIC, Hokofarm, Marknesse, Netherlands), where disappearance was assumed to be caused by intake. Calves were weighed every 28 days in order to calculate ADG and therefore predict daily BW for each calf. Daily weather records, including windchill (°C), solar radiation (W/m2), and maximum relative humidity (%), were obtained through the South Dakota Mesonet automated weather station located 3.86 km from where the calves were housed. A linear mixed effects model with both random intercept and slope were used to account for the within subject correlations. Increased TDWI was associated with increased wind chill (0.38-kg per 1°C; P < 0.0001), increased solar radiation (1.04-kg per 1 W/m2; P < 0.0001), and decreased maximum relative humidity (-0.14 kg per 1%; P < 0.0001). For every kg increase in DMI, TDWI increased by 1.07 kg (P < 0.0001). Lastly, for every kg increase in BW, TDWI increased by 0.05 kg (P < 0.0001). Effects of DMI, BW, SRAD, windchill, RHMax were predictive of TDWI in beef calves fed during the winter. This model will be useful for predicting TDWI during the winter months where calves are raised in regions where temperatures are regularly below freezing.
120 Analytical Strategies for Survey Data in Pet Nutrition and Management
Authors: Rodriguez-Zas Sandra L
Published: October 2021

Companion animal researchers have been at the forefront of using survey methodologies to study dogs’ and cats’ dietary and health patterns in the general population. The reporting of survey results has increased in recent years, facilitated by the rise in internet access, the modest cost of conducting web surveys, and the capability to target surveys to pet owners through address lists collected by services and social media. Data from population surveys have the potential to garner unique and comprehensive information that complements the understanding offered by designed experiments. Recent developments in survey methodologies and the availability of user-friendly survey tools enable the collection of large-scale or even Big Data sets, not only in the number of survey responses but also in the number and type of variables measured. Irrespective of the sample size, the study of survey data necessitates the consideration of complex sampling designs and analysis approaches that reflect the nature of this data. An overview of the characteristics of complex sampling designs typical of survey data with applications to companion animal nutrition is presented. The fundamentals of the analytical approaches that are suitable for survey data are demonstrated, and procedures available to accommodate clustering, stratification, underrepresentation, and nonresponse are reviewed. Examples of survey data visualization and analysis strategies are presented.
132 Early Establishment of the Human Gut Microbiome—a Tale of Moms, Their Diets, and Babes Guts
Authors: Aagaard Kjersti M
Published: October 2021

Human microbial communities are characterized by their metagenomic and metabolic diversity, which varies by distinct body sites and influences human physiology. We are only beginning to characterize the complex set of interactions which alters both community membership and function in early development. With respect to the potential source of microbiota at birth, it has been generally assumed that the majority of seeding microbes originate from the maternal lower genital tract, with microbiota ascending into the otherwise sterile intrauterine. However, we and subsequently others have recently demonstrated that (1) the vaginal and gut microbiome communities are distinctly structured in pregnancy, and (2) the intrauterine environment and the fetus is in fact not sterile, but rather harbors a low-abundance microbiome which varies by several measured exposures, and (3) the maternal diet during both gestation and lactation, and notably a high fat diet, has a particularly strong impact on the developing and early in life microbial community structure. We have taken two dynamic approaches to answering these questions in our studies. First, we use large and robust longitudinal cohorts of maternal-infant dyads collected across gestation and into infancy to gain deeper insight into both source and sink of the early developmental microbiome and its role on determining length of gestation. Second, we utilize our well established primate models of maternal high fat dietary exposure, both in the absence and presence of maternal obesity, to determine the impact of maternal diet on both the microbiome and the resultant offspring metabolic phenotype.
153 Differences in Health and Carcass Characteristics of Yearling Steers That Received Free-choice Garlic-infused Mineral Supplements
Authors: Cheang-Deis Iris Ho In , Oyedeji Oluwatobi , Block Hushton , Rochon Kateryn , Asai-Coakwell Mika , Erickson Nathan , Lardner Herbert , Durunna Obioha N
Published: October 2021

Garlic products have been reported to have antimicrobial effects and may trigger anemia in horses, but their direct impact on feedlot cattle has not been detailed. With increased free-choice feeding of garlic-infused mineral supplements to beef cattle, it is important to evaluate this strategy’s impact on the animals’ health and the potential impact on carcass qualities. This 2-yr study recruited 208 crossbred feedlot steers in a supplementation trial using a completely randomized design. Each year, 104 steers were assigned to 1 of 4 groups that received either non-garlic mineral supplement (MS), MS + 0.3% garlic-oil-based premix (GOil), MS + 2.5% garlic powder (LGP), MS + 5% garlic powder (HGP). Feed and supplements were provided on an ad-lib basis and were measured for each steer with automatic feeding units. The study evaluated health indicators such as blood parameters and internal parasites. At harvest, carcass characteristics (including the incidence of liver abscesses) were assessed for all steers. The groups consumed between 156 and 208 g/d of the supplement over the two years, with the MS group having a lower overall supplement intake than other groups. The average daily consumption of garlic products in GOil, LGP, and HGP were approximately 0.6g/d, 5.2g/d, and 10.1g/d, respectively. There was no difference in total fecal egg counts (P = 0.45) among the groups. There was no association between the treatment groups and incidences of liver abscess scores (P = 0.10) nor carcass grade outcomes (P = 0.84). Further, there were no differences in hot carcass weight (P = 0.90), rib eye area (P = 0.34) and carcass backfat thickness (P = 0.99). All blood parameters evaluated were within normal ranges for all groups. The results suggest that infusing commercial garlic products into mineral supplements is not associated with undesirable effects on cattle health or carcass characteristics.
151 Intake, Growth, and Insectifugal Outcomes Associated with Free-choice Supplementation of Garlic Products to Feedlot Steers
Authors: Cheang-Deis Iris Ho In , Lardner Herbert , Rochon Kateryn , Oyedeji Oluwatobi , Block Hushton , Asai-Coakwell Mika , Erickson Nathan , Durunna Obioha N
Published: October 2021

Conflicting anecdotal accounts from producers about their cattle performance and fly-repellence outcomes while receiving garlic-infused supplements have limited feeding decisions. This study evaluated differences in animal performance and insectifugal outcomes among four groups (26 steers per group) over two years (total = 208 steers). The steers either received non-garlic mineral supplement (MS), MS+0.3% garlic oil-based premix (GOil), MS+2.5% garlic powder (LGP), or MS+5% garlic powder (HGP). A completely randomized design was implemented where each steer was assigned to each treatment group while balancing for bodyweight and breed composition. Steers received a feedlot ration and free-choice mineral supplement for 86 and 108 d in the first and second year, respectively. Individual feed and supplement consumption were measured with automatic feeding units. Fly abundance on each animal was determined using digital images collected during weekly fly surveys. The ADG, feed efficiency, ultrasound body composition, and intake-related activities were also evaluated during the study. Data were analyzed using linear- or generalized linear mixed models in SAS. A significant year and Group×year interactions were observed for daily supplement intake (P < 0.02). Similar interactions (P < 0.04) were observed for feeding behaviors associated with supplement intake. Fly abundance during the peak months was below the economic threshold and was not different among the groups (P = 0.25), but the year and Group×year interactions were significant (P < 0.02). There were no differences among the groups for DMI (P = 0.81), ADG (P = 0.54) and gain to feed ratio (P = 0.34). The Group×year interactions were present for the change in ultrasound rib-fat-thickness. The reasons behind the differences in supplement intake are not clear but may be related to the garlic products’ phytochemical profiles. These results suggest that further studies are required to identify the specific bioactive compounds in garlic that affect supplement intake.
147 Use of Productivity Enhancing Technologies in Beef Steers Reduces Greenhouse Gas Emission Intensity
Authors: Fortier Sydney S , McAllister Tim A , Lardner Herbert , Alemu Aklilu , Legesse Getahun , Ominski Kim , McKinnon John J
Published: October 2021

In the last decade, the cattle industry has witnessed increased demand from domestic and international markets for hormone and antibiotic free beef. However, the environmental consequences of switching from conventional production to “natural” beef have not been extensively examined. This study explored greenhouse gas (GHG) emissions estimated using a whole-farm model, Holos (www.agr.gc.ca/holos-ghg) with model inputs from a 2-year replicated study in which calves were managed from weaning to finishing with 6 treatments based on body weight and feeding strategy. Treatments included Heavy (H), which were directly finished, Medium (M), which were backgrounded prior to finishing, and Light (L), which were backgrounded and then grazed during the summer before being placed on a finishing diet. Each treatment was subdivided into two management practices: Conventional (CON) in which productivity enhancing technologies (PETs) were used (ionophores, steroid implants and beta-adrenergic agonists) and Natural (NAT) in which PETs were removed. Emission intensity (kg CO2e kg-1 boneless beef) of HNAT was 17.3 to 20.1% higher than HCON, MNAT was 20.3 to 20.5% higher than MCON and LNAT were 11.5–12.6% higher than LCON treatment. Conventional treatments, using PET’s, reduced GHG emissions, however grazing should be considered for its potential to store and promote carbon sequestration in perennial grasslands.
159 In vitro Characterization of Potential Pig Calcium-sensing Receptor (CaSR) Ligands and Cell Signaling Pathways Related to CaSR Activation by a Dual-luciferase Reporter Assay
Authors: Zhao Xiaoya , Hui Qianru , Azevedo Paula , O Karmin , Yang Chengbo
Published: October 2021

The calcium-sensing receptor (CaSR) is a pivotal regulator of calcium homeostasis. Our previous study has found that pig CaSR (pCaSR) is widely expressed in intestinal segments in weaned piglets. To characterize the activation of pCaSR by potential ligands and related cell signaling pathways, a dual-luciferase reporter assay was employed for the ligands screening and molecular docking was utilized to predict the binding mode of identified ligands. Our results showed that the dual-luciferase reporter assay system was well suited for pCaSR research and its ligand screening. The extracellular calcium activated pCaSR in a concentration-dependent manner with a half-maximal effective concentration (EC50) = 4.74 mM through the Gq/11 signaling pathway, EC50 = 2.85 mM through extracellular signal-regulated kinases 1 and 2 (ERK1/2) activation signaling pathway, and EC50 = 2.26 mM through the Ras homolog family member A (RhoA) activation signaling pathway. Moreover, the activation of pCaSR stimulated by extracellular calcium showed biased agonism through three main signaling pathways: ERK1/2 phosphorylation signaling, Gq/11 signaling, and G12/13 signaling. Both L-Tryptophan and α-casein (90–95) could activate the pCaSR in the presence of extracellular calcium. Furthermore, we characterized the L-tryptophan binding pocket formed by pCaSR residues TRP 70, SER 147, ALA168, SER 169, SER 170, ASP 190, GLU 297, ALA 298, and ILE 416, as well as the α-casein (90–95) binding pocket formed by pCaSR residues PRO188, ASN189, GLU191, HIS192, LYS225, LEU242, ASP480, VAL486, GLY487, VAL513, and TYR514. In conclusion, similar to the human CaSR, the pCaSR also shows biased agonism through three main signaling pathways and both α-casein (90–95) and L-tryptophan are agonists for pCaSR. Furthermore, the binding sites of α-casein (90–95) and L-tryptophan are mainly located within the extracellular domain of pCaSR.
163 DNA Methylation Across Generation in Bovine
Authors: Sirard Marc Andre A
Published: October 2021

Scientists are starting to realize that some effects from the animal environment may affect their progeny’s phenotype. These epidemiological evidences of early life programming are very well described in humans and rodents but less documented in bovines, especially in relation to the peri-conceptual period. In fact, as other species the bovine gametes may carry non-genetic information that will impact the survival, the fitness and the phenotype of the embryo-fetus-offspring. Using a peri-pubertal age model we have compared the semen of bulls that we obtained at different ages just after puberty for whole genome DNA methylation, miRNA content and open DNA access regions to identify mechanistic relation to gene expression and DNA methylation in embryos created with the same bulls compared to themselves and mated by IVF to the same heifer several times. A similar experiment was also done with pre-peri and post puber heifers using the same adult bull for repetitive IVF. The overall results indicate that the same pathways are affected in embryos from immature parents. The targeted processes are overwhelmingly associated with cellular metabolism involving mitochondria function and the mTOR pathways amongst others. A very similar conclusion was also observed with embryos obtained from adult mothers under negative energy balance and the resulting calves obtained by surrogate gestations using blood DNA methylation to assess the intergenerational legacy. These results support a metabolic programming across generation associated with an energy deficient status of the parent.
162 Fetal Programming and Meat Quality
Authors: Duarte Marcio , Gionbelli Mateus P
Published: October 2021

For many years, variation in carcass and meat quality traits was thought to result from actions taken throughout the animals’ life after birth. However, the quantity and quality of meat obtained at slaughter are not always as good as expected. The past decade has increased the number of evidence of the effects of intrauterine development of skeletal muscle on animal performance that affects the carcass and meat quality traits. The so-called “Fetal Programming” concept sheds light on the biology of skeletal muscle development in meat animals, revealing that this development stage appears to be a pivotal moment to invest efforts aiming to improve animal productivity and the quality of meat. Because most, if not all, of the muscle fibers are formed prenatally in livestock species, the impairment of muscle fiber formation at this stage will limit the overall muscle mass deposition throughout postnatal life. Intramuscular adipocytes also start their formation at the fetal stage. As such, since the intramuscular fat depot has a lower deposition rate than other fat depots, enhancement of intramuscular adipogenesis during the fetal stage may increase marbling deposition postnatally. Muscle fibers, adipocytes, and fibroblasts, which contribute to connective tissue formation, are derived from the same pool of mesenchymal stem (MS) cells. Depending on the insult suffered during intrauterine development, their commitment may shift from myogenic towards adipogenic/fibrogenic lineage. So far, most of the evidence in livestock animals has shown that maternal nutrition during gestation is the main factor that influences the mechanisms underlying the commitment of the MS cells. Although the majority of these studies have shown the consequences of maternal nutrition on myogenesis, adipogenesis, and fibrogenesis, the epigenetic markers that cause the programming of MS cells to undergo to one lineage or another needs to be further investigated.
160 Studies of Sperm DNA Methylation Variations and Their Potential Regulations on Production and Reproduction Traits in Cattle and Pigs
Authors: Yu Ying , Chen Siqian , Liu Shuli , Fang Lingzhao , Zhang Shengli
Published: October 2021

Identification of inter-individual variations of sperm DNA methylation is very essential for elucidating phenotypic variation of reproduction and production traits. We had generated 28 sperm whole genome sequencing (WGBS) data from healthy individuals. We detected 46 variably methylated regions (VMRs) significantly (P < 5.77 × 10−5) associated with reproduction traits. These significant VMRs were also co-localized (±10 kb) with genes related to sperm motility and reproduction, including ZFP36L1, CRISP2 and HGF. To further identify epigenomic markers associated with reproduction and production traits, we generated WGBS dada for a specific pair of monozygotic twin artificial insemination Holstein bulls with moderately different sperm qualities (Bull1 > Bull2). We found 528 differentially methylated regions between the twin bulls, which spanned or overlapped with 309 differentially methylated genes (DMG). These DMG were particularly associated with reproduction, embryo development and the nervous system. To further obtain DNA methylation markers involved in the diversity of porcine reproduction and production traits due to long-term artificial selection, we profiled sperm DNA methylation of three commercial pig breeds--Duroc, Landrace and Large White. we found the hypomethylated regions (HMRs) were highly conserved among pig breeds, while 1040–1666 breed-specific HMRs were identified and associated with the QTLs of embryonic developmental and phenotypic changes. By integrating reduced representation bisulfite sequencing public data of pig testis, we further defined 1743 conservative HMRs between sperm and testis, which may play a role in spermatogenesis process. Overall, our studies demonstrated associations of sperm DNA methylation with bovine and porcine production and reproduction traits, highlighting the potential of epigenomic information in genomic improvement programs for livestock. (*: yuying@cau.edu.cn)