bluuebunny/crossref_metadata_2025 huggingface dataset:
14 Genome-wide Association Studies of Disease Resilience Traits from a Natural Polymicrobial Disease Challenge in Pigs
Authors: Cheng Jian , Fernando Rohan , Cheng Hao , Kachman Stephen D , Lim KyuSang , Harding John , Dyck Michael , Fortin Frederic , Plastow Graham , Dekkers Jack C
Published: October 2021

Infectious diseases cause tremendous financial loss in the pork industry, emphasizing the importance of disease resilience, which is the ability of an animal to maintain performance under disease. The objective of this study was to identify quantitative trait loci (QTL) for disease resilience based on both univariate and bivariate genome-wide association studies (GWAS). Data used were late nursery and finisher growth rates and clinical disease phenotypes, including medical treatment and mortality rates, subjective health scores, feed and water intake traits and carcass traits, collected on 50 batches of 60 or 75 crossbred (LRxY) barrows under a polymicrobial natural disease challenge. Multiple QTL were detected for all traits. The major histocompatibility complex (MHC) region (22–25 Mb on chromosome 7) was found to be associated with multiple traits, including late nursery and finisher growth rates, average daily feed intake and intake rate, average daily water dispensed, water intake duration, and number of visits to the drinker. The MHC region explained ~13% of genetic variance for late nursery growth rate. Further fine mapping identified four QTL in the MHC region for late nursery growth rate that spanned the class I, II, and III regions. Gene set enrichment analyses found genomic regions associated with resilience phenotypes to be enriched for previously identified disease susceptibility and immune capacity QTL, for genes that were differentially expressed following bacterial or virus infection and immune response, and for gene ontology terms related to immune and inflammatory response. In conclusion, MHC and other QTL identified play an important role in host response to infectious diseases and can be incorporated in selection to improve disease resilience. Funded by Genome Canada, Genome Alberta, USDA-NIFA, and PigGen Canada.
20 Profiling circRNA and lncRNA Expression in Key Bovine Metabolic Tissues
Authors: Wang Jian , Sun Hui-Zeng , O’Hara Eóin , Chen Hong , Guan Leluo
Published: October 2021

CircRNAs and lncRNAs are non-coding RNAs that regulate many biological processes at the cellular level. However, knowledge of their function and expression patterns in cattle remains scarce. We investigated circRNA and lncRNA expression profiles in four key metabolic tissues of beef cattle (rumen, liver, muscle, and subcutaneous adipose) using RNA-Seq. Bioinformatic analysis of 189 samples collected from 48 cattle identified 19,766 circRNAs and 10,615 lncRNAs across all four tissues. PCA revealed the expression profiles of both circ- and lncRNA were clearly separated by tissue, suggesting their expression patterns are tissue dependent. Moreover, both datasets contained large numbers of transcripts that were unique to each tissue, underlining the divergence in function across metabolic sites. Further functional analysis of tissue specific circRNAs using the Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that lysine degradation, peroxisome, insulin resistance, and ubiquitin-mediated proteolysis unique to the rumen, liver, muscle, and adipose tissues, respectively. The same analysis of the lncRNAs revealed that purine metabolism, fatty acid degradation, cAMP signaling pathway, and AGE-RAGE signaling pathway in diabetic complications were uniquely enriched in the rumen, liver, muscle, and subcutaneous adipose tissues, respectively. Together, these results revealed tissue specific metabolic pathways that may be regulated by the multiple non-coding RNAs. More specifically, circDLG1 and lncMSTRG.12092.8 were predicted to regulate the expression of Lymphocyte Antigen 6 Family Member G5B (LY6G5B) and pyruvate kinase M1/2 (PKM), Adenylate Kinase 1 (AK1), and Mitofusin 2 (MFN2), respectively, indicating regulatory roles in host immune response, glycolysis, energy balance control, and mitochondrial fusion, all of which may contribute to regulation of energy metabolism. Our findings show that expression profiles of circRNAs and lncRNAs differ among metabolic tissues, and these transcripts may play crucial roles in regulating metabolism in cattle.
26 Are Subjectively Scored Linear Type Traits Suitable Predictors of Genetic Merit for Feed Intake in Grazing Holstein-friesian Dairy Cows?
Authors: Williams Maeve , Murphy Craig P , Sleator Roy D , Ring Siobhan C , Berry Donagh P
Published: October 2021

Measuring dry matter intake (DMI) in grazing dairy cows using currently available techniques is invasive, time consuming, and expensive. An alternative to directly measuring DMI for use in genetic evaluations is to identify a set of readily available data sources that can be used in a multi-trait genetic evaluation with DMI. The objectives of the present study were to estimate the genetic correlations between readily available body-related linear type trait information and DMI in grazing, lactating Irish dairy cows and to estimate the partial genetic correlations between linear traits and DMI, after adjusting for differences in genetic merit for body weight. After edits, a total of 8,055 test-day records of DMI, body weight, and milk yield from 1,331 multiparous dairy cows were available, as were chest width, body depth, and stature scores for 47,141 first lactation dairy cows. In addition to considering the routinely recorded linear type traits individually, novel traits were defined as the product of two or three linear type traits as an approximation of rumen volume. The genetic variance of DMI, body weight, milk yield, and linear type traits were estimated using univariate animal linear mixed models. Sire linear mixed models were used to calculate genetic and phenotypic covariances. All linear type traits were moderately heritable (0.27 to 0.49) and genetically correlated (0.29 to 0.63) with DMI. The genetic correlations between the individual linear type traits and DMI, when the latter was adjusted for differences in the genetic merit for body weight, varied from 0.00 to 0.39. If the (partial) genetic correlations were validated with genetic evaluations, routinely available linear type trait records and live weight data could facilitate the selection of DMI in dairy cows, removing the need to capture large amounts of cost prohibitive feed intake phenotypes.
36 Effect of Blending and Tuning Relationship Matrices in Single-step Genomic BLUP
Authors: McWhorter Taylor M , Garcia Andre , Bermann Matias , Legarra Andres , Aguilar Ignacio , Misztal Ignacy , Lourenco Daniela
Published: October 2021

Single-step GBLUP (ssGBLUP) relies on the combination of genomic (G) and pedigree relationships for all (A) and genotyped animals (A22). The procedure implemented in the BLUPF90 software suite first involves combining a small percentage of A22 into G (blending) to avoid singularity problems, then an adjustment to account for the fact the genetic base in G and A22 is different (tuning). However, blending before tuning may not reflect the actual difference between pedigree and genomic base because the blended matrix already contains a portion of A22. The objective of this study was to evaluate the impact of tuning before blending on predictivity, bias, and inflation of GEBV, indirect predictions (IP), and SNP effects from ssGBLUP using American Angus and US Holstein data. We used four different scenarios to obtain genomic predictions: BlendFirst_TunedG2, TuneFirst_TunedG2, BlendFirst_TunedG4, and TuneFirst_TunedG4. TunedG2 adjusts mean diagonals and off-diagonals of G to be similar to the ones in A22, whereas TunedG4 adjusts based on the fixation index. Over 6 million growth records were available for Angus and 5.9 million udder depth records for Holsteins. Genomic information was available on 51,478 Angus and 105,116 Holstein animals. Predictivity and reliability were obtained for 19,056 and 1,711 validation Angus and Holsteins, respectively. We observed the same predictivity and reliability for GEBV or IP in all four scenarios, ranging from 0.47 to 0.60 for Angus and was 0.67 for Holsteins. Slightly less bias was observed when tuning was done before blending. Correlation of SNP effects between scenarios was > 0.99. Refined tuning before blending had no impact on GEBV and marginally reduced the bias. This option will be implemented in the BLUPF90 software suite.
40 Factors Influencing Accuracy of Genomic Selection with Sequence Information
Authors: Misztal Ignacy , Pocrnic Ivan , Lourenco Daniela
Published: October 2021

Incorporating the sequence information only marginally increases the accuracy of genomic selection. The purpose of this study was to find out why by examining profiles of Quantitative Trait Nucleotides (QTN). Multiple populations were simulated with different effective population sizes and number of animals. 100 equidistant QTN with identical substitution effects were included in 50k SNP genotypes. Analyses were by single-step GBLUP, with solutions converted to SNP values and subsequently to p-values for each SNP. Manhattan plots for standardized SNP solutions were noisy and were elevated only for few QTNs. Manhattan plots for p-values were similar to those for SNP solutions, indicating little impact of population structure. The number of significant QTN was lower with lower effective population size and increased with larger data; at most about 20% of QTNs were detected. A QTN profile was created by averaging SNP solutions ±100 SNP around each QTN. The profile showed a normal-like response but with a distinct peak for the QTN. While the peak was higher with more data and higher effective population size, the normal-like response was smaller with higher effective population size. QTNs explained little variance because of shrinkage. The accuracy of genomic selection would be 100% if all QTNs are identified and their variances known, to prevent shrinking or inflation. This study allows to see limits of application of QTN from sequence data for genomic selection. If all causative SNP are included in the data, only a fraction of them can be identified even under a very simplistic architecture. As variance of QTN are assumed constant or are crude approximations (like in BayesR), the estimated QTN effects are inaccurate. Additional complications in QTN detection are close-spaced QTN and false QTNs due to imputation. Small effective population size allows the genomic selection by GBLUP but complicates the use of QTNs.
41 Using Sequence Data to Increase Accuracy of Genomic Predictions in Livestock: Are We There Yet?
Authors: Lourenco Daniela , Tsuruta Shogo , Jang Sungbong , Fragomeni Breno O , Misztal Ignacy
Published: October 2021

As sequence data is becoming available for many livestock species, there is a question on whether this information can help to boost the accuracy of genomic predictions beyond what has already been achieved with SNP chips. Several studies have been conducted by our group using simulated and real livestock populations that included from 1,000 to 100,000 animals with full or imputed sequence information. For the real datasets, the potential causative variants were identified based on genome-wide association (GWA) and were added to the current SNP chips. Additional scenarios included the use of only causative variants and the use of all sequence SNP. Genomic predictions were obtained based on single-step GBLUP (ssGBLUP), and in some cases, Bayesian regressions. Overall, in real datasets, we observed no significant increase in accuracy by using all sequence SNP, causative variants alone, or combined with SNP currently used for genomic prediction. However, an increase in accuracy of almost 100% was observed in simulated datasets when the causative variants were added to a 60k SNP panel and their simulated variances were accounted for by the prediction model. Our results show that if true causative variants are identified, together with their position and the variance explained, a boost in accuracy can be observed. This raises a question on the effectiveness of the methods and size of the datasets used to select causative variants in real livestock populations. We observed distinct GWA methods work differently depending on the data structure, and the number of genotyped animals with phenotypes. The combination of large-scale sequence and other layers of omics data (e.g., functional data) can help to identify some of the true causative variants. This could possibly promote an increase in the accuracy of genomic predictions in real populations.
529 Late-Breaking: Effects of in Ovo Injection of High Yield Broilers with Nicotinamide Riboside on Pectoralis Major Morphometrics, Muscle Fiber Density, and mRNA Expression
Authors: Xu Xiaoxing , Alcocer Hanna M , Gravely Morgan E , Turner Kari K , Gonzalez John M
Published: October 2021

The objective of this study was to determine the effects of in ovo injection of high yield broilers with nicotinamide riboside (NR) on broiler pectoralis major muscle (PMM) development, growth, and mRNA expression. Fertilized Cobb 700 broiler eggs were randomly assigned to 1 of 4 treatments within a 2×2 factorial design with NR dose (DOS; 0 or 2.5 mM) and injection location (LOC; albumen or yolk) as main effects. Eggs were injected with their assigned treatment at d 10 of incubation. Day-15 and -18 embryos and hatched chicks were euthanized, right PMM and muscle fiber morphometric measurements were collected, and left PMM were utilized for mRNA expression analysis of sirtuin-1 and cyclin D1, 2 and 3. There were no LOC×DOS interactions or main effects for d-15 and -18 PMM measurements (P > 0.23). There were LOC×DOS interactions for hatched chick PMM weight and length, and muscle fiber density (P < 0.04). When NR was injected into the albumen, PMM weight decreased (P = 0.02) and length and fiber density were unaffected (P > 0.33), while PMM weight and fiber density increased when NR was injected into the yolk (P < 0.05). There were no LOC×DOS interactions for all genes analyzed for d-15 and 18-embryos (P > 0.23), but NR embryos had greater expression of all genes (P < 0.03) except d-18 cyclin-D2 (P = 0.08). There were LOC×DOS interactions for hatched chick expression of all genes (P < 0.04). There was no difference in sirturin-1 expression when chicks were injected with 0 mM NR, but 2.5-mM yolk chicks had greater expression than 2.5-mM albumen chicks. When NR was injected into the albumen, expression of all cyclins was unaffected (P > 0.08), while expression increased when NR was injected into the yolk (P < 0.01). Increased expression of sirturin-1 and the cyclins may be responsible for NR catalyzed increase in PMM weight and fiber density.
44 Accuracy of Genomic Predictions over Time in Broilers
Authors: Hidalgo Jorge , Lourenco Daniela , Tsuruta Shogo , Masuda Yutaka , Breen Vivian , Hawken Rachel , Bermann Matias , Misztal Ignacy
Published: October 2021

The objectives of this research were to investigate trends for accuracy of genomic predictions over time in a broiler population accumulating data, and to test if data from distant generations are useful in maintaining the accuracy of genomic predictions in selection candidates. The data contained 820k phenotypes for a growth trait (GROW), 200k for two feed efficiency traits (FE1 and FE2), and 42k for a dissection trait (DT). The pedigree included 1.2M animals across 7 years, over 100k from the last 4 years were genotyped. Accuracy was calculated by the linear regression method. Before genotypes became available for training populations, accuracy was nearly stable despite the accumulation of phenotypes and pedigrees. When the first year of genomic data was included in the training population, accuracy increased 56, 77, 39, and 111% for GROW, FE1, FE2, and DT, respectively. With genomic information, the accuracies increased every year except the last one, when they declined for GROW and FE2. The decay of accuracy over time was evaluated in progeny, grand-progeny, and great-grand-progeny of training populations. Without genotypes, the average decline in accuracy across traits was 41% from progeny to grand-progeny, and 19% from grand-progeny to great-grand-progeny. Whit genotypes, the average decline across traits was 14% from progeny to grand-progeny, and 2% from grand-progeny to great-grand-progeny. The accuracies in the last 3 generations were the same when the training population included 5 or 2 years of data, and a marginal decrease was observed when the training population included only 1 year of data. Training sets including genomic information provided an increased accuracy and persistence of genomic predictions compared to training sets without genomic data. The two most recent years of data were enough to maintain the accuracy of predictions in selection candidates.
50 Using GPS and Genomic Technology to Provide a More Accurate Estimate of Bull Power in Western Intermountain Beef Systems
Authors: Garcia Matthew D , Chapman Kim , Heaton Kevin , Dallin Josh , Rood Kerry , Thacker Eric , Hadfield Jacob , Larsen Ryan
Published: October 2021

The objective of this study was to utilize GPS technology and genomic parentage testing to provide a more accurate measurement of bull power in the intermountain west beef production system. Breeding seasons are typically conducted on large, remote pastures, leading to current estimates of bull:cow ratios (1:20 or 1:25) possibly being inaccurate. With advances in genetic testing, parentage of calves can be obtained allowing producers to review which calves were sired from specific bulls, or how many cows each bull serviced (bull power). Our study fit 5 bulls from the same herd with GPS collars and collected hair samples for future DNA extraction prior to the 2018 breeding season. Bull movement was tracked over a 90-day breeding season on a large grazing allotment on the southern Utah and northern Arizona border. The GPS collars collected measurements of total distance traveled per day and distance traveled away from water, along with geocoordinates. Upon completion of the breeding season, collars were removed and data retrieved. At calving, biological material was collected and parentage testing of 104 calves was conducted and parentage determined. Results of parentage testing revealed that actually 6 bulls sired calves during the 2018 breeding season. The ranch’s bulls sired 72 (69%) calves (30, 16, 14, 10 and 2 calves, respectively). Thirty-two (31%) calves were sired by bulls from herds that grazed nearby. Interesting to note is the producer was unaware of any non-herd bulls co-mingling with this herd. While results from the current study are very preliminary, they do validate the importance of verifying bull power and sire identification to critically evaluate sire performance and increase the accuracy of selection in breeding replacements. The information presented herein may prove useful as a future selection tool to identify bulls that are high performing during breeding season in the intermountain west.
54 Genetics Reloaded: Large-scale Collection of Novel Phenotypes in Turkey
Authors: Baes Christine F , van Staaveren Nienke , Makanjuola Bayode , Leishman Emily M , Abdalla Emhimad , Vanderhout Ryley J , Barbut Shai , Harlander Alexandra , Wood Ben
Published: October 2021

Effective application of genomic selection methodologies require genomic information, population-based pedigree data, and high-quality phenotypes. The implementation of such selection programs can increase the accuracy of breeding values, therefore improving the ability to estimate the genetic merit of livestock. In particular, traits with low heritability are amenable to genomic selection. The objective of this presentation is to outline improvement of traits such as livability, disease resistance, fertility, and other health and welfare traits in turkeys, which could considerably advance breeding programs. The aim of this study was to apply different methodologies (ssGBLUP, random regression approaches, etc.) to novel and conventional traits collected in commercial turkey lines (15,000 turkeys genotyped at 65K). This reference population was used to assess the increase in accuracy of selection using genomic information, which ranged from 0 to +0.3, depending on the trait. A further goal of the study was to monitor inbreeding within the different lines. A large number of high-quality phenotypes related to fertility, growth, production, and carcass composition were collected, as well as additional health and behaviour phenotypes related to livability. These traits are being developed for use in performance testing. Furthermore, meat quality (e.g. white striation, water holding capacity, pH, sheer force and colour, etc.) and total carcass composition phenotypes were analysed. With improved methodology, more detailed phenotypic information, and comprehensive data collection and integration, we present more accurate selection of parent stock for application in applied poultry breeding programs.
64 Feeding Chicory-plantain Silage and Se-yeast on Lactating Ewe Subjected to Intramammary Infection: Effect on Performance and Milk Quality
Authors: Ford Hunter , Bionaz Massimo , Ates Serkan , Klopfenstein Joe , Vanegas Jorge , Hernandez Gracia Puerto , Stowell Callan , Tafoya Paige , McCann Michele , Bozkus Mustafa
Published: October 2021

Our objective was to test the effect on milk yield and quality of feeding a combination of chicory-plantain and Se-yeast in lactating ewes subjected to intramammary infection (IMI). For this purpose, we enrolled 28 Polypay ewes from a prior study where they received chicory (CS) or grass (GC) silage and supplemented with 3.6 mg of Se/day as Se-yeast (DiaMune, Diamond V) (Y) or not (C) for 2 months. For the present study, ewes were kept on the original dietary regiment except the CS group received a chicory-plantain silage (50% each). Ewes were milked twice daily and milk was collected for analysis of components and somatic cell count (SCC). IMI was induced by injecting 2×107 CFU of Strep. uberis in both glands. Data were analyzed using GLIMMIX (SAS) with time, silage, and Se and their interactions as the fixed effects and ewe as random effect with significance declared P ≤ 0.05. SCC increased 8-fold 24h post-IMI and remained at that level until the end of the experiment with higher values pre-IMI in GC-Y animals but no difference post-IMI. Milk yield drastically decreased post-IMI but was not affected by treatments. Protein, fat, solids, amount of de novo fatty acids, and amount of C16:0 were larger in milk of ewes fed chicory-plantain compared to grass silage. Supplementation of Se had minor effect on milk components with a tendency (P = 0.07) to decrease fat, solids, and amount of de novo fatty acids. Amounts of C18:0, C18:1, and preformed fatty acids in milk were increased by Se supplementation in ewes fed grass while decreased in ewes fed chicory. The use of Strep. uberis was effective in inducing IMI in ewes with chicory-plantain improving several milk components while Se supplementation had minor effects. The combination of chicory and Se did not improve the response to IMI.
68 Effects of Intranasal or Parenteral Respiratory Vaccination Administered on Arrival or Delayed in Auction-derived Feedlot Heifers
Authors: McAllister Hudson , Halsted Sherri , Parks Tim , Streeter Marshall N , Hutcheson John P , Richeson John
Published: October 2021

Modified-live virus (MLV) vaccines are used routinely to immunize cattle against bovine respiratory disease (BRD) agents, but differences in the route and timing of MLV administration may exist. The objective was to evaluate the safety and efficacy of a parenteral or intranasal MLV administered on d 0 or 28. Three truckload blocks of heifers (initial BW=208 kg; n = 600) were randomly assigned to treatments in a 2×2 factorial. The generalized complete block design consisted of 15 pens/treatment with pen as the experimental unit and 10 animals/pen. Treatments were: 1) Nasalgen 3/Vista BVD CFP on d 0 (NAS0); 2) Vista 5 SQ on d 0 (VIS0); 3) Nasalgen 3/Vista BVD CFP on d 28 (NAS28); 4) Vista 5 SQ on d 28 (VIS28). Performance, activity, and health data were analyzed in a mixed model and a subset of 3 cattle/pen were selected for antibody titer analyses with repeated measures. Body weight and blood samples were collected on d 0, 28, and 56. No differences existed for performance outcomes (P ≥ 0.19). Activity (351.4 vs. 354.3 min/d) and rumination (282.6 vs. 285.4 min/d) time was less (P < 0.01) for delayed vs. arrival vaccinated heifers. A timing × vaccine × day interaction existed (P < 0.01) for IBRV-specific antibody titers such that VIS0 was greatest, NAS0 was intermediate, and VIS28 and NAS28 were least on d 28 (P < 0.01). Percentage of chronically ill cattle was reduced for arrival vs. delayed (1.3 vs. 4.7%; P = 0.02) and tended (P = 0.06) to be less for VIS vs. NAS (1.7 vs. 4.3%). Arrival vaccinated heifers had a reduction in antimicrobial treatment cost (4.63 vs. $7.31; P = 0.02). These data indicate improvement in some health outcomes for the parenteral route and arrival timing of MLV respiratory vaccination but performance was not affected.
84 The Adoption of AI in the Core Scientific Cycle of Feed Research
Authors: Jacobs Marc
Published: October 2021

The Gartner Hype Cycle methodology highlights five self-explanatory steps through which a technological innovation needs to go: (1) innovation trigger, (2) peak of inflated expectations, (3) trough of disillusionment, (4) slope of enlightenment, and (5) plateau of productivity. It is between step 4 and 5 that any tech innovation really starts to commercially pay off. For Artificial Intelligence (AI), the possibilities and challenges are so diverse that several separate cycles now exist for distinct parts of AI development. For the Animal Sciences / Feed industry the application of AI is not straightforward. In fact, in most industries, application is not straightforward because applications equals implementation. Hence, being able to translate the pains and gains of your customer into the models that you create, and finding a way to implement it, is key and that is more than just applying AI. The majority of (animal) models in the feed industry are mechanistic by nature. Parameters are generated/updated via controlled experiments, and stochasticity is allowed via Monte Carlo simulations and scenario analyses. The validity of the model is its ability to provide usable growth/health predictions, enable least cost formulation, and provide a sustainability footprint. To further support such models, and to offer new services, we have recently begun to combine our near-infrared spectroscopy(NIR), laboratory information management system (LIMS) and mycotoxin databases with climate and geographic data to (1) predict the nutrient composition of raw materials over time, (2) enable risk assessment of mycotoxin co-contamination, (3) improve the feed evaluation of silages, (4) estimate a full nutrient profile, and (5) improve the precision of net energy estimation. In the end, if nurtured carefully, AI is just another technical leap that needs to be integrated into the core scientific cycle.
79 Statistical Graphics and Interactive Visualization in Animal Science
Authors: Morota Gota
Published: October 2021

Statistical graphics has advanced significantly in recent years with the development of statistical computing tools that allow us to create reports dynamically, facilitate reproducible research, and explore data interactively. In particular, data visualization is a fundamental aspect of big data analysis in animal science. However, the static nature of standard visualization limits the information that can be displayed and extracted. The objectives of this hands-on workshop are to learn how to utilize interactive visualization and investigate both global and local structures of graphs with useful zooming in and zooming out capabilities. We will use the Shiny R package, which is a web application framework for R. A Shiny application has great potential to deliver interactive data analysis and visualization in a web browser. Yet there is limited application of this type of tool in agricultural science. We will learn the capabilities of R Shiny and its use with example applications in animal science and how to aid scientific discoveries and decision-making processes using interactive data exploration tools. After taking this workshop, the participants will be able to understand the concept of R Shiny and develop a web-based interactive visualization tool. The interactive and integrative data visualization features embedded in Shiny applications offer a new resource for users to readily extract extensive information from complex data.
87 Beef Heifers Housed in Muddy Environmental Conditions Lose Body Weight and Body Condition but Meet Gestational Requirements for Fetal Growth
Authors: Nickles Kirsten , Relling Alejandro E , Garcia-Guerra Alvaro , Fluharty Francis L , Parker Anthony J
Published: October 2021

Beef heifers experience an exponential increase in energy requirements during late gestation. Heifers must simultaneously grow a fetus, reach mature body weight, and prepare for their first lactation. In spring calving herds, these energy demands coincide with environmental stressors. Future climate projections for the Midwest predict increased winter rainfall, creating muddy conditions. It is likely that muddy conditions increase heifer energy requirements. The increased energy requirements, if not met, may compromise growth of the heifer and fetus. The objectives of this experiment were to evaluate the effects of muddy conditions on heifer body weight (BW), body condition score (BCS), and calf birth weight. Eighteen Angus heifers (n = 9/treatment) were paired based on initial BW. One heifer from each pair was assigned to either the mud (MUD) or control (CON) treatment. Heifers in the CON treatment were housed in pens with sawdust, and heifers in the MUD treatment were housed in pens with mud (20.3 ± 7.6 cm). Heifers were housed individually, and each pair received the same dietary allowance based on the CON heifer’s BW for maintenance, growth, and gestation. From day 196 to 266 of gestation, heifers were weighed and assigned a BCS weekly. Data were analyzed as a randomized complete block design with repeated measurements (SAS 9.4). On day 196 of gestation, heifers were similar in BW and BCS (P > 0.05). By day 266, MUD heifers weighed 43.5 kg less than CON heifers (P < 0.01) and were assigned a BCS of 4.3 compared with CON heifers that were a BCS of 6.1 (P < 0.01). Calf birth weight was not different (P = 0.21). Heifers in both treatments were able to maintain fetal growth, however, MUD heifers did not meet their energy requirements and had decreased BW and BCS compared with the CON heifers.
86 Anthelmintic Resistance in Angus Bulls Participating in Regional Performance Tests
Authors: Rohrbaugh Roger T , Greiner Scott P , Bowdridge Scott A
Published: October 2021

Resistance to anthelmintics, more commonly referred to as “de-wormers,” has been on the rise in parasites that affect cattle. Parasite infection can have severe impacts on calf productivity resulting in reduced profitability. Therefore, we sought to better understand anthelmintic resistance in Appalachia by surveying Angus bulls entering performance tests in VA and WV. During a four-year period, over 1050 Angus bulls were tested at bull development facilities in Wardensville, WV, Culpeper, VA, and Wytheville, VA. Fecal samples were collected at arrival and 14 days later for determination of fecal egg count (FEC) reduction. Upon arrival, all bulls received either fenbendazole (Wardensville, WV) or moxidectin (both VA tests). In Wardensville, treatment with albendazole had a 96.7% FEC reduction, whereas, treatment with moxidectin at Culpeper and Wytheville stations resulted in FEC reduction of 29% and 34.9%, respectively. Gain during these 14 days was significantly lower for bulls from Wytheville (0.87 kg/d) than those of Culpeper and Wardensville (1.87 and 2.1 kg/d; respectively). These data can be partially explained by higher bull FEC after treatment in Wytheville (101 eggs/g) compared to bulls in Wardensville and Culpeper (3.4 and 46.4 eggs/g respectively). Additionally, there was a negative correlation between delivery FEC and average daily gain. Taken together these data demonstrate resistance to moxidectin in bulls from the Appalachian region, and that elevated parasite infection may have contributed to reduced gain during the transition period.
104 Epigenetic Changes Due to Environmental Toxicants: An Animal Health Concern
Authors: Rosenfeld Cheryl S
Published: October 2021

Endocrine disrupting chemicals (EDCs) mimic natural hormones in the body, but they are not subject to normal homeostatic regulatory mechanisms. One such EDC that is particularly important in animal and human health is bisphenol A (BPA) that is an industrial chemical used to harden plastic, and thus, it is prevalent in many common household items. Notably, BPA, and likely other EDCs, persist in the environment. Besides binding to steroid and non-steroid receptors, BPA and other EDCs may induce epigenetic changes directly or by affecting gut bacteria that can promote such host changes. The objective of current studies was to determine whether developmental exposure to BPA and/or genistein, a phytoestrogen, induce persistent epigenetic and transcriptomic changes in various brain regions and the placenta. Additionally, the ability of these chemicals to alter gut microbiota and gut metabolites that may trigger such epigenetic alterations were investigated. Animal models used to examine for such effects included California mice (Peromyscus californicus), deer mice (Peromyscus maniculatus), laboratory mice (Mus musculus), and eastern painted turtles (Chrysemys picta). To link these ‘omics changes to actual phenotypic modifications, several behavioral domains were assessed in these species following developmental exposure to these compounds. Results across taxa clearly show that BPA and genistein leads to behavioral deficits, including cognitive and social impairments, anxiogenic behaviors, and reduced voluntary physical activity. Correspondingly, both chemicals transformed the epigenome and transcriptome in key brain regions and the placenta. Gut dysbiosis and stimulation of harmful bacterial metabolites ensued following early EDC exposure, and such effects persisted through adulthood. By using a one health medicine approached that evaluated various vertebrate animal species, there is solid evidence that perinatal exposure to BPA and genistein reprograms the epigenome and thereby lead to longstanding health consequences. Such findings have important veterinary and human health ramifications.
119 Awardee Talk: A Matter of the Heart: The Use of Pulses in Canine and Feline Nutrition
Authors: de Godoy Maria R
Published: October 2021

In the pet food industry, the popularity of plant-based protein sources has risen as consumer demand for grain-free and novel protein sources increase. However, minimal research has been conducted as regards use of pulses and their effects on acceptability and digestibility in canine and feline nutrition. In addition, market shift towards grain-free and pulse-rich diets has presented concerns about the suitability of pulses as viable protein sources. In July 2018, the FDA published a press release discussing a potential link between diets containing legumes and the development of dilated cardiomyopathy (DCM) in dogs. As such, part of our research program has focused on the 1) characterization of the macronutrient composition and protein quality of plant-based protein sources, 2) evaluation of the effects of plant-based protein sources in extruded canine and feline diets on macronutrient digestibility, and modulation of fecal microbiota and metabolites, and 3) determination of the longitudinal effects of high pulse inclusion in diets on taurine status in dogs. Pulse ingredients contained approximately 20% crude protein, and had methionine or tryptophan as the first-limiting amino acids using the precision-fed cecectomized rooster assay. When incorporated in canine and feline diets, pulses did not result in negative effects on macronutrient digestibility or fecal scores. However, shifts in fecal microbial and metabolites were observed in animals fed pulse-based in contrast with animal-based protein diets. The inclusion of 45% green lentils in extruded diets did not cause decreased plasma or whole blood taurine or methionine levels. Additionally, excess taurine was not depleted from these animals in the urine or feces. Taurine status was considered normal in these dogs, despite changes in fecal bile acid concentrations and microbiota. Although we are currently carrying out further research projects investigating potential association of pulse rich diets and canine DCM. Current research findings from our laboratory suggest the inclusion of pulses may not be the causative factor. The use of plant-based proteins as ingredients in canine and feline diets not only meet consumer demand but also provide a valuable, safe, and nutritionally adequate alternative to traditional protein sources.
145 Conservation Grazing by Goats in Eastern Oak-hickory Forest: Browsing Behavior and Forage Selectivity
Authors: Novais Wanderson , Wenner Benjamin , Block Jeremy , Simon Power , Elizabeth Porteus , Davies G Matt
Published: October 2021

Oak-hickory (Quercus spp. and Carya spp.) recruitment and regeneration are negatively impacted by non-natives species. Goats can provide an initial control of non-native vegetation; however, browsing behavior and preference should be studied before their introduction in the forest. Our objective was to analyze goats’ browsing behavior and preference in an eastern oak-hickory forest. We hypothesized that browsing behavior and preference are dependent on browse biomass composition and grazing duration. This study was conducted in Coshocton, Ohio, and contained two units with nine experimental plots each. Vegetation was surveyed during the summer of 2019 for biomass composition. Cluster analyses were performed using species identity and biomass. Vegetation nutritional analysis including fiber, protein, and sugar was completed. Two stocking rate densities were implemented: high (1,019 goat×day×ha-1) and low (509×goat×day×ha-1). Goats browsed for four or two days for a total of 36 days. Continuous observation was implemented to determine browsing behavior. Forage selectivity was measured using Jacob’s Selectivity Index (JSI). A linear mixed model was calculated using clusters, species, and/or grazing duration (fixed effect), experimental plots (random effect), and JSI (dependent variable). Spicebush (Lindera benzoin), multiflora rose (Rosa multiflora Thunb.), privet (Ligustrum spp.), and oriental bittersweet (Celastrus orbiculatus Thunb.) composed more than 70% of goats’ diet. Species identity, including nutritional components and physical defense mechanisms, was the most important factor in browsing selectivity. Goats preferred spicebush and privet and avoided multiflora irrespective clusters (P 0.001). In the first two days of browsing, goats favored spicebush and privet, avoided multiflora, and had a neutral preference for bittersweet (P-value 0.001). In the last two days, privet was selected and other species had a neutral selection (P 0.001). Goats will target spicebush and privet and avoid multiflora; therefore, an extended browsing period is recommended. Future studies should evaluate the effect of chemical defense mechanisms on browsing.
155 Low Insulin Sensitivity Is Associated with Increased Body Fat and Changes in Gene Expression of Lipogenic Enzymes in the Adipose Tissue of Finishing Pigs
Authors: Salgado Hector H , Palin Marie-France , Lapierre Hélène , Remus Aline , Letourneau-Montminy Marie-Pierre , Pomar Candido
Published: October 2021

Variations in body fat (BF) among pigs can be associated with differences in insulin sensitivity given the insulin anabolic effect in lipid synthesis. The study objectives were to characterize this association and compare the relative mRNA abundance of genes associated with insulin resistance and de novo lipogenesis in the adipose tissue of fat and lean pigs. Thirty 95 kg pigs, catheterized in the jugular vein, received an oral dose of 1.75 g glucose/kg of BW after 18 hours of fasting. Blood samples were collected at -20, -10, 5, 10, 15, 20, 25, 30, 45, 60, 90, 120, 150, 180, 210, 240, 300 and 360 minutes following glucose ingestion. Insulin sensitivity indexes were calculated and analyzed. The BF (%) was estimated by dual X-ray densitometry. The 8 fattest (22 % BF) and the 8 leanest pigs (17.2 % BF) were used to determine the relative mRNA abundance of studied genes using real-time qPCR analyses. Insulin sensitivity was determined using QUICKI and Matsuda indexes, respectively, and their association with body fat was studied with Spearman correlations. Differences in gene expression and insulin sensitivity between fat and lean pigs were studied with a one-way ANOVA. The QUICKI and Matsuda indexes negatively correlated with BF (r = -0.67 and r = -0.59; P < 0.001). Fat pigs had reduced insulin sensitivity and higher relative mRNA abundance of lipogenic enzymes (ACACA, ACLY, FASN; P < 0.05) than lean pigs. The higher expression level of glucose-6-phosphate dehydrogenase (G6PD) combined with the trend (P < 0.10) of lower expression of peroxisome proliferator-activated receptor-gamma (PPAR-γ) in fat pigs may explain part of their reduced insulin sensitivity. These results suggest that an increased BF is associated with reduced insulin sensitivity and greater expression of lipogenic enzymes in pig adipose tissue.
164 Genome-wide DNA Methylation Profiling in in Utero Heat-stressed Pigs as Measured by Whole-genome Bisulfite Sequencing
Authors: Brito Luiz F , Maskal Jacob M , Chen Shi-Yi , Oliveira Hinayah R , Graham Jason R , Schinckel Allan P , Johnson Jay S
Published: October 2021

In utero heat stress (IUHS) has several postnatal consequences in pigs that compromise health, increase stress response, and reduce performance. These phenotypes may be caused by epigenetic modifications such as DNA methylation, which are heritable molecular modifications that impact gene expression and phenotypic outcomes without changing the DNA sequence. Therefore, we aimed to compare the DNA methylation profiles between in-utero thermoneutral (IUTN) and IUHS pigs to identify differentially methylated regions. Twenty-four pregnant gilts were evenly assigned to either a thermoneutral (17.5 ± 2.1°C) or heat stress (cycling 26 to 36°C) chamber from d 0 to 59 of gestation, followed by thermoneutral conditions (20.9 ± 2.3°C) for the rest of gestation and until the piglets were weaned. At 105 d of age, 10 IUTN and 10 IUHS piglets were euthanized and Longissimus dorsi muscle samples were collected and used to perform whole-genome bisulfite sequencing (WGBS). Purified genomic DNA was fragmented and bisulfite conversion was performed. Illumina platforms were used to sequence WGBS libraries. All pigs had similar proportions of methylation at CpG sites. Two-hundred-sixty-eight genomic regions were differentially methylated between IUTN and IUHS pigs. These identified regions are located across all pig chromosomes and ranged from 2 (SSC18) to 40 (SSC10). Eighty-five unique differentially-methylated genes were identified. These genes have been reported to be involved in key biological processes such as transcriptional repressor activity and tRNA processing (e.g., SKOR2,TRMT6, TSEN2), cellular response to heat stress (e.g.,CCAR2), placental vascularization (e.g.,FZD5), central nervous system (e.g.,VEPH1), cholesterol biosynthesis (e.g., CYB5R1), insulin receptor substrate (e.g.,IRS2), synaptic transmission (e.g.,RIMBP2), neurotrophic factor receptor activity (e.g.,LIFR), immune response (e.g., CD84), DNA repair (e.g., CHD1L), and cell proliferation and endocrine signaling (e.g., SSTR1, CYB5R1). These findings contribute to a better understanding of the epigenomic mechanisms underlying postnatal consequences of IUHS in pigs.
168 Use of Genomic Tools to Improve Production Efficiency, Health Resilience and Carbon Footprint of Beef Production
Authors: Basarab John A , Li Changxi , Stothard Paul , Fitzsimmons Carolyn J , Plastow Graham
Published: October 2021

The aim is to present validation studies that demonstrate the benefits of genomic retained heterozygosity, genomic enhanced expected progeny differences (gEPDs) for feed efficiency and carcass traits, as well as DNA pooling technologies, to the beef industry. Team members of Livestock Gentec are global leaders in beef genomics research as evidenced by their leadership roles on the Canadian Cattle Genome Project, 1,000 Bull Genomes Project, gEPDs for Commercial Cattle Project and the Functional Annotation of ANimal Genomes initiative. These large-scale projects have created databases of 380 whole bovine sequence genomes, >24,000 cattle genotypes imputed to sequence variants using Run 6 genotypes from 1000 Bull Genomes project, and >20,000 cattle with associated phenotypes for feed efficiency, carcass quality, cow fertility and methane emissions. The use of admixture analysis, genome wide association studies, and genomic prediction have resulted in new genomic tools that aid in mate selection, improve herd heterosis, female fertility, lifetime productivity and health resilience, and improve accuracy (acc. >0.36) of gEPDs for 18 traits in crossbred cattle. Genomic retained heterozygosity has a benefit of $161/female over five parities while decreasing morbidity of calves and improving the carbon intensity of beef production. Multi-trait selection studies using gEPDs for residual feed intake (acc. > 0.35) have demonstrated annual rates of genetic progress of 0.7%. Validation studies have reported that sires with superior gEPDs for increased marbling, decreased grade fat, increased ribeye and increased carcass weight (acc. > 0.45) produced progeny with improved AAA retail cut yield (59.9 vs 56.7%). DNA pooling shows potential for cheaper genotyping while providing information on pooled records related to sire contribution, heterosis and performance as influenced by genetics. The application of these genomic tools has potential to improve calf crop percentage, health resilience, and retail cut yield while decreasing the carbon footprint of beef production.