Meat Science Commons^™

Big Data Analytics And Precision Animal Agriculture Symposium: Machine Learning And Data Mining Advance Predictive Big Data Analysis In Precision Animal Agriculture, Gota Morota, Ricardo V. Ventura, Fabyano F. Silva, Masanori Koyama, Samodha C. Fernando

Department of Animal Science: Faculty Publications

Precision animal agriculture is poised to rise to prominence in the livestock enterprise in the domains of management, production, welfare, sustainability, health surveillance, and environmental footprint. Considerable progress has been made in the use of tools to routinely monitor and collect information from animals and farms in a less laborious manner than before. These efforts have enabled the animal sciences to embark on information technology-driven discoveries to improve animal agriculture. However, the growing amount and complexity of data generated by fully automated, high-throughput data recording or phenotyping platforms, including digital images, sensor and sound data, unmanned systems, and information obtained …

The Influence Of Fat And Hemicellulose On Methane Production And Energy Utilization In Lactating Jersey Cattle, O. R. Drehmel, T. M. Brown-Brandl, J. V. Judy, S. C. Fernando, P. S. Miller, K. E. Hales, Paul J. Kononoff

Department of Animal Science: Faculty Publications

Feeding fat to lactating dairy cows may reduce methane production. Relative to cellulose, fermentation of hemicellulose is believed to result in less methane; however, these factors have not been studied simultaneously. Eight multiparous, lactating Jersey cows averaging (±SD) 98 ± 30.8 d in milk and body weight of 439.3 ± 56.7 kg were used in a twice-replicated 4 × 4 Latin square to determine the effects of fat and hemicellulose on energy utilization and methane production using a headbox-type indirect calorimetry method. To manipulate the concentration of fat, porcine tallow was included at either 0 or 2% of the diet …

Predictive Ability Of Genome-Assisted Statistical Models Under Various Forms Of Gene Action, Mehdi Momen, Ahmad Ayatollahi Mehrgardi, Ayyub Sheikhi, Andreas Kranis, Llibertat Tussell, Gota Morota, Guilherme J. M. Rosa, Daniel Gianola

Department of Animal Science: Faculty Publications

Recent work has suggested that the performance of prediction models for complex traits may depend on the architecture of the target traits. Here we compared several prediction models with respect to their ability of predicting phenotypes under various statistical architectures of gene action: (1) purely additive, (2) additive and dominance, (3) additive, dominance, and two-locus epistasis, and (4) purely epistatic settings. Simulation and a real chicken dataset were used. Fourteen prediction models were compared: BayesA, BayesB, BayesC, Bayesian LASSO, Bayesian ridge regression, elastic net, genomic best linear unbiased prediction, a Gaussian process, LASSO, random forests, reproducing kernel Hilbert spaces regression, …

Linkage Disequilibrium In Brazilian Santa Inês Breed, Ovis Aries, Amanda Botelho Alvarenga, Gregori Alberto Rovadoscki, Juliana Petrini, Luiz Lehmann Coutinho, Gota Morota, Matthew L. Spangler, Luis Fernando Batista Pinto, Gleidson Giordano Pinto Carvalho, G. B. Mourao

Department of Animal Science: Faculty Publications

For genomic selection to be successful, there must be sufficient linkage disequilibrium between the markers and the causal mutations. The objectives of this study were to evaluate the extent of LD in ovine using the Santa Inês breed and to infer the minimum number of markers required to reach reasonable prediction accuracy. In total, 38,168 SNPs and 395 samples were used. The mean LD between adjacent marker pairs measured by r² and |D′| were 0.166 and 0.617, respectively. LD values between adjacent marker pairs ranged from 0.135 to 0.194 and from 0.568 to 0.650 for r² for |D′| …

Estimates Of Genomic Heritability And Genome-Wide Association Study For Fatty Acids Profile In Santa Inês Sheep, G. A. Rovadoscki, S. F. N. Pertile, A. B. Alvarenga, A. S. M. Cesar, F. Pertille, J. Petrini, V. Franzo, W. V. B. Soares, G. Morota, Matthew L. Spangler, L. F. B. Pinto, G. G. P. Carvalho, D. P. D. Lanna, L. L. Coutinho, G. B. Mourao

Department of Animal Science: Faculty Publications

Background: Despite the health concerns and nutritional importance of fatty acids, there is a relative paucity of studies in the literature that report genetic or genomic parameters, especially in the case of sheep populations. To investigate the genetic architecture of fatty acid composition of sheep, we conducted genome-wide association studies (GWAS) and estimated genomic heritabilities for fatty acid profile in Longissimus dorsi muscle of 216 male sheep.

Results: Genomic heritability estimates for fatty acid content ranged from 0.25 to 0.46, indicating that substantial genetic variation exists for the evaluated traits. Therefore, it is possible to alter fatty acid profiles through …

Effect Of Differing Ingredients And Packaging Technologies On The Color Of High-Pressure Processed Ground Beef, Jhinuk Gupta, Chad G. Bower, Gary Sullivan, George A. Cavender

Department of Animal Science: Faculty Publications

High-pressure processing (HPP) is a nonthermal pasteurization technique to control pathogens, like Escherichia coli. However, color changes in raw beef induced by HPP restrict its use within the beef industry. ­e objectives of this study were to investigate the effects of adding curing agents (nitrite) and packaging with or without reducing compounds (ascorbic acid/erythorbate) on color retention in high-pressure processed ground beef. Color was measured (CIE L*a*b*) before HPP and on days 3, 7, 12, 14, 19, and 21 after HPP. Statistical analysis (SAS GLIMMIX) was run to identify the main effects of adding curing agents, packaging, and …

The Impact Of Truncating Data On The Predictive Ability For Single-Step Genomic Best Linear Unbiased Prediction, Jeremy T. Howard, Thomas A. Rathje, Caitlyn E. Bruns, Danielle F. Wilson-Wells, Stephen D. Kachman, Matthew L. Spangler

Department of Animal Science: Faculty Publications

Simulated and swine industry data sets were utilized to assess the impact of removing older data on the predictive ability of selection candidate estimated breeding values (EBV) when using single-step genomic best linear unbiased prediction (ssGBLUP). Simulated data included thirty replicates designed to mimic the structure of swine data sets. For the simulated data, varying amounts of data were truncated based on the number of ancestral generations back from the selection candidates. The swine data sets consisted of phenotypic and genotypic records for three traits across two breeds on animals born from 2003 to 2017. Phenotypes and genotypes were iteratively …

Do Stronger Measures Of Genomic Connectedness Enhance Prediction Accuracies Across Management Units?, Haipeng Yu, Matthew L. Spangler, Ronald M. Lewis, Gota Morota

Department of Animal Science: Faculty Publications

Genetic connectedness assesses the extent to which estimated breeding values can be fairly compared across management units. Ranking of individuals across units based on best linear unbiased prediction (BLUP) is reliable when there is a sufficient level of connectedness due to a better disentangling of genetic signal from noise. Connectedness arises from genetic relationships among individuals. Although a recent study showed that genomic relatedness strengthens the estimates of connectedness across management units compared with that of pedigree, the relationship between connectedness measures and prediction accuracies only has been explored to a limited extent. In this study, we examined whether increased …

Fecal Microbiota Transplantation Is Associated With Reduced Morbidity And Mortality In Porcine Circovirus Associated Disease, Megan C. Niederwerder, Laura A. Constance, Raymond R. R. Rowland, Waseem Abbas, Samodha C. Fernando, Megan L. Potter, Maureen A. Sheahan, Thomas E. Burkey, Richard A. Hesse, Ada G. Cino-Ozuna

Department of Animal Science: Faculty Publications

Porcine circovirus associated disease (PCVAD) is a term used to describe the multifactorial disease syndromes caused by porcine circovirus type 2 (PCV-2), which can be reproduced in an experimental setting through the co-infection of pigs with PCV-2 and porcine reproductive and respiratory syndrome virus (PRRSV). The resulting PCVAD-affected pigs represent a subpopulation within the co-infected group. In co-infection studies, the presence of increased microbiome diversity is linked to a reduction in clinical signs. In this study, fecal microbiota transplantation (FMT) was investigated as a means to prevent PCVAD in pigs co-infected with PRRSV and PCV-2d. The sources of the FMT …

Generation Of An Equine Biobank To Be Used For Functional Annotation Of Animal Genomes Project, E. N. Burns, M. H. Bordbari, M. J. Mienaltowski, V. K. Affolter, M. V. Barro, F. Gianino, G. Gianino, E. Giulotto, T. S. Kalbfleisch, S. A. Katzman, M. Lassaline, T. Leeb, M. Mack, E. J. Muller, J. N. Macleod, B. Ming-Whitfield, C. R. Alanis, T. Raudsepp, E. Scott, S. Vig, H. Zhou, J. L. Petersen, R. R. Bellone, C. J. Finno

Department of Animal Science: Faculty Publications

The Functional Annotation of Animal Genomes (FAANG) project aims to identify genomic regulatory elements in both sexes across multiple stages of development in domesticated animals. This study represents the first stage of the FAANG project for the horse, Equus caballus. A biobank of 80 tissue samples, two cell lines and six body fluids was created from two adult Thoroughbred mares. Ante-mortem assessments included full physical examinations, lameness, ophthalmologic and neurologic evaluations. Complete blood counts and serum biochemistries were also performed. At necropsy, in addition to tissue samples, aliquots of serum, ethylenediaminetetraacetic acid (EDTA) plasma, heparinized plasma, cerebrospinal fluid, synovial …

Energy Balance And Diurnal Variation In Methane Production As Affected By Feeding Frequency In Jersey Cows In Late Lactation, J. V. Judy, G. C. Bachman, T. M. Brown-Brandl, S. C. Fernando, K. E. Hales, P. S. Miller, R. R. Stowell, P. J. Kononoff

Department of Animal Science: Faculty Publications

Methane (CH₄) production of ruminants typically increases with increased dry matter intake (DMI). However, few studies have observed the effects of feeding multiple times a day and its effects on diurnal variation in CH₄ production and energy balance in late-lactation dairy cattle. A study using headbox-style indirect calorimetry and 12 multiparous (225 ± 16.2 d in milk; mean ± SD) lactating Jersey cows was conducted to determine the effects of feeding twice daily on diurnal variation in CH₄ production and total energy balance. A crossover design with 14-d periods (10 d of adaption and 4 d …

Function And Dysfunction Of Fatty Acid Mobilization: A Review, Joslyn K. Beard, Travis Mulliniks, Dustin T. Yates

Department of Animal Science: Faculty Publications

Western populations have a growing obesity epidemic due in part to excessive nutrient intake from high-fat diets, which are increasingly common. Overindulgence of nutrients is associated with a greater incidence of metabolic dysfunction and a greater risk for obesity, diabetes, hypertension, and other metabolic disorders that lower quality of life. Research in humans and animal models has improved our understanding of how excess circulating free fatty acids negatively impact the ability of muscle and other tissues to regulate nutrient uptake and utilization. It is generally accepted by the scientific community that excess circulating fatty acids lead to insulin resistance, but …

Investigation Of The Skeletal Muscle Transcriptome In Lambs Fed Β Adrenergic Agonists And Subjected To Heat Stress For 21 D, Rachel Kubik, Shauna M. Tietze, Ty B. Schmidt, Dustin Tyler Yates, Jessica Lynn Petersen

Department of Animal Science: Faculty Publications

Dietary β-adrenergic agonists (β-AA) are used in livestock to increase muscle protein accretion and decrease adipose deposition during the last 20 to 40 d of the finishing period (Johnson et al., 2014). These β-AA act through specific seven transmembrane receptors and are classified by the receptor isoform to which they primarily bind (Mersmann, 1998). Two β-AA are approved for use in beef cattle in the United States: ractopamine HCl (RAC, β1 agonist) and zilpaterol HCl (ZH, β2 agonist) (Johnson et al., 2014). Supplementation of β-AA increases efficiency of the animal and results in a leaner carcass (Elam et al., 2009). …

Impact Of Pre-And Postpartum Nutrition On March-Calving Cow And Progeny Productivity, Jacki A. Musgrave, Devin L. Broadhead, L. A. Stalker Stalker, Richard N. Funston

Nebraska Beef Cattle Reports

March-calving cows were fed hay or grazed corn residue prepartum, and then either fed hay or grazed subirrigated meadow postpartum. Combinations of these different feeding strategies impacted body weight (BW) and body condition score (BCS) during the pre-and postpartum period; however, resulted in similar pregnancy rates. Although differences were not observed in cow pregnancy rates, a benefit in pre-weaning growth was observed for calves from the dams in postpartum meadow treatment. A tendency for an improvement in marbling score was observed for steers born to cows fed hay prepartum, perhaps indicating a higher plane of nutrition prepartum may improve quality …

Rumen Bacterial Community Structure Impacts Feed Efficiency In Beef Cattle, Henry A. Paz, Kristin E. Hales, James E. Wells, Larry A. Kuehn, Harvey C. Freetly, Elaine D. Berry, Michael D. Flythe, Matthew L. Spangler, Samodha C. Fernando

Department of Animal Science: Faculty Publications

The importance of the rumen microbiota on nutrient cycling to the animal is well recognized; however, our understanding of the influence of the rumen microbiome composition on feed efficiency is limited. The rumen microbiomes of two large animal cohorts (125 heifers and 122 steers) were characterized to identify specific bacterial members (operational taxonomic units [OTUs]) associated with feed efficiency traits (ADFI, ADG, and G:F) in beef cattle. The heifer and steer cohorts were fed a forage-based diet and a concentrate-based diet, respectively. A rumen sample was obtained from each animal via esophageal tubing and bacterial community composition was …

Using Single Molecule Mrna Fluorescent In Situ Hybridization (Rna-Fish) To Quantify Mrnas In Individual Murine Oocytes And Embryos, Fang Xie, Kelsey A. Timme, Jennifer R. Wood

Department of Animal Science: Faculty Publications

Changes in abundance of mRNAs during oocyte growth and maturation and during pre-implantation embryo development have been documented using quantitative real-time RT-PCR (qPCR), microarray analyses, and whole genome sequencing. However, these techniques require amplification of mRNAs, normalization using housekeeping genes, can be biased for abundant transcripts, and/or require large numbers of oocytes and embryos which can be difficult to acquire from mammalian species. We optimized a single molecule RNA fluorescence in situ hybridization (RNA-FISH) protocol, which amplifies fluorescence signal to detect candidate transcripts, for use with individual oocytes and embryos. Quantification using the software Localize showed patterns of Gdf9 and …

Effects Of Dietary Supplementation Of Formaldehyde And Crystalline Amino Acids On Gut Microbial Composition Of Nursery Pigs, H. E. Williams, R. A. Chochrane, J. C. Woodworth, J. M. Derouchey, S. S. Dritz, M. D. Tokach, C. K. Jones, S. C. Fernando, Thomas E. Burkey, Y. S. Li, R. D. Goodband, R. G. Amachawadi

Department of Animal Science: Faculty Publications

Formaldehyde-based feed additives are approved in the US for Salmonella control and reducing bacterial contamination in animal feed. However, we hypothesize formaldehyde inclusion in swine diets may influence gut microbial composition due to its antimicrobial properties which might negatively influence microbial populations and pig growth performance. Also, formaldehyde inclusion in diets is known to reduce the dietary availability of amino acids. Therefore, our study was conducted to characterize if the effects of feed formaldehyde-treatment are due to influences on microbial population or diet amino acid (AA) sources. Dietary treatments were arranged in a (2 × 2) + 1 factorial with …

Synaptogyrin-2 Influences Replication Of Porcine Circovirus 2, Lianna R. Walker, Taylor B. Engle, Hiep Vu, Emily R. Tosky, Dan J. Nonneman, Timothy P. L. Smith, Tudor Borza, Thomas E. Burkey, Graham S. Plastow, Stephen D. Kachman, Daniel C. Ciobanu

Department of Animal Science: Faculty Publications

Porcine circovirus 2 (PCV2) is a circular single-stranded DNA virus responsible for a group of diseases collectively known as PCV2 Associated Diseases (PCVAD). Variation in the incidence and severity of PCVAD exists between pigs suggesting a host genetic component involved in pathogenesis. A large-scale genome-wide association study of experimentally infected pigs (n = 974), provided evidence of a host genetic role in PCV2 viremia, immune response and growth during challenge. Host genotype explained 64% of the phenotypic variation for overall viral load, with two major Quantitative Trait Loci (QTL) identified on chromosome 7 (SSC7) near the swine leukocyte antigen complex …

Effects Of Syngenta Enogen Feed Corn Containing An Α-Amylase Trait On Finishing Cattle Performance And Carcass Characteristics, M. L. Jolly-Breithaupt, M. E. Harris, B. L. Nuttelman, D. B. Burken, J. C. Macdonald, M. K. Leubbe, T. K. Iragavarapu, G. E. Erickson

Department of Animal Science: Faculty Publications

Two experiments evaluated the effects of feeding a new corn hybrid, containing an α-amylase enzyme trait, Syngenta Enogen Feed Corn (SYT-EFC), on feedlot performance and carcass characteristics at two locations. Experiment 1 utilized 300 calffed steers (298.5 ± 16.3 kg of BW) at the University of Nebraska–Lincoln Eastern Nebraska Research and Extension Center Mead, NE. Treatments were designed as a 2 × 2 + 1– factorial arrangement with factors consisting of 1) corn type (SYT-EFC or conventional [CON]) and 2) byproduct type (with or without Sweet Bran [SB]), or a BLEND of STY-EFC and CON without SB. In Exp. 2, …

Improved Reference Genome For The Domestic Horse Increases Assembly Contiguity And Composition, Theodore S. Kalbfleisch, Edward S. Rice, Michael S. Depriest Jr., Brian P. Walenz, Matthew S. Hestand, Joris R. Vermeesch, Brendan L. O'Connell, Ian T. Fiddes, Alisa O. Vershinina, Nedda F. Saremi, Jessica L. Petersen, Carrie J. Finno, Rebecca R. Bellone, Molly E. Mccue, Samantha A. Brooks, Ernest Bailey, Ludovic Orlando, Richard E. Green, Donald C. Miller, Douglas F. Antczak, James N. Macleod

Department of Animal Science: Faculty Publications

Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. Here, we present EquCab3. The count of …