Genetics and Genomics Commons^™

Comparative Population Genomics Of Latitudinal Variation In Drosophila Simulans And Drosophila Melanogaster, Heather E. Machado, Alan O. Bergland, Katherine R. O'Brien, Emily L. Behrman, Paul S. Schmidt, Dmitri A. Petrov

School of Biological Sciences: Faculty Publications

Examples of clinal variation in phenotypes and genotypes across latitudinal transects have served as important models for understanding how spatially varying selection and demographic forces shape variation within species. Here, we examine the selective and demographic contributions to latitudinal variation through the largest comparative genomic study to date of Drosophila simulans and Drosophila melanogaster, with genomic sequence data from 382 individual fruit flies, collected across a spatial transect of 19 degrees latitude and at multiple time points over 2 years. Consistent with phenotypic studies, we find less clinal variation in D. simulans than D. melanogaster, particularly for the autosomes. Moreover, …

Virus–Host Interactions: Insights From The Replication Cycle Of The Large Paramecium Bursaria Chlorella Virus, Elad Milrot, Yael Mutsafi, Yael Fridmann-Sirkis, Eyal Shimoni, Katya Rechav, James Gurnon, James L. Van Etten, Abraham Minsky

James Van Etten Publications

The increasing interest in cytoplasmic factories generated by eukaryotic-infecting viruses stems from the realization that these highly ordered assemblies may contribute fundamental novel insights to the functional significance of order in cellular biology. Here, we report the formation process and structural features of the cytoplasmic factories of the large dsDNA virus Paramecium bursaria chlorella virus 1 (PBCV-1). By combining diverse imaging techniques, including scanning transmission electron microscopy tomography and focused ion beam technologies, we show that the architecture and mode of formation of PBCV-1 factories are significantly different from those generated by their evolutionary relatives Vaccinia and Mimivirus. Specifically, PBCV-1 …

Evidence For The Fixation Of Gene Duplications By Positive Selection In Drosophila, Margarida Cardoso-Moreira, J. Roman Arguello, Srikanth Gottipati, Lawrence G. Harshman, Jennifer K. Grenier, Andrew G. Clark

Lawrence G. Harshman Publications

Gene duplications play a key role in the emergence of novel traits and in adaptation. But despite their centrality to evolutionary processes, it is still largely unknown how new gene duplicates are initially fixed within populations and later maintained in genomes. Long-standing debates on the evolution of gene duplications could be settled by determining the relative importance of genetic drift vs. positive selection in the fixation of new gene duplicates. Using the Drosophila Global Diversity Lines (GDL), we have combined genome-wide SNP polymorphism data with a novel set of copy number variant calls and gene expression profiles to characterize the …

Enscat: Clustering Of Categorical Data Via Ensembling, Bertrand S. Clarke, Saeid Amiri, Jennifer L. Clarke

Department of Statistics: Faculty Publications

Background: Clustering is a widely used collection of unsupervised learning techniques for identifying natural classes within a data set. It is often used in bioinformatics to infer population substructure. Genomic data are often categorical and high dimensional, e.g., long sequences of nucleotides. This makes inference challenging: The distance metric is often not well-defined on categorical data; running time for computations using high dimensional data can be considerable; and the Curse of Dimensionality often impedes the interpretation of the results. Up to the present, however, the literature and software addressing clustering for categorical data has not yet led to a standard …

Lineage-Specific Differences In The Gp120 Inner Domain Layer 3 Of Human And Simian Immunodeficiency Viruses, Shilei Ding, Halima Medjahed, Jérémie Prévost, Mathieu Coutu, Shi-Hua Xiang, Andrés Finzi

Nebraska Center for Virology: Faculty Publications

Binding of HIV-1 and SIV gp120 exterior envelope glycoprotein to CD4 triggers conformational changes in gp120 that promote its interaction with one of the chemokine receptors, usually CCR5, ultimately leading to gp41-mediated virus-cell membrane fusion and entry. We previously described that topological Layers (Layer 1, Layer 2 and Layer 3) in the gp120 inner domain contribute to gp120-trimer association in the unliganded state but also help secure CD4 binding. Relative to Layer 1 of HIV-1 gp120, the SIVmac239 gp120 Layer 1 plays a more prominent role in maintaining gp120-trimer association but is minimally involved in promoting CD4 binding, which could …

Feeding Wet Distillers Grains Plus Solubles With And Without A Direct-Fed Microbial To Determine Performance, Carcass Characteristics, And Fecal Shedding Of Escherichia Coli O157:H7 In Feedlot Heifers, B. K. Wilson, B. P. Pulsipher, D. L. Step, M. E. Jacob, D. L. Vanoverbeke, C. J. Richards, T. G. Nagaraja, C. R. Krehbiel

Department of Animal Science: Faculty Publications

The inclusion of wet distillers grains plus solubles (WDGS) in feedlot diets has become a common practice in many regions of the United States due to the expanded production of byproducts and fluctuating corn prices related to ethanol production and other factors. In addition, societal concerns over the continued use of antimicrobials in agriculture production combined with an enhanced interest in disease and pathogen prevention in the food supply have led to an increased interest in use of direct-fed microbials (DFM) in growing and finishing cattle. Direct-fed microbials have been shown to improve ADG and feed efficiency, alter ruminal fermentation, …

Joint Mouse–Human Phenome-Wide Association To Test Gene Function And Disease Risk, Xusheng Wang, Ashutosh K. Ciobanu, Megan K. Mulligan, Evan G. Williams, Khyobeni Mozhui, Zhengsheng Li, Virginija Jovaisaite, L. Darryl Quarles, Zhousheng Xiao, Jinsong Huang, John A. Capra, Zugen Chen, William L. Taylor, Lisa Bastarache, Xinnan Niu, Katherine S. Pollard, Daniel C. Ciobanu, Alexander O. Reznik, Artem V. Tishkov, Igor B. Zhulin, Junmin Peng, Stanley F. Nelson, Joshua C. Denny, Johan Auwerx, Lu Lu, Robert W. Williams

Department of Animal Science: Faculty Publications

Phenome-wide association is a novel reverse genetic strategy to analyze genome-tophenome relations in human clinical cohorts. Here we test this approach using a large murine population segregating for ~5 million sequence variants, and we compare our results to those extracted from a matched analysis of gene variants in a large human cohort. For the mouse cohort, we amassed a deep and broad open-access phenome consisting of ~4,500 metabolic, physiological, pharmacological and behavioural traits, and more than 90 independent expression quantitative trait locus (QTL), transcriptome, proteome, metagenome and metabolome data sets—by far the largest coherent phenome for any experimental cohort (www.genenetwork.org). …

Giant Chloroviruses: Five Easy Questions, James L. Van Etten, David Dunigan

Nebraska Center for Virology: Faculty Publications

Chloroviruses are large, icosahedral, dsDNA-containing viruses that replicate in certain unicellular, chlorella-like green algae [1,2]. They exist in freshwater throughout the world with titers as high as thousands of plaque-forming units (PFU) per ml of indigenous water although titers are typically 1–100 PFU/ml. Titers fluctuate during the year with the highest titers typically occurring in the spring and late fall. Known chlorovirus hosts, which are normally symbionts and are often referred to as zoochlorellae, are associated with either the protozoan Paramecium bursaria (Fig 1A), the coelenterate Hydra viridis, or the heliozoan Acanthocystis turfacea. Zoochlorellae are resistant to viruses …

Genetic Barrier To Direct Acting Antivirals In Hcv Sequences Deposited In The European Databank, Dimas Alexandre Kliemann, Cristiane Valle Tovo, Ana Beatriz Gorini Da Veiga, André Luiz Machado, John T. West

Nebraska Center for Virology: Faculty Publications

Background & Aims: Development of resistance results from mutations in the viral genome, and the presence of selective drug pressure leads to the emergence of a resistant virus population. The aim of this study was to analyze the impact of genetic variability on the genetic barrier to drug resistance to DAAs.

Methods: The genetic barrier was quantified based on the number and type of nucleotide mutations required to impart resistance, considering full-length HCV NS3, NS5A and NS5B regions segregated by genotype into subtypes 1a, 1b, 2a, 2b and 3a. This study analyzed 789 NS3 sequences, 708 sequences and 536 NS5B …

Kaposi’S Sarcoma-Associated Herpesvirus Reduces Cellular Myeloid Differentiation Primary-Response Gene 88 (Myd88) Expression Via Modulation Of Its Rna, Amy Lingel, Erica Ehlers, Qianli Wang, Mingxia Cao, Charles Wood, Rongtuan Lin, Luwen Zhang

Nebraska Center for Virology: Faculty Publications

Kaposi’s sarcoma (KS)-associated herpesvirus (KSHV) is a human gammaherpesvirus associated with several human malignancies. The replication and transcription activator (RTA) is necessary and sufficient for the switch from KSHV latency to lytic replication. Interleukin 1 (IL-1) is a major mediator for inflammation and plays an important role in both innate and adaptive immunity. Myeloid differentiation primary response gene 88 (MyD88) is an essential adaptor molecule for IL-1 as well as most Toll-like receptor signaling. In this study, we identified a novel mechanism by which KSHV interferes with host inflammation and immunity. KSHV RTA specifically reduces the steady-state protein levels of …

Nf45 And Nf90 Bind Hiv-1 Rna And Modulate Hiv Gene Expression, Yan Li, Michael Belshan

Nebraska Center for Virology: Faculty Publications

A previous proteomic screen in our laboratory identified nuclear factor 45 (NF45) and nuclear factor 90 (NF90) as potential cellular factors involved in human immunodeficiency virus type 1 (HIV-1) replication. Both are RNA binding proteins that regulate gene expression; and NF90 has been shown to regulate the expression of cyclin T1 which is required for Tat-dependent trans-activation of viral gene expression. In this study the roles of NF45 and NF90 in HIV replication were investigated through overexpression studies. Ectopic expression of either factor potentiated HIV infection, gene expression, and virus production. Deletion of the RNA binding domains of NF45 …

Mucosal Vaccination By Adenoviruses Displaying Reovirus Sigma 1, Eric A. Weaver, Zenaido T. Camacho, Matthew L. Hillestad, Catherine M. Crosby, Mallory A. Turner, Adam J. Guenzel, Hind J. Fadel, George T. Mercier, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

We previously developed adenovirus serotype 5 (Ad5) vectors displaying the sigma 1 protein from reovirus as mucosal vaccines. Ad5-sigma retargets to JAM-1 and sialic acid, but had 40-fold reduced gene delivery when compared to Ad5. While weaker at transduction, Ad5-sigma generated stronger T cell responses than Ad5 when used for mucosal immunization. New Ad5- fiber-sigma vectors were generated here by varying the number of fiber β-spiral shaft repeats (R) fused between fiber tail and the sigma. Ad5 virions encoding R3, R14, and R20 chimeras were rescued. Increasing chimera length led to their decreasing encapsidation of these proteins in the virions. …

Differential Contribution Of Genomic Regions To Marked Genetic Variation And Prediction Of Quantitative Traits In Broiler Chickens, Rostam Abdollaha- Arpanahi, Gota Morota, Bruno D. Valente, Andreas Kranis, Guilherme J. M. Rosa, Daniel Gianola

Department of Animal Science: Faculty Publications

Background: Genome-wide association studies in humans have found enrichment of trait-associated single nucleotide polymorphisms (SNPs) in coding regions of the genome and depletion of these in intergenic regions. However, a recent release of the ENCyclopedia of DNA elements showed that ~80 % of the human genome has a biochemical function. Similar studies on the chicken genome are lacking, thus assessing the relative contribution of its genic and non-genic regions to variation is relevant for biological studies and genetic improvement of chicken populations. Methods: A dataset including 1351 birds that were genotyped with the 600K Affymetrix platform was used. We partitioned …

Epds And Risk, L. Dale Van Vleck

Department of Animal Science: Faculty Publications

About 30 years ago there was concern in both the beef and dairy industries that too much emphasis was being given to accuracy of genetic evaluation. This article will discuss attempts to reduce emphasis on accuracy and, thus increase emphasis on the predictor of genetic value itself which is commonly known as estimated breeding value (EBV). Accuracy is a key component of more useful measures of risk such as standard error of prediction which can be used to create confidence ranges in units of measurement for true breeding value based on the EBV and the standard error of prediction. The …

Effects Of Sorghum Wet Distillers Grains Plus Solubles In Steam-Flaked Corn–Based Finishing Diets On Steer Performance, Carcass Characteristics, And Digestibility Characteristics, E. K. Buttrey, K. H. Noel, F. T. Mccollum Iii, N. A. Cole, L. O. Tedeschi, James C. Macdonald

Department of Animal Science: Faculty Publications

Two studies were conducted to evaluate the effects of sorghum wet distillers grains (SWDGS) in finishing diets on steer performance, carcass characteristics, and nutrient digestibility. In Exp. 1, 240 steers (initial BW = 379 ± 1 kg) were fed steam-flaked corn–based diets with or without 25% SWDGS and 7.5, 10.0, or 12.5% alfalfa hay. There were no effects of alfalfa hay concentration on BW, DMI, ADG, or G:F (P ≥ 0.16). Including SWDGS reduced (P ≤ 0.05) ADG and G:F. Fat thickness decreased (P = 0.03) and DP tended to decrease (P = 0.09) linearly as level of alfalfa hay …

Effects Of Increasing Soybean Hulls In Finishing Diets With Wet Or Modified Distillers Grains Plus Solubles On Performance And Carcass Characteristics Of Beef Steers, Curtis Bittner, Brandon L. Watson, C. J. Schneider, Dirk Burken, L. J. Johnson, Terry J. Klopfenstein, Galen E. Erickson

Department of Animal Science: Faculty Publications

Two experiments evaluated feeding soybean hulls (SBH) in finishing diets that contain distillers grains plus solubles on performance and carcass characteristics. Dietary concentrations of SBH were 0, 12.5, 25, and 37.5% of diet DM. In Exp. 1, 167 crossbred yearling steers (395 ± 22 kg of BW) were fed for 117 d in a randomized block design in which pelleted SBH replaced dry-rolled corn. All diets contained 25% modified distillers grains plus solubles, 15% corn silage, and 5% liquid supplement. As SBH concentration increased, DMI decreased linearly (P = 0.04). Gain and G:F decreased linearly (P < 0.01) in response to increasing concentrations of SBH, which decreased relative energy value from 91 to 79% of corn. Hot carcass weight linearly decreased (P < 0.01) by 24 kg as SBH increased. In Exp. 2, a randomized block design used 160 backgrounded steer calves (363 ± 16 kg of BW) in a 138-d finishing study with 0, 12.5, 25, or 37.5% SBH in the meal form. Basal ingredients consisted of a 1:1 ratio of high-moisture corn and dry-rolled corn, 40% wet distillers grains plus solubles, 8% sorghum silage, and 4% dry meal supplement. There was a tendency (P = 0.12) for a quadratic increase in ADG and G:F as dietary SBH increased, with numerically greatest ADG and G:F with 12.5% SBH. Feeding 12.5 to 25% SBH with 40% wet distillers grains plus solubles (Exp. 2) had little effect on performance but decreased ADG and G:F in diets with 25% modified distillers grains plus solubles (Exp. 1).

Effects Of Fat And/Or Methionine Hydroxy Analog Added To A Molasses-Urea-Based Supplement On Ruminal And Postruminal Digestion And Duodenal Flow Of Nutrients In Beef Steers Consuming Low-Quality Lovegrass Hay, R. Lopez, G. D. Bernhard, J. E. Guerra-Liera, S. A. Soto-Navarro, L. A. Balstad, M. K. Petersen, D. V. Dhuyvetter, M. S. Brown, C. R. Krehbiel

Department of Animal Science: Faculty Publications

Five crossbred beef steers (initial BW = 338.6 ± 7.8 kg) fitted with ruminal and duodenal cannulas were used in a 5 × 5 Latin square design experiment to evaluate the effects of methionine hydroxy analog (MHA) and/or yellow grease (fat) added to a molassesurea- based supplement on intake and characteristics of digestion. Steers were fed low-quality hay (long-stem lovegrass Eragrostis curvula: 3.3% CP, 76.8% NDF; DM basis) ad libitum and supplemented with 0.91 kg/d (as fed) of 1 of 4 supplements in a 2 × 2 + 1 factorial arrangement of treatments. Supplemental treatments were 1) control (no supplement, …

Erratum: Divergent Activity Of The Gonadotropin-Releasing Hormone Receptor Gene Promoter Among Genetic Lines Of Pigs Is Partially Conferred By Nuclear Factor (Nf)- Kb, Specificity Protein (Sp)1-Like And Gata-4 Binding Sites, Emily A. Mcdonald, Jacqueline E. Smith, Rebecca Cederberg, Brett R. White

Department of Animal Science: Faculty Publications

No abstract provided.

Mesh-Informed Enrichment Analysis And Mesh-Guided Semantic Similarity Among Functional Terms And Gene Products In Chicken, Gota Morota, Timothy M. Beissinger, Francisco Peñagaricano

Department of Animal Science: Faculty Publications

Biomedical vocabularies and ontologies aid in recapitulating biological knowledge. The annotation of gene products is mainly accelerated by Gene Ontology (GO) and more recently by Medical Subject Headings (MeSH). Here we report a suite of MeSH packages for chicken in Bioconductor and illustrate some features of different MeSH-based analyses, including MeSH-informed enrichment analysis and MeSH-guided semantic similarity among terms and gene products, using two lists of chicken genes available in public repositories. The two published data sets that were employed represent (i) differentially expressed genes and (ii) candidate genes under selective sweep or epistatic selection. The comparison of MeSH with …

Extension Demonstration Project Outcomes: Industry Adoption And Translation Of Project Deliverables, Matt Spangler

Department of Animal Science: Faculty Publications

Unfortunately, the amount of feed intake data available to U.S. beef breed associations is spars compared to the amount of data available for growth traits. This makes traditional pedigree-based genetic evaluation for feed intake or efficiency challenging. However, progress in this trait complex could be made as we know that dry matter intake and various “efficiency” traits would respond favorably to selection. Table 1 below depicts the heritability (on the diagonal) and genetic correlations (on the off diagonal) of several feed efficiency traits.

Effect Of Increasing Initial Implant Dosage On Feedlot Performance And Carcass Characteristics Of Long-Fed Steer And Heifer Calves1,2, F. H. Hilscher, M. N. Streeter, K. J. Vander Pol, B. D. Dicke, R. J. Cooper, D. J. Jordon, T. L. Scott, A. R. Vogstad, R. E. Peterson, B. E. Depenbusch, G. E. Erickson

Department of Animal Science: Faculty Publications

Three experiments evaluated initial implant strategies for finishing cattle. In Exp. 1, heifers (n = 1,405; initial BW = 282 kg) were given (1) Revalor-IH followed by Revalor-200 (REV-IH/200), (2) Revalor-H followed by Revalor-200 (REV-H/200), or (3) Revalor-200 followed by Revalor-200 (REV-200/200). Intake, ADG, and G:F were not affected (P ≥ 0.14) by implant strategies, nor were HCW and LM area (P ≥ 0.16). Percent USDA Choice was greater (P < 0.01) for Rev-IH/200 compared with Rev-H/200 and Rev-200/200. Experiment 2 used steers (n = 1,858; initial BW = 250 kg) given (1) Revalor-IS reimplanted with Revalor-200 (Rev-IS/200), (2) Revalor-XS followed by Revalor-IS (Rev-XS/IS), (3) Revalor-XS followed by Revalor-S (Rev-XS/S), or (4) Revalor-XS followed by Revalor-200 (Rev-XS/200). Implanting strategies did not affect (P ≥ 0.32) DMI or G:F. Carcass traits were not different (P ≥ 0.18) among treatments, except steers implanted with Rev-XS/200 had greater (P < 0.01) LM area. In Exp. 3, steers (n = 1,408; initial BW = 305 kg) were given (1) Rev-IS/200, (2) Rev-200/200, or (3) Rev-XS/200. Gain and G:F did not differ (P ≥ 0.36) among the 3 implant strategies, nor did HCW or marbling score (P ≥ 0.15). Steers given Rev-XS/200 had greater (P < 0.01) LM area and decreased (P ≤ 0.05) 12th-rib fat and YG compared with Rev-200/200 and Rev-IS/200. Using Rev-200/200 and Rev-XS/200 increased (P = 0.03) USDA Select compared with Rev-IS/200. Using greater-initial-dose implant strategies may not affect ADG or G:F but appears to increase leanness.

Absence Of Mate Choice And Postcopulatory Benefits In A Species With Extreme Sexual Size Dimorphism, Marie-Claire Chelini, Eileen A. Hebets

Eileen Hebets Publications

Most hypotheses related to the evolution of female-biased extreme sexual size dimorphism (SSD) attribute the differences in the size of each sex to selection for reproduction, either through selection for increased female fecundity or selection for male increased mobility and faster development. Very few studies, however, have tested for direct fitness benefits associated with the latter – small male size. Mecaphesa celer is a crab spider with extreme SSD, whose males are less than half the size of females and often weigh 10 times less. Here, we test the hypotheses that larger size in females and smaller size in males …

Corrigendum: The Arabidopsis Homologs Of Trithorax (Atx1) And Enhancer Of Zeste (Clf) Establish ‘Bivalent Chromatin Marks’ At The Silent Agamous Locus, Abdelaty Saleh, Ayed Al-Abdallat, Ivan Ndamukong, Raul Alvarez-Venegas, Zoya Avramova

School of Biological Sciences: Faculty Publications

The authors wish to draw the attention to two irregularities in Figures 2a and 4. Both concern errors in duplicating images of "empty" lanes illustrating absence of DNA bands. We regret these omissions and apologize to readers for the inconvenience caused. The results and conclusions remain valid.

Comparison Of Joint Angles For Feet And Leg Conformation Traits Between Gilts At Selection And At Their Second Gestation And Sows Parity 5 And Above, Joseph D. Stock, Julia A. Calderón Díaz, Benny E. Mote, Kenneth J. Stalder

Department of Animal Science: Faculty Publications

This study is a portion from the validation process of an objective methodology to measure feet and leg joint angles and to evaluate their relationship with sow longevity. Joint angle measurements from five feet and leg conformation traits (knee, hock, front and rear pasterns and rear stance) that have been previously described in the literature as being related with sow longevity were obtained from maternal gilts at selection and during their second gestation and compared with those obtained from 45 crossbred sows parity 5 and above. Significant differences (P < 0.05) between parities were identified in the knee, both pasterns, hock and rear stance joint angle measurements. These results suggest that as pigs age, structural changes occur. The range of which these changes occur could carry implications for the use of objective feet and leg angles towards future selection programs and protocols.

Genomic Differences Between Preweaning Survival And Mortality Of Piglets Following Pedv Outbreaks, Francesca Bertolini, John C.S. Harding, Benny Mote, Graham S. Plastow, Max Rothschild

Department of Animal Science: Faculty Publications

Porcine Epidemic Diarrhea (PED) is a serious and potentially devastating disease in the US and Canadian pig industries. To investigate if there is genetic resistance to PEDV a total of 156 dead and 106 surviving neonatal piglets infected with PEDV were genotyped with over 60,000 genetic markers to investigate genetic differences between the two groups. This allows for the identification of genomic regions that could be linked to susceptibility/resistance to virus infection and in cellular components that are involved in the PED virus infection cycle, providing new insights on the genetic resistance to this disease.

Joint Angles For Feet And Leg Conformation Traits In Second Gestation Sows, Joseph D. Stock, Julia A. Calderón Díaz, Benny Mote, Kenneth J. Stalder

Department of Animal Science: Faculty Publications

This study is a portion from the validation process of an

objective methodology to measure feet and leg joint angles

and to evaluate their relationship with sow longevity. Five

feet and leg conformation traits (knee, hock, front and rear

pasterns and rear stance) that have been described in the

literature as being related with sow longevity were selected

for this study. Profile and rear stance digital images were

obtained from 277 sows during their 2nd gestation (26.7 ±

17.2 days of gestation; range 0 to 87 days). Sows were

obtained from a single gilt population and were moved to

three …

Genetic And Genomic Basis Of Antibody Response To Porcine Reproductive And Respiratory Syndrome (Prrs) In Gilts And Sows, Nick V. Serão, Robert A. Kemp, Benny Mote, Philip Willson, John C.S. Harding, Stephen C. Bishop, Graham S. Plastow, Jack C.M. Dekkers

Department of Animal Science: Faculty Publications

Background: Our recent research showed that antibody response to porcine reproductive and respiratory syndrome (PRRS), measured as sample-to-positive (S/P) ratio, is highly heritable and has a high genetic correlation with reproductive performance during a PRRS outbreak. Two major quantitative trait loci (QTL) on Sus scrofa chromosome 7 (SSC7; QTL_MHC and QTL₁₃₀) accounted for ~40 % of the genetic variance for S/P. Objectives of this study were to estimate genetic parameters for PRRS S/P in gilts during acclimation, identify regions associated with S/P, and evaluate the accuracy of genomic prediction of S/P across populations with different prevalences of …

Rumen Bacterial Community Composition In Holstein And Jersey Cows Is Different Under Same Dietary Condition And Is Not Affected By Sampling Method, Henry A. Paz, Christopher L., Makala J. Muller, Paul J. Kononoff, Samodha C. Fernando

Department of Animal Science: Faculty Publications

The rumen microbial community in dairy cows plays a critical role in efficient milk production. However, there is a lack of data comparing the composition of the rumen bacterial community of the main dairy breeds. This study utilizes 16S rRNA gene sequencing to describe the rumen bacterial community composition in Holstein and Jersey cows fed the same diet by sampling the rumen microbiota via the rumen cannula (Holstein cows) or esophageal tubing (both Holstein and Jersey cows). After collection of the rumen sample via esophageal tubing, particles attached to the strainer were added to the sample to ensure representative sampling …

Results Of Survey Of Stakeholders Regarding Knowledge Of And Attitudes Towards Feed Intake, Efficiency And Genetic Improvement Concepts, R. L. Weaber, J. E. Kerley, H. C. Freetly, D. J. Garrick, S. L. Hansen, K. A. Johnson, M. S. Kerley, D. D. Loy, E. Marques, H. L. Neibergs, E. J. Pollak, R. D. Schnabel, C. M. Seabury, D. W. Shike, M. L. Spangler, J. F. Taylor

Department of Animal Science: Faculty Publications

Individual animal feed efficiency plays a key role in the profitability and sustainability of the US beef industry. During the growing and finishing phase of production, a 10% improvement in feed efficiency has a two-fold greater impact on profit than a 10% increase in rate of gain (Fox et al., 2001). The traits that beef producers routinely record are outputs which determine the value of product sold and not the inputs defining the cost of beef production. The inability to routinely measure feed intake and feed efficiency on large numbers of cattle has precluded the efficient application of selection despite …

Development Of Economic Selection Indices For Beef Cattle Improvement, Kathleen P. Ochsner

Department of Animal Science: Faculty Publications

Profitability is the primary goal for most beef cattle producers. The main source of long-term profitability for a beef cattle operation lies in its production efficiency relative to other operations (Harris, 1970). There are numerous approaches to achieve greater efficiency including nutrition, reproduction, management, and genetics. The goal in animal breeding and genetics is to improve animal populations and future generations of animals (Dekkers et al., 2004). Expected progeny differences (EPD) are the traditional genetic tools used to select parents. A drawback to EPD is that they represent genetic merit in only one trait while in reality multiple traits influence …