Us Meat Animal Research Center Usmarc

Clay Center, NE, United States

Us Meat Animal Research Center Usmarc

Clay Center, NE, United States
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Heaton M.P.,Us Meat Animal Research Center Usmarc | Smith T.P.,Us Meat Animal Research Center Usmarc | Carnahan J.K.,Us Meat Animal Research Center Usmarc | Basnayake V.,A Neogen Company | And 3 more authors.
F1000Research | Year: 2016

The availability of whole genome sequence (WGS) data has made it possible to discover protein variants in silico. However, existing bovine WGS databases do not show data in a form conducive to protein variant analysis, and tend to under represent the breadth of genetic diversity in U.S. beef cattle. Thus, our first aim was to use 96 beef sires, sharing minimal pedigree relationships, to create a searchable and publicly viewable set of mapped genomes relevant for 19 popular breeds of U.S. cattle. Our second aim was to identify protein variants encoded by the bovine endothelial PAS domain-containing protein 1 gene ( EPAS1), a gene associated with high-altitude pulmonary hypertension in Angus cattle. The identity and quality of genomic sequences were verified by comparing WGS genotypes to those derived from other methods. The average read depth, genotype scoring rate, and genotype accuracy exceeded 14, 99%, and 99%, respectively. The 96 genomes were used to discover four amino acid variants encoded by EPAS1 (E270Q, P362L, A671G, and L701F) and confirm two variants previously associated with disease (A606T and G610S). The six EPAS1 missense mutations were verified with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry assays, and their frequencies were estimated in a separate collection of 1154 U.S. cattle representing 46 breeds. A rooted phylogenetic tree of eight polypeptide sequences provided a framework for evaluating the likely order of mutations and potential impact of EPAS1 alleles on the adaptive response to chronic hypoxia in U.S. cattle. This public, whole genome resource facilitates in silico identification of protein variants in diverse types of U.S. beef cattle, and provides a means of translating WGS data into a practical biological and evolutionary context for generating and testing hypotheses. © 2016 Heaton MP et al.

Heaton M.P.,Us Meat Animal Research Center Usmarc | Kalbfleisch T.S.,University of Louisville | Kalbfleisch T.S.,Intrepid Bioinformatics | Petrik D.T.,a Neogen company | And 6 more authors.
PLoS ONE | Year: 2013

In sheep, small ruminant lentiviruses cause an incurable, progressive, lymphoproliferative disease that affects millions of animals worldwide. Known as ovine progressive pneumonia virus (OPPV) in the U.S., and Visna/Maedi virus (VMV) elsewhere, these viruses reduce an animal's health, productivity, and lifespan. Genetic variation in the ovine transmembrane protein 154 gene (TMEM154) has been previously associated with OPPV infection in U.S. sheep. Sheep with the ancestral TMEM154 haplotype encoding glutamate (E) at position 35, and either form of an N70I variant, were highly-susceptible compared to sheep homozygous for the K35 missense mutation. Our current overall aim was to characterize TMEM154 in sheep from around the world to develop an efficient genetic test for reduced susceptibility. The average frequency of TMEM154 E35 among 74 breeds was 0.51 and indicated that highly-susceptible alleles were present in most breeds around the world. Analysis of whole genome sequences from an international panel of 75 sheep revealed more than 1,300 previously unreported polymorphisms in a 62 kb region containing TMEM154 and confirmed that the most susceptible haplotypes were distributed worldwide. Novel missense mutations were discovered in the signal peptide (A13V) and the extracellular domains (E31Q, I74F, and I102T) of TMEM154. A matrix-assisted laser desorption/ionization-time-of flight mass spectrometry (MALDI-TOF MS) assay was developed to detect these and six previously reported missense and two deletion mutations in TMEM154. In blinded trials, the call rate for the eight most common coding polymorphisms was 99.4% for 499 sheep tested and 96.0% of the animals were assigned paired TMEM154 haplotypes (i.e., diplotypes). The widespread distribution of highly-susceptible TMEM154 alleles suggests that genetic testing and selection may improve the health and productivity of infected flocks.

Heaton M.P.,Us Meat Animal Research Center Usmarc | Leymaster K.A.,Us Meat Animal Research Center Usmarc | Kalbfleisch T.S.,University of Louisville | Kijas J.W.,CSIRO | And 8 more authors.
PLoS ONE | Year: 2014

DNA-based parentage determination accelerates genetic improvement in sheep by increasing pedigree accuracy. Single nucleotide polymorphism (SNP) markers can be used for determining parentage and to provide unique molecular identifiers for tracing sheep products to their source. However, the utility of a particular ''parentage SNP'' varies by breed depending on its minor allele frequency (MAF) and its sequence context. Our aims were to identify parentage SNPs with exceptional qualities for use in globally diverse breeds and to develop a subset for use in North American sheep. Starting with genotypes from 2,915 sheep and 74 breed groups provided by the International Sheep Genomics Consortium (ISGC), we analyzed 47,693 autosomal SNPs by multiple criteria and selected 163 with desirable properties for parentage testing. On average, each of the 163 SNPs was highly informative (MAF$0.3) in 4865 breed groups. Nearby polymorphisms that could otherwise confound genetic testing were identified by whole genome and Sanger sequencing of 166 sheep from 54 breed groups. A genetic test with 109 of the 163 parentage SNPs was developed for matrix-assisted laser desorption/ionization- time-of-flight mass spectrometry. The scoring rates and accuracies for these 109 SNPs were greater than 99% in a panel of North American sheep. In a blinded set of 96 families (sire, dam, and non-identical twin lambs), each parent of every lamb was identified without using the other parent's genotype. In 74 ISGC breed groups, the median estimates for probability of a coincidental match between two animals (PI), and the fraction of potential adults excluded from parentage (PE) were 1.1610(239) and 0.999987, respectively, for the 109 SNPs combined. The availability of a well-characterized set of 163 parentage SNPs facilitates the development of high-throughput genetic technologies for implementing accurate and economical parentage testing and traceability in many of the world's sheep breeds.

Kelley C.M.,Rush University Medical Center | Kelley C.M.,Us Meat Animal Research Center Usmarc | Ash J.A.,Cornell University | Ash J.A.,University of Oxford | And 9 more authors.
Current Alzheimer Research | Year: 2016

Down syndrome (DS), caused by trisomy of chromosome 21, is marked by intellectual disability (ID) and early onset of Alzheimer’s disease (AD) neuropathology including hippocampal cholinergic projection system degeneration. Here we determined the effects of age and maternal choline supplementation (MCS) on hippocampal cholinergic deficits in Ts65Dn mice compared to 2N mice sacrificed at 6-8 and 14-18 months of age. Ts65Dn mice and disomic (2N) littermates sacrificed at ages 6-8 and 14-18 mos were used for an aging study and Ts65Dn and 2N mice derived from Ts65Dn dams were maintained on either a choline-supplemented or a choline-controlled diet (conception to weaning) and examined at 14-18 mos for MCS studies. In the latter, mice were behaviorally tested on the radial arm Morris water maze (RAWM) and hippocampal tissue was examined for intensity of choline acetyltransferase (ChAT) immunoreactivity. Hippocampal ChAT activity was evaluated in a separate cohort. ChAT-positive fiber innervation was significantly higher in the hippocampus and dentate gyrus in Ts65Dn mice compared with 2N mice, independent of age or maternal diet. Similarly, hippocampal ChAT activity was significantly elevated in Ts65Dn mice compared to 2N mice, independent of maternal diet. A significant increase with age was seen in hippocampal cholinergic innervation of 2N mice, but not Ts65Dn mice. Degree of ChAT intensity correlated negatively with spatial memory ability in unsupplemented 2N and Ts65Dn mice, but positively in MCS 2N mice. The increased innervation produced by MCS appears to improve hippocampal function, making this a therapy that may be exploited for future translational approaches in human DS. © 2016 Bentham Science Publishers.

Nonneman D.,Us Meat Animal Research Center Usmarc | Lindholm-Perry A.K.,Us Meat Animal Research Center Usmarc | Shackelford S.D.,Us Meat Animal Research Center Usmarc | King D.A.,Us Meat Animal Research Center Usmarc | And 7 more authors.
Journal of Animal Science | Year: 2011

The identification of predictive DNA markers for pork quality would allow US pork producers and breeders to select genetically superior animals more quickly and efficiently for the production of consistent, high-quality meat. Genome scans have identified QTL for tenderness on SSC 2, which have been fine-mapped to the calpastatin locus. The objectives of this study were to identify the sequence variation in calpastatin that likely affects tenderness in commerciallevel pig populations and to develop definitive DNA markers that are predictive of pork tenderness for use in marker-assisted selection programs. We resequenced the calpastatin regulatory and transcribed regions in pigs with divergently extreme shear force values to identify possible mutstions that could affect tenderness. A total of 194 SNP were identified in this sequence, and 31 SNP were found in predicted transcription factor binding sites. We tested 131 polymorphisms in our research population and a subset (40) of these in samples of industry pigs for their association with objective measures of tenderness. We identified 4 SNP that were consistently associated with pork tenderness in all the populations studied, representing 2,826 pigs rom 4 distinct populations. Gel shift assays were designed for these SNP and 12 other polymorphic sites. Six sites demonstrated a gel shift when probes were incubated with nuclear extract from muscle, heart, or testis. Four of these sites, a specificity protein 1 (Sp1) site around nucleotides 12978 and 12979, a potential thyrotroph embryonic factor (Tef) site at nucleotide 25587, an unknown site at nucleotide 48699, and myocyte enhancer factor-2 (Mef-2)/TATA sites with SNP at positions 49223 and 49228 were allele specific in binding nuclear roteins. The allele frequencies for the tender alleles were similar (0.11 to 0.36) in the 4 different commercial populations. These 4 SNP were not in complete linkage disequilibrium with each other and may independently affect calpastatin expression, tenderness, or both. These markers should be predictive of pork tenderness in industry populations. © 2011 American Society of Animal Science.

Pinto T.L.C.,Federal University of Lavras | Nogueira M.B.R.,Federal University of Lavras | Sales J.N.S.,Federal University of Lavras | de Carvalho R.R.,Federal University of Lavras | And 2 more authors.
Ciencia e Agrotecnologia | Year: 2015

High milk production, heat, physiological status and management impair reproduction in Holstein cows. The use of in vivo-produced embryos has been reported as an alternative to enhance pregnancy outcome in the tropics; however there are several limitations for its production, especially from variations in superovulatory responses. The in vitro production of embryos would avoid such variations, but few studies have been reported. This study aims to verify the effects of variables related to recipients under a program of routine in vitro embryo transfer on a commercial dairy farm in southeastern Brazil. It was hypothesized that pregnancy rates after transfer of ovum pick up or OPU-derived embryos (ET) to lactating Holstein recipients may be influenced by recipient GnRH-treatment at ET, parity, milk production and body condition score. Recipients (267) were allocated to one of three i.m. treatments given at ET: Control (92) – 2.5 ml saline; Buserelin (86) – 10 μg Buserelin acetate; Deslorelin (89) – 750 μg Deslorelin acetate. Ultrasound images and blood samples were taken at ET and seven days later. The first pregnancy diagnosis was performed between 30-40 days and the second between 60-80 days post ET. Data were analyzed by GENMOD (SAS®). The proportion of pregnant cows was greater (P<0.05) in Buserelin-treated recipients (38.3%) at the first pregnancy diagnosis than Controls (24.1%), but similar to Deslorelin and control cows at the second diagnosis (13.0, 20.9 and 14.6% in Control, Buserelin and Deslorelin, respectively). In conclusion, Buserelin improved pregnancy rate only transitorily, under the present conditions. © 2015, Federal University of Lavras. All rights reserved.

PubMed | Us Meat Animal Research Center Usmarc, a Neogen Company and University of Louisville
Type: | Journal: F1000Research | Year: 2016

The availability of whole genome sequence (WGS) data has made it possible to discover protein variants

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