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You searched for: Author "Tad S. Sonstegard" Remove constraint Author: "Tad S. Sonstegard"
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1. Effects of the SLICK1 mutation in PRLR on regulation of core body temperature and global gene expression in liver in cattle

Author:
Tad S. Sonstegard,   et al.   ; Froylan Sosa; José E.P. Santos; D. Owen Rae; Colleen C. Larson; Marissa Macchietto; Juan E. Abrahante; Thiago F. Amaral; Anna C. Denicol; Peter J. Hansen;     Show all 10 Authors
Source:
Animal 2022 v.16 no.5 pp. 100523
ISSN:
1751-7311
Subject:
Holstein; Senepol; adults; alleles; amino acid metabolism; body temperature; cohort studies; fatty acids; gene expression; gene expression regulation; heat stress; heterozygosity; homozygosity; immune response; liver; phenotype; prolactin; sequence deletion
Abstract:
... The SLICK1 mutation in bovine PRLR (c.1382del; rs517047387) is a deletion mutation resulting in a protein with a truncated intracellular domain. Cattle carrying at least one allele have a phenotype characterized by a short hair coat (slick phenotype) and increased resistance to heat stress. Given the pleiotropic nature of prolactin, the mutation may affect other physiological characteristics. The ...
DOI:
10.1016/j.animal.2022.100523

2. Evaluating Large Spontaneous Deletions in a Bovine Cell Line Selected for Bovine Viral Diarrhea Virus Resistance

Author:
Tad S. Sonstegard,   et al.   ; Aspen M. Workman; Michael P. Heaton; Dennis A. Webster; Gregory P. Harhay; Theodore S. Kalbfleisch; Timothy P. L. Smith; Shollie M. Falkenberg; Daniel F. Carlson;     Show all 9 Authors
Source:
Viruses 2021 v.13 no.11 pp. -
ISSN:
1999-4915
Subject:
Bovine viral diarrhea virus 1; CRISPR-Cas systems; cattle; cell lines; genes; genetic variation; kidneys; pH; phenotype; viruses
Abstract:
... Bovine viral diarrhea virus’s (BVDV) entry into bovine cells involves attachment of virions to cellular receptors, internalization, and pH-dependent fusion with endosomal membranes. The primary host receptor for BVDV is CD46; however, the complete set of host factors required for virus entry is unknown. The Madin-Darby bovine kidney (MDBK) cell line is susceptible to BVDV infection, while a deriva ...
DOI:
10.3390/v13112147

3. BGVD: An Integrated Database for Bovine Sequencing Variations and Selective Signatures

Author:
Tad S. Sonstegard,   et al.   ; Ningbo Chen; Weiwei Fu; Jianbang Zhao; Jiafei Shen; Qiuming Chen; Zhuqing Zheng; Hong Chen; Chuzhao Lei; Yu Jiang;     Show all 10 Authors
Source:
Genomics, proteomics & bioinformatics 2020 v.18 no.2 pp. 186-193
ISSN:
1672-0229
Subject:
artificial selection; bioinformatics; cattle; data collection; databases; genes; genetic variation; genomics; proteomics
Abstract:
... Next-generation sequencing has yielded a vast amount of cattle genomic data for global characterization of population genetic diversity and identification of genomic regions under natural and artificial selection. However, efficient storage, querying, and visualization of such large datasets remain challenging. Here, we developed a comprehensive database, the Bovine Genome Variation Database (BGVD ...
DOI:
10.1016/j.gpb.2019.03.007

4. Simulation of introgression of the POLLED allele into the Jersey breed via conventional breeding vs. gene editing1

Author:
Tad S. Sonstegard,   et al.   ; Maci L. Mueller; John B. Cole; Alison L. Van Eenennaam;     Show all 4 Authors
Source:
Translational Animal Science 2018 v.2 no.suppl.1 pp. 1-4
ISSN:
2573-2102
Subject:
Jersey; USDA; alleles; cattle husbandry; dairy cattle; introgression
Abstract:
... Dehorning, a standard cattle management practice to protect animals and humans from injury, is unpleasant, costly, and subject to public scrutiny (Stafford and Mellor, 2011). In the United States, 94% of dairy cattle producers report routine dehorning (USDA, 2009). Horns are recessively inherited; an alternative is to breed for polled (Long and Gregory, 1978). ...
DOI:
10.1093/tas/txy054
CHORUS:
10.1093/tas/txy054

5. Genomic Regions Associated with Sheep Resistance to Gastrointestinal Nematodes

Author:
Tad S. Sonstegard,   et al.   ; Magda Vieira Benavides; Curtis Van Tassell;     Show all 3 Authors
Source:
Trends in parasitology 2016 v.32 no.6 pp. 470-480
ISSN:
1471-4922
Subject:
eggs; farmers; flocks; gastrointestinal nematodes; gastrointestinal system; genetic markers; genomics; hemostasis; interferon-gamma; livestock and meat industry; major histocompatibility complex; mucus; sheep
Abstract:
... Genetic markers for sheep resistance to gastrointestinal parasites have long been sought by the livestock industry as a way to select more resistant individuals and to help farmers reduce parasite transmission by identifying and removing high egg shedders from the flock. Polymorphisms related to the major histocompatibility complex and interferon (IFN)-γ genes have been the most frequently reporte ...
DOI:
10.1016/j.pt.2016.03.007

6. Chickspress: a resource for chicken gene expression

Author:
Tad S. Sonstegard,   et al.   ; Fiona M. McCarthy; Ken Pendarvis; Amanda M. Cooksey; Cathy R. Gresham; Matt Bomhoff; Sean Davey; Eric Lyons; Susan M. Bridges; Shane C. Burgess;     Show all 10 Authors
Source:
Database 2019 v.2019 no. pp. -
ISSN:
0162-4105
Subject:
chickens; databases; gene expression; genes; microRNA; peptides; prediction; proteome; proteomics
Abstract:
... High-throughput sequencing and proteomics technologies are markedly increasing the amount of RNA and peptide data that are available to researchers, which are typically made publicly available via data repositories such as the NCBI Sequence Read Archive and proteome archives, respectively. These data sets contain valuable information about when and where gene products are expressed, but this infor ...
DOI:
10.1093/database/baz058
CHORUS:
10.1093/database/baz058

7. Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo (Bubalus bubalis)

Author:
Tad S. Sonstegard,   et al.   ; Shuli Liu; Xiaolong Kang; Claudia R. Catacchio; Mei Liu; Lingzhao Fang; Steven G. Schroeder; Wenli Li; Benjamin D. Rosen; Daniela Iamartino; Leopoldo Iannuzzi; Curtis P. Van Tassell; Mario Ventura; Wai Yee Low; John L. Williams; Derek M. Bickhart; George E. Liu;     Show all 17 Authors
Source:
Functional & integrative genomics 2019 v.19 no.3 pp. 409-419
ISSN:
1438-793X
Subject:
Bubalus bubalis; buffaloes; cattle; comparative genomic hybridization; copy number variation; evolution; fluorescence in situ hybridization; genes; genome-wide association study; high-throughput nucleotide sequencing; immune response; oxygen; phenotype; prediction; quantitative polymerase chain reaction; regression analysis; selection methods; sensory system; signal transduction
Abstract:
... Duplicated sequences are an important source of gene evolution and structural variation within mammalian genomes. Using a read depth approach based on next-generation sequencing, we performed a genome-wide analysis of segmental duplications (SDs) and associated copy number variations (CNVs) in the water buffalo (Bubalus bubalis). By aligning short reads of Olimpia (the reference water buffalo) to ...
DOI:
10.1007/s10142-019-00657-4
CHORUS:
10.1007/s10142-019-00657-4

8. Identification of a nonsense mutation in APAF1 that is likely causal for a decrease in reproductive efficiency in Holstein dairy cattle

Author:
Tad S. Sonstegard,   et al.   ; Heather A. Adams; Paul M. VanRaden; Daniel J. Null; Curt P. Van Tassell; Denis M. Larkin; Harris A. Lewin;     Show all 7 Authors
Source:
Journal of dairy science 2016 v.99 no.8 pp. 6693-6701
ISSN:
0022-0302
Subject:
Holstein; alleles; apoptosis; breeding; chromosomes; conception rate; dairy cattle; daughters; farms; genotyping; haplotypes; heterozygosity; homozygosity; mice; mutants; neurodegenerative diseases; nonsense mutation; protein-protein interactions; proteinases; reproductive efficiency; screening; sons
Abstract:
... The HH1 haplotype on chromosome 5 is associated with a reduced conception rate and a deficit of homozygotes at the population level in Holstein cattle. The source HH1 haplotype was traced to the bull Pawnee Farm Arlinda Chief (Chief), who was born in 1962 and has sired more than 16,000 daughters. We identified a nonsense mutation in APAF1 (apoptotic protease activating factor 1;APAF1 p.Q579X) with ...
DOI:
10.3168/jds.2015-10517

9. Variants at the ASIP locus contribute to coat color darkening in Nellore cattle

Author:
Tad S. Sonstegard,   et al.   ; Beatriz B. Trigo; Adam T. H. Utsunomiya; Alvaro A. A. D. Fortunato; Marco Milanesi; Rafaela B. P. Torrecilha; Harrison Lamb; Loan Nguyen; Elizabeth M. Ross; Ben Hayes; Rômulo C. M. Padula; Thayla S. Sussai; Ludmilla B. Zavarez; Rafael S. Cipriano; Maria M. T. Caminhas; Flavia L. Lopes; Cassiano Pelle; Tosso Leeb; Danika Bannasch; Derek Bickhart; Timothy P. L. Smith; José F. Garcia; Yuri T. Utsunomiya;     Show all 23 Authors
Source:
Genetics, selection, evolution 2021 v.53 no.1 pp. 40
ISSN:
1297-9686
Subject:
Brahman; Nellore; ancestry; color; eumelanin; evolution; exons; genome-wide association study; genotyping; head; heat tolerance; loci; nanopores; neck; pigmentation; single nucleotide polymorphism; transposons; zebu
Abstract:
... BACKGROUND: Nellore cattle (Bos indicus) are well-known for their adaptation to warm and humid environments. Hair length and coat color may impact heat tolerance. The Nellore breed has been strongly selected for white coat, but bulls generally exhibit darker hair ranging from light grey to black on the head, neck, hump, and knees. Given the potential contribution of coat color variation to the ada ...
DOI:
10.1186/s12711-021-00633-2

10. Whole genome structural analysis of Caribbean hair sheep reveals quantitative link to West African ancestry

Author:
Tad S. Sonstegard,   et al.   ; Gordon L. Spangler; Benjamin D. Rosen; Moses Babatunde Ilori; Olivier Hanotte; Eui-Soo Kim; Joan M. Burke; James L.M. Morgan; David R. Notter; Curtis P. Van Tassell;     Show all 10 Authors
Source:
PloS one 2017 v.12 no.6 pp. 16-32
ISSN:
1932-6203
Subject:
Barbados Blackbelly; ancestry; drug resistance; ecotypes; gastrointestinal nematodes; genome; humans; introgression; phylogeny; population structure; production costs; provenance; sheep; sheep industry; single nucleotide polymorphism; trade; wool; Africa; Caribbean; Europe; South America; United States
Abstract:
... Hair sheep of Caribbean origin have become an important part of the U.S. sheep industry. Their lack of wool eliminates a number of health concerns and drastically reduces the cost of production. More importantly, Caribbean hair sheep demonstrate robust production performance even in the presence of drug-resistant gastrointestinal nematodes, a rising concern to the industry. Despite the growing imp ...
Handle:
10113/5931470
DOI:
10.1371/journal.pone.0179021
PubMed:
28662044
PubMed Central:
PMC5490989

11. A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle

Author:
Tad S. Sonstegard,   et al.   ; Lingyang Xu; Yali Hou; Derek M. Bickhart; Jiuzhou Song; Curtis P. Van Tassell; George E. Liu;     Show all 7 Authors
Source:
Functional & integrative genomics 2014 v.14 no.2 pp. 333-339
ISSN:
1438-793X
Subject:
Angus; cattle; gastrointestinal nematodes; gastrointestinal system; gene expression; genes; haplotypes; linear models; linkage disequilibrium; nematode infections; regression analysis; single nucleotide polymorphism; surveys
Abstract:
... Gastrointestinal (GI) nematode infections are a worldwide threat to human health and animal production. In this study, we performed a genome-wide association study between copy number variations (CNVs) and resistance to GI nematodes in an Angus cattle population. Using a linear regression analysis, we identified one deletion CNV which reaches genome-wide significance after Bonferroni correction. W ...
DOI:
10.1007/s10142-014-0371-6
PubMed:
24718732

12. Short-Read Sequencing for Genomic Analysis of the Brown Rot Fungus Fibroporia radiculosa

Author:
Tad S. Sonstegard,   et al.   ; Juliet D. Tang; Andy D. Perkins; Steven G. Schroeder; Shane C. Burgess; Susan V. Diehl;     Show all 6 Authors
Source:
Applied and environmental microbiology 2012 v.78 no.7 pp. 2272-2281
ISSN:
0099-2240
Subject:
sequence analysis; lignocellulose; decayed wood; Serpula lacrymans; Rhodonia placenta; brown-rot fungi; reading; genes; signal peptide; filters
Abstract:
... The feasibility of short-read sequencing for genomic analysis was demonstrated for Fibroporia radiculosa, a copper-tolerant fungus that causes brown rot decay of wood. The effect of read quality on genomic assembly was assessed by filtering Illumina GAIIx reads from a single run of a paired-end library (75-nucleotide read length and 300-bp fragment size) at three different stringency levels and th ...
DOI:
10.1128/AEM.06745-11
PubMed:
22247176
PubMed Central:
PMC3302605

13. RAPTR-SV: a hybrid method for the detection of structural variants

Author:
Tad S. Sonstegard,   et al.   ; Derek M. Bickhart; Jana L. Hutchison; Lingyang Xu; Robert D. Schnabel; Jeremy F. Taylor; James M. Reecy; Steven Schroeder; Curt P. Van Tassell; George E. Liu;     Show all 10 Authors
Source:
Bioinformatics 2015 v.31 no.13 pp. 2084-2090
ISSN:
1367-4803
Subject:
algorithms; computer analysis; computer software; data collection; genetic techniques and protocols; genome; prediction
Abstract:
... Motivation: Identification of structural variants (SVs) in sequence data results in a large number of false positive calls using existing software, which overburdens subsequent validation. Results: Simulations using RAPTR-SV and other, similar algorithms for SV detection revealed that RAPTR-SV had superior sensitivity and precision, as it recovered 66.4% of simulated tandem duplications with a pre ...
Handle:
10113/61483
DOI:
10.1093/bioinformatics/btv086

14. The development of genomics applied to dairy breeding

Author:
Tad S. Sonstegard,   et al.   ; Marcos V.B. Silva; Daniel J.A. dos Santos; Solomon A. Boison; Adam T.H. Utsunomiya; Adriana S. Carmo; John B. Cole; Curt P. Van Tassell;     Show all 8 Authors
Source:
Livestock science 2014 v.166 pp. 66-75
ISSN:
1871-1413
Subject:
breeding value; cattle breeding; dairy cattle; genetic markers; genome; genomics; marker-assisted selection; models; program evaluation; quantitative trait loci; single nucleotide polymorphism; Australia; Canada; Europe; New Zealand; United States
Abstract:
... Genomic selection (GS) has profoundly changed dairy cattle breeding in the last decade and can be defined as the use of genomic breeding values (GEBV) in selection programs. The GEBV is the sum of the effects of dense DNA markers across the whole genome, capturing all the quantitative trait loci (QTL) that contribute to variation in a trait. This technology was successfully implemented in the Unit ...
Handle:
10113/60899
DOI:
10.1016/j.livsci.2014.05.017

15. Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions

Author:
Tad S. Sonstegard,   et al.   ; Ana M. Pérez O’Brien; Gábor Mészáros; Yuri T. Utsunomiya; J. Fernando Garcia; Curtis P. Van Tassell; Roberto Carvalheiro; Marcos V.B. da Silva; Johann Sölkner;     Show all 9 Authors
Source:
Livestock science 2014 v.166 pp. 121-132
ISSN:
1871-1413
Subject:
alleles; animal breeding; animal genetics; cattle; gene frequency; genomics; genotype; genotyping; linkage disequilibrium; loci; single nucleotide polymorphism; taurine; zebu; zebu breeds
Abstract:
... Linkage disequilibrium (LD), the observed correlation between alleles at different loci in the genome, is a determinant parameter in many applications of molecular genetics. With the wider use of genomic technologies in animal breeding and animal genetics, it is worthwhile revising and improving the current knowledge and understanding of cattle LD.This study analyzes levels of LD assessed through ...
DOI:
10.1016/j.livsci.2014.05.007

16. Bovine Exome Sequence Analysis and Targeted SNP Genotyping of Recessive Fertility Defects BH1, HH2, and HH3 Reveal a Putative Causative Mutation in SMC2 for HH3

Author:
Tad S. Sonstegard,   et al.   ; Matthew C. McClure; Derek Bickhart; Dan Null; Paul VanRaden; Lingyang Xu; George Wiggans; George Liu; Steve Schroeder; Jarret Glasscock; Jon Armstrong; John B. Cole; Curtis P. Van Tassell;     Show all 13 Authors
Source:
PloS one 2014 v.9 no.3 pp. 1-9
ISSN:
1932-6203
Subject:
Brown Swiss; DNA repair; Holstein; Jersey; cattle; cell division; chromosomes; embryogenesis; exons; genotyping; haplotypes; sequence analysis; single nucleotide polymorphism
Abstract:
... The recent discovery of bovine haplotypes with negative effects on fertility in the Brown Swiss, Holstein, and Jersey breeds has allowed producers to identify carrier animals using commercial single nucleotide polymorphism (SNP) genotyping assays. This study was devised to identify the causative mutations underlying defective bovine embryo development contained within three of these haplotypes (Br ...
Handle:
10113/58860
DOI:
10.1371/journal.pone.0092769
PubMed:
24667746
PubMed Central:
PMC3965462

17. Effect of Artificial Selection on Runs of Homozygosity in U.S. Holstein Cattle

Author:
Tad S. Sonstegard,   et al.   ; Eui-Soo Kim; John B. Cole; Heather Huson; George R. Wiggans; Curtis P. Van Tassell; Brian A. Crooker; George Liu; Yang Da; Zhanjiang Liu;     Show all 10 Authors
Source:
PloS one 2013 v.8 no.11 pp. -
ISSN:
1932-6203
Subject:
Holstein; animal breeding; artificial insemination; artificial selection; cattle; genome; haplotypes; homozygosity; inbreeding coefficient; loci; milk; milk fat yield; milk protein yield; quantitative trait loci; United States
Abstract:
... The intensive selection programs for milk made possible by mass artificial insemination increased the similarity among the genomes of North American (NA) Holsteins tremendously since the 1960s. This migration of elite alleles has caused certain regions of the genome to have runs of homozygosity (ROH) occasionally spanning millions of continuous base pairs at a specific locus. In this study, genome ...
Handle:
10113/58857
DOI:
10.1371/journal.pone.0080813
PubMed:
24348915
PubMed Central:
PMC3858116

18. Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle

Author:
Tad S Sonstegard,   et al.   ; Ana M Pérez O’Brien; Yuri T Utsunomiya; Gábor Mészáros; Derek M Bickhart; George E Liu; Curtis P Van Tassell; Marcos VB Da Silva; José Fernando Garcia; Johann Sölkner;     Show all 10 Authors
Source:
Genetics, selection, evolution 2014 v.46 no.1 pp. 2607
ISSN:
0999-193X
Subject:
Angus; Brown Swiss; Nellore; beef cattle; genes; genetic variation; genome assembly; linkage disequilibrium
Abstract:
... BACKGROUND: Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium (LD) patterns. METHODS: By comparing the differences in regional LD variation b ...
DOI:
10.1186/1297-9686-46-19
PubMed:
24592996
PubMed Central:
PMC4014805

19. Accuracy of genotype imputation in Nelore cattle

Author:
Tad S Sonstegard,   et al.   ; Roberto Carvalheiro; Solomon A Boison; Haroldo H R Neves; Mehdi Sargolzaei; Flavio S Schenkel; Yuri T Utsunomiya; Ana Maria Pérez O’Brien; Johann Sölkner; John C McEwan; Curtis P Van Tassell; José Fernando Garcia;     Show all 12 Authors
Source:
Genetics, selection, evolution 2014 v.46 no.1 pp. 69
ISSN:
0999-193X
Subject:
Nellore; bulls; computer software; cost effectiveness; cows; gene frequency; genetic markers; genotype; genotyping; linkage disequilibrium; marker-assisted selection; prediction; single nucleotide polymorphism; sires; zebu; zebu breeds
Abstract:
... BACKGROUND: Genotype imputation from low-density (LD) to high-density single nucleotide polymorphism (SNP) chips is an important step before applying genomic selection, since denser chips tend to provide more reliable genomic predictions. Imputation methods rely partially on linkage disequilibrium between markers to infer unobserved genotypes. Bos indicus cattle (e.g. Nelore breed) are characteriz ...
DOI:
10.1186/s12711-014-0069-1
PubMed:
25927950
PubMed Central:
PMC4192291

20. Signatures of selection and environmental adaptation across the goat genome post-domestication

Author:
Tad S. Sonstegard,   et al.   ; Francesca Bertolini; Bertrand Servin; Andrea Talenti; Estelle Rochat; Eui Soo Kim; Claire Oget; Isabelle Palhière; Alessandra Crisà; Gennaro Catillo; Roberto Steri; Marcel Amills; Licia Colli; Gabriele Marras; Marco Milanesi; Ezequiel Nicolazzi; Benjamin D. Rosen; Curtis P. Van Tassell; Bernt Guldbrandtsen; Gwenola Tosser-Klopp; Alessandra Stella; Max F. Rothschild; Stéphane Joost; Paola Crepaldi; the AdaptMap consortium;     Show all 25 Authors
Source:
Genetics, selection, evolution 2018 v.50 no.1 pp. 57
ISSN:
0999-193X
Subject:
artificial selection; circadian clocks; climatic factors; color; data collection; domestication; genes; genotyping; geographical coordinates; geographical distribution; glucose; goat breeds; goats; humans; oxidative stress; phenotype; stress response
Abstract:
... BACKGROUND: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in term ...
DOI:
10.1186/s12711-018-0421-y
PubMed:
30449276
PubMed Central:
PMC6240954