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Animal genetics2018; 49(6); 564-570; doi: 10.1111/age.12717

Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project.

Abstract: 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 fluid, urine and microbiome samples from all regions of the gastrointestinal and urogenital tracts were collected. Epidermal keratinocytes and dermal fibroblasts were cultured from skin samples. All tissues were grossly and histologically evaluated by a board-certified veterinary pathologist. The results of the clinical and pathological evaluations identified subclinical eosinophilic and lymphocytic infiltration throughout the length of the gastrointestinal tract as well as a mild clinical lameness in both animals. Each sample was cryo-preserved in multiple ways, and nuclei were extracted from selected tissues. These samples represent the first published systemically healthy equine-specific biobank with extensive clinical phenotyping ante- and post-mortem. The tissues in the biobank are intended for community-wide use in the functional annotation of the equine genome. The use of the biobank will improve the quality of the reference annotation and allow all equine researchers to elucidate unknown genomic and epigenomic causes of disease.
© 2018 Stichting International Foundation for Animal Genetics.
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Publication Date: 2018-10-11 PubMed ID: 30311254PubMed Central: PMC6264908DOI: 10.1111/age.12717Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research paper discusses the first stage of the Functional Annotation of Animal Genomes (FAANG) project for horses, in which an equine biobank was created from two Thoroughbred mares. This biobank, intended for community-wide use, will help in the functional annotation of the equine genome, enhance reference annotation quality, and enable researchers to discover unknown genomic and epigenomic causes of disease.

Overview of the FAANG Project

  • The Functional Annotation of Animal Genomes (FAANG) is a project designed to identify genomic regulatory elements, that is, the parts of the genome that control gene activity, in both males and females across multiple stages of animal development.
  • This article describes the first phase of the FAANG venture for horses, or more specifically, the species Equus caballus.

Creation of the Equine Biobank

  • A biobank consisting of 80 tissue samples, two cell lines (cultures of cells obtained from a single animal cell), and six types of body fluids was generated. All these samples were derived from two fully grown Thoroughbred mares.
  • Various examinations and tests, like full physical examinations, prognosis for lameness, ophthalmologic and neurologic evaluations, complete blood counts and serum biochemistry, were conducted while the horses were still alive (ante-mortem).
  • At post-mortem, tissue samples were taken from across the body along with serum (a component of blood), plasma (another component of blood treated with two different compounds – EDTA and heparin), cerebrospinal fluid, synovial fluid (found in the cavities of joints), and urine.
  • Microbiome samples, or samples of the microorganisms living in and on the animals, were taken from the entire lengths of the gastrointestinal and the urogenital tracts.
  • Apart from body fluids and tissues, epidermal keratinocytes and dermal fibroblasts, two types of skin cells, were cultured from skin samples.

Evaluation of Samples

  • A certified-veterinary pathologist conducted an overall assessment of the tissue samples, both through the naked eye (gross evaluation) and microscope (histologic evaluation).
  • The clinical and pathological evaluations showed light indications of an eosinophilic and lymphocytic infiltration throughout the entire gastrointestinal tract. Such infiltration could be indicative of parasitic infection or other types of inflammation.
  • Both horses were found to have a slight clinical lameness. Despite this, they were overall found to be systemically healthy.
  • Each sample was frozen (cryo-preserved) in a variety of ways for future research, with nuclei extracted from certain tissues.

Conclusions

  • The diverse samples from these horses present the first systematically healthy horse-specific biobank to be published, inclusive of extensive clinical phenotyping both before and after death.
  • The intended use of this biobank is to facilitate a community-wide annotation of the horse genome. It will prove invaluable in enhancing the quality of the reference annotation and in enabling equine researchers to uncover unknown genomic and epigenomic causes of diseases in horses.

Cite This Article

APA
Burns EN, Bordbari MH, Mienaltowski MJ, Affolter VK, Barro MV, Gianino F, Gianino G, Giulotto E, Kalbfleisch TS, Katzman SA, Lassaline M, Leeb T, Mack M, Müller EJ, MacLeod JN, Ming-Whitfield B, Alanis CR, Raudsepp T, Scott E, Vig S, Zhou H, Petersen JL, Bellone RR, Finno CJ. (2018). Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project. Anim Genet, 49(6), 564-570. https://doi.org/10.1111/age.12717

Publication

Animal genetics
ISSN: 1365-2052
NlmUniqueID: 8605704
Country: England
Language: English
Volume: 49
Issue: 6
Pages: 564-570

Researcher Affiliations

Burns, E N
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.
Bordbari, M H
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.
Mienaltowski, M J
  • Department of Animal Science, College of Agricultural and Environmental Sciences, University of California-Davis, Davis, CA, 95616, USA.
Affolter, V K
  • Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.
Barro, M V
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.
Gianino, F
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.
Gianino, G
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.
Giulotto, E
  • Department of Biology and Biotechnology, University of Pavia, via Ferrata 1, Pavia, I-27100, Italy.
Kalbfleisch, T S
  • Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, 40292, USA.
Katzman, S A
  • Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95618, USA.
Lassaline, M
  • Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95618, USA.
Leeb, T
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.
Mack, M
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.
Müller, E J
  • Department of Biomedical Research, Molecular Dermatology and Stem Cell Research, Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.
  • Department of Dermatology, Inselspital, Bern University Hospital, University of Bern, Bern, 3001, Switzerland.
MacLeod, J N
  • Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, 40546, USA.
Ming-Whitfield, B
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.
Alanis, C R
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.
Raudsepp, T
  • Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77845, USA.
Scott, E
  • Department of Animal Science, College of Agricultural and Environmental Sciences, University of California-Davis, Davis, CA, 95616, USA.
Vig, S
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.
Zhou, H
  • Department of Animal Science, College of Agricultural and Environmental Sciences, University of California-Davis, Davis, CA, 95616, USA.
Petersen, J L
  • Department of Animal Science, University of Nebraska - Lincoln, Lincoln, NE, 68583, USA.
Bellone, R R
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.
  • Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.
Finno, C J
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.

MeSH Terms

  • Animals
  • Biological Specimen Banks
  • Female
  • Genomics
  • Horses / genetics
  • Phenotype

Grant Funding

  • UC Davis Agriculture Experiment Station
  • Grayson Jockey Club Foundation
  • L40 TR001136 / NCATS NIH HHS
  • NRSP-8 / U.S. Department of Agriculture
  • 1K01OD015134 / NIH Office of the Director
  • Center for Equine Health, UC Davis
  • 20143842021796 / National Institute of Food and Agriculture
  • L40 TR001136 / National Center for Advancing Translational Sciences
  • K01 OD015134 / NIH HHS

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