Generation of a Biobank From Two Adult Thoroughbred Stallions for the Functional Annotation of Animal Genomes Initiative.
Abstract: Following the successful creation of a biobank from two adult Thoroughbred mares, this study aimed to recapitulate sample collection in two adult Thoroughbred stallions as part of the Functional Annotation of the Animal Genome (FAANG) initiative. Both stallions underwent thorough physical, lameness, neurologic, and ophthalmic (including electroretinography) examinations prior to humane euthanasia. Epididymal sperm was recovered from both stallions immediately postmortem and cryopreserved. Aseptically collected full thickness skin biopsies were used to isolate, culture and cryopreserve dermal fibroblasts. Serum, plasma, cerebrospinal fluid, urine, and gastrointestinal content from various locations were collected and cryopreserved. Under guidance of a board-certified veterinary anatomic pathologist, 102 representative tissue samples were collected from both horses. Whole tissue samples were flash-frozen and prioritized tissues had nuclei isolated and cryopreserved. Spatially contemporaneous samples of each tissue were submitted for histologic examination. Antemortem and gross pathologic examination revealed mild abnormalities in both stallions. One stallion (ECA_UCD_AH3) had unilateral thoracic limb lameness and bilateral chorioretinal scars. The second stallion (ECA_UCD_AH4) had subtle symmetrical pelvic limb ataxia, symmetrical prostatomegally, and moderate gastrointestinal nematodiasis. DNA from each was whole-genome sequenced and genotyped using the GGP Equine 70K SNP array. The genomic resources and banked biological samples from these animals augments the existing resource available to the equine genomics community. Importantly we may now improve the resolution of tissue-specific gene regulation as affected by sex, as well as add sex-specific tissues and gametes.
Copyright © 2021 Donnelly, Bellone, Hales, Nguyen, Katzman, Dujovne, Knickelbein, Avila, Kalbfleisch, Giulotto, Kingsley, Tanaka, Esdaile, Peng, Dahlgren, Fuller, Mienaltowski, Raudsepp, Affolter, Petersen and Finno.
Publication Date: 2021-03-08 PubMed ID: 33763124PubMed Central: PMC7982670DOI: 10.3389/fgene.2021.650305Google Scholar: Lookup
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Summary
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The researchers conducted a study to generate a biobank from two adult Thoroughbred stallions, expanding the genetic resources available to the equine genomics community. This advance could boost the understanding of tissue-specific gene regulation and effects of gender on it.
Study Aim
- The primary purpose of this study was to replicate the biobank production of two adult Thoroughbred mares using male stallions. This effort is part of a bigger initiative, the Functional Annotation of the Animal Genome (FAANG)
Process of Sample Collection
- Each of the stallions underwent comprehensive physical, lameness, neurologic, and ophthalmic examinations.
- Post-euthanasia, the researchers recovered and cryopreserved epididymal sperm from both stallions.
- Dermal fibroblasts were isolated, cultured, and cryopreserved from aseptically collected full-thickness skin biopsies.
- Samples of serum, plasma, cerebrospinal fluid, urine, and gastrointestinal content were also collected and cryopreserved.
- A total of 102 representative tissue samples were collected under the guidance of a certified veterinary anatomic pathologist, leading to the collection of a comprehensive set of tissue samples for a broad range of genetic analyses.
Observations and Results
- Mild abnormalities were found in both stallions during the examinations before and after death, and the thorough genomic sequencing and genotyping of DNA samples provided substantial insight into any potential genetic basis for these health issues.
- One of the stallions exhibited unilateral thoracic limb lameness and bilateral chorioretinal scars, while the second had subtle symmetrical pelvic limb ataxia, symmetrical prostatomegally, and moderate gastrointestinal nematodiasis.
- The stallions’ whole-genome sequences were used along with a GGP Equine 70K SNP array for genotyping.
Implications of the Study
- This research effectively expanded the equine genetics resources by including male genetic material, thereby it contributes to the effort of understanding the functioning of different genes in the equine genome.
- Moreover, these added resources also paved the way for studying how gender could affect tissue-specific gene regulation, as well as the study of gender-specific tissues and gametes.
- This is a significant stride in the equine genomics community, opening up new avenues in genomics and potential therapeutic discoveries.
Cite This Article
APA
Donnelly CG, Bellone RR, Hales EN, Nguyen A, Katzman SA, Dujovne GA, Knickelbein KE, Avila F, Kalbfleisch TS, Giulotto E, Kingsley NB, Tanaka J, Esdaile E, Peng S, Dahlgren A, Fuller A, Mienaltowski MJ, Raudsepp T, Affolter VK, Petersen JL, Finno CJ.
(2021).
Generation of a Biobank From Two Adult Thoroughbred Stallions for the Functional Annotation of Animal Genomes Initiative.
Front Genet, 12, 650305.
https://doi.org/10.3389/fgene.2021.650305 Publication
Researcher Affiliations
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
- Morris Animal Foundation, Denver, CO, United States.
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
- Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States.
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States.
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States.
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States.
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States.
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.
Grant Funding
- L40 TR001136 / NCATS NIH HHS
Conflict of Interest Statement
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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Citations
This article has been cited 10 times.- Peng S, Dahlgren AR, Donnelly CG, Hales EN, Petersen JL, Bellone RR, Kalbfleisch T, Finno CJ. Functional annotation of the animal genomes: An integrated annotation resource for the horse. PLoS Genet 2023 Mar;19(3):e1010468.
- Peng S, Magdesian KG, Dowd J, Blea J, Carpenter R, Ho W, Finno CJ. Investigation of high gamma-glutamyltransferase syndrome in California Thoroughbred racehorses. J Vet Intern Med 2022 Nov;36(6):2203-2212.
- Peng S, Petersen JL, Bellone RR, Kalbfleisch T, Kingsley NB, Barber AM, Cappelletti E, Giulotto E, Finno CJ. Decoding the Equine Genome: Lessons from ENCODE. Genes (Basel) 2021 Oct 27;12(11).
- Sharma M, Singh A, Kumar V, Olla N, Arora R, Sharma R, Mohan NH, Ahlawat S. Advances in Equine Genomics: Decoding the Genetic Architecture of Morphology, Performance, Behavior, and Adaptation. Mol Biotechnol 2025 Dec 19;.
- Cullen JN, Cieslak J, Petersen JL, Bellone RR, Finno CJ, Kalbfleisch TS, Calloe K, Capomaccio S, Cappelli K, Coleman SJ, Distl O, Durward-Akhurst SA, Giulotto E, Hamilton NA, Hill EW, Katz LM, Klaerke DA, Lindgren G, MacHugh DE, Mackowski M, MacLeod JN, Metzger J, Murphy BA, Orlando L, Raudsepp T, Silvestrelli M, Strand E, Tozaki T, Trachsel DS, Valderrama Figueroa LS, Velie BD, Wade CM, Waud B, Mickelson JR, McCue ME. Charting the equine miRNA landscape: An integrated pipeline and browser for annotating, quantifying, and visualizing expression. PLoS Genet 2025 Sep;21(9):e1011835.
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