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Hinkley S, Tait RG. Sampling and Laboratory Logistics: How to Collect DNA Samples and Overview of Techniques for Laboratory Analysis. Vet Clin North Am Food Anim Pract 2024:S0749-0720(24)00027-6. [PMID: 39181793 DOI: 10.1016/j.cvfa.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024] Open
Abstract
This article discusses different options and best practices for sample types and sample collection devices for downstream genotyping in today's sophisticated animal husbandry systems. Best practices for sample collection, shipping, and submission of samples are shown and an overview of techniques for laboratory analysis is provided. The ultimate goal is to facilitate the generation of useful and meaningful results for the client.
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Affiliation(s)
- Susanne Hinkley
- Clinical Diagnostics, Neogen Genomics, 4131 North 48th Street, Lincoln, NE 68504, USA.
| | - Richard G Tait
- Genetics Product Development, Neogen Genomics, 4131 North 48th Street, Lincoln, NE 68504, USA
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Reith RR, Beever JE, Paschal JC, Banta J, Porter BF, Steffen DJ, Hairgrove TB, Petersen JL. A de novo mutation in CACNA1A is associated with autosomal dominant bovine familial convulsions and ataxia in Angus cattle. Anim Genet 2024; 55:344-351. [PMID: 38426585 DOI: 10.1111/age.13409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/03/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
Bovine familial convulsions and ataxia (BFCA) is considered an autosomal dominant syndrome with incomplete penetrance. Nine Angus calves from the same herd were diagnosed with BFCA within days of birth. Necropsy revealed cerebellar and spinal cord lesions associated with the condition. Parentage testing confirmed that all affected calves had a common sire. The sire was then bred to 36 cows across two herds using artificial insemination, producing an additional 14 affected calves. The objective of this investigation was to identify hypothesized dominant genetic variation underlying the condition. Whole-genome sequencing was performed on the sire, six affected and seven unaffected paternal half-sibling calves and combined with data from 135 unrelated controls. The sire and five of the six affected calves were heterozygous for a nonsense variant (Chr7 g.12367906C>T, c.5073C>T, p.Arg1681*) in CACNA1A. The other affected calves (N = 8) were heterozygous for the variant but it was absent in the other unaffected calves (N = 7) and parents of the sire. This variant was also absent in sequence data from over 6500 other cattle obtained via public repositories and collaborator projects. The variant in CACNA1A is expressed in the cerebellum of the ataxic calves as detected in the transcriptome and was not differentially expressed compared with controls. The CACNA1A protein is part of a highly expressed cerebellar calcium voltage gated channel. The nonsense variant is proposed to cause haploinsufficiency, preventing proper transmission of neuronal signals through the channel and resulting in BFCA.
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Affiliation(s)
- Rachel R Reith
- Department of Animal Science, University of Nebraska - Lincoln, Lincoln, Nebraska, USA
| | - Jonathan E Beever
- Department of Animal Science, University of Tennessee Institute of Agriculture, Knoxville, Tennessee, USA
| | - Joe C Paschal
- Texas A&M AgriLife Extension, Texas A&M University, College Station, Texas, USA
| | - Jason Banta
- Texas A&M AgriLife Extension, Texas A&M University, College Station, Texas, USA
| | - Brian F Porter
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - David J Steffen
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska - Lincoln, Lincoln, Nebraska, USA
| | - Thomas B Hairgrove
- Texas A&M AgriLife Extension, Texas A&M University, College Station, Texas, USA
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska - Lincoln, Lincoln, Nebraska, USA
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Reith RR, Batt MC, Fuller AM, Meekins JM, Diehl KA, Zhou Y, Bedwell PS, Ward JA, Sanders SK, Petersen JL, Steffen DJ. A recessive CLN3 variant is responsible for delayed-onset retinal degeneration in Hereford cattle. J Vet Diagn Invest 2024; 36:438-446. [PMID: 38516801 PMCID: PMC11110775 DOI: 10.1177/10406387241239918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024] Open
Abstract
Thirteen American Hereford cattle were reported blind with presumed onset when ~12-mo-old. All blind cattle shared a common ancestor through both the maternal and paternal pedigrees, suggesting a recessive genetic origin. Given the pedigree relationships and novel phenotype, we characterized the ophthalmo-pathologic changes associated with blindness and identified the responsible gene variant. Ophthalmologic examinations of 5 blind cattle revealed retinal degeneration. Histologically, 2 blind cattle had loss of the retinal photoreceptor layer. Whole-genome sequencing (WGS) of 7 blind cattle and 9 unaffected relatives revealed a 1-bp frameshift deletion in ceroid lipofuscinosis neuronal 3 (CLN3; chr25 g.26043843del) for which the blind cattle were homozygous and their parents heterozygous. The identified variant in exon 16 of 17 is predicted to truncate the encoded protein (p. Pro369Argfs*8) battenin, which is involved in lysosomal function necessary for photoreceptor layer maintenance. Of 462 cattle genotyped, only blind cattle were homozygous for the deletion. A query of WGS data of > 5,800 animals further revealed that the variant was only observed in related Hereford cattle. Mutations in CLN3 are associated with human juvenile neuronal ceroid lipofuscinosis (JNCL), or Batten disease, which results in early-onset retinal degeneration and lesions similar to those observed in our cases. Our data support the frameshift variant of CLN3 as causative of blindness in these Hereford cattle, and provide additional evidence of the role of this gene in retinal lesions, possibly as a model for human non-syndromic JNCL.
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Affiliation(s)
- Rachel R. Reith
- Department of Animal Science, University of Nebraska–Lincoln, Lincoln, NE, USA
| | - Mackenzie C. Batt
- Department of Animal Science, University of Nebraska–Lincoln, Lincoln, NE, USA
| | - Anna M. Fuller
- Department of Animal Science, University of Nebraska–Lincoln, Lincoln, NE, USA
| | - Jessica M. Meekins
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Kathryn A. Diehl
- College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - You Zhou
- Center for Biotechnology, University of Nebraska–Lincoln, Lincoln, NE, USA
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska–Lincoln, Lincoln, NE, USA
| | | | - Jack A. Ward
- American Hereford Association, Breed Improvement, Kansas City, MO, USA
| | - Stacy K. Sanders
- American Hereford Association, Breed Improvement, Kansas City, MO, USA
| | - Jessica L. Petersen
- Department of Animal Science, University of Nebraska–Lincoln, Lincoln, NE, USA
| | - David J. Steffen
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska–Lincoln, Lincoln, NE, USA
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Batt MC, Venzor LG, Gardner K, Reith RR, Roberts KA, Herrera NJ, Fuller AM, Sullivan GA, Mulliniks JT, Spangler ML, Valberg SJ, Steffen DJ, Petersen JL. An autosomal recessive variant in PYGM causes myophosphorylase deficiency in Red Angus composite cattle. BMC Genomics 2024; 25:417. [PMID: 38678201 PMCID: PMC11055281 DOI: 10.1186/s12864-024-10330-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Between 2020 and 2022, eight calves in a Nebraska herd (composite Simmental, Red Angus, Gelbvieh) displayed exercise intolerance during forced activity. In some cases, the calves collapsed and did not recover. Available sire pedigrees contained a paternal ancestor within 2-4 generations in all affected calves. Pedigrees of the calves' dams were unavailable, however, the cows were ranch-raised and retained from prior breeding seasons, where bulls used for breeding occasionally had a common ancestor. Therefore, it was hypothesized that a de novo autosomal recessive variant was causative of exercise intolerance in these calves. RESULTS A genome-wide association analysis utilizing SNP data from 6 affected calves and 715 herd mates, followed by whole-genome sequencing of 2 affected calves led to the identification of a variant in the gene PYGM (BTA29:g.42989581G > A). The variant, confirmed to be present in the skeletal muscle transcriptome, was predicted to produce a premature stop codon (p.Arg650*). The protein product of PYGM, myophosphorylase, breaks down glycogen in skeletal muscle. Glycogen concentrations were fluorometrically assayed as glucose residues demonstrating significantly elevated glycogen concentrations in affected calves compared to cattle carrying the variant and to wild-type controls. The absence of the PYGM protein product in skeletal muscle was confirmed by immunohistochemistry and label-free quantitative proteomics analysis; muscle degeneration was confirmed in biopsy and necropsy samples. Elevated skeletal muscle glycogen persisted after harvest, resulting in a high pH and dark-cutting beef, which is negatively perceived by consumers and results in an economic loss to the industry. Carriers of the variant did not exhibit differences in meat quality or any measures of animal well-being. CONCLUSIONS Myophosphorylase deficiency poses welfare concerns for affected animals and negatively impacts the final product. The association of the recessive genotype with dark-cutting beef further demonstrates the importance of genetics to not only animal health but to the quality of their product. Although cattle heterozygous for the variant may not immediately affect the beef industry, identifying carriers will enable selection and breeding strategies to prevent the production of affected calves.
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Affiliation(s)
- Mackenzie C Batt
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Leila G Venzor
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Keri Gardner
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Rachel R Reith
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Kelsey A Roberts
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Nicolas J Herrera
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Anna M Fuller
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Gary A Sullivan
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - J Travis Mulliniks
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Matthew L Spangler
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Stephanie J Valberg
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - David J Steffen
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA.
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Petersen JL, Sieck RL, Steffen DJ. White coat color of a Black Angus calf attributed to an occurrence of the delR217 variant of MITF. Anim Genet 2023; 54:549-552. [PMID: 37062854 DOI: 10.1111/age.13327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/16/2023] [Accepted: 04/01/2023] [Indexed: 04/18/2023]
Abstract
A white calf, with minimal pigmented markings, was born to two registered Black Angus parents. Given the possibility of an unknown recessive or de novo dominant mutation, whole-genome sequencing was conducted on the trio of individuals. A 3-bp in-frame deletion in MITF was identified; this mutation was unique to the calf but identical to the delR217 variant reported in both humans and murine models of Waardenburg syndrome type 2A and Tietz syndrome. Given the coat color phenotype and identity of the mutation, our data support that this calf represents the first instance of this recurring MITF mutation in cattle.
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Affiliation(s)
- Jessica L Petersen
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Renae L Sieck
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - David J Steffen
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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Todd ET, Fromentier A, Sutcliffe R, Running Horse Collin Y, Perdereau A, Aury JM, Èche C, Bouchez O, Donnadieu C, Wincker P, Kalbfleisch T, Petersen JL, Orlando L. Imputed genomes of historical horses provide insights into modern breeding. iScience 2023; 26:107104. [PMID: 37416458 PMCID: PMC10319840 DOI: 10.1016/j.isci.2023.107104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/25/2023] [Accepted: 06/08/2023] [Indexed: 07/08/2023] Open
Abstract
Historical genomes can provide important insights into recent genomic changes in horses, especially the development of modern breeds. In this study, we characterized 8.7 million genomic variants from a panel of 430 horses from 73 breeds, including newly sequenced genomes from 20 Clydesdales and 10 Shire horses. We used this modern genomic variation to impute the genomes of four historically important horses, consisting of publicly available genomes from 2 Przewalski's horses, 1 Thoroughbred, and a newly sequenced Clydesdale. Using these historical genomes, we identified modern horses with higher genetic similarity to those in the past and unveiled increased inbreeding in recent times. We genotyped variants associated with appearance and behavior to uncover previously unknown characteristics of these important historical horses. Overall, we provide insights into the history of Thoroughbred and Clydesdale breeds and highlight genomic changes in the endangered Przewalski's horse following a century of captive breeding.
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Affiliation(s)
- Evelyn T. Todd
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
| | - Aurore Fromentier
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
| | - Richard Sutcliffe
- Glasgow Museums Resource Centre, 200 Woodhead Road, Nitshill, G53 7NN Glasgow, UK
| | - Yvette Running Horse Collin
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
| | - Aude Perdereau
- Genoscope, Institut de biologie François Jacob, CEA, Université d’Evry, Université Paris-Saclay, 91042 Evry, France
| | - Jean-Marc Aury
- Genoscope, Institut de biologie François Jacob, CEA, Université d’Evry, Université Paris-Saclay, 91042 Evry, France
| | - Camille Èche
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 31326 Castanet-Tolosan Cedex, France
| | - Olivier Bouchez
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 31326 Castanet-Tolosan Cedex, France
| | - Cécile Donnadieu
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, 31326 Castanet-Tolosan Cedex, France
| | - Patrick Wincker
- Genoscope, Institut de biologie François Jacob, CEA, Université d’Evry, Université Paris-Saclay, 91042 Evry, France
| | - Ted Kalbfleisch
- MH Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546-0091, USA
| | - Jessica L. Petersen
- Department of Animal Science, University of Nebraska-Lincoln, 3940 Fair St, Lincoln, NE 68583-0908, USA
| | - Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, 37 Allées Jules Guesde, Bâtiment A, 31000 Toulouse, France
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Modorov MV, Kleshcheva AA, Osintseva KR, Tkachenko IV, Sevost’yanov MY, Zezin NN. The Use of KASP Technology to Study Associations of Single Nucleotide Polymorphisms in the GPAD4, CCL3, DGKG, PPARGC1A, STAT1, and TLR4 Genes with Milk Production in Cattle. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422120080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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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. Generation of a Biobank From Two Adult Thoroughbred Stallions for the Functional Annotation of Animal Genomes Initiative. Front Genet 2021; 12:650305. [PMID: 33763124 PMCID: PMC7982670 DOI: 10.3389/fgene.2021.650305] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/15/2021] [Indexed: 12/27/2022] Open
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.
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Affiliation(s)
- Callum G Donnelly
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Rebecca R Bellone
- 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
| | - Erin N Hales
- Morris Animal Foundation, Denver, CO, United States
| | - Annee Nguyen
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Scott A Katzman
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Ghislaine A Dujovne
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Kelly E Knickelbein
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Felipe Avila
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Ted S Kalbfleisch
- Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States
| | - Elena Giulotto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Nicole B Kingsley
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Jocelyn Tanaka
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Elizabeth Esdaile
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Sichong Peng
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Anna Dahlgren
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Anna Fuller
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Michael J Mienaltowski
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Verena K Affolter
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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