1
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Heaton MP, Harhay GP, Bassett AS, Clark HJ, Carlson JM, Jobman EE, Sadd HR, Pelster MC, Workman AM, Kuehn LA, Kalbfleisch TS, Piscatelli H, Carrie M, Krafsur GM, Grotelueschen DM, Vander Ley BL. Association of ARRDC3 and NFIA variants with bovine congestive heart failure in feedlot cattle. F1000Res 2024; 11:385. [PMID: 38680232 PMCID: PMC11046187 DOI: 10.12688/f1000research.109488.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 05/01/2024] Open
Abstract
Background Bovine congestive heart failure (BCHF) has become increasingly prevalent among feedlot cattle in the Western Great Plains of North America with up to 7% mortality in affected herds. BCHF is an untreatable complex condition involving pulmonary hypertension that culminates in right ventricular failure and death. Genes associated with BCHF in feedlot cattle have not been previously identified. Our aim was to search for genomic regions associated with this disease. Methods A retrospective, matched case-control design with 102 clinical BCHF cases and their unaffected pen mates was used in a genome-wide association study. Paired nominal data from approximately 560,000 filtered single nucleotide polymorphisms (SNPs) were analyzed with McNemar's test. Results Two independent genomic regions were identified as having the most significant association with BCHF: the arrestin domain-containing protein 3 gene ( ARRDC3), and the nuclear factor IA gene ( NFIA, mid- p-values, 1x10 -8 and 2x10 -7, respectively). Animals with two copies of risk alleles at either gene were approximately eight-fold more likely to have BCHF than their matched pen mates with either one or zero risk alleles at both genes (CI 95 = 3-17). Further, animals with two copies of risk alleles at both genes were 28-fold more likely to have BCHF than all others ( p-value = 1×10 -7, CI 95 = 4-206). A missense variant in ARRDC3 (C182Y) represents a potential functional variant since the C182 codon is conserved among all other jawed vertebrate species observed. A two-SNP test with markers in both genes showed 29% of 273 BCHF cases had homozygous risk genotypes in both genes, compared to 2.5% in 198 similar unaffected feedlot cattle. This and other DNA tests may be useful for identifying feedlot animals with the highest risk for BCHF in the environments described here. Conclusions Although pathogenic roles for variants in the ARRDC3 and NFIA genes are unknown, their discovery facilitates classifying animals by genetic risk and allows cattle producers to make informed decisions for selective breeding and animal health management.
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Affiliation(s)
- Michael P. Heaton
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Gregory P. Harhay
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Adam S. Bassett
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Halden J. Clark
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Jaden M. Carlson
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Erin E. Jobman
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Helen R. Sadd
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Madeline C. Pelster
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Aspen M. Workman
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Larry A. Kuehn
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | | | | | | | - Greta M. Krafsur
- Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado, 80045, USA
| | - Dale M. Grotelueschen
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Brian L. Vander Ley
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
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2
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Workman AM, Harhay GP, Groves JT, Vander Ley BL. Two bovine hepacivirus genome sequences from U.S. cattle. J Vet Diagn Invest 2024; 36:274-277. [PMID: 38414254 DOI: 10.1177/10406387231225656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024] Open
Abstract
Bovine hepacivirus (BoHV) is closely related to the hepatitis C virus (HCV) in humans and can cause both acute and chronic liver infections in cattle. BoHV was first identified in Ghana and Germany in 2015 and since then it has been detected and characterized in other countries around the world, but no strains have been sequenced from U.S. cattle. To date, BoHV has been classified into 2 genotypes (1 and 2), with genotype 1 being further divided into 11 subtypes (A-K). However, the true genetic diversity of BoHV is likely underestimated given limited surveillance and a lack of published genome sequences. Here, we sequenced 2 nearly complete BoHV genomes from serum samples collected in 2019 from beef cattle in Missouri. Sequence comparisons and phylogenetic analysis showed that isolate MARC/2019/60 had high sequence homology with genotype 1, subtype E isolates from China. In contrast, isolate MARC/2019/50 represented a novel BoHV subtype within genotype 2. Thus, we report the first genomic characterization of BoHV isolates from U.S. cattle, and the second complete BoHV2 genome worldwide. This work increases our knowledge of the global genetic diversity of BoHV and demonstrates the co-circulation of divergent BoHV strains in U.S. cattle.
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Affiliation(s)
- Aspen M Workman
- U.S. Meat Animal Research Center, U.S. Department of Agriculture, Agricultural Research Service, Clay Center, NE, USA
| | - Gregory P Harhay
- U.S. Meat Animal Research Center, U.S. Department of Agriculture, Agricultural Research Service, Clay Center, NE, USA
| | | | - Brian L Vander Ley
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, NE, USA
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3
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Workman AM, Heaton MP, Vander Ley BL, Webster DA, Sherry L, Bostrom JR, Larson S, Kalbfleisch TS, Harhay GP, Jobman EE, Carlson DF, Sonstegard TS. First gene-edited calf with reduced susceptibility to a major viral pathogen. PNAS Nexus 2023; 2:pgad125. [PMID: 37181049 PMCID: PMC10167990 DOI: 10.1093/pnasnexus/pgad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/03/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023]
Abstract
Bovine viral diarrhea virus (BVDV) is one of the most important viruses affecting the health and well-being of bovine species throughout the world. Here, we used CRISPR-mediated homology-directed repair and somatic cell nuclear transfer to produce a live calf with a six amino acid substitution in the BVDV binding domain of bovine CD46. The result was a gene-edited calf with dramatically reduced susceptibility to infection as measured by reduced clinical signs and the lack of viral infection in white blood cells. The edited calf has no off-target edits and appears normal and healthy at 20 months of age without obvious adverse effects from the on-target edit. This precision bred, proof-of-concept animal provides the first evidence that intentional genome alterations in the CD46 gene may reduce the burden of BVDV-associated diseases in cattle and is consistent with our stepwise, in vitro and ex vivo experiments with cell lines and matched fetal clones.
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Affiliation(s)
- Aspen M Workman
- US Meat Animal Research Center, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), 844 Road 313 Clay Center, NE 68933, USA
| | - Michael P Heaton
- US Meat Animal Research Center, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), 844 Road 313 Clay Center, NE 68933, USA
| | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska–Lincoln, 820 Road 313 Clay Center, NE 68933, USA
| | - Dennis A Webster
- Recombinetics Inc., 3388 Mike Collins Drive, Eagan, MN 55121, USA
| | - Luke Sherry
- Recombinetics Inc., 3388 Mike Collins Drive, Eagan, MN 55121, USA
| | | | - Sabreena Larson
- Acceligen Inc., 3388 Mike Collins Drive, Eagan, MN 55121, USA
| | - Theodore S Kalbfleisch
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, 1400 Nicholasville Rd Lexington, KY 40546, USA
| | - Gregory P Harhay
- US Meat Animal Research Center, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), 844 Road 313 Clay Center, NE 68933, USA
| | - Erin E Jobman
- Great Plains Veterinary Educational Center, University of Nebraska–Lincoln, 820 Road 313 Clay Center, NE 68933, USA
| | - Daniel F Carlson
- Recombinetics Inc., 3388 Mike Collins Drive, Eagan, MN 55121, USA
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4
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Leonard AS, Crysnanto D, Fang ZH, Heaton MP, Vander Ley BL, Herrera C, Bollwein H, Bickhart DM, Kuhn KL, Smith TPL, Rosen BD, Pausch H. Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies. Nat Commun 2022; 13:3012. [PMID: 35641504 PMCID: PMC9156671 DOI: 10.1038/s41467-022-30680-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 05/10/2022] [Indexed: 12/12/2022] Open
Abstract
Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Here we generate haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT is sufficient to produce two haplotype-resolved assemblies meeting standards set by the Vertebrate Genomes Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrate significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identifies 90 thousand structural variants including 931 overlapping with coding sequences; this approach reveals variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46, and GC that have potential to affect phenotype.
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Affiliation(s)
- Alexander S Leonard
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland.
| | - Danang Crysnanto
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Zih-Hua Fang
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Michael P Heaton
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Carolina Herrera
- Clinic of Reproductive Medicine, Department for Farm Animals, University of Zurich, 8057, Zurich, Switzerland
| | - Heinrich Bollwein
- Clinic of Reproductive Medicine, Department for Farm Animals, University of Zurich, 8057, Zurich, Switzerland
| | - Derek M Bickhart
- Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI, 53706, USA
| | - Kristen L Kuhn
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Timothy P L Smith
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD, 20705, USA.
| | - Hubert Pausch
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland.
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5
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Larson-Peine JM, Heller MC, Rathert-Williams AR, Pearl KA, Duncan NB, Vander Ley BL, Meyer AM. Blood chemistry and rectal temperature changes in a population of healthy, fall-born, suckling beef calves from birth to 72 h of age. Theriogenology 2022; 188:145-155. [DOI: 10.1016/j.theriogenology.2022.05.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/10/2022] [Accepted: 05/28/2022] [Indexed: 10/18/2022]
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6
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Heaton MP, Harhay GP, Bassett AS, Clark HJ, Carlson JM, Jobman EE, Sadd HR, Pelster MC, Workman AM, Kuehn LA, Kalbfleisch TS, Piscatelli H, Carrie M, Krafsur GM, Grotelueschen DM, Vander Ley BL. Association of ARRDC3 and NFIA variants with bovine congestive heart failure in feedlot cattle. F1000Res 2022. [DOI: 10.12688/f1000research.109488.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Background: Bovine congestive heart failure (BCHF) has become increasingly prevalent among feedlot cattle in the Western Great Plains of North America with up to 7% mortality in affected herds. BCHF is an untreatable complex condition involving pulmonary hypertension that culminates in right ventricular failure and death. Genes associated with BCHF in feedlot cattle have not been previously identified. Our aim was to search for genomic regions associated with this disease. Methods: A retrospective, matched case-control design with 102 clinical BCHF cases and their unaffected pen mates was used in a genome-wide association study. Paired nominal data from approximately 560,000 filtered single nucleotide polymorphisms (SNPs) were analyzed with McNemar’s test. Results: The most significant genome-wide association was in the arrestin domain-containing protein 3 gene (ARRDC3), followed by the nuclear factor IA gene (NFIA, mid-p-values, 1x10-8 and 2x10-7, respectively). Animals with homozygous risk alleles at either gene were approximately eight-fold more likely to have BCHF than their matched pen mates without those risk alleles (CI95 = 3-17). Animals with homozygous risk alleles at both genes were 28-fold more likely to have BCHF than all others (p-value = 1x10-7, CI95 = 4-206). A linked missense variant in ARRDC3 (C182Y) represents a potential functional variant as the C182 codon is conserved among all other jawed vertebrate species observed. A DNA test with two markers showed 29% of 273 BCHF cases had homozygous risk alleles in both genes, compared to 2.5% in 198 similar unaffected feedlot cattle. This DNA test may be useful for identifying feedlot animals with the highest risk for BCHF in the environments described here. Conclusions: Although pathogenic roles for ARRDC3 and NFIA variants associated with BCHF are unknown, their discovery facilitates classifying animals by genetic risk and allows cattle producers to make informed decisions for selective breeding and animal health management.
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7
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Heaton MP, Smith TPL, Bickhart DM, Vander Ley BL, Kuehn LA, Oppenheimer J, Shafer WR, Schuetze FT, Stroud B, McClure JC, Barfield JP, Blackburn HD, Kalbfleisch TS, Davenport KM, Kuhn KL, Green RE, Shapiro B, Rosen BD. Erratum to: A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus. J Hered 2021; 112:565. [PMID: 34436588 DOI: 10.1093/jhered/esab039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Michael P Heaton
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | | | | | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Larry A Kuehn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Jonas Oppenheimer
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | | | | | - Brad Stroud
- Stroud Veterinary Embryo Services, Weatherford, TX, USA
| | | | - Jennifer P Barfield
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | | | | | - Kimberly M Davenport
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, ID, USA
| | - Kristen L Kuhn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Benjamin D Rosen
- USDA, ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, USA
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8
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Heaton MP, Smith TPL, Bickhart DM, Vander Ley BL, Kuehn LA, Oppenheimer J, Shafer WR, Schuetze FT, Stroud B, McClure JC, Barfield JP, Blackburn HD, Kalbfleisch TS, Davenport KM, Kuhn KL, Green RE, Shapiro B, Rosen BD. A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus. J Hered 2021; 112:184-191. [PMID: 33438035 PMCID: PMC8006815 DOI: 10.1093/jhered/esab002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/11/2021] [Indexed: 12/22/2022] Open
Abstract
Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison-cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS_Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.
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Affiliation(s)
| | | | | | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE
| | - Larry A Kuehn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE
| | - Jonas Oppenheimer
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
| | | | | | - Brad Stroud
- Stroud Veterinary Embryo Services, Weatherford, TX
| | | | - Jennifer P Barfield
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | | | | | - Kimberly M Davenport
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, ID
| | - Kristen L Kuhn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA
| | - Benjamin D Rosen
- USDA, ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD
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9
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Oppenheimer J, Rosen BD, Heaton MP, Vander Ley BL, Shafer WR, Schuetze FT, Stroud B, Kuehn LA, McClure JC, Barfield JP, Blackburn HD, Kalbfleisch TS, Bickhart DM, Davenport KM, Kuhn KL, Green RE, Shapiro B, Smith TPL. A Reference Genome Assembly of American Bison, Bison bison bison. J Hered 2021; 112:174-183. [PMID: 33595645 PMCID: PMC8006816 DOI: 10.1093/jhered/esab003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/13/2021] [Indexed: 11/14/2022] Open
Abstract
Bison are an icon of the American West and an ecologically, commercially, and culturally important species. Despite numbering in the hundreds of thousands today, conservation concerns remain for the species, including the impact on genetic diversity of a severe bottleneck around the turn of the 20th century and genetic introgression from domestic cattle. Genetic diversity and admixture are best evaluated at genome-wide scale, for which a high-quality reference is necessary. Here, we use trio binning of long reads from a bison-Simmental cattle (Bos taurus taurus) male F1 hybrid to sequence and assemble the genome of the American plains bison (Bison bison bison). The male haplotype genome is chromosome-scale, with a total length of 2.65 Gb across 775 scaffolds (839 contigs) and a scaffold N50 of 87.8 Mb. Our bison genome is ~13× more contiguous overall and ~3400× more contiguous at the contig level than the current bison reference genome. The bison genome sequence presented here (ARS-UCSC_bison1.0) will enable new research into the evolutionary history of this iconic megafauna species and provide a new tool for the management of bison populations in federal and commercial herds.
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Affiliation(s)
- Jonas Oppenheimer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Benjamin D Rosen
- USDA, ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, USA
| | - Michael P Heaton
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | | | - Brad Stroud
- Stroud Veterinary Embryo Services, Weatherford, TE, USA
| | - Larry A Kuehn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | | | - Jennifer P Barfield
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | | | | | | | - Kimberly M Davenport
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, ID, USA
| | - Kristen L Kuhn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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10
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Gamsjäger L, Vander Ley BL, Knych HK, McArthur GR, Heller MC. Efficacy of sodium iodide for prevention of respiratory disease in preweaned dairy calves. Am J Vet Res 2020; 81:673-680. [PMID: 32700995 DOI: 10.2460/ajvr.81.8.673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To determine the pharmacokinetics of sodium iodide (NaI) following oral administration to preweaned dairy calves, and to assess the efficacy of NaI for prevention of bovine respiratory disease (BRD) in preweaned calves at a commercial calf-raising facility. ANIMALS 434 healthy preweaned dairy calves. PROCEDURES In the first of 2 experimental trials, each of 7 calves received NaI (20 mg/kg, PO) once. Blood and nasal fluid samples were collected at predetermined times before (baseline) and for 72 hours after NaI administration for determination of iodine concentrations. Pharmacokinetic parameters were determined by noncompartmental analysis. In the second trial, 427 calves at a calf-raising facility were randomly assigned to receive NaI (20 mg/kg, PO, 2 doses 72 hours apart; n = 211) or serve as untreated controls (216). Health outcomes were compared between the 2 groups. RESULTS For all 7 calves in the pharmacokinetic trial, the iodine concentration in both serum and nasal fluid samples was significantly increased from the baseline concentration and exceeded the presumed therapeutic iodine concentration (6.35 μg/mL) throughout the sampling period. In the on-farm trial, the odds of being treated for BRD before weaning for NaI-treated calves were twice those for control calves (OR, 2.04; 95% CI, 1.38 to 3.00). CONCLUSIONS AND CLINICAL RELEVANCE Results suggested that, although oral administration of NaI (20 mg/kg) to preweaned dairy calves achieved iodine concentrations presumed to be effective in both serum and nasal fluid, it was not effective for prevention of BRD in preweaned calves at a commercial calf-raising facility.
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11
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Carlson JM, Vander Ley BL, Lee SI, Grotelueschen DM, Walz PH, Workman AM, Heaton MP, Boxler DJ. Detection of bovine viral diarrhea virus in stable flies following consumption of blood from persistently infected cattle. J Vet Diagn Invest 2020; 32:108-111. [PMID: 31967528 DOI: 10.1177/1040638719898688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Control of bovine viral diarrhea virus (BVDV) relies on resource-intensive sampling to detect and remove persistently infected (PI) cattle. Herd-level surveillance tools would be useful for herds with unknown BVDV status and for monitoring herds with BVDV-free status. Our objective was to determine the feasibility of using stable flies as a sampling tool to detect BVDV at the herd level. Stable flies (Stomoxys calcitrans) were fed citrated blood from either BVDV-PI or BVDV-free cattle to establish pools of 100 flies with various proportions of BVDV-fed flies (0%, 1%, 10%, 20%, 40%, or 100% in each pool). BVDV-fed flies in these pools were harvested either 1, 2, or 3 d after consuming BVDV-PI blood to determine the impact of time after feeding. Two replicates of a 3-d by 6-dilution level matrix were produced. BVDV RNA was consistently detected on day 1 when ≥10% of the flies in the pool consumed PI blood. On days 2 and 3, positive BVDV RNA detection was variable and became less consistent. Our results demonstrate that BVDV RNA can be detected in stable flies after feeding on blood from PI cattle. Successful use of stable flies as a surveillance tool will require validation under field conditions.
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Affiliation(s)
- Jaden M Carlson
- Department of Veterinary Medicine and Biomedical Sciences, Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Clay Center, NE (Carlson, Vander Ley, Grotelueschen).,Department of Food Science and Technology, Oregon State University, Corvallis, OR (Lee).,Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL (Walz).,Genetics, USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE (Workman, Heaton).,Department of Entomology, West Central Research and Extension Center, University of Nebraska-Lincoln, North Platte, NE (Boxler)
| | - Brian L Vander Ley
- Department of Veterinary Medicine and Biomedical Sciences, Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Clay Center, NE (Carlson, Vander Ley, Grotelueschen).,Department of Food Science and Technology, Oregon State University, Corvallis, OR (Lee).,Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL (Walz).,Genetics, USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE (Workman, Heaton).,Department of Entomology, West Central Research and Extension Center, University of Nebraska-Lincoln, North Platte, NE (Boxler)
| | - Sang I Lee
- Department of Veterinary Medicine and Biomedical Sciences, Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Clay Center, NE (Carlson, Vander Ley, Grotelueschen).,Department of Food Science and Technology, Oregon State University, Corvallis, OR (Lee).,Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL (Walz).,Genetics, USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE (Workman, Heaton).,Department of Entomology, West Central Research and Extension Center, University of Nebraska-Lincoln, North Platte, NE (Boxler)
| | - Dale M Grotelueschen
- Department of Veterinary Medicine and Biomedical Sciences, Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Clay Center, NE (Carlson, Vander Ley, Grotelueschen).,Department of Food Science and Technology, Oregon State University, Corvallis, OR (Lee).,Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL (Walz).,Genetics, USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE (Workman, Heaton).,Department of Entomology, West Central Research and Extension Center, University of Nebraska-Lincoln, North Platte, NE (Boxler)
| | - Paul H Walz
- Department of Veterinary Medicine and Biomedical Sciences, Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Clay Center, NE (Carlson, Vander Ley, Grotelueschen).,Department of Food Science and Technology, Oregon State University, Corvallis, OR (Lee).,Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL (Walz).,Genetics, USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE (Workman, Heaton).,Department of Entomology, West Central Research and Extension Center, University of Nebraska-Lincoln, North Platte, NE (Boxler)
| | - Aspen M Workman
- Department of Veterinary Medicine and Biomedical Sciences, Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Clay Center, NE (Carlson, Vander Ley, Grotelueschen).,Department of Food Science and Technology, Oregon State University, Corvallis, OR (Lee).,Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL (Walz).,Genetics, USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE (Workman, Heaton).,Department of Entomology, West Central Research and Extension Center, University of Nebraska-Lincoln, North Platte, NE (Boxler)
| | - Michael P Heaton
- Department of Veterinary Medicine and Biomedical Sciences, Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Clay Center, NE (Carlson, Vander Ley, Grotelueschen).,Department of Food Science and Technology, Oregon State University, Corvallis, OR (Lee).,Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL (Walz).,Genetics, USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE (Workman, Heaton).,Department of Entomology, West Central Research and Extension Center, University of Nebraska-Lincoln, North Platte, NE (Boxler)
| | - David J Boxler
- Department of Veterinary Medicine and Biomedical Sciences, Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Clay Center, NE (Carlson, Vander Ley, Grotelueschen).,Department of Food Science and Technology, Oregon State University, Corvallis, OR (Lee).,Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL (Walz).,Genetics, USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE (Workman, Heaton).,Department of Entomology, West Central Research and Extension Center, University of Nebraska-Lincoln, North Platte, NE (Boxler)
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Heaton MP, Bassett AS, Whitman KJ, Krafsur GM, Lee SI, Carlson JM, Clark HJ, Smith HR, Pelster MC, Basnayake V, Grotelueschen DM, Vander Ley BL. Evaluation of EPAS1 variants for association with bovine congestive heart failure. F1000Res 2019; 8:1189. [PMID: 31543958 PMCID: PMC6733380 DOI: 10.12688/f1000research.19951.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/18/2019] [Indexed: 11/25/2022] Open
Abstract
Background: Bovine congestive heart failure (BCHF) has become increasingly prevalent in feedlot cattle in the Western Great Plains of North America. BCHF is an untreatable complex condition involving pulmonary hypertension that culminates in right ventricular failure and death. A protein variant of hypoxia-inducible factor 2 alpha (HIF2α, encoded by the endothelial PAS domain-containing protein 1 gene,
EPAS1) was previously reported to be associated with pulmonary hypertension at altitudes exceeding 2,000 m. Our aim was to evaluate
EPAS1 haplotypes for association with BCHF in feedlot cattle raised at moderate altitudes (1,200 m). Methods: Paired samples of clinical cases and unaffected controls were collected at four feedlots in Nebraska and Wyoming. Each pair (n =102) was matched for source, pen, breed type, sex, arrival date, and management conditions. Cases were identified by animal caretakers, euthanized, and diagnosis was confirmed at necropsy. Cases were derived from 30 different ranch operations, with the largest source contributing 32. Animals were tested for eight
EPAS1 haplotypes encoding 36 possible different diploid combinations. Results: The common, ancestral
EPAS1 haplotype encoding HIF2α with alanine (A) at position 606 and glycine (G) at position 610 was equally frequent in cases and controls (0.67). The
EPAS1 variant haplotype reported to be associated with disease (encoding threonine (T) at position 606 and serine (S) at position 610) was not enriched in cases compared with controls (0.21 and 0.25, respectively). Frequencies of other
EPAS1 haplotypes (e.g., encoding Q270, L362, or G671) were each less than 0.05 overall. McNemar’s test with 45 discordant pairs showed the linked T606/S610 variant was not associated with BCHF (OR = 0.73, CI
95 0.38 -1.4,
p-value = 0.37). Conclusions: HIF2α polypeptide variants were not significantly associated with BCHF in feedlot cattle at moderate altitudes. Thus, a wider search is needed to identify genetic risk factors underlying this disease.
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Affiliation(s)
- Michael P Heaton
- U.S. Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Adam S Bassett
- University of Nebraska-Lincoln, Clay Center, Nebraska, 68933, USA
| | | | - Greta M Krafsur
- Anschutz School of Medicine, University of Colorado Denver, Aurora, Colorado, 80045, USA
| | - Sang In Lee
- University of Nebraska-Lincoln, Clay Center, Nebraska, 68933, USA
| | - Jaden M Carlson
- University of Nebraska-Lincoln, Clay Center, Nebraska, 68933, USA
| | - Halden J Clark
- University of Nebraska-Lincoln, Clay Center, Nebraska, 68933, USA
| | - Helen R Smith
- U.S. Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
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Gatson GA, Gunn PJ, Busby WD, Wiegand BR, Vander Ley BL, Meyer AM. Effects of dry or wet conditions during the preweaning phase on subsequent feedlot performance and carcass composition of beef cattle. Transl Anim Sci 2018; 3:247-255. [PMID: 32704796 PMCID: PMC7200500 DOI: 10.1093/tas/txy095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 08/01/2018] [Indexed: 11/13/2022] Open
Abstract
Our objective was to determine the effects of dry and wet conditions during the preweaning on subsequent feedlot performance and carcass characteristics of beef cattle. Steers (n = 7,432) and heifers (n = 2,361) finished in 16 feedlots in southwestern Iowa through the Tri-County Steer Carcass Futurity Cooperative were used for a retrospective analysis. Cattle originated in the Midwest (Iowa, Missouri, Indiana, Illinois, and Minnesota) and were born in February, March, or April of 2002 through 2013. Feedlot performance and carcass composition data were obtained for each animal. Palmer Drought Severity Index (PDSI) values were obtained for each animal's preweaning environment on a monthly basis. Mean PDSI values were used to classify conditions as dry (≤-2.0), normal (>-2.0 and <2.0), or wet (≥2.0) for the cool (April and May), warm (June through August), and combined (April through August) forage growing seasons preweaning. Mixed models were used to evaluate the effects of PDSI class on subsequent performance. Calf sex, date of birth (as day of year), year, and feedlot were also included as fixed effects. When considering PDSI class during the cool season, cattle from normal and wet classes had a greater feedlot delivery BW (P < 0.0001) than dry. Dry and normal classes had greater (P ≤ 0.02) delivery BW than wet during the warm and combined seasons, however. For the cool season, average daily gain was greater (P < 0.0001) for the dry class than normal and wet. Cattle from the normal class for the cool season had greater (P = 0.001) final BW than wet, but the wet class had the greatest (P < 0.04) and dry class had the lowest (P < 0.01) final BW during the warm season. During the cool season, HCW was greater (P < 0.007) for the normal than wet class, although HCW was greater (P ≤ 0.02) for wet compared with dry and normal during the warm season. Calculated yield grade was lower (P ≤ 0.006) for the normal class during the cool season compared with dry and wet. For both the warm and combined seasons, the dry class had lower (P ≤ 0.004) calculated yield grade compared with normal and wet. Carcasses from cattle that experienced normal or wet warm seasons had greater (P ≤ 0.0005) marbling scores than dry, and normal had greater (P = 0.0009) marbling score than dry for the combined seasons. In conclusion, these data indicate that both dry and wet conditions during the preweaning phase may impact ultimate feedlot performance and carcass composition.
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Affiliation(s)
- Garth A Gatson
- Division of Animal Sciences, University of Missouri, Columbia, MO
| | - Patrick J Gunn
- Department of Animal Science, Iowa State University, Ames, IA
| | | | - Bryon R Wiegand
- Division of Animal Sciences, University of Missouri, Columbia, MO
| | | | - Allison M Meyer
- Division of Animal Sciences, University of Missouri, Columbia, MO
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14
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Vander Ley BL, Ridpath JF, Sweiger SH. Bovine viral diarrhea virus antigen detection across whole cattle hides using two antigen-capture enzyme-linked immunosorbent assays. J Vet Diagn Invest 2012; 24:546-8. [DOI: 10.1177/1040638712443057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Bovine viral diarrhea virus is a costly disease of cattle that can be controlled by vaccination, biosecurity, and removal of persistently infected cattle. Development and proficiency testing of assays to identify persistently infected cattle requires substantial quantities of known positive- and negative-sample material. The objective of this study was to determine what sections of bovine skin contained Bovine viral diarrhea virus antigen. Two commercially available antigen-capture enzyme-linked immunoassays were used to test subsamples representing the entire skin of 3 persistently infected calves. Both assays detected Bovine viral diarrhea virus antigen in the samples indicated for use by assay protocol. However, one assay identified all subsamples as positive, while the second assay identified 64.4% of subsamples as positive. These results show that use of samples other than those specified by the assay protocol must be validated for each individual assay. In this study, alternative sample sites and use of the entire hide for proficiency testing would be acceptable for only one of the assays tested.
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Affiliation(s)
- Brian L. Vander Ley
- Cattle Stats, Oklahoma City, OK (Vander Ley, Sweiger)
- Iowa State University, Ames, IA (Vander Ley, Sweiger)
- Ruminant Diseases and Immunology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Ames, IA (Ridpath)
| | - Julia F. Ridpath
- Cattle Stats, Oklahoma City, OK (Vander Ley, Sweiger)
- Iowa State University, Ames, IA (Vander Ley, Sweiger)
- Ruminant Diseases and Immunology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Ames, IA (Ridpath)
| | - Shaun H. Sweiger
- Cattle Stats, Oklahoma City, OK (Vander Ley, Sweiger)
- Iowa State University, Ames, IA (Vander Ley, Sweiger)
- Ruminant Diseases and Immunology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Ames, IA (Ridpath)
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