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Mullen KR, Tammen I, Matentzoglu NA, Mather M, Mungall CJ, Haendel MA, Nicholas FW, Toro S. The Vertebrate Breed Ontology: Towards Effective Breed Data Standardization. ARXIV 2024:arXiv:2406.02623v1. [PMID: 38883236 PMCID: PMC11177956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Background – Limited universally adopted data standards in veterinary science hinders data interoperability and therefore integration and comparison; this ultimately impedes application of existing information-based tools to support advancement in veterinary diagnostics, treatments, and precision medicine. Hypothesis/Objectives – Creation of a Vertebrate Breed Ontology (VBO) as a single, coherent logic-based standard for documenting breed names in animal health, production and research-related records will improve data use capabilities in veterinary and comparative medicine. Animals – No live animals were used in this study. Methods – A list of breed names and related information was compiled from relevant sources, organizations, communities, and experts using manual and computational approaches to create VBO. Each breed is represented by a VBO term that includes all provenance and the breed's related information as metadata. VBO terms are classified using description logic to allow computational applications and Artificial Intelligence-readiness. Results – VBO is an open, community-driven ontology representing over 19,000 livestock and companion animal breeds covering 41 species. Breeds are classified based on community and expert conventions (e.g., horse breed, cattle breed). This classification is supported by relations to the breeds' genus and species indicated by NCBI Taxonomy terms. Relationships between VBO terms, e.g. relating breeds to their foundation stock, provide additional context to support advanced data analytics. VBO term metadata includes common names and synonyms, breed identifiers/codes, and attributed cross-references to other databases. Conclusion and clinical importance – Veterinary data interoperability and computability can be enhanced by the adoption of VBO as a source of standard breed names in databases and veterinary electronic health records.
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Esdaile E, Knickelbein KE, Donnelly CG, Ferneding M, Motta MJ, Story BD, Avila F, Finno CJ, Gilger BC, Sandmeyer L, Thomasy S, Bellone RR. Additional evidence supports GRM6 p.Thr178Met as a cause of congenital stationary night blindness in three horse breeds. Vet Ophthalmol 2024; 27:248-255. [PMID: 37815029 DOI: 10.1111/vop.13151] [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: 06/09/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023]
Abstract
Congenital stationary night blindness (CSNB) is an ocular disorder characterized by nyctalopia. An autosomal recessive missense mutation in glutamate metabotropic receptor 6 (GRM6 c.533C>T, p.(Thr178Met)), called CSNB2, was previously identified in one Tennessee Walking Horse and predicted to reduce binding affinity of the neurotransmitter glutamate, impacting the retinal rod ON-bipolar cell signaling pathway. Thus, the first aim was to identify the allele frequency (AF) of CSNB2 in breeds with reported cases of CSNB and breeds closely related to the Tennessee Walking Horse. The second aim was to perform ocular examinations in multiple breeds to confirm the link between genotype and CSNB phenotype. In evaluating 3518 horses from 14 breeds, the CSNB2 allele was identified in nine previously unreported breeds. The estimated AF was highest in pacing Standardbreds (0.17) and lowest in American Quarter Horses (0.0010). Complete ophthalmic examinations and electroretinograms (ERG) were performed on 19 horses from three breeds, including one CSNB2 homozygote from each breed. All three CSNB2/CSNB2 horses had an electronegative ERG waveform under scotopic light conditions consistent with CSNB. The remaining 16 horses (seven CSNB2/N and nine N/N) had normal scotopic ERG results. All horses had normal photopic ERGs. This study provides additional evidence that GRM6 c.533C>T homozygosity is likely causal to CSNB in Tennessee Walking Horses, Standardbreds, and Missouri Fox Trotting Horses. Genetic testing is recommended for breeds with the CSNB2 allele to limit the production of affected horses. This study represents the largest across-breed identification of CSNB in the horse and suggests that this disorder is likely underdiagnosed.
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Affiliation(s)
- Elizabeth Esdaile
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Kelly E Knickelbein
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Callum G Donnelly
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Michelle Ferneding
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Monica J Motta
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Brett D Story
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Felipe Avila
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Brian C Gilger
- Department of Clinical Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Department of Ophthalmology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Lynne Sandmeyer
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sara Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
- Department of Ophthalmology & Vision Science, School of Medicine, University of California, Davis, Sacramento, California, USA
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
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3
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Gu LH, Wu RR, Zheng XL, Fu A, Xing ZY, Chen YY, He ZC, Lu LZ, Qi YT, Chen AH, Zhang YP, Xu TS, Peng MS, Ma C. Genomic insights into local adaptation and phenotypic diversity of Wenchang chickens. Poult Sci 2024; 103:103376. [PMID: 38228059 PMCID: PMC10823079 DOI: 10.1016/j.psj.2023.103376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/02/2023] [Accepted: 12/08/2023] [Indexed: 01/18/2024] Open
Abstract
Wenchang chicken, a prized local breed in Hainan Province of China renowned for its exceptional adaptability to tropical environments and good meat quality, is deeply favored by the public. However, an insufficient understanding of its population architecture and the unclear genetic basis that governs its typical attributes have posed challenges in the protection and breeding of this precious breed. To address these gaps, we conducted whole-genome resequencing on 200 Wenchang chicken samples derived from 10 distinct strains, and we gathered data on an array of 21 phenotype traits. Population genomics analysis unveiled distinctive population structures in Wenchang chickens, primarily attributed to strong artificial selection for different feather colors. Selection sweep analysis identified a group of candidate genes, including PCDH9, DPF3, CDIN1, and SUGCT, closely linked to adaptations that enhance resilience in tropical island habitats. Genome-wide association studies (GWAS) highlighted potential candidate genes associated with diverse feather color traits, encompassing TYR, RAB38, TRPM1, GABARAPL2, CDH1, ZMIZ1, LYST, MC1R, and SASH1. Through the comprehensive analysis of high-quality genomic and phenotypic data across diverse Wenchang chicken resource groups, this study unveils the intricate genetic backgrounds and population structures of Wenchang chickens. Additionally, it identifies multiple candidate genes linked to environmental adaptation, feather color variations, and production traits. These insights not only provide genetic reference for the purification and breeding of Wenchang chickens but also broaden our understanding of the genetic basis of phenotypic diversity in chickens.
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Affiliation(s)
- Li-Hong Gu
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571199, China
| | - Ran-Ran Wu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin-Li Zheng
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571199, China
| | - An Fu
- Wenchang City Wenchang Chicken Research Institute, Wenchang 571300, China
| | - Zeng-Yang Xing
- Wenchang Long-quan Wenchang Chicken Industrial Co., Ltd., Wenchang 571346, China
| | - Yi-Yong Chen
- Hainan Chuang Wen Wenchang Chicken Industry Co., Ltd., Wenchang 571321, China
| | - Zhong-Chun He
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571199, China
| | - Li-Zhi Lu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yan-Tao Qi
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571199, China
| | - An-Hong Chen
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571199, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tie-Shan Xu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Min-Sheng Peng
- Wenchang City Wenchang Chicken Research Institute, Wenchang 571300, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Ma
- Wenchang City Wenchang Chicken Research Institute, Wenchang 571300, China.
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Zhou Y, Bennett TM, Ruzycki PA, Guo Z, Cao YQ, Shahidullah M, Delamere NA, Shiels A. A Cataract-Causing Mutation in the TRPM3 Cation Channel Disrupts Calcium Dynamics in the Lens. Cells 2024; 13:257. [PMID: 38334649 PMCID: PMC10854584 DOI: 10.3390/cells13030257] [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: 01/04/2024] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/10/2024] Open
Abstract
TRPM3 belongs to the melastatin sub-family of transient receptor potential (TRPM) cation channels and has been shown to function as a steroid-activated, heat-sensitive calcium ion (Ca2+) channel. A missense substitution (p.I65M) in the TRPM3 gene of humans (TRPM3) and mice (Trpm3) has been shown to underlie an inherited form of early-onset, progressive cataract. Here, we model the pathogenetic effects of this cataract-causing mutation using 'knock-in' mutant mice and human cell lines. Trpm3 and its intron-hosted micro-RNA gene (Mir204) were strongly co-expressed in the lens epithelium and other non-pigmented and pigmented ocular epithelia. Homozygous Trpm3-mutant lenses displayed elevated cytosolic Ca2+ levels and an imbalance of sodium (Na+) and potassium (K+) ions coupled with increased water content. Homozygous TRPM3-mutant human lens epithelial (HLE-B3) cell lines and Trpm3-mutant lenses exhibited increased levels of phosphorylated mitogen-activated protein kinase 1/extracellular signal-regulated kinase 2 (MAPK1/ERK2/p42) and MAPK3/ERK1/p44. Mutant TRPM3-M65 channels displayed an increased sensitivity to external Ca2+ concentration and an altered dose response to pregnenolone sulfate (PS) activation. Trpm3-mutant lenses shared the downregulation of genes involved in insulin/peptide secretion and the upregulation of genes involved in Ca2+ dynamics. By contrast, Trpm3-deficient lenses did not replicate the pathophysiological changes observed in Trpm3-mutant lenses. Collectively, our data suggest that a cataract-causing substitution in the TRPM3 cation channel elicits a deleterious gain-of-function rather than a loss-of-function mechanism in the lens.
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Affiliation(s)
- Yuefang Zhou
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thomas M. Bennett
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Philip A. Ruzycki
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zhaohua Guo
- Department of Anesthesiology and Washington University Pain Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yu-Qing Cao
- Department of Anesthesiology and Washington University Pain Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mohammad Shahidullah
- Department of Physiology, University of Arizona College of Medicine, Tucson, AZ 85724, USA
| | - Nicholas A. Delamere
- Department of Physiology, University of Arizona College of Medicine, Tucson, AZ 85724, USA
| | - Alan Shiels
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
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McFadden A, Vierra M, Martin K, Brooks SA, Everts RE, Lafayette C. Spotting the Pattern: A Review on White Coat Color in the Domestic Horse. Animals (Basel) 2024; 14:451. [PMID: 38338094 PMCID: PMC10854722 DOI: 10.3390/ani14030451] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Traits such as shape, size, and color often influence the economic and sentimental value of a horse. Around the world, horses are bred and prized for the colors and markings that make their unique coat patterns stand out from the crowd. The underlying genetic mechanisms determining the color of a horse's coat can vary greatly in their complexity. For example, only two genetic markers are used to determine a horse's base coat color, whereas over 50 genetic variations have been discovered to cause white patterning in horses. Some of these white-causing mutations are benign and beautiful, while others have a notable impact on horse health. Negative effects range from slightly more innocuous defects, like deafness, to more pernicious defects, such as the lethal developmental defect incurred when a horse inherits two copies of the Lethal White Overo allele. In this review, we explore, in detail, the etiology of white spotting and its overall effect on the domestic horse to Spot the Pattern of these beautiful (and sometimes dangerous) white mutations.
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Affiliation(s)
- Aiden McFadden
- Etalon Inc., Menlo Park, CA 94025, USA; (M.V.); (K.M.); (R.E.E.); (C.L.)
| | - Micaela Vierra
- Etalon Inc., Menlo Park, CA 94025, USA; (M.V.); (K.M.); (R.E.E.); (C.L.)
| | - Katie Martin
- Etalon Inc., Menlo Park, CA 94025, USA; (M.V.); (K.M.); (R.E.E.); (C.L.)
| | - Samantha A. Brooks
- Department of Animal Sciences, UF Genetics Institute, University of Florida, Gainesville, FL 32611, USA;
| | - Robin E. Everts
- Etalon Inc., Menlo Park, CA 94025, USA; (M.V.); (K.M.); (R.E.E.); (C.L.)
| | - Christa Lafayette
- Etalon Inc., Menlo Park, CA 94025, USA; (M.V.); (K.M.); (R.E.E.); (C.L.)
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6
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Benítez-Burraco A, Uriagereka J, Nataf S. The genomic landscape of mammal domestication might be orchestrated by selected transcription factors regulating brain and craniofacial development. Dev Genes Evol 2023; 233:123-135. [PMID: 37552321 PMCID: PMC10746608 DOI: 10.1007/s00427-023-00709-7] [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: 02/26/2023] [Accepted: 07/27/2023] [Indexed: 08/09/2023]
Abstract
Domestication transforms once wild animals into tamed animals that can be then exploited by humans. The process entails modifications in the body, cognition, and behavior that are essentially driven by differences in gene expression patterns. Although genetic and epigenetic mechanisms were shown to underlie such differences, less is known about the role exerted by trans-regulatory molecules, notably transcription factors (TFs) in domestication. In this paper, we conducted extensive in silico analyses aimed to clarify the TF landscape of mammal domestication. We first searched the literature, so as to establish a large list of genes selected with domestication in mammals. From this list, we selected genes experimentally demonstrated to exhibit TF functions. We also considered TFs displaying a statistically significant number of targets among the entire list of (domestication) selected genes. This workflow allowed us to identify 5 candidate TFs (SOX2, KLF4, MITF, NR3C1, NR3C2) that were further assessed in terms of biochemical and functional properties. We found that such TFs-of-interest related to mammal domestication are all significantly involved in the development of the brain and the craniofacial region, as well as the immune response and lipid metabolism. A ranking strategy, essentially based on a survey of protein-protein interactions datasets, allowed us to identify SOX2 as the main candidate TF involved in domestication-associated evolutionary changes. These findings should help to clarify the molecular mechanics of domestication and are of interest for future studies aimed to understand the behavioral and cognitive changes associated to domestication.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Seville, Spain.
- Área de Lingüística General, Departamento de Lengua Española, Lingüística y Teoría de la Literatura, Facultad de Filología, Universidad de Sevilla, C/ Palos de la Frontera s/n., 41007-, Sevilla, España.
| | - Juan Uriagereka
- Department of Linguistics and School of Languages, Literatures & Cultures, University of Maryland, College Park, MD, USA
| | - Serge Nataf
- Stem-cell and Brain Research Institute, 18 avenue de Doyen Lépine, F-69500, Bron, France
- University of Lyon 1, 43 Bd du 11 Novembre 1918, F-69100, Villeurbanne, France
- Bank of Tissues and Cells, Hospices Civils de Lyon, Hôpital Edouard Herriot, Place d'Arsonval, F-69003, Lyon, France
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7
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Bellone RR, Tanaka J, Esdaile E, Sutton RB, Payette F, Leduc L, Till BJ, Abdel-Ghaffar AK, Hammond M, Magdesian KG. A de novo 2.3 kb structural variant in MITF explains a novel splashed white phenotype in a Thoroughbred family. Anim Genet 2023; 54:752-762. [PMID: 37697831 DOI: 10.1111/age.13352] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/12/2023] [Accepted: 08/19/2023] [Indexed: 09/13/2023]
Abstract
Splashed white in horses is characterized by extensive white patterning on the legs, face and abdomen and may be accompanied by deafness. To date, seven variants in microphthalmia-associated transcription factor (MITF) and two variants in Paired Box 3 (PAX3) have been identified to explain this phenotype. A splashed white Thoroughbred stallion, whose sire and dam were not patterned, was hypothesized to have a de novo variant leading to his white coat pattern. A whole-genome sequencing candidate gene approach identified two single nucleotide variants (SNVs) in SOX10, four SNVs in MITF and a 2.3 kb deletion in MITF with the alternative allele present in this stallion but absent in the other 18 horses analyzed. All six SNVs were annotated as modifiers and were not further considered. The deletion in MITF (NC_009159.3:g.21555811_21558139delinsAAAT) encompasses exon 9 encoding a part of the helix-loop-helix domain required for DNA binding. Sanger sequencing and parentage testing confirmed that this deletion was a de novo mutation of maternal origin. Consistent with the published nomenclature, we denote this likely causal variant as SW8. Genotyping three of this stallion's offspring identified SW8 only in the nearly all-white foal that was confirmed deaf by brainstem auditory evoked response testing. This foal was also a compound heterozygote for dominant white variants (W20/W22), but to date, W variants alone have not been connected to deafness. SW8 marks the fourth de novo MITF variant in horses reported to cause white patterning. The link between deafness and all MITF variants with and without other variants impacting melanocyte development and function needs to be further explored.
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Affiliation(s)
- R R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - J Tanaka
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - E Esdaile
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - R B Sutton
- Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - F Payette
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, University School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania, USA
| | - L Leduc
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, University School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania, USA
| | - B J Till
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - A K Abdel-Ghaffar
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - M Hammond
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - K G Magdesian
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
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8
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Kingsley NB, Sandmeyer L, Parker SE, Dwyer A, Heden S, Reilly C, Hallendar-Edman A, Archer S, Bellone RR. Risk factors for insidious uveitis in the Knabstrupper breed. Equine Vet J 2023; 55:820-830. [PMID: 36199161 DOI: 10.1111/evj.13879] [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: 04/29/2022] [Accepted: 09/23/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Equine recurrent uveitis (ERU) is the leading cause of blindness for horses; previous research implicated the leopard complex spotting allele (LP) as a genetic risk factor for insidious uveitis in the Appaloosa. There is limited information about risk in the Knabstrupper. OBJECTIVE To evaluate clinical manifestations, disease frequency and potential risk factors for ERU in Knabstrupper horses. STUDY DESIGN Cross-sectional study. METHODS Ocular examinations were performed on 116 horses, and based on identified anomalies, horses were classified as suspect, ERU-affected or having no clinical signs. Microagglutination testing (MAT) of serum assessed exposure to Leptospira spp. Clinical signs, age, sex, base colour, coat pattern, LP and PATN1 genotypes, percent white at birth, progressive roaning and Leptospira were assessed as risk factors using multivariable exact logistic regression, accounting for clustering at the barn level. Additionally, a pedigree analysis was performed (n = 20 cases and 21 controls), and coefficients of coancestry (CC) and inbreeding were calculated. RESULTS Prevalence of insidious uveitis in this sample of Knabstruppers was 20.7%. Similar to findings for Appaloosas, LP homozygotes had higher odds of uveitis compared with true solid (N/N) horses (LP/LP OR = 7.64, 95% CI [0.8 to +INF], p = 0.04) and age was also identified as a risk factor. After accounting for LP, the 16-20 age group had higher odds compared with the youngest group (OR = 13.36, 95% CI [1.4-213.4], p = 0.009). The distributions of average CC were significantly different between cases and controls (p = 0.01). MAIN LIMITATIONS A relatively small sample size decreased the power for detecting additional associations. The progressive nature of insidious uveitis may have prevented identification of younger affected horses. CONCLUSIONS Our data support genotyping for LP to assess risk of ERU in Knabstruppers. Additional studies are necessary to develop more robust risk models across LP breeds for earlier detection and improved clinical management.
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Affiliation(s)
- Nicole B Kingsley
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - Lynne Sandmeyer
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sarah E Parker
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ann Dwyer
- Genesee Valley Equine Clinic, LLC, Scottsville, New York, USA
| | | | | | - Anna Hallendar-Edman
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sheila Archer
- Independent Researcher, Sayward, British Columbia, Canada
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
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9
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Koller D, Benítez-Burraco A, Polimanti R. Enrichment of self-domestication and neural crest function loci in the heritability of neurodevelopmental disorders. Hum Genet 2023; 142:1271-1279. [PMID: 36930228 PMCID: PMC10472204 DOI: 10.1007/s00439-023-02541-5] [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: 12/27/2022] [Accepted: 03/01/2023] [Indexed: 03/18/2023]
Abstract
Self-domestication could contribute to shaping the biology of human brain and consequently the predisposition to neurodevelopmental disorders. Leveraging genome-wide data from the Psychiatric Genomics Consortium, we tested the enrichment of self-domestication and neural crest function loci with respect to the heritability of autism spectrum disorder, schizophrenia (SCZ in East Asian and European ancestries, EAS and EUR, respectively), attention-deficit/hyperactivity disorder, obsessive-compulsive disorder, and Tourette's syndrome (TS). Considering only self-domestication and neural-crest-function annotations in the linkage disequilibrium score regression (LDSC) model, our partitioned heritability analysis revealed statistically significant enrichments across all disorders investigated. The estimates of the heritability enrichments for self-domestication loci were similar across neurodevelopmental disorders, ranging from 0.902 (EAS SCZ, p = 4.55 × 10-20) to 1.577 (TS, p = 5.85 × 10-5). Conversely, a wider spectrum of heritability enrichment estimates was present for neural crest function with the highest enrichment observed for TS (enrichment = 3.453, p = 2.88 × 10-3) and the lowest for EAS SCZ (enrichment = 1.971, p = 3.81 × 10-3). Although these estimates appear to be strong, the enrichments for self-domestication and neural crest function were null once we included additional annotations related to different genomic features. This indicates that the effect of self-domestication on the polygenic architecture of neurodevelopmental disorders is not independent of other functions of human genome.
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Affiliation(s)
- Dora Koller
- Department of Psychiatry, Yale School of Medicine, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA
- VA CT Healthcare Center, West Haven, CT, 06516, USA
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028, Barcelona, Catalonia, Spain
| | - Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, 41004, Seville, Spain
| | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine, VA CT 116A2, 950 Campbell Avenue, West Haven, CT, 06516, USA.
- VA CT Healthcare Center, West Haven, CT, 06516, USA.
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10
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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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11
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Zhao P, Peng C, Fang L, Wang Z, Liu GE. Taming transposable elements in livestock and poultry: a review of their roles and applications. Genet Sel Evol 2023; 55:50. [PMID: 37479995 PMCID: PMC10362595 DOI: 10.1186/s12711-023-00821-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/30/2023] [Indexed: 07/23/2023] Open
Abstract
Livestock and poultry play a significant role in human nutrition by converting agricultural by-products into high-quality proteins. To meet the growing demand for safe animal protein, genetic improvement of livestock must be done sustainably while minimizing negative environmental impacts. Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. However, compared to other species, research on TE in livestock and poultry is still in its early stages. In this review, we analyze 72 studies published in the past 20 years, summarize the TE composition in livestock and poultry genomes, and focus on their potential roles in functional genomics. We also discuss bioinformatic tools and strategies for integrating multi-omics data with TE, and explore future directions, feasibility, and challenges of TE research in livestock and poultry. In addition, we suggest strategies to apply TE in basic biological research and animal breeding. Our goal is to provide a new perspective on the importance of TE in livestock and poultry genomes.
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Affiliation(s)
- Pengju Zhao
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China
| | - Chen Peng
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark.
| | - Zhengguang Wang
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
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12
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Kingsley NB, Sandmeyer L, Norton EM, Speed D, Dwyer A, Lassaline M, McCue M, Bellone RR. Heritability of insidious uveitis in Appaloosa horses. Anim Genet 2022; 53:872-877. [DOI: 10.1111/age.13267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/09/2022] [Accepted: 09/20/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Nicole B. Kingsley
- Veterinary Genetics Laboratory, School of Veterinary Medicine University of California – Davis Davis California USA
- Department of Population Health and Reproduction, School of Veterinary Medicine University of California – Davis Davis California USA
| | - Lynne Sandmeyer
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine University of Saskatchewan Saskatoon Saskatchewan Canada
| | - Elaine M. Norton
- School of Animal and Comparative Biomedical Sciences University of Arizona Tucson Arizona USA
| | - Doug Speed
- Center for Quantitative Genetics and Genomics Aarhus University Aarhus Denmark
| | - Ann Dwyer
- Genesee Valley Equine Clinic, LLC Scottsville New York USA
| | - Mary Lassaline
- School of Veterinary Medicine University of Pennsylvania Philadelphia Pennsylvania USA
| | - Molly McCue
- Veterinary Population Medicine Department, College of Veterinary Medicine University of Minnesota St Paul Minnesota USA
| | - Rebecca R. Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine University of California – Davis Davis California USA
- Department of Population Health and Reproduction, School of Veterinary Medicine University of California – Davis Davis California USA
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13
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Characterization of the Sarcidano Horse Coat Color Genes. Animals (Basel) 2022; 12:ani12192677. [PMID: 36230420 PMCID: PMC9558981 DOI: 10.3390/ani12192677] [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: 08/30/2022] [Revised: 09/24/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022] Open
Abstract
The goal of this study was to contribute to the general knowledge of the Sarcidano Horse, both by the identification of the genetic basis of the coat color and by updating the exact locations of the genotyping sites, based on the current EquCab3.0 genome assembly version. One-hundred Sarcidano Horses, living in semi-feral condition, have been captured to perform health and biometric checks. From that total number, 70 individual samples of whole blood were used for DNA extraction, aimed to characterize the genetic basis of the coat color. By genotyping and sequencing analyses of the MC1R Exon 1 and ASIP Exon 3, a real image of the coat color distribution in the studied population has been obtained. Chestnut and Black resulted in the most representative coat colors both from a phenotypic and genotypic point of view, that is suggestive of no human domestication or crossbreeding with domestic breed. Due to its ancient origin and genetic isolation, an active regional plan for the conservation of this breed would be desirable, focused on maintenance of resident genotypes and genetic resources. Collection and management of DNA, sperm, embryos, with the involvement of research centers and Universities, could be a valid enhancing strategy.
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14
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Breed Distribution and Allele Frequencies of Base Coat Color, Dilution, and White Patterning Variants across 28 Horse Breeds. Genes (Basel) 2022; 13:genes13091641. [PMID: 36140807 PMCID: PMC9498372 DOI: 10.3390/genes13091641] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
Since domestication, horses have been selectively bred for various coat colors and white spotting patterns. To investigate breed distribution, allele frequencies, and potential lethal variants for recommendations on genetic testing, 29 variants within 14 genes were investigated in 11,281 horses from 28 breeds. The recessive chestnut ea allele in melanocortin 1 receptor (MC1R) (p.D84N) was identified in four breeds: Knabstrupper, Paint Horse, Percheron, and Quarter Horse. After filtering for relatedness, ea allele frequency in Knabstruppers was estimated at 0.035, thus illustrating the importance of testing for mate selection for base coat color. The Rocky Mountain Horse breed had the highest allele frequency for two of the dilution variants under investigation (Za.f. = 0.32 and Cha.f. = 0.026); marker-assisted selection in this breed could aid in the production of horses with desirable dilute coats with less severe ocular anomalies caused by the silver (Z) allele. With regard to white patterning, nine horses homozygous for the paired box 3 (PAX3) splashed white 2 (SW2) allele (p.C70Y) and six horses homozygous for the KIT proto-oncogene, receptor tyrosine kinase (KIT) sabino 1 (SB1) allele (ECA3g.79544206A>T) were identified, thus determining they are rare and confirming that homozygosity for SW2 is not embryonic lethal. The KIT dominant white 20 (W20) allele (p.R682H) was identified in all but three breeds: Arabian (n = 151), Icelandic Horse (n = 66), and Norwegian Fjord Horse (n = 90). The role of W20 in pigmentation across breeds is not well understood; given the different selection regimes of the breeds investigated, these data provide justification for further evaluating the functional role of this allele in pigmentation. Here, we present the largest dataset reported for coat color variants in horses to date, and these data highlight the importance of breed-specific studies to inform on the proper use of marker-assisted selection and to develop hypotheses related to pigmentation for further testing in horses.
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15
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Kingsley NB, Sandmeyer L, Bellone RR. A review of investigated risk factors for developing equine recurrent uveitis. Vet Ophthalmol 2022; 26:86-100. [PMID: 35691017 DOI: 10.1111/vop.13002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/25/2022] [Accepted: 05/27/2022] [Indexed: 12/01/2022]
Abstract
Equine recurrent uveitis (ERU) is an ocular inflammatory disease that can be difficult to manage clinically. As such, it is the leading cause of bilateral blindness for horses. ERU is suspected to have a complex autoimmune etiology with both environmental and genetic risk factors contributing to onset and disease progression in some or all cases. Work in recent years has aimed at unraveling the primary triggers, such as infectious agents and inherited breed-specific risk factors, for disease onset, persistence, and progression. This review has aimed at encompassing those factors that have been associated, implicated, or substantiated as contributors to ERU, as well as identifying areas for which additional knowledge is needed to better understand risk for disease onset and progression. A greater understanding of the risk factors for ERU will enable earlier detection and better prognosis through prevention and new therapeutics.
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Affiliation(s)
- Nicole B Kingsley
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, California, USA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, California, USA
| | - Lynne Sandmeyer
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, California, USA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, California, USA
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16
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Esdaile E, Till B, Kallenberg A, Fremeux M, Bickel L, Bellone RR. A de novo missense mutation in KIT is responsible for dominant white spotting phenotype in a Standardbred horse. Anim Genet 2022; 53:534-537. [PMID: 35641888 DOI: 10.1111/age.13222] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 05/04/2022] [Indexed: 12/31/2022]
Affiliation(s)
- Elizabeth Esdaile
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - Brad Till
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - Angelica Kallenberg
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - Michelle Fremeux
- InfogeneNZ, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - Leslie Bickel
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
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17
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Finno CJ. Science-in-brief: Genomic and transcriptomic approaches to the investigation of equine diseases. Equine Vet J 2022; 54:444-448. [PMID: 35133024 PMCID: PMC9095347 DOI: 10.1111/evj.13549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/17/2021] [Indexed: 12/01/2022]
Affiliation(s)
- Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
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18
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Niego A, Benítez-Burraco A. Are feralization and domestication truly mirror processes? ETHOL ECOL EVOL 2021. [DOI: 10.1080/03949370.2021.1975314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Amy Niego
- PhD Program, Faculty of Philology, University of Seville, C/Palos de la Frontera s/n, 41004 Sevilla, Spain
| | - Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, C/Palos de la Frontera s/n, 41004 Sevilla, Spain (E-mail: )
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19
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Derks MFL, Steensma M. Review: Balancing Selection for Deleterious Alleles in Livestock. Front Genet 2021; 12:761728. [PMID: 34925454 PMCID: PMC8678120 DOI: 10.3389/fgene.2021.761728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/19/2021] [Indexed: 01/04/2023] Open
Abstract
Harmful alleles can be under balancing selection due to an interplay of artificial selection for the variant in heterozygotes and purifying selection against the variant in homozygotes. These pleiotropic variants can remain at moderate to high frequency expressing an advantage for favorable traits in heterozygotes, while harmful in homozygotes. The impact on the population and selection strength depends on the consequence of the variant both in heterozygotes and homozygotes. The deleterious phenotype expressed in homozygotes can range from early lethality to a slightly lower fitness in the population. In this review, we explore a range of causative variants under balancing selection including loss-of-function variation (i.e., frameshift, stop-gained variants) and regulatory variation (affecting gene expression). We report that harmful alleles often affect orthologous genes in different species, often influencing analogous traits. The recent discoveries are mainly driven by the increasing genomic and phenotypic resources in livestock populations. However, the low frequency and sometimes subtle effects in homozygotes prevent accurate mapping of such pleiotropic variants, which requires novel strategies to discover. After discovery, the selection strategy for deleterious variants under balancing selection is under debate, as variants can contribute to the heterosis effect in crossbred animals in various livestock species, compensating for the loss in purebred animals. Nevertheless, gene-assisted selection is a useful tool to decrease the frequency of the harmful allele in the population, if desired. Together, this review marks various deleterious variants under balancing selection and describing the functional consequences at the molecular, phenotypic, and population level, providing a resource for further study.
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Affiliation(s)
- Martijn F L Derks
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands.,Topigs Norsvin Research Center, Beuningen, Netherlands
| | - Marije Steensma
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
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20
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Identification of W13 in the American Miniature Horse and Shetland Pony Populations. Genes (Basel) 2021; 12:genes12121985. [PMID: 34946933 PMCID: PMC8702037 DOI: 10.3390/genes12121985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/07/2021] [Accepted: 12/11/2021] [Indexed: 11/16/2022] Open
Abstract
Coat color is a trait of economic significance in horses. Variants in seven genes have been documented to cause white patterning in horses. Of the 34 variants that have been identified in KIT proto-oncogene, receptor tyrosine kinase (KIT), 27 have only been reported in a single individual or family and thus not all are routinely offered for genetic testing. Therefore, to enable proper use of marker-assisted selection, determining breed specificity for these alleles is warranted. Screening 19 unregistered all-white Shetland ponies for 16 white patterning markers identified 14 individuals whose phenotype could not be explained by testing results. In evaluating other known dominant white variants, 14 horses were heterozygous for W13. W13 was previously only reported in two quarter horses and a family of Australian miniature horses. Genotyping known white spotting variants in 30 owner-reported white animals (25 Miniature Horses and five Shetland ponies) identified two additional W13/N American Miniature Horses. The estimated allele frequency of W13 in the American Miniature Horse was 0.0063 (79 N/N, 1 W13/N) and the allele was not detected in a random sample (n = 59) of Shetland ponies. No homozygous W13 individuals were identified and W13/N ponies had a similar all-white coat with pink skin phenotype, regardless of the other white spotting variants present, demonstrating that W13 results in a Mendelian inherited dominant white phenotype and homozygosity is likely lethal. These findings document the presence of W13 in the American Miniature Horse and Shetland pony populations at a low frequency and illustrate the importance of testing for this variant in additional breeds.
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21
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Abstract
Background Ocular adverse events are common dose-limiting toxicities in cancer patients treated with HSP90 inhibitors, such as AUY922; however, the pathology and molecular mechanisms that mediate AUY922-induced retinal toxicity remain undescribed. Methods The impact of AUY922 on mouse retinas and cell lines was comprehensively investigated using isobaric tags for relative and absolute quantitation (iTRAQ)‑based proteomic profiling and pathway enrichment analysis, immunohistochemistry and immunofluorescence staining, terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay, MTT assay, colony formation assay, and western blot analysis. The effect of AUY922 on the Transient Receptor Potential cation channel subfamily M member 1 (TRPM1)-HSP90 chaperone complex was characterized by coimmunoprecipitation. TRPM1-regulated gene expression was analyzed by RNAseq analysis and gene set enrichment analysis (GSEA). The role of TRPM1 was assessed using both loss-of-function and gain-of-function approaches. Results Here, we show that the treatment with AUY922 induced retinal damage and cell apoptosis, dysregulated the photoreceptor and retinal pigment epithelium (RPE) layers, and reduced TRPM1 expression. Proteomic profiling and functional annotation of differentially expressed proteins reveals that those related to stress responses, protein folding processes, regulation of apoptosis, cell cycle and growth, reactive oxygen species (ROS) response, cell junction assembly and adhesion regulation, and proton transmembrane transport were significantly enriched in AUY922-treated cells. We found that AUY922 triggered caspase-3-dependent cell apoptosis, increased ROS production and inhibited cell growth. We determined that TRPM1 is a bona fide HSP90 client and characterized that AUY922 may reduce TRPM1 expression by disrupting the CDC37-HSP90 chaperone complex. Additionally, GSEA revealed that TRPM1-regulated genes were associated with retinal morphogenesis in camera-type eyes and the JAK-STAT cascade. Finally, gain-of-function and loss-of-function analyses validated the finding that TRPM1 mediated the cell apoptosis, ROS production and growth inhibition induced by AUY922. Conclusions Our study demonstrates the pathology of AUY922-induced retinal toxicity in vivo. TRPM1 is an HSP90 client, regulates photoreceptor morphology and function, and mediates AUY922-induced cytotoxicity. Supplementary Information The online version contains supplementary material available at 10.1186/s12929-021-00751-5.
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22
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Benítez-Burraco A, Chekalin E, Bruskin S, Tatarinova T, Morozova I. Recent selection of candidate genes for mammal domestication in Europeans and language change in Europe: a hypothesis. Ann Hum Biol 2021; 48:313-320. [PMID: 34241552 DOI: 10.1080/03014460.2021.1936634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND AND AIM Human evolution resulted from changes in our biology, behaviour, and culture. One source of these changes has been hypothesised to be our self-domestication (that is, the development in humans of features commonly found in domesticated strains of mammals, seemingly as a result of selection for reduced aggression). Signals of domestication, notably brain size reduction, have increased in recent times. METHODS In this paper, we compare whole-genome data between the Late Neolithic/Bronze Age individuals and modern Europeans. RESULTS We show that genes associated with mammal domestication and with neural crest development and function are significantly differently enriched in nonsynonymous single nucleotide polymorphisms between these two groups. CONCLUSION We hypothesise that these changes might account for the increased features of self-domestication in modern humans and, ultimately, for subtle recent changes in human cognition and behaviour, including language.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature, Faculty of Philology, University of Seville, Seville, Spain
| | - Evgeny Chekalin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Bruskin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana Tatarinova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Department of Biology, University of La Verne, La Verne, CA, USA.,A. A. Kharkevich Institute for Information Transmission Problems, Moscow, Russia.,Department of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
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23
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Magdesian KG, Tanaka J, Bellone RR. A De Novo MITF Deletion Explains a Novel Splashed White Phenotype in an American Paint Horse. J Hered 2021; 111:287-293. [PMID: 32242630 PMCID: PMC7238438 DOI: 10.1093/jhered/esaa009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/01/2020] [Indexed: 11/14/2022] Open
Abstract
Splashed white is a coat color pattern in horses characterized by extensive white patterning on the legs, belly, and face often accompanied by blue eyes and deafness. Three mutations in microphthalmia-associated transcription factor (MITF) and two mutations in Paired Box 3 (PAX3) have been identified that explain splashed white patterns (SW1-SW5). An American Paint Horse stallion with a splashed white phenotype and blue eyes, whose parents were not white patterned, was negative for the 5 known splashed white variants and other known white spotting alleles. This novel splashed white phenotype (SW6) was hypothesized to be caused by a de novo mutation in MITF or PAX3. Analysis of whole-genome sequencing using the EquCab3.0 reference genome for comparison identified an 8.7 kb deletion in MITF on ECA16 (NC_009159.3:g.21551060-21559770del). The deletion encompassed part of intron 7 through the 3' UTR of exon 9 of MITF, including the helix-loop-helix DNA-binding domain (ENSECAT00000006375.3). This variant is predicted to truncate protein and impair binding to DNA. Sanger sequencing confirmed the stallion was heterozygous for the MITF deletion. No single nucleotide polymorphisms (SNPs) or structural variants were identified in PAX3 or any of the other candidate genes that were unique to the stallion or predicted to affect protein function. Genotyping five of the stallion's splashed white offspring, including one all white foal, found that they were also heterozygous for the deletion. Given the role of MITF in producing white pattern phenotypes, and the predicted deleterious effect of this mutation, this 8.7 kb deletion is the likely causal variant for SW6.
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Affiliation(s)
- K Gary Magdesian
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California-Davis, Davis, CA
| | - Jocelyn Tanaka
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA
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24
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Kingsley NB, Hamilton NA, Lindgren G, Orlando L, Bailey E, Brooks S, McCue M, Kalbfleisch TS, MacLeod JN, Petersen JL, Finno CJ, Bellone RR. "Adopt-a-Tissue" Initiative Advances Efforts to Identify Tissue-Specific Histone Marks in the Mare. Front Genet 2021; 12:649959. [PMID: 33841506 PMCID: PMC8033197 DOI: 10.3389/fgene.2021.649959] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Affiliation(s)
- N B Kingsley
- 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
| | - Natasha A Hamilton
- Faculty of Science, School of Life and Environmental Science, University of Sydney, Camperdown, NSW, Australia
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Ludovic Orlando
- Centre d'Anthropobiologie et Génomique de Toulouse (CAGT), Faculté de Médecine Purpan, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Ernie Bailey
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, United States
| | - Samantha Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Molly McCue
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - T S Kalbfleisch
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, United States
| | - James N MacLeod
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, 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
| | - Rebecca R Bellone
- 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
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25
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Orlando L. The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics. Annu Rev Genet 2020; 54:563-581. [PMID: 32960653 DOI: 10.1146/annurev-genet-021920-011805] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The domestication of the horse some 5,500 years ago followed those of dogs, sheep, goats, cattle, and pigs by ∼2,500-10,000 years. By providing fast transportation and transforming warfare, the horse had an impact on human history with no equivalent in the animal kingdom. Even though the equine sport industry has considerable economic value today, the evolutionary history underlying the emergence of the modern domestic horse remains contentious. In the last decade, novel sequencing technologies have revolutionized our capacity to sequence the complete genome of organisms, including from archaeological remains. Applied to horses, these technologies have provided unprecedented levels of information and have considerably changed models of horse domestication. This review illustrates how ancient DNA, especially ancient genomes, has inspired researchers to rethink the process by which horses were first domesticated and then diversified into a variety of breeds showing a range of traits that are useful to humans.
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Affiliation(s)
- Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse, Faculté de Médecine Purpan, Université Toulouse III-Paul Sabatier, 31000 Toulouse, France;
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26
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Hack YL, Crabtree EE, Avila F, Sutton RB, Grahn R, Oh A, Gilger B, Bellone RR. Whole-genome sequencing identifies missense mutation in GRM6 as the likely cause of congenital stationary night blindness in a Tennessee Walking Horse. Equine Vet J 2020; 53:316-323. [PMID: 32654228 DOI: 10.1111/evj.13318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/01/2020] [Accepted: 06/25/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND The only known genetic cause of congenital stationary night blindness (CSNB) in horses is a 1378 bp insertion in TRPM1. However, an affected Tennessee Walking Horse was found to have no copies of this variant. OBJECTIVES To identify the genetic cause for CSNB in an affected Tennessee Walking Horse. STUDY DESIGN Case report detailing a whole-genome sequencing (WGS) approach to identify a causal variant. METHODS A complete ophthalmic exam, including an electroretinogram (ERG), was performed on suspected CSNB-affected horse. WGS data were generated from the case and compared with data from seven other breeds (n = 29). One hundred candidate genes were evaluated for coding variants homozygous in the case and absent in all other horses. Protein modelling was used to assess the functional effects of the identified variant. A random cohort of 90 unrelated Tennessee Walking Horses and 273 horses from additional breeds were screened to estimate allele frequency of the GRM6 variant. RESULTS ERG results were consistent with CSNB. WGS analysis identified a missense mutation in metabotropic glutamate receptor 6 (GRM6) (c.533C>T p.Thr178Met). This single nucleotide polymorphism (SNP) is predicted to be deleterious and protein modelling supports impaired binding of the neurotransmitter glutamate. This variant was not detected in 273 horses from three additional breeds. The estimated allele frequency in Tennessee Walking Horses is 10%. MAIN LIMITATIONS Limited phenotype information for controls and no additional cases with which to replicate this finding. CONCLUSIONS We identified a likely causal recessive missense variant in GRM6. Based on protein modelling, this variant alters GRM6 binding, and thus signalling from the retinal rod cell to the ON-bipolar cell, impairing vision in low light conditions. Given the 10% population allele frequency, it is likely that additional affected horses exist in this breed and further work is needed to identify and examine these animals.
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Affiliation(s)
- Yael L Hack
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Elizabeth E Crabtree
- College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Felipe Avila
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Roger B Sutton
- Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Robert Grahn
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Annie Oh
- College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Brian Gilger
- College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA.,Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
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27
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Abstract
The sequencing and assembly of a reference genome for the horse has been revolutionary for investigation of horse health and performance. Next-generation sequencing (NGS) methods represent a second revolution in equine genomics. Researchers can align and compare DNA and RNA sequencing data to the reference genome to explore variation that may contribute or be attributed to disease. NGS has also facilitated the translation of research discovery to clinically relevant applications. This article discusses the history and development of NGS, details some of the available sequencing platforms, and describes currently available applications in the context of both discovery and clinical settings.
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28
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Abstract
Horses perform in a variety of disciplines that are visually demanding, and any disease impacting the eye has the potential to threaten vision and thus the utility of the horse. Advances in equine genetics have enabled the understanding of some inherited ocular disorders and ocular manifestations and are enabling cross-species comparisons. Genetic testing for multiple congenital ocular anomalies, congenital stationary night blindness, equine recurrent uveitis, and squamous cell carcinoma can identify horses with or at risk for disease and thus can assist in clinical management and breeding decisions. This article describes the current knowledge of inherited ocular disorders.
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Affiliation(s)
- Rebecca R Bellone
- Department of Population Health and Reproduction, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA.
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29
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Brooks SA, Palermo KM, Kahn A, Hein J. Impact of white‐spotting alleles, including
W20
, on phenotype in the American Paint Horse. Anim Genet 2020; 51:707-715. [DOI: 10.1111/age.12960] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2020] [Indexed: 01/09/2023]
Affiliation(s)
- S. A. Brooks
- Department of Animal Sciences UF Genetics Institute University of Florida Gainesville FL 32611‐0910 USA
| | - K. M. Palermo
- Department of Animal Sciences UF Genetics Institute University of Florida Gainesville FL 32611‐0910 USA
| | - A. Kahn
- Department of Animal Sciences UF Genetics Institute University of Florida Gainesville FL 32611‐0910 USA
| | - J. Hein
- American Paint Horse Association Fort Worth TX 76161‐0023 USA
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30
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Abstract
Genetic testing in horses began in the 1960s, when parentage testing using blood group markers became the standard. In the 1990s, parentage testing shifted from evaluating blood groups to DNA testing. The development of genetics and genomics in both human and veterinarian medicine, along with continued technological advances in the last 2 decades, has helped unravel the causal variants for many horse traits. Genetic testing is also now possible for a variety of phenotypic and disease traits and is used to assist in breeding and clinical management decisions. This article describes the genetic tests that are currently available for horses.
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Affiliation(s)
- Rebecca R Bellone
- Department of Population Health and Reproduction Davis, CA 95616, USA; Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA.
| | - Felipe Avila
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
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31
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Corbin LJ, Pope J, Sanson J, Antczak DF, Miller D, Sadeghi R, Brooks SA. An Independent Locus Upstream of ASIP Controls Variation in the Shade of the Bay Coat Colour in Horses. Genes (Basel) 2020; 11:E606. [PMID: 32486210 PMCID: PMC7349280 DOI: 10.3390/genes11060606] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/20/2020] [Accepted: 05/27/2020] [Indexed: 01/09/2023] Open
Abstract
Novel coat colour phenotypes often emerge during domestication, and there is strong evidence of genetic selection for the two main genes that control base coat colour in horses-ASIP and MC1R. These genes direct the type of pigment produced, red pheomelanin (MC1R) or black eumelanin (ASIP), as well as the relative concentration and the temporal-spatial distribution of melanin pigment deposits in the skin and hair coat. Here, we describe a genome-wide association study (GWAS) to identify novel genic regions involved in the determination of the shade of bay. In total, 126 horses from five different breeds were ranked according to the extent of the distribution of eumelanin: spanning variation in phenotype from black colour restricted only to the extremities to the presence of some black pigment across nearly all the body surface. We identified a single region associated with the shade of bay ranking spanning approximately 0.5 MB on ECA22, just upstream of the ASIP gene (p = 9.76 × 10-15). This candidate region encompasses the distal 5' end of the ASIP transcript (as predicted from other species) as well as the RALY gene. Both loci are viable candidates based on the presence of similar alleles in other species. These results contribute to the growing understanding of coat colour genetics in the horse and to the mapping of genetic determinants of pigmentation on a molecular level. Given pleiotropic phenotypes in behaviour and obesity for ASIP alleles, especially those in the 5' regulatory region, improved understanding of this new Shade allele may have implications for health management in the horse.
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Affiliation(s)
- Laura J. Corbin
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK;
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol BS8 2BN, UK
| | - Jessica Pope
- Bristol Veterinary School, University of Bristol, Bristol BS8 1QU, UK;
| | - Jacqueline Sanson
- Department of Animal Sciences, University of Florida, Gainesville, FL 32610, USA;
| | - Douglas F. Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; (D.F.A.); (D.M.); (R.S.)
| | - Donald Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; (D.F.A.); (D.M.); (R.S.)
| | - Raheleh Sadeghi
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; (D.F.A.); (D.M.); (R.S.)
| | - Samantha A. Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL 32610, USA;
- UF Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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32
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Abstract
The domestication of animals led to a major shift in human subsistence patterns, from a hunter-gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have enabled the sequencing of whole ancient genomes. These genomes have helped reconstruct the process by which animals entered into domestic relationships with humans and were subjected to novel selection pressures. Here, we discuss and update key concepts in animal domestication in light of recent contributions from ancient genomics.
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33
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Winkler PA, Occelli LM, Petersen-Jones SM. Large Animal Models of Inherited Retinal Degenerations: A Review. Cells 2020; 9:cells9040882. [PMID: 32260251 PMCID: PMC7226744 DOI: 10.3390/cells9040882] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 12/13/2022] Open
Abstract
Studies utilizing large animal models of inherited retinal degeneration (IRD) have proven important in not only the development of translational therapeutic approaches, but also in improving our understanding of disease mechanisms. The dog is the predominant species utilized because spontaneous IRD is common in the canine pet population. Cats are also a source of spontaneous IRDs. Other large animal models with spontaneous IRDs include sheep, horses and non-human primates (NHP). The pig has also proven valuable due to the ease in which transgenic animals can be generated and work is ongoing to produce engineered models of other large animal species including NHP. These large animal models offer important advantages over the widely used laboratory rodent models. The globe size and dimensions more closely parallel those of humans and, most importantly, they have a retinal region of high cone density and denser photoreceptor packing for high acuity vision. Laboratory rodents lack such a retinal region and, as macular disease is a critical cause for vision loss in humans, having a comparable retinal region in model species is particularly important. This review will discuss several large animal models which have been used to study disease mechanisms relevant for the equivalent human IRD.
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34
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Sandmeyer LS, Kingsley NB, Walder C, Archer S, Leis ML, Bellone RR, Bauer BS. Risk factors for equine recurrent uveitis in a population of Appaloosa horses in western Canada. Vet Ophthalmol 2020; 23:515-525. [PMID: 32086865 DOI: 10.1111/vop.12749] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To characterize clinical manifestations, measure frequency, and evaluate risk factors for equine recurrent uveitis (ERU) in Appaloosa horses in western Canada. ANIMALS 145 Appaloosa horses. PROCEDURES Ophthalmic examinations were completed and eyes were classified as having no or mild clinical signs, or moderate, or severe damage from ERU. Clinical signs, age, sex, base coat color, and pattern were recorded. Whole blood and/or mane hair follicles were collected for DNA extraction, and all horses were tested for the leopard complex (LP) spotting pattern allele. Pedigree analysis was completed on affected and unaffected horses, and coefficients of coancestry (CC) and inbreeding (COI) were determined. RESULTS Equine recurrent uveitis was confirmed in 20 (14%) horses. The mean age of affected horses was 12.3 years (±5.3; range 3-25). Age was a significant risk factor for ERU diagnosis (ORyear = 1.15) and classification (ORyear = 1.19). The fewspot coat pattern was significantly associated with increased risk for ERU compared to horses that were minimally patterned or true solids. The LP/LP genotype was at a significantly greater risk for ERU compared to lp/lp (OR = 19.4) and LP/lp (OR = 6.37). Classification of ERU was greater in the LP/LP genotype compared to LP/lp. Affected horses had an average CC of 0.066, and there was a significant difference in the distribution of CC for affected horses versus the control group (P = .021). One affected horse was the sire or grandsire of nine other affected. CONCLUSIONS Age, coat pattern, and genetics are major risk factors for the diagnosis and classification of ERU in the Appaloosa.
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Affiliation(s)
- Lynne S Sandmeyer
- Small Animal Clinical Sciences, University of Saskatchewan, Saskatoon, Sask, Canada
| | - Nicole B Kingsley
- Equine Research Unit, University of California Davis Veterinary Genetics Laboratory, Davis, CA, USA
| | - Cheryl Walder
- Large Animal Clinical Sciences, University of Saskatchewan College of Veterinary Medicine, Saskatoon, Sask, Canada
| | | | - Marina L Leis
- Small Animal Clinical Sciences, University of Saskatchewan, Saskatoon, Sask, Canada
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory and the Department of Population Health and Reproduction, University of California-Davis, Davis, CA, USA
| | - Bianca S Bauer
- Small Animal Clinical Sciences, University of Saskatchewan, Saskatoon, Sask, Canada
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35
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Shiels A. TRPM3_miR-204: a complex locus for eye development and disease. Hum Genomics 2020; 14:7. [PMID: 32070426 PMCID: PMC7027284 DOI: 10.1186/s40246-020-00258-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/06/2020] [Indexed: 02/07/2023] Open
Abstract
First discovered in a light-sensitive retinal mutant of Drosophila, the transient receptor potential (TRP) superfamily of non-selective cation channels serve as polymodal cellular sensors that participate in diverse physiological processes across the animal kingdom including the perception of light, temperature, pressure, and pain. TRPM3 belongs to the melastatin sub-family of TRP channels and has been shown to function as a spontaneous calcium channel, with permeability to other cations influenced by alternative splicing and/or non-canonical channel activity. Activators of TRPM3 channels include the neurosteroid pregnenolone sulfate, calmodulin, phosphoinositides, and heat, whereas inhibitors include certain drugs, plant-derived metabolites, and G-protein subunits. Activation of TRPM3 channels at the cell membrane elicits a signal transduction cascade of mitogen-activated kinases and stimulus response transcription factors. The mammalian TRPM3 gene hosts a non-coding microRNA gene specifying miR-204 that serves as both a tumor suppressor and a negative regulator of post-transcriptional gene expression during eye development in vertebrates. Ocular co-expression of TRPM3 and miR-204 is upregulated by the paired box 6 transcription factor (PAX6) and mutations in all three corresponding genes underlie inherited forms of eye disease in humans including early-onset cataract, retinal dystrophy, and coloboma. This review outlines the genomic and functional complexity of the TRPM3_miR-204 locus in mammalian eye development and disease.
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Affiliation(s)
- Alan Shiels
- Ophthalmology and Visual Sciences, Washington University School of Medicine, 660 S. Euclid Ave., Box 8096, St. Louis, MO, 63110, USA.
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36
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Grilz-Seger G, Reiter S, Neuditschko M, Wallner B, Rieder S, Leeb T, Jagannathan V, Mesarič M, Cotman M, Pausch H, Lindgren G, Velie B, Horna M, Brem G, Druml T. A Genome-Wide Association Analysis in Noriker Horses Identifies a SNP Associated With Roan Coat Color. J Equine Vet Sci 2020; 88:102950. [PMID: 32303326 DOI: 10.1016/j.jevs.2020.102950] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 01/20/2023]
Abstract
The roan coat color in horses is characterized by dispersed white hair and dark points. This phenotype segregates in a broad range of horse breeds, while the underlying genetic background is still unknown. Previous studies mapped the roan locus to the KIT gene on equine chromosome 3 (ECA3). However, this association could not be validated across different horse breeds. Performing a genome-wide association analysis (GWAS) in Noriker horses, we identified a single nucleotide polymorphism (SNP) (ECA3:g.79,543.439 A > G) in the intron 17 of the KIT gene. The G -allele of the top associated SNP was present in other roan horses, namely Quarter Horse, Murgese, Slovenian, and Belgian draught horse, while it was absent in a panel of 15 breeds, including 657 non-roan horses. In further 379 gray Lipizzan horses, eight animals exhibited a heterozygous genotype (A/G). Comparative whole-genome sequence analysis of the KIT region revealed two deletions in the downstream region (ECA3:79,533,217_79,533,224delTCGTCTTC; ECA3:79,533,282_79,533,285delTTCT) and a 3 bp deletion combined with 17 bp insertion in intron 20 of KIT (ECA3:79,588,128_79,588,130delinsTTATCTCTATAGTAGTT). Within the Noriker sample, these loci were in complete linkage disequilibrium (LD) with the identified top SNP. Based upon pedigree information and historical records, we were able to trace back the genetic origin of roan coat color to a baroque gene pool. Furthermore, our data suggest allelic heterogeneity and the existence of additional roan alleles in ponies and breeds related to the English Thoroughbred. In order to study the roan phenotype segregating in those breeds, further association and verification studies are required.
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Affiliation(s)
- Gertrud Grilz-Seger
- Department of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Vienna, Austria.
| | - Simone Reiter
- Department of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Vienna, Austria
| | | | - Barbara Wallner
- Department of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Vienna, Austria
| | | | - Tosso Leeb
- Department of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vidhya Jagannathan
- Department of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Matjaz Mesarič
- Clinic for Reproduction and Large Animals, University of Ljubljana, Veterinary Faculty, Ljubljana, Slovenia
| | - Markus Cotman
- Department for Preclinical Sciences, University of Ljubljana, Veterinary Faculty, Ljubljana, Slovenia
| | | | - Gabriella Lindgren
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Brandon Velie
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Michaela Horna
- Department of Animal Husbandry, Slovak University of Agriculture in Nitra, Nitra, Slovakia
| | - Gottfried Brem
- Department of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Vienna, Austria
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Benítez-Burraco A. Genes Positively Selected in Domesticated Mammals Are Significantly Dysregulated in the Blood of Individuals with Autism Spectrum Disorders. Mol Syndromol 2020; 10:306-312. [PMID: 32021604 PMCID: PMC6995977 DOI: 10.1159/000505116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2019] [Indexed: 12/27/2022] Open
Abstract
Human self-domestication (i.e., the presence of traits in our species that are commonly found in domesticated animals) has been hypothesized to have contributed to the emergence of many human-specific features, including aspects of our cognition and behavior. Signs of self-domestication have been claimed to be attenuated in individuals with autism spectrum disorders (ASD), this conceivably accounting for facets of their distinctive cognitive and behavioral profile, although this possibility needs to be properly tested. In this study, we have found that candidate genes for mammal domestication, but not for neural crest development and function, are significantly dysregulated in the blood of subjects with ASD. The set of differentially expressed genes (DEGs) is enriched in biological and molecular processes, as well as in pathological phenotypes, of relevance for the etiology of ASD, like lipid metabolism, cell apoptosis, the activity of the insulin-like growth factor, gene expression regulation, skin/hair anomalies, musculoskeletal abnormalities, and hearing impairment. Moreover, among the DEGs, there are known candidates for ASD and/or genes involved in biological processes known to be affected in ASD. Our findings give support to the view that one important aspect of the etiopathogenesis of ASD is the abnormal manifestation of features of human self-domestication.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Seville, Spain
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38
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Rockwell H, Mack M, Famula T, Sandmeyer L, Bauer B, Dwyer A, Lassaline M, Beeson S, Archer S, McCue M, Bellone RR. Genetic investigation of equine recurrent uveitis in Appaloosa horses. Anim Genet 2019; 51:111-116. [PMID: 31793009 DOI: 10.1111/age.12883] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2019] [Indexed: 01/05/2023]
Abstract
Equine recurrent uveitis (ERU) is characterized by intraocular inflammation that often leads to blindness in horses. Appaloosas are more likely than any other breed to develop insidious ERU, distinguished by low-grade chronic intraocular inflammation, suggesting a genetic predisposition. Appaloosas are known for their white coat spotting patterns caused by the leopard complex spotting allele (LP) and the modifier PATN1. A marker linked to LP on ECA1 and markers near MHC on ECA20 were previously associated with increased ERU risk. This study aims to further investigate these loci and identify additional genetic risk factors. A GWAS was performed using the Illumina Equine SNP70 BeadChip in 91 horses. Additive mixed model approaches were used to correct for relatedness. Although they do not reach a strict Bonferroni genome-wide significance threshold, two SNPs on ECA1 and one SNP each on ECA12 and ECA29 were among the highest ranking SNPs and thus warranted further analysis (P = 1.20 × 10-5 , P = 5.91 × 10-6 , P = 4.91 × 10-5 , P = 6.46 × 10-5 ). In a second cohort (n = 98), only an association with the LP allele on ECA1 was replicated (P = 5.33 × 10-5 ). Modeling disease risk with LP, age and additional depigmentation factors (PATN1 genotype and extent of roaning) supports an additive role for LP and suggests an additive role for PATN1. Genotyping for LP and PATN1 may help predict ERU risk (AUC = 0.83). The functional role of LP and PATN1 in ERU development requires further investigation. Testing samples across breeds with leopard complex spotting patterns and a denser set of markers is warranted to further refine the genetic components of ERU.
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Affiliation(s)
- H Rockwell
- Veterinary Genetics Laboratory, Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, 95616, CA, USA
| | - M Mack
- Veterinary Genetics Laboratory, Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, 95616, CA, USA
| | - T Famula
- Appaloosa Project, Davis, 95616, CA, USA
| | - L Sandmeyer
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - B Bauer
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - A Dwyer
- Genesee Valley Equine Clinic, LLC, Scottsville, NY, 14546, USA
| | - M Lassaline
- Department of Radiological and Surgical Sciences, School of Veterinary Medicine, University of California - Davis, Davis, CA, 95616, USA
| | - S Beeson
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St Paul, MN, 55108, USA
| | - S Archer
- Appaloosa Project, Sayward, V0P 1R0, BC, Canada
| | - M McCue
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St Paul, MN, 55108, USA
| | - R R Bellone
- Veterinary Genetics Laboratory, Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, 95616, CA, USA
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39
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Brosnahan MM. Genetics, Evolution, and Physiology of Donkeys and Mules. Vet Clin North Am Equine Pract 2019; 35:457-467. [PMID: 31672199 DOI: 10.1016/j.cveq.2019.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The genus Equus is made up of donkeys, horses, and zebras. Despite significant variation in chromosome number across these species, interspecies breeding results in healthy, although infertile, hybrid offspring. Most notable among these are the horse-donkey hybrids, the mule and hinny. Donkeys presently are used for everything from companion animals to beasts of burden. Although closely related from an evolutionary standpoint, differences in anatomy and physiology preclude the assumption that they can be treated identically to the domestic horse. Veterinarians should be aware of these differences and adjust their practice accordingly.
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Affiliation(s)
- Margaret M Brosnahan
- College of Veterinary Medicine, Midwestern University, 19555 North 59th Avenue, Cactus Wren Hall 336-P, Glendale, AZ 85308, USA.
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40
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Das RG, Becker D, Jagannathan V, Goldstein O, Santana E, Carlin K, Sudharsan R, Leeb T, Nishizawa Y, Kondo M, Aguirre GD, Miyadera K. Genome-wide association study and whole-genome sequencing identify a deletion in LRIT3 associated with canine congenital stationary night blindness. Sci Rep 2019; 9:14166. [PMID: 31578364 PMCID: PMC6775105 DOI: 10.1038/s41598-019-50573-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/05/2019] [Indexed: 01/11/2023] Open
Abstract
Congenital stationary night blindness (CSNB), in the complete form, is caused by dysfunctions in ON-bipolar cells (ON-BCs) which are secondary neurons of the retina. We describe the first disease causative variant associated with CSNB in the dog. A genome-wide association study using 12 cases and 11 controls from a research colony determined a 4.6 Mb locus on canine chromosome 32. Subsequent whole-genome sequencing identified a 1 bp deletion in LRIT3 segregating with CSNB. The canine mutant LRIT3 gives rise to a truncated protein with unaltered subcellular expression in vitro. Genetic variants in LRIT3 have been associated with CSNB in patients although there is limited evidence regarding its apparently critical function in the mGluR6 pathway in ON-BCs. We determine that in the canine CSNB retina, the mutant LRIT3 is correctly localized to the region correlating with the ON-BC dendritic tips, albeit with reduced immunolabelling. The LRIT3-CSNB canine model has direct translational potential enabling studies to help understand the CSNB pathogenesis as well as to develop new therapies targeting the secondary neurons of the retina.
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Affiliation(s)
- Rueben G Das
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Pennsylvania, United States of America
| | - Doreen Becker
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Pennsylvania, United States of America.,Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | | | - Orly Goldstein
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Evelyn Santana
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Pennsylvania, United States of America
| | - Kendall Carlin
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Pennsylvania, United States of America
| | - Raghavi Sudharsan
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Pennsylvania, United States of America
| | - Tosso Leeb
- Institute of Genetics, University of Bern, Bern, Switzerland
| | - Yuji Nishizawa
- Department of Biomedical Sciences, Chubu University, Kasugai, Aichi, Japan
| | - Mineo Kondo
- Department of Ophthalmology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | - Gustavo D Aguirre
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Pennsylvania, United States of America
| | - Keiko Miyadera
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Pennsylvania, United States of America.
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41
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Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era. Anim Genet 2019; 50:569-597. [PMID: 31568563 PMCID: PMC6825885 DOI: 10.1111/age.12857] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 12/14/2022]
Abstract
The horse reference genome from the Thoroughbred mare Twilight has been available for a decade and, together with advances in genomics technologies, has led to unparalleled developments in equine genomics. At the core of this progress is the continuing improvement of the quality, contiguity and completeness of the reference genome, and its functional annotation. Recent achievements include the release of the next version of the reference genome (EquCab3.0) and generation of a reference sequence for the Y chromosome. Horse satellite‐free centromeres provide unique models for mammalian centromere research. Despite extremely low genetic diversity of the Y chromosome, it has been possible to trace patrilines of breeds and pedigrees and show that Y variation was lost in the past approximately 2300 years owing to selective breeding. The high‐quality reference genome has led to the development of three different SNP arrays and WGSs of almost 2000 modern individual horses. The collection of WGS of hundreds of ancient horses is unique and not available for any other domestic species. These tools and resources have led to global population studies dissecting the natural history of the species and genetic makeup and ancestry of modern breeds. Most importantly, the available tools and resources, together with the discovery of functional elements, are dissecting molecular causes of a growing number of Mendelian and complex traits. The improved understanding of molecular underpinnings of various traits continues to benefit the health and performance of the horse whereas also serving as a model for complex disease across species.
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Affiliation(s)
- T Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Research, Texas A&M University, College Station, TX, 77843, USA
| | - C J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - R R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.,School of Veterinary Medicine, Veterinary Genetics Laboratory, University of California-Davis, Davis, CA, 95616, USA
| | - J L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE, 68583-0908, USA
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Grilz-Seger G, Druml T, Neuditschko M, Mesarič M, Cotman M, Brem G. Analysis of ROH patterns in the Noriker horse breed reveals signatures of selection for coat color and body size. Anim Genet 2019; 50:334-346. [PMID: 31199540 PMCID: PMC6617995 DOI: 10.1111/age.12797] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2019] [Indexed: 12/24/2022]
Abstract
Overlapping runs of homozygosity (ROH islands) shared by the majority of a population are hypothesized to be the result of selection around a target locus. In this study we investigated the impact of selection for coat color within the Noriker horse on autozygosity and ROH patterns. We analyzed overlapping homozygous regions (ROH islands) for gene content in fragments shared by more than 50% of horses. Long‐term assortative mating of chestnut horses and the small effective population size of leopard spotted and tobiano horses resulted in higher mean genome‐wide ROH coverage (SROH) within the range of 237.4–284.2 Mb, whereas for bay, black and roan horses, where rotation mating is commonly applied, lower autozygosity (SROH from 176.4–180.0 Mb) was determined. We identified seven common ROH islands considering all Noriker horses from our dataset. Specific islands were documented for chestnut, leopard spotted, roan and bay horses. The ROH islands contained, among others, genes associated with body size (ZFAT, LASP1 and LCORL/NCAPG), coat color (MC1R in chestnut and the factor PATN1 in leopard spotted horses) and morphogenesis (HOXB cluster in all color strains except leopard spotted horses). This study demonstrates that within a closed population sharing the same founders and ancestors, selection on a single phenotypic trait, in this case coat color, can result in genetic fragmentation affecting levels of autozygosity and distribution of ROH islands and enclosed gene content.
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Affiliation(s)
- G Grilz-Seger
- Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, Vienna, A-1210, Austria
| | - T Druml
- Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, Vienna, A-1210, Austria
| | - M Neuditschko
- Swiss National Stud Farm, Agroscope, Les Longs Prés, Avenches, CH-1580, Switzerland
| | - M Mesarič
- Clinic for Reproduction and Large Animals, University of Ljubljana, Veterinary Faculty, Cesta v Mestni log 47, Ljubljana, 1000, Slovenia
| | - M Cotman
- Institute for Preclinical Sciences, University of Ljubljana, Veterinary Faculty, Gerbičeva 60, Ljubljana, 1000, Slovenia
| | - G Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, Vienna, A-1210, Austria
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Knickelbein KE, Lassaline ME, Singer-Berk M, Reilly CM, Clode AB, Famula TR, Michau TM, Bellone RR. A missense mutation in damage-specific DNA binding protein 2 is a genetic risk factor for ocular squamous cell carcinoma in Belgian horses. Equine Vet J 2019; 52:34-40. [PMID: 30903710 DOI: 10.1111/evj.13116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 03/15/2019] [Indexed: 01/15/2023]
Abstract
BACKGROUND Belgian horses are commonly affected with ocular squamous cell carcinoma (SCC), the most common cancer of the equine eye. A missense mutation in damage-specific DNA binding protein 2 (DDB2 c.1013C>T, p.Thr338Met) has been established as a recessive genetic risk factor for ocular SCC in the Haflinger breed. A sample of Belgian horses with unknown SCC phenotype was shown to possess this variant at a similar frequency to the Haflinger breed. Retrospective studies indicate that chestnut coat colour may predispose to the development of SCC. OBJECTIVES To determine if DDB2 c.1013C>T is a risk factor for ocular SCC in a strictly phenotyped sample of Belgian horses. To investigate associations between coat colour loci genotypes and ocular SCC. STUDY DESIGN Retrospective and prospective case identification, genetic investigation. METHODS Genomic DNA was isolated from blood, hair or formalin-fixed paraffin-embedded tissue from 25 Belgian horses with histologically confirmed ocular SCC and 18 unaffected Belgian horses. Association testing of 34 single nucleotide variants from 11 genomic loci and genotyping for DDB2 c.1013C>T and coat colour alleles were performed. Exons of DDB2 were sequenced in four cases and two controls. Associations were analysed by Chi-square or Fisher's exact tests and relative risk was calculated. RESULTS Homozygosity for DDB2 c.1013C>T was significantly associated with ocular SCC (P = 7.4 × 10-7 ). Seventy-six per cent of affected horses were homozygous for the variant. Relative risk for homozygous horses developing SCC was 4.0 (P = 1.0 × 10-4 ). Sequencing DDB2 did not identify a variant more concordant with disease phenotype. An association between disease and coat colour loci was not identified. MAIN LIMITATIONS Phenotyping was determined at a single timepoint. Each included horse genotyped as chestnut, so association with this MC1R variant could not be investigated. CONCLUSIONS A missense variant, DDB2 c.1013C>T, p.Thr338Met, is a risk factor for ocular SCC in Belgian horses. A genetic risk test is commercially available.
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Affiliation(s)
- K E Knickelbein
- Veterinary Medical Teaching Hospital, University of California-Davis, Davis, California, USA.,Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - M E Lassaline
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - M Singer-Berk
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - C M Reilly
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - A B Clode
- New England Equine Medical & Surgical Center, PLLC, Dover, New Hampshire, USA
| | - T R Famula
- Department of Animal Science, University of California-Davis, Davis, California, USA
| | - T M Michau
- Blue Pearl Specialty and Emergency Pet Hospital, Tampa, Florida, USA
| | - R R Bellone
- Veterinary Medical Teaching Hospital, University of California-Davis, Davis, California, USA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
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Owen N, Moosajee M. RNA-sequencing in ophthalmology research: considerations for experimental design and analysis. Ther Adv Ophthalmol 2019; 11:2515841419835460. [PMID: 30911735 PMCID: PMC6421592 DOI: 10.1177/2515841419835460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/08/2019] [Indexed: 12/13/2022] Open
Abstract
High-throughput, massively parallel sequence analysis has revolutionized the way that researchers design and execute scientific investigations. Vast amounts of sequence data can be generated in short periods of time. Regarding ophthalmology and vision research, extensive interrogation of patient samples for underlying causative DNA mutations has resulted in the discovery of many new genes relevant to eye disease. However, such analysis remains functionally limited. RNA-sequencing accurately snapshots thousands of genes, capturing many subtypes of RNA molecules, and has become the gold standard for transcriptome gene expression quantification. RNA-sequencing has the potential to advance our understanding of eye development and disease; it can reveal new candidates to improve our molecular diagnosis rates and highlight therapeutic targets for intervention. But with a wide range of applications, the design of such experiments can be problematic, no single optimal pipeline exists, and therefore, several considerations must be undertaken for optimal study design. We review the key steps involved in RNA-sequencing experimental design and the downstream bioinformatic pipelines used for differential gene expression. We provide guidance on the application of RNA-sequencing to ophthalmology and sources of open-access eye-related data sets.
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Affiliation(s)
- Nicholas Owen
- Development, Ageing and Disease Theme, UCL Institute of Ophthalmology, University College London, London, UK
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Henkel J, Lafayette C, Brooks SA, Martin K, Patterson-Rosa L, Cook D, Jagannathan V, Leeb T. Whole-genome sequencing reveals a large deletion in the MITF gene in horses with white spotted coat colour and increased risk of deafness. Anim Genet 2019; 50:172-174. [PMID: 30644113 DOI: 10.1111/age.12762] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2018] [Indexed: 01/18/2023]
Abstract
White spotting phenotypes in horses are highly valued in some breeds. They are quite variable and may range from the common white markings up to completely white horses. EDNRB, KIT, MITF, PAX3 and TRPM1 represent known candidate genes for white spotting phenotypes in horses. For the present study, we investigated an American Paint Horse family segregating a phenotype involving white spotting and blue eyes. Six of eight horses with the white-spotting phenotype were deaf. We obtained whole-genome sequence data from an affected horse and specifically searched for structural variants in the known candidate genes. This analysis revealed a heterozygous ~63-kb deletion spanning exons 6-9 of the MITF gene (chr16:21 503 211-21 566 617). We confirmed the breakpoints of the deletion by PCR and Sanger sequencing. PCR-based genotyping revealed that all eight available affected horses from the family carried the deletion. The finding of an MITF variant fits well with the syndromic phenotype involving both depigmentation and an increased risk for deafness and corresponds to human Waardenburg syndrome type 2A. Our findings will enable more precise genetic testing for depigmentation phenotypes in horses.
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Affiliation(s)
- J Henkel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | | | - S A Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611-0910, USA
| | - K Martin
- Etalon Inc., Menlo Park, CA, 94025, USA
| | - L Patterson-Rosa
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611-0910, USA
| | - D Cook
- Etalon Inc., Menlo Park, CA, 94025, USA
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
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Tavares E, Tang CY, Vig A, Li S, Billingsley G, Sung W, Vincent A, Thiruvahindrapuram B, Héon E. Retrotransposon insertion as a novel mutational event in Bardet-Biedl syndrome. Mol Genet Genomic Med 2018; 7:e00521. [PMID: 30484961 PMCID: PMC6393654 DOI: 10.1002/mgg3.521] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/23/2018] [Accepted: 10/26/2018] [Indexed: 01/12/2023] Open
Abstract
Background Bardet‐Biedl syndrome (BBS) is an autosomal recessive pleiotropic disorder of the primary cilia that leads to severe visual loss in the teenage years. Approximately 80% of BBS cases are explained by mutations in one of the 21 identified genes. Documented causative mutation types include missense, nonsense, copy number variation (CNV), frameshift deletions or insertions, and splicing variants. Methods Whole genome sequencing was performed on a patient affected with BBS for whom no mutations were identified using clinically approved genetic testing of the known genes. Analysis of the WGS was done using internal protocols and publicly available algorithms. The phenotype was defined by retrospective chart review. Results We document a female affected with BBS carrying the most common BBS1 mutation (BBS1: Met390Arg) on the maternal allele and an insertion of a ~1.7‐kb retrotransposon in exon 13 on the paternal allele. This retrotransposon insertion was not automatically annotated by the standard variant calling protocols used. This novel variant was identified by visual inspection of the alignment file followed by specific genome analysis with an available algorithm for transposable elements. Conclusion This report documents a novel mutation type associated with BBS and highlights the importance of systematically performing transposon detection analysis on WGS data of unsolved cases.
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Affiliation(s)
- Erika Tavares
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Chen Yu Tang
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anjali Vig
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Shuning Li
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gail Billingsley
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wilson Sung
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ajoy Vincent
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,Ophthalmology and Vision Sciences, Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Elise Héon
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,Ophthalmology and Vision Sciences, Hospital for Sick Children, Toronto, Ontario, Canada
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47
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Improved reference genome for the domestic horse increases assembly contiguity and composition. Commun Biol 2018; 1:197. [PMID: 30456315 PMCID: PMC6240028 DOI: 10.1038/s42003-018-0199-z] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 10/16/2018] [Indexed: 11/30/2022] Open
Abstract
Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. Here, we present EquCab3. The count of non-N bases in the incorporated chromosomes is improved from 2.33 Gb in EquCab2 to 2.41 Gb in EquCab3. Contiguity has also been improved nearly 40-fold with a contig N50 of 4.5 Mb and scaffold contiguity enhanced to where all but one of the 32 chromosomes is comprised of a single scaffold. Theodore Kalbfleisch et al. present an improved genome assembly for the domestic horse by combining short- and long-read data, as well as proximity ligation data. They improve contiguity of the assembly by 40-fold, with a 10-fold reduction in gaps.
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48
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Zeng L, Pederson SM, Cao D, Qu Z, Hu Z, Adelson DL, Wei C. Genome-Wide Analysis of the Association of Transposable Elements with Gene Regulation Suggests that Alu Elements Have the Largest Overall Regulatory Impact. J Comput Biol 2018; 25:551-562. [DOI: 10.1089/cmb.2017.0228] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Lu Zeng
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Stephen M. Pederson
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Danfeng Cao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhipeng Qu
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Zhiqiang Hu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - David L. Adelson
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Chaochun Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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49
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Affiliation(s)
- E. N. Adam
- Gluck Equine Research Center; University of Kentucky; Lexington USA
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50
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Affiliation(s)
- Gustavo D Aguirre
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
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