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Panigrahi M, Kumar H, Saravanan KA, Rajawat D, Sonejita Nayak S, Ghildiyal K, Kaisa K, Parida S, Bhushan B, Dutt T. Trajectory of livestock genomics in South Asia: A comprehensive review. Gene 2022; 843:146808. [PMID: 35973570 DOI: 10.1016/j.gene.2022.146808] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 02/07/2023]
Abstract
Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.
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Affiliation(s)
- Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - K A Saravanan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Kaiho Kaisa
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Holmes TQ, Brown AF. Champing at the Bit for Improvements: A Review of Equine Welfare in Equestrian Sports in the United Kingdom. Animals (Basel) 2022; 12:1186. [PMID: 35565612 PMCID: PMC9100173 DOI: 10.3390/ani12091186] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/20/2022] [Accepted: 04/30/2022] [Indexed: 01/10/2023] Open
Abstract
Equestrian sports, including racing (e.g., flat, steeple-chasing, harness or donkey derby); show-jumping; cross-country; dressage; polo; polocrosse; endurance; carriage driving; vaulting and hunting; are hugely popular in the UK, and they involve a significant number of people, both as participants and spectators, and tens of thousands of equids. In this paper, we discuss animal welfare as a complex and disputed issue, clarifying what the term means and how it can be measured. We review many aspects of welfare risk to equids used for sport, addressing issues encountered throughout their lives, including housing, feeding, veterinary intervention, shoeing, handling, training, breeding and equipment. This is followed by a unique exploration of the institutions and social processes influencing equine welfare. The institutional components comprise the rules of competition, the equids, attributes of the stakeholders and the space where participants strive to achieve a common purpose. We endeavour to untangle the most significant elements that create barriers or provide opportunities for equine welfare improvement. We expose the challenges faced by a broad range of stakeholders with differing ethics, attitudes and values. Evidently, there are many welfare risks to which equids used in sports continue to be exposed. It is also evident that significant improvements have occurred in recent times, but there remains a barrier to reducing the risks to an acceptable level. We conclude with recommendations regarding a process for change, involvement of stakeholders and management of knowledge to improve equine welfare that involves identifying and prioritising the risk factors and ultimately leading to interventions, further research and/or education.
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Muñoz L, Donaire C, Salazar T, Ortiz R, Cruces J, Briones M. Heritability of Locomotor Stereotypies in Chilean Horses. J Equine Vet Sci 2021; 105:103702. [PMID: 34607683 DOI: 10.1016/j.jevs.2021.103702] [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] [Received: 06/07/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 10/20/2022]
Abstract
The Chilean horse is a breed of closed registry. Stall-walking and weaving are locomotor stereotypies that affect this breed, and genetic predisposition has been suggested for both conditions. The objective of the present study was to estimate heritability of stall-walking and weaving in Chilean horses. Owners of 2,098 horses registered in the Chilean horse Stud Book, which were or had been stabled for at least 1 year, were asked to provide for identification data of the animal and presence or absence of stall-walking and/or weaving. The Chilean Horse Stud Book was accessed online, to collect information on name and registration number of the sire and dam of each horse. The prevalence of stall-walking and weaving was calculated from the sample (n = 2,098). The database to estimate the heritability (h2) included all the sample horses (n = 2,098) and their sires and dams. Additionally, all the ancestors available in the Chilean Horse Stud Book were included in the database for 297 sampled horses including those with locomotor stereotypies. The genealogical database consisted of 7,187 individuals. The prevalence of stall-walking was 2.05% and prevalence of weaving was 1.43%, being more frequent in males (P < .05) for stall-walking. Heritability of stall-walking was low (h2 = 0.213 ± 0.08) and moderate for weaving (h2 = 0.435 ± 0.06). Heritability and prevalence of locomotor stereotypies found in the Chilean horse suggest that they are hereditary disorders, highly influenced by environmental factors.
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Affiliation(s)
- Lisandro Muñoz
- Departamento de Ciencias Clínicas, Universidad de Concepción, Victoria, Concepción, Chile.
| | - Camila Donaire
- Departamento de Ciencias Clínicas, Universidad de Concepción, Victoria, Concepción, Chile
| | - Tomás Salazar
- Departamento de Ciencias Clínicas, Universidad de Concepción, Victoria, Concepción, Chile
| | - Reinaldo Ortiz
- Departamento de Ciencias Clínicas, Universidad de Concepción, Victoria, Concepción, Chile
| | - Jaime Cruces
- Departamento de Ciencias Clínicas, Universidad de Concepción, Victoria, Concepción, Chile
| | - Mario Briones
- Departamento de Ciencia Animal, Facultad de Ciencias Veterinaria, Chillán, Chile
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4
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Muñoz L, Salazar T, Donaire C, Ortiz R, Cruces J, Briones M. Heritability of crib-biting in Chilean horses. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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5
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Abstract
The Arabian horse, one of the world’s oldest breeds of any domesticated animal, is characterized by natural beauty, graceful movement, athletic endurance, and, as a result of its development in the arid Middle East, the ability to thrive in a hot, dry environment. Here we studied 378 Arabian horses from 12 countries using equine single nucleotide polymorphism (SNP) arrays and whole-genome re-sequencing to examine hypotheses about genomic diversity, population structure, and the relationship of the Arabian to other horse breeds. We identified a high degree of genetic variation and complex ancestry in Arabian horses from the Middle East region. Also, contrary to popular belief, we could detect no significant genomic contribution of the Arabian breed to the Thoroughbred racehorse, including Y chromosome ancestry. However, we found strong evidence for recent interbreeding of Thoroughbreds with Arabians used for flat-racing competitions. Genetic signatures suggestive of selective sweeps across the Arabian breed contain candidate genes for combating oxidative damage during exercise, and within the “Straight Egyptian” subgroup, for facial morphology. Overall, our data support an origin of the Arabian horse in the Middle East, no evidence for reduced global genetic diversity across the breed, and unique genetic adaptations for both physiology and conformation.
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Pinzon-Arteaga C, Snyder MD, Lazzarotto CR, Moreno NF, Juras R, Raudsepp T, Golding MC, Varner DD, Long CR. Efficient correction of a deleterious point mutation in primary horse fibroblasts with CRISPR-Cas9. Sci Rep 2020; 10:7411. [PMID: 32366884 PMCID: PMC7198616 DOI: 10.1038/s41598-020-62723-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 03/04/2020] [Indexed: 12/26/2022] Open
Abstract
Phenotypic selection during animal domestication has resulted in unwanted incorporation of deleterious mutations. In horses, the autosomal recessive condition known as Glycogen Branching Enzyme Deficiency (GBED) is the result of one of these deleterious mutations (102C > A), in the first exon of the GBE1 gene (GBE1102C>A). With recent advances in genome editing, this type of genetic mutation can be precisely repaired. In this study, we used the RNA-guided nuclease CRISPR-Cas9 (clustered regularly-interspaced short palindromic repeats/CRISPR-associated protein 9) to correct the GBE1102C>A mutation in a primary fibroblast cell line derived from a high genetic merit heterozygous stallion. To correct this mutation by homologous recombination (HR), we designed a series of single guide RNAs (sgRNAs) flanking the mutation and provided different single-stranded donor DNA templates. The distance between the Cas9-mediated double-stranded break (DSB) to the mutation site, rather than DSB efficiency, was the primary determinant for successful HR. This framework can be used for targeting other harmful diseases in animal populations.
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Affiliation(s)
- Carlos Pinzon-Arteaga
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas, USA
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Matthew D Snyder
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas, USA
| | | | - Nicolas F Moreno
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas, USA
| | - Rytis Juras
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Michael C Golding
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas, USA
| | - Dickson D Varner
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX, USA
| | - Charles R Long
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas, USA.
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Campbell MLH, McNamee MJ. Ethics, Genetic Technologies and Equine Sports: The Prospect of Regulation of a Modified Therapeutic Use Exemption Policy. SPORT ETHICS AND PHILOSOPHY 2020. [DOI: 10.1080/17511321.2020.1737204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- M. L. H Campbell
- Department of Production and Population Sciences, The Royal Veterinary College, South Mymms, UK
| | - M. J. McNamee
- School of Sport and Exercise Sciences, Swansea University, Swansea, UK
- Faculty of Kinesiology and Rehabilitation Sciences, KU Leuven, Leuven, Belgium
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8
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Khusro A, Aarti C, Rivas-Caceres RR, Barbabosa-Pliego A. Equine Herpesvirus-I Infection in Horses: Recent Updates on its Pathogenicity, Vaccination, and Preventive Management Strategies. J Equine Vet Sci 2020; 87:102923. [PMID: 32172913 DOI: 10.1016/j.jevs.2020.102923] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 12/31/2022]
Abstract
Equine herpesvirus-1 (EHV-1) is one of the most common and ubiquitous viral pathogens infecting equines, particularly horses worldwide. The EHV-1 is known to induce not only humoral but also cellular immune responses in horses. Respiratory distress, abortion in pregnant mares, neurological disorders, and neonatal foal deaths represent EHV-1 infection. Despite the limited success of inactivated, subunit, live, and DNA vaccines, over the past few decades, vaccination remains the prime preventive option to combat EHV-1 infection in horses. However, current vaccines lack the potentiality to protect the neurological form of infections in horses. There is desperate necessity to search effectual EHV-1 vaccines that may stimulate not only mucosal and systemic cellular immunity but also humoral immunity in the horses. This review highlights the state of knowledge regarding EHV-1 biology, EHV-1 pathogenesis, and disparate vaccines studied in the past to prevent EHV-1 infection. The review also underlines the best management strategies which certainly need to be adopted by veterinarians in order to avoid and prevent EHV-1 infection and outbreak in horses in the future.
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Affiliation(s)
- Ameer Khusro
- Research Department of Plant Biology and Biotechnology, Loyola College, Chennai, Tamil Nadu, India
| | - Chirom Aarti
- Research Department of Plant Biology and Biotechnology, Loyola College, Chennai, Tamil Nadu, India
| | | | - Alberto Barbabosa-Pliego
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Toluca, Mexico.
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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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10
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Zanzarini Delfiol DJ, de Oliveira-Filho JP, Badial PR, Battazza A, Araujo Junior JP, Borges AS. Estimation of the Allele Frequency of Type 1 Polysaccharide Storage Myopathy and Malignant Hyperthermia in Quarter Horses in Brazil. J Equine Vet Sci 2018. [DOI: 10.1016/j.jevs.2018.06.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Lewczuk D, Hecold M, Ruść A, Frąszczak M, Bereznowski A, Korwin-Kossakowska A, Kamiński S, Szyda J. Single nucleotide polymorphisms associated with osteochondrosis dissecans in Warmblood horses at different stages of training. ANIMAL PRODUCTION SCIENCE 2017. [DOI: 10.1071/an15450] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The genetic background of osteochondrosis dissecans (OCD) has been studied for years, but the compatibility of the position of markers has not been reached between results, probably because of unknown additional effects that may influence the results, such as definition of the trait, gene–environmental interactions and the dynamics of trait development. The aim of the study was to identify single nucleotide polymorphisms (SNP) associated with the occurrence of OCD in Polish Warmblood sport breed horses in two different stages of training. Warmblood horses (87 stallions and 114 mares) were phenotyped and genotyped. Horses were X-rayed twice, at the beginning and at the end of the tests (100 days for stallions and 60 days for mares). Ten images per horse were collected using digital equipment for the fetlocks, stifles and hocks. The DNA was genotyped using the Illumina Neogen Equine Array. Statistical analysis included the Cochran–Armitage test and logistic regression assuming an additive model of inheritance. The Monte Carlo Markov Chain method was also applied to determine heritability coefficients. Nineteen and twenty SNP were identified that were significantly associated with OCD using logistic regression at the first and second stage of training, respectively. Four SNP were significant for both stages of training. The estimation of the heritability of a horse’s OCD status does not achieve the same level at different stages of training. The study on the genetic background of horse OCD should include as much detailed information on their training as possible.
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Staiger EA, Tseng CT, Miller D, Cassano JM, Nasir L, Garrick D, Brooks SA, Antczak DF. Host genetic influence on papillomavirus-induced tumors in the horse. Int J Cancer 2016; 139:784-92. [PMID: 27037728 DOI: 10.1002/ijc.30120] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/27/2016] [Accepted: 02/16/2016] [Indexed: 01/26/2023]
Abstract
The common equine skin tumors known as sarcoids have been causally associated with infection by bovine papillomavirus (BPV). Additionally, there is evidence for host genetic susceptibility to sarcoids. We investigated the genetic basis of susceptibility to sarcoid tumors on a cohort of 82 affected horses and 270 controls genotyped on a genome-wide platform and two custom panels. A Genome Wide Association Study (GWAS) identified candidate regions on six chromosomes. Bayesian probability analysis of the same dataset verified only the regions on equine chromosomes (ECA) 20 and 22. Fine mapping using custom-produced SNP arrays for ECA20 and ECA22 regions identified two marker loci with high levels of significance: SNP BIEC2-530826 (map position 32,787,619) on ECA20 in an intron of the DQA1 gene in the Major Histocompatibility Complex (MHC) class II region (p = 4.6e-06), and SNP BIEC2-589604 (map position 25,951,536) on ECA22 in a 200 kb region containing four candidate genes: PROCR, EDEM2, EIF6 and MMP24 (p = 2.14e-06). The marker loci yielded odds ratios of 5.05 and 4.02 for ECA20 and ECA22, respectively. Associations between genetic MHC class II variants and papillomavirus-induced tumors have been reported for human papillomavirus and cottontail rabbit papillomavirus infections. This suggests a common mechanism for susceptibility to tumor progression that may involve subversion of the host immune response. This study also identified a genomic region other than MHC that influenced papillomavirus-induced tumor development in the studied population.
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Affiliation(s)
| | - Chia T Tseng
- Baker Institute for Animal Health, Cornell University, Ithaca, NY
| | - Donald Miller
- Baker Institute for Animal Health, Cornell University, Ithaca, NY
| | | | - Lubna Nasir
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Dorian Garrick
- Department of Animal Science, Iowa State University, Ames, IA
| | - Samantha A Brooks
- Department of Animal Science, University of Florida, Gainesville, FL
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Sánchez MJ, Azor PJ, Molina A, Parkin T, Rivero JLL, Valera M. Prevalence, risk factors and genetic parameters of cresty neck in Pura Raza Español horses. Equine Vet J 2016; 49:196-200. [DOI: 10.1111/evj.12569] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 02/06/2016] [Indexed: 11/28/2022]
Affiliation(s)
- M. J. Sánchez
- Department of Agro–Forestry Sciences ETSIA University of SevilleSeville Spain
| | - P. J. Azor
- Department of Agro–Forestry Sciences ETSIA University of SevilleSeville Spain
| | - A. Molina
- Department of Genetics University of Cordoba Seville Spain
| | - T. Parkin
- School of Veterinary Medicine College of Medical Veterinary and Life Sciences University of Glasgow Glasgow UK
| | - J. L. L. Rivero
- Department of Comparative Anatomy and Pathological Anatomy University of Cordoba Cordoba Spain
| | - M. Valera
- Department of Agro–Forestry Sciences ETSIA University of SevilleSeville Spain
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Stout TA.E, Troedsson MHT. Report of the Havemeyer Foundation Workshop on Equine Implantation: Is early pregnancy loss the only important potential consequence of disturbed preimplantation development? Equine Vet J 2015; 47:381-3. [DOI: 10.1111/evj.12382] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- T. A .E. Stout
- Department of Equine Sciences; Faculty of Veterinary Medicine; Utrecht University; The Netherlands
- Section of Reproduction; Faculty of Veterinary Science; University of Pretoria; Onderstepoort South Africa
| | - M. H. T. Troedsson
- Gluck Equine Research Center; Department of Veterinary Science; University of Kentucky; Lexington USA
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15
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Finno CJ, Bannasch DL. Applied equine genetics. Equine Vet J 2014; 46:538-44. [PMID: 24802051 DOI: 10.1111/evj.12294] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 04/27/2014] [Indexed: 01/13/2023]
Abstract
Genome sequencing of the domestic horse and subsequent advancements in the field of equine genomics have led to an explosion in the development of tools for mapping traits and diseases and evaluating gene expression. The objective of this review is to discuss the current progress in the field of equine genomics, with specific emphasis on assembly and analysis of the reference sequence and subsequent sequencing of a Quarter Horse mare; the genomic tools currently available to researchers and their implications in genomic investigations in the horse; the genomics of Mendelian and non-Mendelian traits; the genomics of performance traits and considerations regarding genetic testing in the horse. The whole-genome sequencing of a Quarter Horse mare has provided additional variants within the equine genome that extend past single nucleotide polymorphisms to include insertions/deletions and copy number variants. Equine single nucleotide polymorphism arrays have allowed for the investigation of both simple and complex genetic traits while DNA microarrays have provided a tool for examining gene expression across various tissues and with certain disease conditions. Recently, next-generation sequencing has become more affordable and both whole-genome DNA sequencing and transcriptome-wide RNA sequencing are methodologies that are being applied to equine genomic research. Research in the field of equine genomics continues to expand rapidly as the cost of genotyping and sequencing decreases, resulting in a need for quality bioinformatics software and expertise to appropriately handle both the size and complexity of these data.
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Affiliation(s)
- C J Finno
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, USA
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Identification of genomic loci associated with Rhodococcus equi susceptibility in foals. PLoS One 2014; 9:e98710. [PMID: 24892408 PMCID: PMC4043894 DOI: 10.1371/journal.pone.0098710] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/04/2014] [Indexed: 11/30/2022] Open
Abstract
Pneumonia caused by Rhodococcus equi is a common cause of disease and death in foals. Although agent and environmental factors contribute to the incidence of this disease, the genetic factors influencing the clinical outcomes of R. equi pneumonia are ill-defined. Here, we performed independent single nucleotide polymorphism (SNP)- and copy number variant (CNV)-based genome-wide association studies to identify genomic loci associated with R. equi pneumonia in foals. Foals at a large Quarter Horse breeding farm were categorized into 3 groups: 1) foals with R. equi pneumonia (clinical group [N = 43]); 2) foals with ultrasonographic evidence of pulmonary lesions that never developed clinical signs of pneumonia (subclinical group [N = 156]); and, 3) foals without clinical signs or ultrasonographic evidence of pneumonia (unaffected group [N = 49]). From each group, 24 foals were randomly selected and used for independent SNP- and CNV-based genome-wide association studies (GWAS). The SNP-based GWAS identified a region on chromosome 26 that had moderate evidence of association with R. equi pneumonia when comparing clinical and subclinical foals. A joint analysis including all study foals revealed a 3- to 4-fold increase in odds of disease for a homozygous SNP within the associated region when comparing the clinical group with either of the other 2 groups of foals or their combination. The region contains the transient receptor potential cation channel, subfamily M, member 2 (TRPM2) gene, which is involved in neutrophil function. No associations were identified in the CNV-based GWAS. Collectively, these data identify a region on chromosome 26 associated with R. equi pneumonia in foals, providing evidence that genetic factors may indeed contribute to this important disease of foals.
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Gerber V, Tessier C, Marti E. Genetics of upper and lower airway diseases in the horse. Equine Vet J 2014; 47:390-7. [PMID: 24773614 DOI: 10.1111/evj.12289] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 04/12/2014] [Indexed: 11/30/2022]
Abstract
Genetic predispositions for guttural pouch tympany, recurrent laryngeal neuropathy and recurrent airway obstruction (RAO) are well documented. There is also evidence that exercise-induced pulmonary haemorrhage and infectious diseases of the respiratory tract in horses have a genetic component. The clinical expression of equine respiratory diseases with a genetic basis results from complex interactions between the environment and the genetic make-up of each individual horse. The genetic effects are likely to be due to variations in several genes, i.e. they are polygenic. It is therefore unlikely that single gene tests will be diagnostically useful in these disorders. Genetic profiling panels, combining several genetic factors with an assessment of environmental risk factors, may have greater value, but much work is still needed to uncover diagnostically useful genetic markers or even causative variants for equine respiratory diseases. Nonetheless, chromosomal regions associated with guttural pouch tympany, recurrent laryngeal neuropathy and RAO have been identified. The association of RAO with other hypersensitivities and with resistance to intestinal parasites requires further study. This review aims to provide an overview of the available data and current thoughts on the genetics of equine airway diseases.
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Affiliation(s)
- V Gerber
- Swiss Institute of Equine Medicine (ISME), DKV, Vetsuisse Faculty, University of Berne and ALP-Haras Avenches, Switzerland
| | - C Tessier
- ONIRIS, Ecole Nationale Vétérinaire, Agro-Alimentaire et de l'Alimentation Nantes-Atlantique, Equine Surgery, Nantes, France
| | - E Marti
- Division of Clinical Immunology, DCR-VPH, University of Berne, Switzerland
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Signer-Hasler H, Neuditschko M, Koch C, Froidevaux S, Flury C, Burger D, Leeb T, Rieder S. A chromosomal region on ECA13 is associated with maxillary prognathism in horses. PLoS One 2014; 9:e86607. [PMID: 24466169 PMCID: PMC3897735 DOI: 10.1371/journal.pone.0086607] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 12/12/2013] [Indexed: 12/22/2022] Open
Abstract
Hereditary variations in head morphology and head malformations are known in many species. The most common variation encountered in horses is maxillary prognathism. Prognathism and brachygnathism are syndromes of the upper and lower jaw, respectively. The resulting malocclusion can negatively affect teeth wear, and is considered a non-desirable trait in breeding programs. We performed a case-control analysis for maxillary prognathism in horses using 96 cases and 763 controls. All horses had been previously genotyped with a commercially available 50 k SNP array. We analyzed the data with a mixed-model considering the genomic relationships in order to account for population stratification. Two SNPs within a region on the distal end of chromosome ECA 13 reached the Bonferroni corrected genome-wide significance level. There is no known prognathism candidate gene located within this region. Therefore, our findings in the horse offer the possibility of identifying a novel gene involved in the complex genetics of prognathism that might also be relevant for humans and other livestock species.
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Affiliation(s)
- Heidi Signer-Hasler
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | | | - Christoph Koch
- Swiss Institute of Equine Medicine ISME, Vetsuisse Faculty University of Bern and Agroscope, Bern, Switzerland
| | - Sylvie Froidevaux
- Swiss Institute of Equine Medicine ISME, Vetsuisse Faculty University of Bern and Agroscope, Bern, Switzerland
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Dominik Burger
- Swiss Institute of Equine Medicine ISME, Vetsuisse Faculty University of Bern and Agroscope, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Stefan Rieder
- Swiss National Stud Farm, Agroscope, Avenches, Switzerland
- * E-mail:
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The Role of Genomics in Conservation and Reproductive Sciences. REPRODUCTIVE SCIENCES IN ANIMAL CONSERVATION 2014; 753:71-96. [DOI: 10.1007/978-1-4939-0820-2_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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A genome-wide association study reveals loci influencing height and other conformation traits in horses. PLoS One 2012; 7:e37282. [PMID: 22615965 PMCID: PMC3353922 DOI: 10.1371/journal.pone.0037282] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 04/17/2012] [Indexed: 11/19/2022] Open
Abstract
The molecular analysis of genes influencing human height has been notoriously difficult. Genome-wide association studies (GWAS) for height in humans based on tens of thousands to hundreds of thousands of samples so far revealed ∼200 loci for human height explaining only 20% of the heritability. In domestic animals isolated populations with a greatly reduced genetic heterogeneity facilitate a more efficient analysis of complex traits. We performed a genome-wide association study on 1,077 Franches-Montagnes (FM) horses using ∼40,000 SNPs. Our study revealed two QTL for height at withers on chromosomes 3 and 9. The association signal on chromosome 3 is close to the LCORL/NCAPG genes. The association signal on chromosome 9 is close to the ZFAT gene. Both loci have already been shown to influence height in humans. Interestingly, there are very large intergenic regions at the association signals. The two detected QTL together explain ∼18.2% of the heritable variation of height in horses. However, another large fraction of the variance for height in horses results from ECA 1 (11.0%), although the association analysis did not reveal significantly associated SNPs on this chromosome. The QTL region on ECA 3 associated with height at withers was also significantly associated with wither height, conformation of legs, ventral border of mandible, correctness of gaits, and expression of the head. The region on ECA 9 associated with height at withers was also associated with wither height, length of croup and length of back. In addition to these two QTL regions on ECA 3 and ECA 9 we detected another QTL on ECA 6 for correctness of gaits. Our study highlights the value of domestic animal populations for the genetic analysis of complex traits.
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