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Azcona F, Karlau A, Trigo P, Molina A, Demyda-Peyrás S. Genomic tools for early selection among Thoroughbreds and Polo Argentino horses for practicing polo. J Equine Vet Sci 2024; 138:105098. [PMID: 38763367 DOI: 10.1016/j.jevs.2024.105098] [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: 12/15/2023] [Revised: 03/28/2024] [Accepted: 05/16/2024] [Indexed: 05/21/2024]
Abstract
The Polo Argentino (PA) horse is a recognized breed, developed originally by mixing crossbred and Thoroughbred (TB) horses to play polo. Early PA selection is difficult due to unreliable performance estimations. This study investigated the usefulness of genomic markers previously linked to morphological and functional traits as a tool for the early selection of PA. To this, we genotyped 520 PA and 30 TB horses using the Equine GGPArray (Illumina, n = 71,778 SNPs). Analyses included a genetic characterization of six genetic markers associated with behavioral (DRD4), muscular development (MSTN), and body size (LCORL, HMGA6, ZFAT, and LASP1) genes. Genetic differences in the DRD4, MSTN, and LCORL SNP were found between the two breeds, in the last two FST index between breeds was 0.13 and 0.6, respectively (p < 0.01). In DRD4, G allele was the more prevalent in PA (0.56 vs 0.45 in TB, p < 0.05), but no differences were observed between the genotypes associated with phenotypes. In MSTN, heterozygous genotypes were the most common in PA (48 %), with a significant decrease in AA (Hardy-Weinberg p < 0.05), suggesting a negative selection against it in polo horses. In body size, HMGA2 was monomorphic in all horses, while ZFAT and LASP1 SNP showed higher variability. Interestingly, 99 % of PA showed a TT genotype in LCORL (only 66 % in TB), demonstrating selection for smaller horses. Our results suggest that empirical selection in PA has generated an incipient genomic differentiation in discrete traits which could be used as a marker-assisted selection tool for early selection of polo horses.
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Affiliation(s)
- F Azcona
- Cátedra de Medicina Equina, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, calle 60 y 118 s/n, 1900-La Plata, Argentina; CONICET, CCT La Plata, 1900-La Plata, Argentina; Cátedra de Genética de Poblaciones y Mejoramiento Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, calle 60 y 118 s/n, 1900-La Plata, Argentina.
| | - A Karlau
- CONICET, CCT La Plata, 1900-La Plata, Argentina; Cátedra de Genética de Poblaciones y Mejoramiento Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, calle 60 y 118 s/n, 1900-La Plata, Argentina
| | - P Trigo
- CONICET, CCT La Plata, 1900-La Plata, Argentina; Cátedra de Producción Equina, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, calle 60 y 118 s/n, 1900-La Plata, Argentina
| | - A Molina
- Departamento de Genética, Universidad de Córdoba, CN IV KM 396 Edificio Gregor Mendel, 14007-Córdoba, España
| | - S Demyda-Peyrás
- Departamento de Genética, Universidad de Córdoba, CN IV KM 396 Edificio Gregor Mendel, 14007-Córdoba, España
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De Coster T, Zhao Y, Tšuiko O, Demyda-Peyrás S, Van Soom A, Vermeesch JR, Smits K. Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection. Sci Rep 2024; 14:2003. [PMID: 38263320 PMCID: PMC10805710 DOI: 10.1038/s41598-023-48103-7] [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: 06/28/2023] [Accepted: 11/22/2023] [Indexed: 01/25/2024] Open
Abstract
In different species, embryonic aneuploidies and genome-wide errors are a major cause of developmental failure. The increasing number of equine embryos being produced worldwide provides the opportunity to characterize and rank or select embryos based on their genetic profile prior to transfer. Here, we explored the possibility of generic, genome-wide preimplantation genetic testing concurrently for aneuploidies (PGT-A) and monogenic (PGT-M) traits and diseases in the horse, meanwhile assessing the incidence and spectrum of chromosomal and genome-wide errors in in vitro-produced equine embryos. To this end, over 70,000 single nucleotide polymorphism (SNP) positions were genotyped in 14 trophectoderm biopsies and corresponding biopsied blastocysts, and in 26 individual blastomeres from six arrested cleavage-stage embryos. Subsequently, concurrent genome-wide copy number detection and haplotyping by haplarithmisis was performed and the presence of aneuploidies and genome-wide errors and the inherited parental haplotypes for four common disease-associated genes with high carrier frequency in different horse breeds (GBE1, PLOD1, B3GALNT2, MUTYH), and for one color coat-associated gene (STX17) were compared in biopsy-blastocyst combinations. The euploid (n = 12) or fully aneuploid (n = 2) state and the inherited parental haplotypes for 42/45 loci of interest of the biopsied blastocysts were predicted by the biopsy samples in all successfully analyzed biopsy-blastocyst combinations (n = 9). Two biopsies showed a loss of maternal chromosome 28 and 31, respectively, which were confirmed in the corresponding blastocysts. In one of those biopsies, additional complex aneuploidies not present in the blastocyst were found. Five out of six arrested embryos contained chromosomal and/or genome-wide errors in most of their blastomeres, demonstrating their contribution to equine embryonic arrest in vitro. The application of the described PGT strategy would allow to select equine embryos devoid of genetic errors and pathogenetic variants, and with the variants of interest, which will improve foaling rate and horse quality. We believe this approach will be a gamechanger in horse breeding.
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Affiliation(s)
- T De Coster
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Y Zhao
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - O Tšuiko
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - S Demyda-Peyrás
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Department of Animal Production, Veterinary School, National University of La Plata, La Plata, Argentina
| | - A Van Soom
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium
| | - J R Vermeesch
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - K Smits
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium.
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White-Springer SH, Bruemmer J, Coleman RJ. The Past, Present, and Future of Equine Science. J Equine Vet Sci 2023; 124:104297. [PMID: 37236727 DOI: 10.1016/j.jevs.2023.104297] [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: 03/01/2023] [Accepted: 03/23/2023] [Indexed: 05/28/2023]
Abstract
A core group of 27 equine nutritionists and physiologists joined together in the late 1960s to formally address and enhance the direction of equine research, creating the Equine Nutrition and Physiology Society. In 2003, that growing society transformed into the Equine Science Society, which now serves as the preeminent, internationally recognized scientific equine organization. In recent years, it has been appreciated that equine science encompasses a wide range of focus areas, including exercise science, nutrition, genetics, reproductive physiology, teaching and extension, production and management, and mix of other specialties, qualified as biosciences. Additionally, trainees are highly valued in the society, with the clear understanding that young people are the future of equine science. Amongst tightening budgets, equine researchers must focus on timely dissemination of high-quality research studies and development of strong, interdisciplinary, cross-species, and multi-institutional collaborations to ensure sustainability of academic research programs. With a little creativity, equine science will continue to thrive for the betterment of the horse and all involved in the equine industry.
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Affiliation(s)
- Sarah H White-Springer
- Department of Animal Science, Texas A&M University and Texas A&M AgriLife Research, College Station, TX.
| | - Jason Bruemmer
- USDA-APHIS National Wildlife Research Center, Fort Collins, CO
| | - Robert J Coleman
- Department of Food and Animal Science, University of Kentucky, Lexington, KY
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Prevalence of Sex-Related Chromosomal Abnormalities in a Large Cohort of Spanish Purebred Horses. Animals (Basel) 2023; 13:ani13030539. [PMID: 36766428 PMCID: PMC9913619 DOI: 10.3390/ani13030539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 02/09/2023] Open
Abstract
Chromosomal abnormalities are largely associated with fertility impairments in the domestic horse. To date, over 600 cases of individuals carrying abnormal chromosome complements have been reported, making the domestic horse the species with the highest prevalence. However, studies analyzing the prevalence of chromosomal diseases in whole populations are scarce. We, therefore, employed a two-step molecular tool to screen and diagnose chromosomal abnormalities in a large population of 25,237 Pura Raza Español horses. Individuals were first screened using short tandem repeats parentage testing results and phenotypic evaluations. Those animals showing results suggesting chromosomal abnormalities were re-tested using a single nucleotide polymorphism (SNP)-based diagnostic methodology to accurately determine the chromosomal complements. Thirteen individuals showed a positive screening, all of which were diagnosed as chromosomally abnormal, including five 64,XY mares with sex development disorders (DSD) and four cases of blood chimerism (two male/female and two female/female cases). In addition, we detected one Turner and one Klinefelter syndrome and two individuals carrying complex karyotypes. The overall prevalence in the entire population was ~0.05%, with the prevalence of 64,XY DSD and blood chimerism ~0.02% and ~0.016%, respectively. However, the overall results should be taken with caution since the individuals carrying Turner syndrome (in full (63,X) or mosaic (mos 63,X/64,XX) forms) cannot be detected due to limitations in the methodology employed. Finally, the lack of agreement between populational studies performed using karyotyping or molecular methods is discussed. To our knowledge, this is the largest populational study performed evaluating the prevalence of the most common chromosomal abnormalities in the domestic horse.
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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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Reich P, Falker-Gieske C, Pook T, Tetens J. Development and validation of a horse reference panel for genotype imputation. Genet Sel Evol 2022; 54:49. [PMID: 35787788 PMCID: PMC9252005 DOI: 10.1186/s12711-022-00740-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/23/2022] [Indexed: 11/10/2022] Open
Abstract
Background Genotype imputation is a cost-effective method to generate sequence-level genotypes for a large number of animals. Its application can improve the power of genomic studies, provided that the accuracy of imputation is sufficiently high. The purpose of this study was to develop an optimal strategy for genotype imputation from genotyping array data to sequence level in German warmblood horses, and to investigate the effect of different factors on the accuracy of imputation. Publicly available whole-genome sequence data from 317 horses of 46 breeds was used to conduct the analyses. Results Depending on the size and composition of the reference panel, the accuracy of imputation from medium marker density (60K) to sequence level using the software Beagle 5.1 ranged from 0.64 to 0.70 for horse chromosome 3. Generally, imputation accuracy increased as the size of the reference panel increased, but if genetically distant individuals were included in the panel, the accuracy dropped. Imputation was most precise when using a reference panel of multiple but related breeds and the software Beagle 5.1, which outperformed the other two tested computer programs, Impute 5 and Minimac 4. Genome-wide imputation for this scenario resulted in a mean accuracy of 0.66. Stepwise imputation from 60K to 670K markers and subsequently to sequence level did not improve the accuracy of imputation. However, imputation from higher density (670K) was considerably more accurate (about 0.90) than from medium density. Likewise, imputation in genomic regions with a low marker coverage resulted in a reduced accuracy of imputation. Conclusions The accuracy of imputation in horses was influenced by the size and composition of the reference panel, the marker density of the genotyping array, and the imputation software. Genotype imputation can be used to extend the limited amount of available sequence-level data from horses in order to boost the power of downstream analyses, such as genome-wide association studies, or the detection of embryonic lethal variants. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00740-8.
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Affiliation(s)
- Paula Reich
- Department of Animal Sciences, Georg-August-University Göttingen, 37077, Göttingen, Germany.
| | - Clemens Falker-Gieske
- Department of Animal Sciences, Georg-August-University Göttingen, 37077, Göttingen, Germany.,Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, 37075, Göttingen, Germany
| | - Torsten Pook
- Department of Animal Sciences, Georg-August-University Göttingen, 37077, Göttingen, Germany.,Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, 37075, Göttingen, Germany
| | - Jens Tetens
- Department of Animal Sciences, Georg-August-University Göttingen, 37077, Göttingen, Germany.,Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, 37075, Göttingen, Germany
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Poyato-Bonilla J, Laseca N, Demyda-Peyrás S, Molina A, Valera M. 500 years of breeding in the Carthusian Strain of Pura Raza Español horse: An evolutional analysis using genealogical and genomic data. J Anim Breed Genet 2021; 139:84-99. [PMID: 34363624 DOI: 10.1111/jbg.12641] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/19/2021] [Accepted: 07/25/2021] [Indexed: 01/19/2023]
Abstract
The Carthusian horse is a Pura Raza Español (PRE) strain (CS), bred as a closed population since its creation more than 500 years ago. The aim of this study was to analyse for the first time its population structure and situation of variability combining both genealogical (GEL) and genomic (GEN) data. The GEL data comprised 348,429 pedigree records (56,105 CS horses), while the GEN analysis included the high-density genotypes (670,804 SNPs) of 287 horses. Pedigree completeness demonstrated its accuracy, showing a good correlation of GEL (F) and GEN (FROH ) inbreeding coefficient in the case of PRE subpopulations partially related and non-related to Carthusian strain (0.68) but a lower value in the 100% Carthusian horses (0.42), due to the high weight of founders not detected by GEL analysis. GEN (PCA, AMOVA, and Admixture) and GEL analysis showed a good differentiation of subpopulations, but also a high level of introgression of the CS in the breed during past decades. A recent change in this trend was noteworthy, with a considerable reduction in CS variability and a genetic bottleneck (effective population sizes of 31.57 and 30.20 in GEL and GEN analysis, respectively, in last generation). The PRE has maintained its variability, and a considerable difference in estimated Ne by GEL (60.77) and GEN (188.0) data was observed. Using two sources of complementary information, it was found the existence of an ancient PRE strain with a unique genetic landmark, practically free from the influence of other equine populations.
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Affiliation(s)
- Julia Poyato-Bonilla
- Dpto. Agronomía. Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Sevilla, Spain
| | - Nora Laseca
- Dpto. Genética. Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Sebastián Demyda-Peyrás
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Buenos Aires, Argentina.,CONICET, CCT La Plata, La Plata, Argentina
| | - Antonio Molina
- Dpto. Genética. Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Mercedes Valera
- Dpto. Agronomía. Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Sevilla, Spain
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Pirosanto Y, Laseca N, Valera M, Molina A, Moreno-Millán M, Bugno-Poniewierska M, Ross P, Azor P, Demyda-Peyrás S. Screening and detection of chromosomal copy number alterations in the domestic horse using SNP-array genotyping data. Anim Genet 2021; 52:431-439. [PMID: 34013628 DOI: 10.1111/age.13077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 03/25/2021] [Accepted: 04/22/2021] [Indexed: 12/27/2022]
Abstract
Chromosomal abnormalities are a common cause of infertility in horses. However, they are difficult to detect using automated methods. Here, we propose a simple methodology based on single nucleotide polymorphism (SNP)-array data that allows us to detect the main chromosomal abnormalities in horses in a single procedure. As proof of concept, we were able to detect chromosomal abnormalities in 33 out of 268 individuals, including monosomies, chimerisms, and male and female sex-reversions, by analyzing the raw signal intensity produced by an SNP array-based genotyping platform. We also demonstrated that the procedure is not affected by the SNP density of the array employed or by the inbreeding level of the individuals. Finally, the methodology proposed in this study could be performed in an open bioinformatic environment, thus permitting its integration as a flexible screening tool in diagnostic laboratories and genomic breeding programs.
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Affiliation(s)
- Y Pirosanto
- Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 s/n, La Plata, 1900, Argentina.,IGEVET (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, UNLP, Calle 60 y 118 s/n, La Plata, 1900, Argentina
| | - N Laseca
- Laboratorio de Diagnóstico Genético Veterinario, Departamento de Genética, Universidad de Córdoba, CN IV KM 396, Edificio Gregor Mendel, Campus Rabanales, Córdoba, 14071, España
| | - M Valera
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Ctra. de Utrera km 1, Sevilla, 41013, España
| | - A Molina
- Laboratorio de Diagnóstico Genético Veterinario, Departamento de Genética, Universidad de Córdoba, CN IV KM 396, Edificio Gregor Mendel, Campus Rabanales, Córdoba, 14071, España
| | - M Moreno-Millán
- Laboratorio de Diagnóstico Genético Veterinario, Departamento de Genética, Universidad de Córdoba, CN IV KM 396, Edificio Gregor Mendel, Campus Rabanales, Córdoba, 14071, España
| | - M Bugno-Poniewierska
- Katedra Rozrodu, Anatomii i Genomiki Zwierząt Wydział Hodowli i Biologii Zwierząt, Uniwersytet Rolniczy im. Hugona Kołłątaja w Krakowie, al. Mickiewicza 24/28, Krakow, 30-059, Poland
| | - P Ross
- Department of Animal Science, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA
| | - P Azor
- Asociación Nacional de Criadores de Caballos de Pura Raza Española (ANCCE), Edif. Indotorre · Avda. del Reino Unido 11, pl. 3ª 2, Sevilla, 41012, España
| | - S Demyda-Peyrás
- Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 s/n, La Plata, 1900, Argentina.,IGEVET (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, UNLP, Calle 60 y 118 s/n, La Plata, 1900, Argentina
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Wallis N, Raffan E. The Genetic Basis of Obesity and Related Metabolic Diseases in Humans and Companion Animals. Genes (Basel) 2020; 11:E1378. [PMID: 33233816 PMCID: PMC7699880 DOI: 10.3390/genes11111378] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 12/18/2022] Open
Abstract
Obesity is one of the most prevalent health conditions in humans and companion animals globally. It is associated with premature mortality, metabolic dysfunction, and multiple health conditions across species. Obesity is, therefore, of importance in the fields of medicine and veterinary medicine. The regulation of adiposity is a homeostatic process vulnerable to disruption by a multitude of genetic and environmental factors. It is well established that the heritability of obesity is high in humans and laboratory animals, with ample evidence that the same is true in companion animals. In this review, we provide an overview of how genes link to obesity in humans, drawing on a wealth of information from laboratory animal models, and summarise the mechanisms by which obesity causes related disease. Throughout, we focus on how large-scale human studies and niche investigations of rare mutations in severely affected patients have improved our understanding of obesity biology and can inform our ability to interpret results of animal studies. For dogs, cats, and horses, we compare the similarities in obesity pathophysiology to humans and review the genetic studies that have been previously reported in those species. Finally, we discuss how veterinary genetics may learn from humans about studying precise, nuanced phenotypes and implementing large-scale studies, but also how veterinary studies may be able to look past clinical findings to mechanistic ones and demonstrate translational benefits to human research.
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Affiliation(s)
| | - Eleanor Raffan
- Anatomy Building, Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK;
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