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Sobotková E, Kopec T, Mikule V, Kuřitková D. Influence of horse demographics, country of training and race distance on the rating of Thoroughbreds. Arch Anim Breed 2023; 66:299-313. [PMID: 38039343 PMCID: PMC10654610 DOI: 10.5194/aab-66-299-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/07/2023] [Indexed: 12/03/2023] Open
Abstract
The aim of the research was to assess how age, sex, sire, country of foaling, country of training and race distance influenced the international racing and performance of Thoroughbreds. The research was based on performance ratings of 6216 horses assigned by the International Federation of Racing Authorities between 2004 and 2022. The most common sex was stallion (58.54 %) and more than half of the population consisted of 3- and 4-year-old horses (54.68 %). The majority of the horses had the USA as their country of foaling (25.92 %) and also as their country of training (24.87 %). The sire with the largest number of offspring in the International Federation of Horseracing Authorities (IFHA) databases was Galileo (IRE) (193 horses). Four of the 10 most frequently represented sires belonged to the Sadler's Wells (USA) paternal line. The analysis of the statistics in the database as a whole established a significant (p < 0.001 ) influence of all observed factors. Stallions achieved a significantly higher rating (117.85) compared to geldings (117.17) and mares (117.13). The horses originating in Ireland achieved a statistically higher rating (117.99) than horses from Argentina, Australia, Brazil, New Zealand, a group of other countries designated "Others" and South Africa. Statistically conclusive differences were found between horses trained in Ireland (118.80) and all other countries except Great Britain and France. Five of the 10 sires with the best offspring rating belong to the Mr. Prospector (USA) paternal line.
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Affiliation(s)
- Eva Sobotková
- Department of Animal Science, Mendel University in Brno, Zemědělská 1, Brno, 613 00, Czech Republic
| | - Tomáš Kopec
- Department of Animal Science, Mendel University in Brno, Zemědělská 1, Brno, 613 00, Czech Republic
| | - Vladimír Mikule
- Department of Animal Science, Mendel University in Brno, Zemědělská 1, Brno, 613 00, Czech Republic
| | - Dana Kuřitková
- Department of Animal Science, Mendel University in Brno, Zemědělská 1, Brno, 613 00, Czech Republic
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Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Nagata SI. Construction of an individual identification panel for horses using insertion and deletion markers. J Equine Sci 2023; 34:83-92. [PMID: 37781568 PMCID: PMC10534061 DOI: 10.1294/jes.34.83] [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: 05/29/2023] [Accepted: 07/21/2023] [Indexed: 10/03/2023] Open
Abstract
Individual identification and paternity testing are important for avoiding inbreeding in the management of small populations of wild and domestic animals. In horse racing industries, they are extremely important for identifying and registering individuals and doping control to ensure fair competition. In this study, we constructed an individual identification panel for horses by using insertion and deletion (INDEL) markers. The panel included 39 INDEL markers selected from a whole-genome INDEL database. Genotyping of 89 Thoroughbreds showed polymorphisms with minor allele frequencies (MAFs) of 0.180-0.489 in all markers. The total probability of exclusion for paternity testing, power of discrimination, and probability of identity were 0.9994271269, >0.9999999999, and 0.9999999987, respectively. The panel was applied to 13 trios (sires, dams, and foals), and no contradictions were observed in genetic inheritance among the trios. When this panel was applied to the trios (52 trios) containing false fathers, an average of 7.3 markers excluded parentage relationships. In addition, genomic DNA extracted from the urine of six horses was partially genotyped for 39 markers, and 6-28 markers were successfully genotyped. The newly constructed panel has two advantages: a low marker mutation rate compared with short tandem repeats and a genotyping procedure that is as simple as short tandem repeat typing compared with single nucleotide variant typing. This panel can be applied for individual identification, paternity determination, and urine-sample identification in Thoroughbred horses.
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Affiliation(s)
- Teruaki Tozaki
- Genetic Analysis Department, Laboratory of
Racing Chemistry, Tochigi 320-0851, Japan
| | - Aoi Ohnuma
- Genetic Analysis Department, Laboratory of
Racing Chemistry, Tochigi 320-0851, Japan
| | - Mio Kikuchi
- Genetic Analysis Department, Laboratory of
Racing Chemistry, Tochigi 320-0851, Japan
| | - Taichiro Ishige
- Genetic Analysis Department, Laboratory of
Racing Chemistry, Tochigi 320-0851, Japan
| | - Hironaga Kakoi
- Genetic Analysis Department, Laboratory of
Racing Chemistry, Tochigi 320-0851, Japan
| | - Kei-ichi Hirota
- Genetic Analysis Department, Laboratory of
Racing Chemistry, Tochigi 320-0851, Japan
| | - Shun-ichi Nagata
- Genetic Analysis Department, Laboratory of
Racing Chemistry, Tochigi 320-0851, Japan
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Analysis of Genetic Variability in the Argentine Polo Horse With a Panel of Microsatellite Markers. J Equine Vet Sci 2020; 96:103320. [PMID: 33349401 DOI: 10.1016/j.jevs.2020.103320] [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: 09/22/2020] [Revised: 11/02/2020] [Accepted: 11/02/2020] [Indexed: 11/24/2022]
Abstract
Argentine Polo (AP) is a young horse breed with a fast expansion because of an open registry policy and the application of assisted reproduction technologies. In the last years, AP showed a remarkable progress associated with the use of embryo transfer technology and intensive selection based on sport performance. However, these practices could have affected the genetic variability of the breed. To monitor these potential changes, a parentage panel of 11-15 microsatellites was investigated for changes in allele frequencies, heterozygosity, and exclusion probability over a 16 year period. Frequency of 36 alleles in 13 markers showed significant departures from expected changes because of random genetic drift. Six markers showed both allelic frequency increase and expected heterozygosity (He) reduction, suggesting the influence of selective breeding or hitchhiking effects. The average He decreased significantly although was lower than the observed heterozygosity, indicating a still low inbreeding level. Although the exclusion probability of the panel showed a trend to decrease, it is over 0.9995, the recommended value for equine parentage exclusion.
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McGivney BA, Han H, Corduff LR, Katz LM, Tozaki T, MacHugh DE, Hill EW. Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population. Sci Rep 2020; 10:466. [PMID: 31949252 PMCID: PMC6965197 DOI: 10.1038/s41598-019-57389-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/30/2019] [Indexed: 02/07/2023] Open
Abstract
The Thoroughbred horse is a highly valued domestic animal population under strong selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of inbreeding in the population that may form the basis for evidence-based discussion amid concerns in the breeding industry over the increasing use of small numbers of popular sire lines, which may accelerate a loss of genetic diversity. In the most comprehensive globally representative sample of Thoroughbreds to-date (n = 10,118), including prominent stallions (n = 305) from the major bloodstock regions of the world, we show using pan-genomic SNP genotypes that there has been a highly significant decline in global genetic diversity during the last five decades (FIS R2 = 0.942, P = 2.19 × 10-13; FROH R2 = 0.88, P = 1.81 × 10-10) that has likely been influenced by the use of popular sire lines. Estimates of effective population size in the global and regional populations indicate that there is some level of regional variation that may be exploited to improve global genetic diversity. Inbreeding is often a consequence of selection, which in managed animal populations tends to be driven by preferences for cultural, aesthetic or economically advantageous phenotypes. Using a composite selection signals approach, we show that centuries of selection for favourable athletic traits among Thoroughbreds acts on genes with functions in behaviour, musculoskeletal conformation and metabolism. As well as classical selective sweeps at core loci, polygenic adaptation for functional modalities in cardiovascular signalling, organismal growth and development, cellular stress and injury, metabolic pathways and neurotransmitters and other nervous system signalling has shaped the Thoroughbred athletic phenotype. Our results demonstrate that genomics-based approaches to identify genetic outcrosses will add valuable objectivity to augment traditional methods of stallion selection and that genomics-based methods will be beneficial to actively monitor the population to address the marked inbreeding trend.
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Affiliation(s)
| | - Haige Han
- Plusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, Ireland
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Leanne R Corduff
- Plusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, Ireland
| | - Lisa M Katz
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Teruaki Tozaki
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, Japan
| | - David E MacHugh
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Emmeline W Hill
- Plusvital Ltd, The Highline, Dun Laoghaire Business Park, Dublin, Ireland.
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.
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Amano T, Tozaki T, Takasu M, Onogi A, Yamada F, Kawai M, Ueda J. Changes of sires in a breeding farm enables maintenance of DNA-level genetic variation in a produced herd of Hokkaido Native Horses. Anim Sci J 2019; 91:e13318. [PMID: 31755177 DOI: 10.1111/asj.13318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/06/2019] [Accepted: 10/23/2019] [Indexed: 11/29/2022]
Abstract
We investigated whether regular changes of the sire in a breeding farm of Hokkaido Native Horses (HKDs) enables the DNA-level genetic variation of the produced animals to be maintained. The genotypes of 31 microsatellite markers were identified and analyzed in 207 animals produced in a breeding farm in which the sire was replaced every 3 to 5 years. The mean allele number indicating the degree of genetic variation was 5.97 and was similar to those reported previously. The mean observed heterozygosity was 0.74 and was higher than the expected heterozygosity, 0.69; FIS was -0.07, indicating that the analyzed animals reflected frequent outbreeding and had maintained genetic variation. Based on genetic structural analysis, the number of genetic subpopulations of the animals was estimated to be as 6, and the majority (more than 50%) of each subpopulation corresponded to the progeny of one of the sires used in the breeding farm; these observations suggested that genetic variation in the analyzed animals reflected the genetic differences among sires. Pedigree records indicated that the average co-ancestry coefficient between sires used in the breeding farm was 0.015 corresponding to second cousin. This level of kinship among sires is acceptable for producing HKDs that maintain genetic variation.
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Affiliation(s)
- Tomoko Amano
- College of Agriculture, Food and Environment Sciences, Department of Sustainable Agriculture, Laboratory of Animal Genetics, Rakuno Gakuen University, Hokkaido, Japan
| | - Teruaki Tozaki
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi, Japan.,Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Masaki Takasu
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Akio Onogi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Fumihiro Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Masahito Kawai
- Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Junji Ueda
- College of Agriculture, Food and Environment Sciences, Department of Sustainable Agriculture, Laboratory of Animal Genetics, Rakuno Gakuen University, Hokkaido, Japan
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