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PATEL ASHISHC, PARIKH RC, MACWAN SHEFALI, TANK PH, MARADIA MG, RANK DN. Genetic characterization of horse breeds (Equus caballus) of Western India. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2020. [DOI: 10.56093/ijans.v90i3.102522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Assessment of genetic diversity and population structure of population through molecular markers allows determining their extinction risk and to manage and conserve the respective population. The present study was undertaken for population genetic analysis at a molecular level of horse breeds for planning conservation, utilization and improvement in the livelihood. Gujarat has three recognized horse breeds Kathiawari, Marwari and Kachchhi- Sindhi. The genetic characterization and differentiation analysis among and within these breeds was analyzed using 26 microsatellite markers out of which 25 markers were polymorphic while one was monomorphic. The present study indicated that Marwari and Kathiawari horse breeds are genetically nearer as compared to Kathiawari— Kachchhi-Sindhi and Marwari—Kachchhi-Sindhi. The observed number of alleles in all three breeds ranged from 2 (NVHEQ21) to 16 (ASB17). The within population in breeding estimate (FIS) was less than zero, indicating absence of inbreeding in Kathiawari, Marwari and Kachchhi-Sindhi breed. The Wilcox text, sign test and standardized difference test in present study revealed the presence of significant heterozygotic excess in both IAM and SMM model demonstrating that these three breeds of horse has showed recent genetic bottleneck.
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Gupta AK, Chauhan M, Bhardwaj A. Genetic diversity and bottleneck studies in endangered Bhutia and Manipuri pony breeds. Mol Biol Rep 2013; 40:6935-43. [PMID: 24150726 DOI: 10.1007/s11033-013-2813-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/16/2013] [Indexed: 10/26/2022]
Abstract
For studying the genetic diversity and bottleneck problem in Bhutia and Manipuri pony breeds of India, we analysed DNA samples of 34 Bhutia and 50 Manipuri, true to breed, ponies using 47 polymorphic microsatellite markers. All the microsatellites were observed to be highly polymorphic in nature in both Bhutia and Manipuri breeds with mean no. of alleles as 8.702 ± 0.0493 and 8.416 ± 0.0548 respectively. Genetic diversity values in terms of heterozygosity values within individual breeds were also high with very low inbreeding (Fis 0.102 and 0.055 in Bhutia and Manipuri ponies, respectively). Number of alleles in both the populations together ranged from 3 to 18 with an average of 10.851 ± 1.583 per locus. The mean effective number of alleles was observed to 5.34 ± 0.253. All loci except ASB017 and HTG004 showed high values of allele richness (>5.0). The mean observed and expected heterozygosities were 0.7159 ± 0.022, 0.7986 ± 0.011 (Levene's) and 0.7936 ± 0.011 (Nei's), respectively. The high mean values of heterozygosity indicated the presence of high genetic diversity in both the pony populations. The overall mean value of within-population inbreeding estimates (Fis) was low (0.101 ± 0.023) indicating low to moderate level of inbreeding. Bottleneck studies revealed that no recent bottleneck problem has taken place in both the populations. Both pony populations were found to be in mutation drift equilibrium. The study reveals that both the pony breeds have high diversity and timely action needs to be taken to conserve them.
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Affiliation(s)
- A K Gupta
- National Research Centre on Equines, Sirsa Road, Hisar, 125 001, India,
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Kusza S, Priskin K, Ivankovic A, Jedrzejewska B, Podgorski T, Jávor A, Mihók S. Genetic characterization and population bottleneck in the Hucul horse based on microsatellite and mitochondrial data. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Katalin Priskin
- Biological Research Center of the Hungarian Academy of Sciences; Szeged; Hungary
| | | | | | - Tomasz Podgorski
- Mammal Research Institute; Polish Academy of Science; Białowieża; Poland
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Gupta AK, Chauhan M, Bhardwaj A, Tandon SN. Microsatellite markers based genetic diversity and bottleneck studies in Zanskari pony. Gene 2012; 499:357-61. [PMID: 22445609 DOI: 10.1016/j.gene.2012.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 03/04/2012] [Indexed: 10/28/2022]
Abstract
Genetic diversity in Zanskari pony breed was evaluated at 48 microsatellite loci using fifty adult, healthy and unrelated animals. Allele frequency data was used to detect genetic diversity and bottleneck. The estimated average number of alleles (±s.e.) was 8.5208±2.5010 with a total of 409 alleles. A high level of genetic diversity within this breed was observed in terms of number of alleles, observed heterozygosity (0.6763±0.1704), expected Leven's heterozygosity (0.7724±0.795), expected Nei's heterozygosity (0.7644±0.0787) and polymorphism information content (>0.5). In-breeding coefficient (F(is)) was 0.115±0.0209, suggesting moderately high in-breeding in Zanskari breed. Although analysis of bottleneck revealed no bottleneck in recent past but population of Zanskari ponies has decreased drastically and only a few thousand pure-bred animals are left. The information is useful for proposing effective population management strategies for future.
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Affiliation(s)
- A K Gupta
- National Research Centre on Equines, Hisar 125 001, India
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Machado FB, de Vasconcellos Machado L, Bydlowski CR, Bydlowski SP, Medina-Acosta E. Gametic phase disequilibrium between the syntenic multiallelic HTG4 and HMS3 markers widely used for parentage testing in Thoroughbred horses. Mol Biol Rep 2011; 39:1447-52. [PMID: 21607619 DOI: 10.1007/s11033-011-0881-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 05/14/2011] [Indexed: 10/18/2022]
Abstract
Validation of parentage and horse breed registries through DNA typing relies on estimates of random match probabilities with DNA profiles generated from multiple polymorphic loci. Of the twenty-seven microsatellite loci recommended by the International Society for Animal Genetics for parentage testing in Thoroughbred horses, eleven are located on five chromosomes. An important aspect in determining combined exclusion probabilities is the ascertainment of the genetic linkage status of syntenic markers, which may affect reliable use of the product rule in estimating random match probabilities. In principle, linked markers can be in gametic phase disequilibrium (GD). We aimed at determining the extent, by frequency and strength, of GD between the HTG4 and HMS3 multiallelic loci, syntenic on chromosome 9. We typed the qualified offspring (n (1) = 27; n (2) = 14) of two Quarter Bred stallions (registered by the Brazilian Association of Quarter Horse Breeders) and 121 unrelated horses from the same breed. In the 41 informative meioses analyzed, the frequency of recombination between the HTG4 and HMS3 loci was 0.27. Consistent with genetic map distances, this recombination rate does not fit to the theoretical distribution for independently segregated markers. We estimated sign-based D' coefficients as a measure of GD, and showed that the HTG4 and HMS3 loci are in significant, yet partial and weak, disequilibrium, with two allele pairs involved (HTG4 M/HMS3 P, D'(+) = 0.6274; and HTG4 K/HMS3 P, D'(-) = -0.6096). These results warn against the inadequate inclusion of genetically linked markers in the calculation of combined power of discrimination for Thoroughbred parentage validation.
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Affiliation(s)
- Filipe Brum Machado
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes, 3900, Monte Alegre, Ribeirão Preto, SP, CEP 14049-900, Brazil
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Lucas ZL, McLoughlin PD, Coltman DW, Barber C. Multiscale analysis reveals restricted gene flow and a linear gradient in heterozygosity for an island population of feral horses. CAN J ZOOL 2009. [DOI: 10.1139/z09-019] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We studied the genetic (microsatellite) diversity of a feral population of horses ( Equus caballus L., 1758) on Sable Island, Nova Scotia, Canada (1983–2003), at two spatial scales: (1) for the island as a whole and (2) at the level of four equally sized subdivisions along the length of Sable Island, which is a long (42 km) and narrow (1.5 km) vegetated sand bar. At the island scale (n = 264 horses), observed heterozygosity over 10 loci was 0.647 ± 0.035 (mean ± 1 SE), while expected heterozygosity was 0.696 ± 0.029; we observed significant heterozygote deficiency with all loci considered (P < 0.0001). At the subdivision scale, observed heterozygosity ranged from 0.589 to 0.694 in a gradient from west to east. We observed a corresponding gradient in effective number of alleles and allelic richness. Pairwise values of FST were significant for most subdivision pairs, ranging as high as 0.067 from west to east. Western areas showed highest levels of inbreeding (FIS = 0.113) with outbreeding indicated in the east (FIS = –0.008). Our results suggest that for a large mammal that lives in polygynous social groups, like the feral horse, gene flow along linear habitats (corridors) may be restricted (relative to the dispersal capabilities of the species), even over short distances.
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Affiliation(s)
- Z. L. Lucas
- Sable Island Green Horse Society, P.O. Box 64, Halifax CRO, Halifax, NS B3J 2L4, Canada
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS B3H 3C3, Canada
| | - P. D. McLoughlin
- Sable Island Green Horse Society, P.O. Box 64, Halifax CRO, Halifax, NS B3J 2L4, Canada
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS B3H 3C3, Canada
| | - D. W. Coltman
- Sable Island Green Horse Society, P.O. Box 64, Halifax CRO, Halifax, NS B3J 2L4, Canada
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS B3H 3C3, Canada
| | - C. Barber
- Sable Island Green Horse Society, P.O. Box 64, Halifax CRO, Halifax, NS B3J 2L4, Canada
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS B3H 3C3, Canada
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