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Nguyen AT, Kövér G, Tóth P, Curik I, Bokor Á, Nagy I. Population Subdivision and Migration Assessment of Mangalica Pig Breeds Based on Pedigree Analysis. Animals (Basel) 2024; 14:653. [PMID: 38396621 PMCID: PMC10886115 DOI: 10.3390/ani14040653] [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: 12/08/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
In conserving the genetic diversity of domestic animal breeds, strategies that emphasise between-breed diversity may not be optimal, as they neglect within-breed variation. The aim of the present study was to assess the extent of population subdivision in three Mangalica pig breeds and the contribution of migration to their substructure. Wright's FST coefficient was calculated based on genealogical data with breeding animals born between 1981 and 2023, with three colour variants (Blonde, Swallow-Belly and Red). These Wright's FST coefficients were analysed using multidimensional scaling to reveal the population substructure. The average FST coefficient was 0.04 for the Blonde breed and 0.047 for the Swallow-Belly and Red Mangalica breeds, while these parameters were lower in the active herds at 0.03 and 0.04, respectively. The migration of individuals between herds was 61.63% for the Blonde breed and 75.53% and 63.64% for the Swallow-Belly and Red Magalica breeds, respectively. No population substructure was observed in any of the Mangalica breeds, which can be explained by the extensive migration between herds.
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Affiliation(s)
- Anh Thi Nguyen
- Institute of Animal Sciences, Hungarian University of Agriculture and Life Sciences (MATE), Guba Sándor u. 40, 7400 Kaposvár, Hungary; (A.T.N.); (G.K.); (Á.B.)
- Department of Veterinary Medicine, Faculty of Biology Applied Sciences, Vinh Long University of Technology Education, 73 Nguyen Hue, Ward 2, Vinh Long 85000, Vietnam
| | - György Kövér
- Institute of Animal Sciences, Hungarian University of Agriculture and Life Sciences (MATE), Guba Sándor u. 40, 7400 Kaposvár, Hungary; (A.T.N.); (G.K.); (Á.B.)
| | - Péter Tóth
- Hungarian National Association of Mangalica Breeders, Piac u. 77, 4025 Debrecen, Hungary;
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia;
| | - Árpád Bokor
- Institute of Animal Sciences, Hungarian University of Agriculture and Life Sciences (MATE), Guba Sándor u. 40, 7400 Kaposvár, Hungary; (A.T.N.); (G.K.); (Á.B.)
| | - István Nagy
- Institute of Animal Sciences, Hungarian University of Agriculture and Life Sciences (MATE), Guba Sándor u. 40, 7400 Kaposvár, Hungary; (A.T.N.); (G.K.); (Á.B.)
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Genetic Differentiation among Livestock Breeds—Values for Fst. Animals (Basel) 2022; 12:ani12091115. [PMID: 35565543 PMCID: PMC9103131 DOI: 10.3390/ani12091115] [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: 04/01/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary The degree of relationship among livestock breeds can be quantified by the Fst statistic, which measures the extent of genetic differentiation between them. An Fst value of 0.1 has often been taken as indicating that two breeds are indeed genetically distinct, but this concept has not been evaluated critically. Here, Fst values have been collated for the six major livestock species: cattle, sheep, goats, pigs, horses, and chickens. These values are remarkably variable both within and between species, demonstrating that Fst > 0.1 is not a reliable criterion for breed distinctiveness. However, the large body of Fst data accumulated in the last 20–30 years represents an untapped database that could contribute to the development of interdisciplinary research involving livestock breeds. Abstract (1) Background: The Fst statistic is widely used to characterize between-breed relationships. Fst = 0.1 has frequently been taken as indicating genetic distinctiveness between breeds. This study investigates whether this is justified. (2) Methods: A database was created of 35,080 breed pairs and their corresponding Fst values, deduced from microsatellite and SNP studies covering cattle, sheep, goats, pigs, horses, and chickens. Overall, 6560 (19%) of breed pairs were between breeds located in the same country, 7395 (21%) between breeds of different countries within the same region, 20,563 (59%) between breeds located far apart, and 562 (1%) between a breed and the supposed wild ancestor of the species. (3) Results: General values for between-breed Fst were as follows, cattle: microsatellite 0.06–0.12, SNP 0.08–0.15; sheep: microsatellite 0.06–0.10, SNP 0.06–0.17; horses: microsatellite 0.04–0.11, SNP 0.08–0.12; goats: microsatellite 0.04–0.14, SNP 0.08–0.16; pigs: microsatellite 0.06–0.27, SNP 0.15–0.22; chickens: microsatellite 0.05–0.28, SNP 0.08–0.26. (4) Conclusions: (1) Large amounts of Fst data are available for a substantial proportion of the world’s livestock breeds, (2) the value for between-breed Fst of 0.1 is not appropriate owing to its considerable variability, and (3) accumulated Fst data may have value for interdisciplinary research.
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Dell A, Curry M, Yarnell K, Starbuck G, Wilson PB. Genetic analysis of the endangered Cleveland Bay horse: A century of breeding characterised by pedigree and microsatellite data. PLoS One 2020; 15:e0240410. [PMID: 33119607 PMCID: PMC7595272 DOI: 10.1371/journal.pone.0240410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/27/2020] [Indexed: 11/29/2022] Open
Abstract
The Cleveland Bay horse is one of the oldest equines in the United Kingdom, with pedigree data going back almost 300 years. The studbook is essentially closed and because of this, there are concerns about loss of genetic variation across generations. The breed is one of five equine breeds listed as “critical” (<300 registered adult breeding females) by the UK Rare Breeds Survival Trust in their annual Watchlist. Due to their critically endangered status, the current breadth of their genetic diversity is of concern, and assessment of this can lead to improved breed management strategies. Herein, both genealogical and molecular methods are combined in order to assess founder representation, lineage, and allelic diversity. Data from 15 microsatellite loci from a reference population of 402 individuals determined a loss of 91% and 48% of stallion and dam lines, respectively. Only 3 ancestors determine 50% of the genome in the living population, with 70% of maternal lineage being derived from 3 founder females, and all paternal lineages traced back to a single founder stallion. Methods and theory are described in detail in order to demonstrate the scope of this analysis for wider conservation strategies. We quantitatively demonstrate the critical nature of the genetic resources within the breed and offer a perspective on implementing this data in considered breed management strategies.
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Affiliation(s)
- Andrew Dell
- Department of Biological Sciences, University of Lincoln, Brayford Way, Brayford Pool, Lincoln, United Kingdom
- Rare Breeds Survival Trust, Stoneleigh Park, Stoneleigh, Warwickshire, United Kingdom
- * E-mail: (AD); (PBW)
| | - Mark Curry
- Department of Biological Sciences, University of Lincoln, Brayford Way, Brayford Pool, Lincoln, United Kingdom
| | - Kelly Yarnell
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Brackenhurst Campus, Southwell, Nottinghamshire, United Kingdom
| | - Gareth Starbuck
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Brackenhurst Campus, Southwell, Nottinghamshire, United Kingdom
| | - Philippe B. Wilson
- Rare Breeds Survival Trust, Stoneleigh Park, Stoneleigh, Warwickshire, United Kingdom
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Brackenhurst Campus, Southwell, Nottinghamshire, United Kingdom
- * E-mail: (AD); (PBW)
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Baena MM, Diaz S, Moura RS, Meirelles SLC. Genetic Characterization of Mangalarga Marchador Breed Horses Based on Microsatellite Molecular Markers. J Equine Vet Sci 2020; 95:103231. [PMID: 33276913 DOI: 10.1016/j.jevs.2020.103231] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/09/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022]
Abstract
The Mangalarga Marchador (MM) horse breed has expressive importance in the Brazilian economy. Thus, the aim of this study was to investigate diversity in the MM breed. A database with a total of 3,193 genotyped horses was used (MM, n = 2,829; Andalusian - AND, n = 67; Pure Blood Lusitano - LUS, n = 43; English Thoroughbred - THO, n = 54; Arabian - ARA, n = 99; Campolina - CAM, n = 61; and Mangalarga - MAN, n = 40) for 13 microsatellite. Diversity parameters were estimates, such as mean number of alleles (Nma) and the number of rare alleles (AR), expected heterozygosity (He), F statistics, genetic distances, Hardy-Weinberg equilibrium test (HWE), population structure, and others. The Nma was 10.85, the AR was prevalent in the MM, and the He was 0.7402. In MM, the values of Fis (-0.0195), Fit (0.0566), Fst (0.0748), and deviations of HWE were observed. The genetic distances of the ARA and THO breeds with the other breeds were greater than the distances between the Brazilian breeds and between these and the breeds in the Iberian Peninsula. The population structure indicated that MM was substructured, yet there were some more genetically defined breeding farms. The genetic diversity is satisfactory for MM conservation, but the population is substructure, and parameters indicate moderate gene flow and the existence, though few, of crosses with other horse breeds. Immediate implementation of a genetic breeding program is required, especially seeking to conserve the structure of the MM breed as a well-defined genetic entity.
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Affiliation(s)
- Marielle M Baena
- Department Animal Science, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Silvina Diaz
- Faculty of Veterinary Sciences, Universidad Nacional de La Plata, La Plata, Province of Buenos Aires, Argentina
| | - Raquel S Moura
- Department Animal Science, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Sarah L C Meirelles
- Department Animal Science, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil.
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Machmoum M, Boujenane I, Azelhak R, Badaoui B, Petit D, Piro M. Genetic Diversity and Population Structure of Arabian Horse Populations Using Microsatellite Markers. J Equine Vet Sci 2020; 93:103200. [PMID: 32972687 DOI: 10.1016/j.jevs.2020.103200] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/09/2020] [Accepted: 07/27/2020] [Indexed: 11/17/2022]
Abstract
Understanding the genetic diversity and the relationships among the show Arabian horse populations is a current issue for breeders and professionals. This study aimed to define the relationship among the Desert breed, the Straight Egyptian, and the Polish Arabian populations by considering the historical background of their origin and to verify their genetic diversity. All selected samples were related to Arabian show activities. One hundred forty four hair samples were collected from horses at stud farms having notoriety in the breeding of Arabians from different geographic regions. A set of 17 microsatellites markers for parentage control were used for genotyping. Genetic diversity among and between these populations were evaluated using several statistical methods. All the microsatellites were informative and the marker set analyzed provided 145 alleles. The average number of alleles per locus was 6.52, 6.35, and 7 for the Desert breed, Straight Egyptian, and Polish Arabian, respectively. The high genetic diversity observed within the three populations (0.63-0.71) was associated with a high number of effective alleles. Desert breed and Polish Arabian populations appeared the closest, whereas the Egyptian population was more distant. The significant positive inbreeding coefficient FIS found in Desert breed, Straight Egyptian, and Polish Arabian horses (0.09, 0.14, and 0.11, respectively) confirmed the deficit of heterozygosity observed in these populations. These results suggested that the three populations have high levels of gene flow or share the same origin and have a recent divergence. This study may highlight the risk of the loss of gene diversity in these populations and help to implement appropriate breeding programs to preserve genetic diversity.
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Affiliation(s)
- Mohamed Machmoum
- Veterinary Genetic Laboratory, Department of Medicine, Surgery and Reproduction, Institut Agronomique et Vétérinaire Hassan II, Rabat, Morocco.
| | - Ismaïl Boujenane
- Department of Animal Production and Biotechnology, Institut Agronomique et Vétérinaire Hassan II, Rabat, Morocco
| | | | - Bouabid Badaoui
- Biodiversity, Ecology and Genome Laboratory, Department of Biology, Mohammed V University, Faculty of Science, Rabat, Morocco
| | - Daniel Petit
- Laboratoire Peirene, EA7500, University of Limoges, Limoges, France
| | - Mohammed Piro
- Veterinary Genetic Laboratory, Department of Medicine, Surgery and Reproduction, Institut Agronomique et Vétérinaire Hassan II, Rabat, Morocco
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Grilz-Seger G, Druml T, Neuditschko M, Dobretsberger M, Horna M, Brem G. High-resolution population structure and runs of homozygosity reveal the genetic architecture of complex traits in the Lipizzan horse. BMC Genomics 2019; 20:174. [PMID: 30836959 PMCID: PMC6402180 DOI: 10.1186/s12864-019-5564-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/25/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The sample ascertainment bias due to complex population structures remains a major challenge in genome-wide investigations of complex traits. In this study we derived the high-resolution population structure and levels of autozygosity of 377 Lipizzan horses originating from five different European stud farms utilizing the SNP genotype information of the high density 700 k Affymetrix Axiom™ Equine genotyping array. Scanning the genome for overlapping runs of homozygosity (ROH) shared by more than 50% of horses, we identified homozygous regions (ROH islands) in order to investigate the gene content of those candidate regions by gene ontology and enrichment analyses. RESULTS The high-resolution population network approach revealed well-defined substructures according to the origin of the horses (Austria, Slovakia, Croatia and Hungary). The highest mean genome coverage of ROH (SROH) was identified in the Austrian (SROH = 342.9), followed by Croatian (SROH = 214.7), Slovakian (SROH = 205.1) and Hungarian (SROH = 171.5) subpopulations. ROH island analysis revealed five common islands on ECA11 and ECA14, hereby confirming a closer genetic relationship between the Hungarian and Croatian as well as between the Austrian and Slovakian samples. Private islands were detected for the Hungarian and the Austrian Lipizzan subpopulations. All subpopulations shared a homozygous region on ECA11, nearly identical in position and length containing among other genes the homeobox-B cluster, which was also significantly (p < 0.001) highlighted by enrichment analysis. Gene ontology terms were mostly related to biological processes involved in embryonic morphogenesis and anterior/posterior specification. Around the STX17 gene (causative for greying), we identified a ROH island harbouring the genes NR4A3, STX17, ERP44 and INVS. Within further islands on ECA14, ECA16 and ECA20 we detected the genes SPRY4, NDFIP1, IMPDH2, HSP90AB1, whereas SPRY4 and HSP90AB1 are involved in melanoma metastasis and survival rate of melanoma patients in humans. CONCLUSIONS We demonstrated that the assessment of high-resolution population structures within one single breed supports the downstream genetic analyses (e.g. the identification of ROH islands). By means of ROH island analyses, we identified the genes SPRY4, NDFIP1, IMPDH2, HSP90AB1, which might play an important role for further studies on equine melanoma. Furthermore, our results highlighted the impact of the homeobox-A and B cluster involved in morphogenesis of Lipizzan horses.
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Affiliation(s)
- Gertrud Grilz-Seger
- Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Thomas Druml
- Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Markus Neuditschko
- Agroscope, Swiss National Stud Farm, Les Longs Prés, CH-1580 Avenches, Switzerland
| | - Max Dobretsberger
- Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Michaela Horna
- Department of Animal Husbandry, Slovak University of Agriculture in Nitra, Nitra-Chrenová, Slovak Republic
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
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Senokuchi A, Ishikawa S, Tozaki T, Takasu M, Kakoi H, Misumi K, Hobo S. Genetic analyses for conservation of the traditional Tokara horse using 31 microsatellite markers. J Equine Sci 2018; 29:97-104. [PMID: 30607133 PMCID: PMC6306296 DOI: 10.1294/jes.29.97] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/29/2018] [Indexed: 11/16/2022] Open
Abstract
In order to promote conservation of the traditional Tokara horse in its remaining three
breeding areas in Japan (Nakanoshima, Kaimondake, and Iriki), we genotyped 123 horses
using 31 microsatellite markers and determined their genetic diversity. On average, the
number of alleles (NA), observed heterozygosity (HO), expected
heterozygosity (HE), and inbreeding coefficient (FIS) among all
horses were 3.0, 0.424, 0.481, and 0.108, respectively. Compared with other endangered
horse breeds, we found that, even though the size of the Tokara horse population has
recently increased, the NA, HO, and HE of Tokara horses
are still notably lower than those of other breeds. Neighbor-joining tree and STRUCTURE
analysis showed that the current population of Tokara horses is divided into three
subpopulations, corresponding to their respective feeding and breeding areas: Nakanoshima,
Kaimondake, and Iriki. This subdivision was also reflected in the NA of
microsatellite DNAs, with four, three, and four different loci showing single alleles in
Nakanoshima, Kaimondake, and Iriki horses, respectively. These alleles are considered to
have become fixed as a consequence of breeding within the limited number of horses in each
area. Since Tokara horses are currently strongly divided into subpopulations, it is
vitally important to exchange several horses among their different breeding units in order
to maintain the genetic diversity of the Tokara horse as a unique breed. The data obtained
in this study contribute toward explaining the history of Tokara horses and also provide
important information for future monitoring of population diversity and guiding
conservation measures for this endangered breed.
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Affiliation(s)
- Akane Senokuchi
- Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
| | - Shingo Ishikawa
- Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
| | - Teruaki Tozaki
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan.,Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Masaki Takasu
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Hironaga Kakoi
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan
| | - Kazuhiro Misumi
- Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
| | - Seiji Hobo
- Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
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8
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Sánchez-Guerrero MJ, Negro-Rama S, Demyda-Peyras S, Solé-Berga M, Azor-Ortiz PJ, Valera-Córdoba M. Morphological and genetic diversity of Pura Raza Español horse with regard to the coat colour. Anim Sci J 2018; 90:14-22. [PMID: 30467923 DOI: 10.1111/asj.13102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 07/04/2018] [Accepted: 07/13/2018] [Indexed: 11/27/2022]
Abstract
Gene mutations influencing melanocytes also impact on physiological and behavioural functions. In this study, we investigated their association with four different coat colours in the Pura Raza Español (PRE) horse using morphological traits and molecular datasets. Four different subpopulations were identified according to individual coat colour: grey, bay, chestnut and black. Coat colour significantly associated with morphological measurements. Observed and expected heterozygosity values were low in grey compared with the other three subpopulations, suggesting the presence of unique ancestral alleles probably arisen by genetic drift and selection mechanism effects. Nei's distance demonstrated a clear division among subpopulations, the grey being the most divergent group. Gene flow estimates were similar, showing the lowest values in grey. Divergence times among subpopulations assessed with the average square distance suggested that grey was the original PRE population which diverged from bay, chestnut and black. Our results also demonstrated a clear morphological differentiation according to coat colour. The close genetic structure of bay and chestnut PRE subpopulations and the clear differences in most morphological traits of grey and chestnut PRE mares would suggest the pleiotropic effect of genomic regions determining coat colour in horses. However, further analysis including genomic information would be necessary to elucidate the mechanisms involved.
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Affiliation(s)
| | - Sara Negro-Rama
- Departamento de Ciencias Agroforestales, ETSIA, Universidad de Sevilla, Sevilla, España
| | - Sebastián Demyda-Peyras
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina
| | - Marina Solé-Berga
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Pedro J Azor-Ortiz
- Departamento de Ciencias Agroforestales, ETSIA, Universidad de Sevilla, Sevilla, España
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Vázquez-Armijo JF, Parra-Bracamonte GM, Velazquez MA, Sifuentes-Rincón AM, Tinoco-Jaramillo JL, Ambriz-Morales P, Arellano-Vera W, Moreno-Medina VR. Diversity and effective population size of four horse breeds from microsatellite DNA markers in South-Central Mexico. Arch Anim Breed 2017. [DOI: 10.5194/aab-60-137-2017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. The South-Central region of Mexico has experienced a sizeable introduction of purebred horses for recreational aims. A study was designed to assess effective population sizes and genetic diversity and to verify the genetic integrity of four horse breeds. Using a 12-microsatellite panel, Quarter Horse, Azteca, Thoroughbred and Creole (CRL) horses were sampled and analysed for diversity and genetic structure. Genetic diversity parameters showed high numbers of heterozygous horses but small effective population sizes in all breeds. Population structure results suggested some degree of admixture of CRL with the other reference breeds. The highly informative microsatellite panel allowed the verification of diversity in introduced horse populations and the confirmation of small effective population sizes, which suggests a risk for future breed integrity.
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10
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Anaya G, Molina A, Valera M, Moreno-Millán M, Azor P, Peral-García P, Demyda-Peyrás S. Sex chromosomal abnormalities associated with equine infertility: validation of a simple molecular screening tool in the Purebred Spanish Horse. Anim Genet 2017; 48:412-419. [DOI: 10.1111/age.12543] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2016] [Indexed: 11/27/2022]
Affiliation(s)
- G. Anaya
- Laboratorio de Diagnóstico Genético Veterinario; Departamento de Genética; Universidad de Córdoba; CN IV KM 396 Edificio Gregor Mendel Campus Rabanales Córdoba 14071 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. Valera
- Departamento de Ciencias Agroforestales; Escuela Tecnica Superior de Ingeniería Agronómica; Universidad de Sevilla; Ctra de Utrera km 1 41013 Sevilla España
| | - M. Moreno-Millán
- Laboratorio de Citogenética Animal Aplicada y Molecular; Departamento de Genética; Universidad de Córdoba; CN IV KM 396 Edificio Gregor Mendel Campus Rabanales Córdoba 14071 España
| | - P. Azor
- Departamento de Ciencias Agroforestales; Escuela Tecnica Superior de Ingeniería Agronómica; Universidad de Sevilla; Ctra de Utrera km 1 41013 Sevilla España
| | - P. Peral-García
- Instituto de Genética Veterinaria “Ing. Fernando N. Dulout” (UNLP - CONICET LA PLATA); Facultad de Ciencias Veterinarias; Universidad Nacional de La Plata; Calle 60 y 118 s/n 1900 La Plata Argentina
| | - S. Demyda-Peyrás
- Instituto de Genética Veterinaria “Ing. Fernando N. Dulout” (UNLP - CONICET LA PLATA); Facultad de Ciencias Veterinarias; Universidad Nacional de La Plata; Calle 60 y 118 s/n 1900 La Plata Argentina
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11
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Senju N, Tozaki T, Kakoi H, Shinjo A, Matsuyama R, Almunia J, Takasu M. Genetic diversity of the Yonaguni horse based on polymorphisms in microsatellites and mitochondrial DNA. J Vet Med Sci 2016; 79:425-431. [PMID: 28049866 PMCID: PMC5326952 DOI: 10.1292/jvms.16-0040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Thirty-two microsatellites and a mitochondrial DNA haplotypes of endangered Yonaguni
horses were analyzed to establish a pedigree registration system and to understand their
genetic diversity for planning effective conservation. Blood samples were collected from
78 of the 130 horses in existence, and DNA was extracted and genotyped. There were two
major findings. One is that it is possible to use microsatellites for Yonaguni horse
pedigree registration in the future because the power of exclusion of parentage testing is
reliable at 0.999998. The second is the clarification of the current genetic diversity of
Yonaguni horses. The average number of alleles, observed heterozygosity, expected
heterozygosity and fixation index were 4.4, 0.591, 0.601 and 0.016, respectively, for the
analyzed horses. The probability of a genetic bottleneck, under the assumptions of the
stepwise mutation model, was 0.432, suggesting that the genetic structure of the horses
was not influenced by a recent bottleneck. Genetic distance between individuals was
visualized by a phylogenetic tree based on the proportion of shared alleles. Structure
analysis based on Bayesian clustering revealed the possibility that Yonaguni horses
comprise four or five subpopulations. Consequently, although only two haplotypes were
identified in the mitochondrial analysis, genetic diversity of Yonaguni horses was not
particularly low in comparison with that of other breeds that are at risk of
extinction.
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Affiliation(s)
- Natsuko Senju
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University,1-1 Yanagido, Gifu 501-1193, Japan
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12
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Kasarda R, Vostrý L, Moravčíková N, Vostrá-Vydrová H, Dovč P, Kadlečík O. Detailed insight into genetic diversity of the Old Kladruber horse substructure in comparison to the Lipizzan breed. ACTA AGR SCAND A-AN 2016. [DOI: 10.1080/09064702.2016.1249400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- R. Kasarda
- Department of Animal Genetics and Breeding Biology, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - L. Vostrý
- Department of Genetics and Breeding, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - N. Moravčíková
- Department of Animal Genetics and Breeding Biology, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | | | - P. Dovč
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - O. Kadlečík
- Department of Animal Genetics and Breeding Biology, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
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13
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Negro S, Solé M, Pelayo R, Gómez M, Azor P, Valera M. Molecular diversity between two cohorts of six Spanish riding-horse breeds: Impact of selection in Crossbred vs Purebred populations. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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14
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Senju N, Tozaki T, Kakoi H, Almunia J, Maeda M, Matsuyama R, Takasu M. Genetic characterization of the Miyako horse based on polymorphisms of microsatellites and mitochondrial DNA. J Vet Med Sci 2016; 79:218-223. [PMID: 27795462 PMCID: PMC5289264 DOI: 10.1292/jvms.16-0111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
To help plan conservation of the endangered Miyako horse, a biological resource of the Miyako Islands in Japan, we characterized the genetics of the breed by
genotyping 32 microsatellites and identifying mitochondrial DNA haplotypes. We also calculated genetic distances between individuals based on the proportion of
shared alleles and visualized the genetic relationships with a phylogenetic tree. Two important results were obtained. One is that accurate pedigree
registration of the horse by using microsatellites is possible, as the exclusion power of parentage testing is 0.999998. Another is that the current genetic
diversity of the horses was clarified. The average number of alleles, observed heterozygosity and expected heterozygosity were 4.2, 0.701 and 0.649,
respectively, for the 35 analyzed horses. The probability values for bottleneck models (infinite allele model: 0.00000; stepwise mutation model: 0.00026; and
two-phase model: 0.00000) suggested that Miyako horses have experienced a recent genetic bottleneck. Only one mitochondrial haplotype was identified.
Consequently, genetic diversity within the population is relatively well-maintained despite a very small population size (41 at the time of the study), and the
first priority in conservation of the Miyako horse is to increase the population size.
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Affiliation(s)
- Natsuko Senju
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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15
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Stasiol LD, Perrotta G, Blasi M, Lisa C. Genetic characterization of the Bardigiano horse using microsatellite markers. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2008.243] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Elbeltagy A, Aboul-Naga A, Hassen H, Rischkowsky B, Mwacharo J. Genetic diversity and structure in Egyptian indigenous sheep populations mirror patterns of anthropological interactions. Small Rumin Res 2015. [DOI: 10.1016/j.smallrumres.2015.10.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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17
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Felicetti M, Lopes MS, Verini-Supplizi A, Machado ADC, Silvestrelli M, Mendonça D, Distl O. Genetic diversity in the Maremmano horse and its relationship with other European horse breeds. Anim Genet 2015; 41 Suppl 2:53-5. [PMID: 21070276 DOI: 10.1111/j.1365-2052.2010.02102.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Maremmano is an Italian warmblood horse breed from central Italy. We characterized the genetic diversity and the degree of admixture in Maremmano in comparison to 14 other European horse breeds using 30 microsatellites. Between-breed diversity explained about 9 per cent of the total genetic diversity. Cluster analysis, genetic distances and genetic differentiation coefficients showed a close relationship of Maremmano with Hanoverian and Lusitano in accordance with breed history.
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Affiliation(s)
- M Felicetti
- Department of Pathology, Diagnostic and Veterinary Clinic, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy
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18
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Delgado J, De Andrés N, Valera M, Gutiérrez J, Cervantes I. Assessment of population structure depending on breeding objectives in Spanish Arabian horse by genealogical and molecular information. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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19
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Genetic diversity and conservation in a small endangered horse population. J Appl Genet 2013; 54:285-92. [PMID: 23649723 DOI: 10.1007/s13353-013-0151-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 04/14/2013] [Accepted: 04/17/2013] [Indexed: 02/04/2023]
Abstract
The Old Kladruber horses arose in the 17th century as a breed used for ceremonial purposes. Currently, grey and black coat colour varieties exist as two sub-populations with different recent breeding history. As the population underwent historical bottlenecks and intensive inbreeding, loss of genetic variation is considered as the major threat. Therefore, genetic diversity in neutral and non-neutral molecular markers was examined in the current nucleus population. Fifty microsatellites, 13 single nucleotide polymorphisms (SNPs) in immunity-related genes, three mutations in coat colour genes and one major histocompatibility (MHC-DRA) gene were studied for assessing genetic diversity after 15 years of conservation. The results were compared to values obtained in a similar study 13 years ago. The extent of genetic diversity of the current population was comparable to other breeds, despite its small size and isolation. The comparison between 1997 and 2010 did not show differences in the extent of genetic diversity and no loss of allele richness and/or heterozygosity was observed. Genetic differences identified between the black and grey sub-populations observed 13 years ago persisted. Deviations from the Hardy-Weinberg equilibrium found in 19 microsatellite loci and in five SNP loci are probably due to selective breeding. No differences between neutral and immunity-related markers were found. No changes in the frequencies of markers associated with two diseases, melanoma and insect bite hypersensitivity, were observed, due probably to the short interval of time between comparisons. It, thus, seems that, despite its small size, previous bottlenecks and inbreeding, the molecular variation of Old Kladruber horses is comparable to other horse breeds and that the current breeding policy does not compromise genetic variation of this endangered population.
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20
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Genetic diversity and admixture among Canadian, Mountain and Moorland and Nordic pony populations. Animal 2013; 6:19-30. [PMID: 22436150 DOI: 10.1017/s1751731111001212] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
As part of the requirements of the Convention on Biological Diversity, Canada has been investigating the genetic diversity of its native equine and pony populations. Along with examining four indigenous Canadian equine populations (Canadian horse, Lac La Croix pony, Newfoundland pony and Sable Island population), another 10 Mountain and Moorland, three Nordic, four horse and two feral equine populations (thought to have influenced some pony breeds) were also investigated. In total, 821 individuals were genotyped at 38 microsatellite loci. Results of the analysis of molecular variance indicated that 13.3% of genetic diversity was explained by breed differences, whereas 84.6% and 2.1% of diversity came from within and among individuals, respectively. The average effective number of alleles and allelic richness was the lowest in the Eriskay (2.51 and 3.98) and Lac La Croix (2.83 and 4.01) populations, whereas it was highest in the New Forest (4.31 and 6.01) and Welsh (4.33 and 5.87) breeds, followed closely by the Newfoundland-CDN (4.23 and 5.86) population. Expected heterozygosities varied from 0.61 in the Lac La Croix to 0.74 in the Welsh and in Newfoundland. Observed heterozygosities ranged from 0.57 in the Exmoor and 0.58 in the Sable Island herd to 0.77 in the Kerry Bog and 0.76 in the New Forest breeds. Structure and admixture analyses revealed that the most likely number of clusters was 21, although some substructure was also observed when K = 16, compared with the 24 predefined populations. Information gathered from this study should be combined with other available phenotypic and pedigree data to develop, or amend, a suitable conservation strategy for all populations examined.
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Pirault P, Danvy S, Verrier E, Leroy G. Genetic structure and gene flows within horses: a genealogical study at the french population scale. PLoS One 2013; 8:e61544. [PMID: 23630596 PMCID: PMC3632587 DOI: 10.1371/journal.pone.0061544] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 03/11/2013] [Indexed: 11/21/2022] Open
Abstract
Since horse breeds constitute populations submitted to variable and multiple outcrossing events, we analyzed the genetic structure and gene flows considering horses raised in France. We used genealogical data, with a reference population of 547,620 horses born in France between 2002 and 2011, grouped according to 55 breed origins. On average, individuals had 6.3 equivalent generations known. Considering different population levels, fixation index decreased from an overall species FIT of 1.37%, to an average of −0.07% when considering the 55 origins, showing that most horse breeds constitute populations without genetic structure. We illustrate the complexity of gene flows existing among horse breeds, a few populations being closed to foreign influence, most, however, being submitted to various levels of introgression. In particular, Thoroughbred and Arab breeds are largely used as introgression sources, since those two populations explain together 26% of founder origins within the overall horse population. When compared with molecular data, breeds with a small level of coancestry also showed low genetic distance; the gene pool of the breeds was probably impacted by their reproducer exchanges.
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Affiliation(s)
- Pauline Pirault
- AgroParisTech, Unité Mixte de Recherche 1313 Génétique Animale et Biologie Intégrative, Paris, France
| | - Sophy Danvy
- Institut Français du Cheval et de l'Equitation, Le Pin au Haras, France
| | - Etienne Verrier
- AgroParisTech, Unité Mixte de Recherche 1313 Génétique Animale et Biologie Intégrative, Paris, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1313 Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
| | - Grégoire Leroy
- AgroParisTech, Unité Mixte de Recherche 1313 Génétique Animale et Biologie Intégrative, Paris, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1313 Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- * E-mail:
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Barcaccia G, Felicetti M, Galla G, Capomaccio S, Cappelli K, Albertini E, Buttazzoni L, Pieramati C, Silvestrelli M, Verini Supplizi A. Molecular analysis of genetic diversity, population structure and inbreeding level of the Italian Lipizzan horse. Livest Sci 2013. [DOI: 10.1016/j.livsci.2012.11.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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23
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Petersen JL, Mickelson JR, Cothran EG, Andersson LS, Axelsson J, Bailey E, Bannasch D, Binns MM, Borges AS, Brama P, da Câmara Machado A, Distl O, Felicetti M, Fox-Clipsham L, Graves KT, Guérin G, Haase B, Hasegawa T, Hemmann K, Hill EW, Leeb T, Lindgren G, Lohi H, Lopes MS, McGivney BA, Mikko S, Orr N, Penedo MCT, Piercy RJ, Raekallio M, Rieder S, Røed KH, Silvestrelli M, Swinburne J, Tozaki T, Vaudin M, M Wade C, McCue ME. Genetic diversity in the modern horse illustrated from genome-wide SNP data. PLoS One 2013; 8:e54997. [PMID: 23383025 PMCID: PMC3559798 DOI: 10.1371/journal.pone.0054997] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 12/20/2012] [Indexed: 11/18/2022] Open
Abstract
Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. F(ST) calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.
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Affiliation(s)
- Jessica L Petersen
- University of Minnesota, College of Veterinary Medicine, St Paul, MN, USA.
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24
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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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Khanshour AM, Juras R, Cothran EG. Microsatellite analysis of genetic variability in Waler horses from Australia. AUST J ZOOL 2013. [DOI: 10.1071/zo13062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Waler horse breed is an integral part of Australian history. The purposes of this study were to analyse the genetic variability in Waler horses from Australia and to investigate genetic relationships with other horse breeds. We examined the genetic diversity of 70 Waler horses sampled from seven breeding stations in Australia. Also we analysed the relationships of these horses with 11 other horse breeds. Analysis of the genetic structure was carried out using 15 microsatellite loci, genetic distances, AMOVA, factorial correspondence analysis and a Bayesian method. We found that the genetic diversity in the Waler was greater than the domestic horse mean and exceeded that of all endangered horse breeds. Our findings also revealed moderate population subdivision rather than inbreeding. All genetic similarity measures indicated that the Thoroughbred might be a key ancestor to the Waler. This study indicates that there is no immediate concern for loss of variation in Waler horses. Also, there clearly has been a strong input from the Thoroughbred into the Waler horse breed. However, the genetic evidence suggests that this input was not just direct but also came through other types of horses with a Thoroughbred cross background.
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Dumasy JF, Daniaux C, Donnay I, Baret PV. Genetic diversity and networks of exchange: a combined approach to assess intra-breed diversity. Genet Sel Evol 2012; 44:17. [PMID: 22620856 PMCID: PMC3406966 DOI: 10.1186/1297-9686-44-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 05/23/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cryopreservation of three endangered Belgian sheep breeds required to characterize their intra-breed genetic diversity. It is assumed that the genetic structure of a livestock breed depends mostly on gene flow due to exchanges between herds. To quantify this relation, molecular data and analyses of the exchanges were combined for three endangered Belgian breeds. METHODS For each breed, between 91 and 225 sheep were genotyped with 19 microsatellites. Genetic differentiations between breeds and among herds within a breed were evaluated and the genetic structure of the breeds was described using Bayesian clustering (Structure). Exchanges of animals between 20, 46 and 95 herds according to breed were identified via semi-directed interviews and were analyzed using the concepts of the network theory to calculate average degrees and shortest path lengths between herds. Correlation between the Reynolds' genetic distances and the shortest path lengths between each pair of herds was assessed by a Mantel test approach. RESULTS Genetic differentiation between breeds was high (0.16). Overall Fst values among herds were high in each breed (0.17, 0.11 and 0.10). Use of the Bayesian approach made it possible to identify genetic groups of herds within a breed. Significant correlations between the shortest path lengths and the Reynolds' genetic distances were found in each breed (0.87, 0.33 and 0.41), which demonstrate the influence of exchanges between herds on the genetic diversity. Correlation differences between breeds could be explained by differences in the average degree of the animal exchange networks, which is a measure of the number of exchanges per herd. The two breeds with the highest average degree showed the lowest correlation. Information from the exchange networks was used to assign individuals to the genetic groups when molecular information was incomplete or missing to identify donors for a cryobank. CONCLUSIONS A fine-scale picture of the population genetic structure at the herd level was obtained for the three breeds. Network analysis made it possible to highlight the influence of exchanges on genetic structure and to complete or replace molecular information in establishing a conservation program.
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Affiliation(s)
- Jean-François Dumasy
- Université catholique de Louvain, Institut des Sciences de la Vie, Embryologie moléculaire et cellulaire animale, Louvain-la-Neuve, Belgium.
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Piro M, Benjouad A, Karom A, Nabich A, Benbihi N, El Allali K, Machmoum M, Ouragh L. Genetic Structure of Severe Combined Immunodeficiency Carrier Horses in Morocco Inferred by Microsatellite Data. J Equine Vet Sci 2011. [DOI: 10.1016/j.jevs.2011.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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28
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Traoré A, Álvarez I, Tambourá H, Fernández I, Kaboré A, Royo L, Gutiérrez J, Sangaré M, Ouédraogo-Sanou G, Toguyeni A, Sawadogo L, Goyache F. Genetic characterisation of Burkina Faso goats using microsatellite polymorphism. Livest Sci 2009. [DOI: 10.1016/j.livsci.2008.11.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Padilla JÁ, Sansinforiano E, Parejo JC, Rabasco A, Martínez-Trancón M. Inference of admixture in the endangered Blanca Cacereña bovine breed by microsatellite analyses. Livest Sci 2009. [DOI: 10.1016/j.livsci.2008.09.016] [Citation(s) in RCA: 4] [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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30
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Microsatellite analysis of genetic diversity and population structure of Chinese mitten crab (Eriocheir sinensis). J Genet Genomics 2009; 35:171-6. [PMID: 18355760 DOI: 10.1016/s1673-8527(08)60023-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 07/12/2007] [Accepted: 07/12/2007] [Indexed: 11/22/2022]
Abstract
Chinese mitten crab (Eriocheir sinensis) has higher commercial value as food source than any other species of Eriocheir in China. To evaluate the germplasm resources and characterize the genetic diversity and population structure of the crabs in different water systems, two stocks and two farming populations were assessed with 25 polymorphic microsallite loci available in public GenBank. Basic statistics showed that the average observed heterozygosity (Ho) amongst populations ranged from 0.5789 to 0.6824. However, a remarkable presence of inbreeding and heterozygote deficiencies were observed. To analyze population structure, pairwise F(ST) coefficients explained only approximately 10.3% variability from the subdivision of mitten crab populations, the remaining variability stems from the subdivision within subpopulations. Although the four populations had slight differentiation, different allelic frequencies resulted in distinct population structures. Two stocks and one farming population were clustered together to the phylogenetic branch of Yangtze crab, with an approximate membership of 95%. Whereas, another farming population was clustered singly to the phylogenetic branch of the Liaohe crab, with a membership of 97.1%. The tests for individual admixture showed that Yangtze crab had probably been contaminated with individuals from other water systems. Genetic relationships between populations also supported the conclusion that Yangtze crab and Liaohe crab had different gene pools in spite of the origins of the same species.
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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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Thirstrup JP, Pertoldi C, Loeschcke V. Genetic analysis, breed assignment and conservation priorities of three native Danish horse breeds. Anim Genet 2008; 39:496-505. [PMID: 18840148 DOI: 10.1111/j.1365-2052.2008.01767.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A genetic analysis was performed on three indigenous Danish horse breeds using 12 microsatellite markers from a standard kit for parental testing. These three breeds are all considered endangered based on their small population sizes. Genetic variation in these three breeds was comparable to other horse breeds in Europe, and they do not seem to be at immediate danger of extinction caused by genetic deterioration. The Knabstrupper breed had more genetic variation, as measured by expected heterozygosity and allelic richness, than the other two breeds (Frederiksborg and Jutland). F(ST) statistics and population assignments confirmed population differentiation into three distinct breeds. The Frederiksborg and Knabstrupper breeds were closer to each other than to the Jutland breed. When establishing conservation priorities for the breeds, the priorities will depend on the conservation goals. Different methods for establishing conservation priorities are also discussed.
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Affiliation(s)
- J P Thirstrup
- Department of Biological Science, University of Aarhus, Ny Munkegade, DK, Denmark
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Abstract
Hispano-Breton (HB) is a horse breed with a recent mixed ancestry. It was developed in the 1930s by crossing local mares with Breton draught horses imported from France. Nowadays it is considered to be in a vulnerable situation due to census decline. To genetically characterize the breed and to set up the basis for a conservation programme, we have employed two types of molecular markers: a 347-bp D-loop mitochondrial DNA (mtDNA) fragment and 13 microsatellite loci. A representative sample of 53 HB individuals was analysed together with a sample of 40 Pura Raza Española horses for comparison. Both types of markers revealed a high level of genetic diversity in the HB breed, emphasizing the importance of its conservation. The construction of a phylogenetic network with mtDNA sequences including various Iberian breeds and European heavy horses provided an overall picture of the ubiquitous appearance of HB matrilines with respect to other breeds and revealed the singularity of certain HB maternal lineages. Despite the high allelic richness found in HB horses, microsatellite analysis evidenced a certain degree of inbreeding as a consequence of the type of management generally used for local breeds.
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Affiliation(s)
- L M Pérez-Gutiérrez
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
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Ćinkulov M, Tapio M, Ozerov M, Kiselyova T, Marzanov N, Pihler I, Olsaker I, Vegara M, Kantanen J. Genetic differentiation between the Old and New types of SerbianTsigaisheep. Genet Sel Evol 2008. [DOI: 10.1051/gse:2008006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Vijh RK, Tantia MS, Mishra B, Kumar STB. Genetic diversity and differentiation of dromedarian camel of India. Anim Biotechnol 2008; 18:81-90. [PMID: 17453647 DOI: 10.1080/10495390600648741] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Estimation of genetic variability and relationship among different livestock breeds is important for management of genetic resources for their sustainable utilization and conservation. This is more important when the livestock species, like camel, have shown a sharp decline in head count during the last decade. In the present study we estimated genetic variability and relationship among four camel breeds of India using 23 microsatellite loci. A total of 252 alleles were observed across all the four populations with mean number of alleles per locus as 8.04, 7.30, 6.39, and 7.43 for Bikaneri, Jaisalmeri, Kutchi, and Mewari breeds, respectively. The mean observed heterozygosity of the four breeds were 0.58, 0.57, 0.56, and 0.60 for Bikaneri, Jaisalmeri, Kutchi, and Mewari breeds, respectively and were lower than expected heterozygosity values. The mean estimates of F statistics were 0.227+/-0.044 (F(IT)), 0.157+/-0.038 (F(IS)), and 0.082+/-0.019 (F(ST)). The values were significantly different from zero for all the three measures and point towards the existence of population structure and moderate differentiation in four camel breeds. The exact test also indicated significant population differentiation (P < 0.001). The analysis of molecular variance revealed 12% of the variation attributed to among populations and 88% within populations. Sixty-nine percent of the individuals could be correctly assigned using "leave one out" procedure. All the individuals of Mewari and 42 out of 44 Jaisalmeri were correctly assigned. The existence of strong population structure in Jaisalmeri and Mewari camel was further substantiated by Nei's standard genetic distance as well as interindividual allele sharing distance. Thus these two breeds owing to selection for specific traits are distinct from other camel breeds.
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Affiliation(s)
- R K Vijh
- Division of Animal Genetics, National Bureau of Animal Genetic Resources, Karnal, Haryana, India.
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36
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Reis SP, Gonçalves EC, Silva A, Schneider MP. Genetic variability and efficiency of DNA microsatellite markers for paternity testing in horse breeds from the Brazilian Marajó archipelago. Genet Mol Biol 2008. [DOI: 10.1590/s1415-47572008000100014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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37
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Genetic diversity and admixture analysis of Sanfratellano and three other Italian horse breeds assessed by microsatellite markers. Animal 2008; 2:991-8. [DOI: 10.1017/s1751731108002255] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Javier Azor P, Valera M, Gómez MD, Goyache F, Molina A. Genetic characterization of the Spanish Trotter horse breed using microsatellite markers. Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000100009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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39
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40
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Behl R, Behl J, Gupta N, Gupta SC, Ahlawat SPS, Ragnekar M, Ahmed Z. Genetic characterization of Zanskari breed of horse. J Genet 2006; 85:199-203. [PMID: 17406094 DOI: 10.1007/bf02935331] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Rahul Behl
- National Bureau of Animal Genetic Resources, P.O. Box 129, GT By-Pass Road, Karnal 132 001, India.
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Jones BW, Lopez JE, Huttenburg J, Nishiguchi MK. Population structure between environmentally transmitted vibrios and bobtail squids using nested clade analysis. Mol Ecol 2006; 15:4317-29. [PMID: 17107468 DOI: 10.1111/j.1365-294x.2006.03073.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Squids from the genus Euprymna (Cephalopoda: Sepiolidae) and their symbiotic bacteria Vibrio fischeri form a mutualism in which vibrios inhabit a complex light organ within the squid host. A host-mediated daily expulsion event seeds surrounding seawater with symbiotically capable V. fischeri that environmentally colonize newly hatched axenic Euprymna juveniles. Competition experiments using native and non-native Vibrio have shown that this expulsion/re-colonization phenomenon has led to cospeciation in this system in the Pacific Ocean; however, the genetic architecture of these symbiotic populations has not been determined. Using genetic diversity and nested clade analyses we have examined the variation and history of three allopatric Euprymna squid species (E. scolopes of Hawaii, E. hyllebergi of Thailand, and E. tasmanica from Australia) and their respective Vibrio symbionts. Euprymna populations appear to be very genetically distinct from each other, exhibiting little or no migration over large geographical distances. In contrast, Vibrio symbiont populations contain more diverse haplotypes, suggesting both host presence and unidentified factors facilitating long-distance migration structure in Pacific Vibrio populations. Findings from this study highlight the importance of how interactions between symbiotic organisms can unexpectedly shape population structure in phylogeographical studies.
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Affiliation(s)
- B W Jones
- Department of Biology, MSC 3AF, New Mexico State University, PO Box 30001, Las Cruces, NM 88003-8001, USA
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42
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Druml T, Curik I, Baumung R, Aberle K, Distl O, Sölkner J. Individual-based assessment of population structure and admixture in Austrian, Croatian and German draught horses. Heredity (Edinb) 2006; 98:114-22. [PMID: 17035951 DOI: 10.1038/sj.hdy.6800910] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
All over Europe, the number of draught horses has decreased drastically during the last 50 years. As a prerequisite for efficient management decisions, we analysed the conservation status in Austrian (Noriker Carinthia - NC, Noriker Salzburg - NS), Croatian (Croatian Coldblood - C, Posavina horse - P) and German (Altmaerkisch Coldblood - A, Black Forest horse - BF, Mecklenburg Coldblood - M, Rhenish German Draught horse - R, Saxon Thuringa Coldblood - ST, Schleswig Draught horse - Sch, South German Coldblood - SG) draught horses (434) using multilocus genotypic information from 30 (effectively 27) microsatellite loci. Populations located in areas with less intensive agricultural production (C, NC, NS, P and SG) had greater diversity within the population and estimated effective population size than A, BF, Sch, M, R and ST populations. The PCA plots revealed that populations form five separate groups. The 'Noriker' group (NC, NS and SG) and the 'Rhenish' group (A, M, R and ST) were the most distinctive (pairwise F(ST) values ranged from 0.078 to 0.094). The 'Croatian' group (C and P) was in the centre, while the BF and Sch populations formed two out-groups. A posterior Bayesian analysis detected further differentiation, mainly caused by political and geographical factors. Thus, it was possible to separate the South German Coldblood from the Austrian Noriker population where no subpopulation structure was detected. The admixture analysis revealed imprecise classification between C and P populations. A small but notable separation of R from A, M and ST populations was detected, while Sch and BF populations remained as out-groups. The information obtained should aid in making efficient conservation decisions.
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Affiliation(s)
- T Druml
- BOKU - University of Natural Resources and Applied Life Sciences Vienna, Vienna, Austria
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Marletta D, Tupac-Yupanqui I, Bordonaro S, García D, Guastella AM, Criscione A, Cañón J, Dunner S. Analysis of genetic diversity and the determination of relationships among western Mediterranean horse breeds using microsatellite markers. J Anim Breed Genet 2006; 123:315-25. [PMID: 16965404 DOI: 10.1111/j.1439-0388.2006.00603.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The distribution of genetic diversity and the genetic relationships among western Mediterranean horse breeds were investigated using microsatellite markers. The examined sample included seven Spanish and three Italian local horse breeds and populations, plus a Spanish Thoroughbred outgroup. The total number of animals examined was 682 (on average 62 animals per breed; range 20-122). The microsatellite marker set analysed provided 128 alleles (10.7 alleles per locus). Within-breed genetic diversity was always high (>0.70), with breeds contributing about 8% of the total genetic variability. The mean molecular coancestry of the entire population examined was 0.205, Losino being the breed that contributed most. In addition to Nei's standard and Reynolds' genetic distances, pair-wise kinship distance and molecular coancestry were estimated. Remarkably similar breed rankings were obtained with all methods. Clustering analysis provided an accurate representation of the current genetic relationships among the breeds. Determining coancestry is useful for analysing genetic diversity distribution between and within breeds and provides a good framework for jointly analysing molecular markers and pedigree information. An integrated analysis was undertaken to obtain information on the population dynamics in western Mediterranean native horse populations, and to better determine conservation priorities.
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Affiliation(s)
- D Marletta
- DACPA, Sez. di Scienze delle Produzioni Animali, Facoltà di Agraria, Università degli studi di Catania, Catania, Italy.
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Abstract
The development and a brief history of the Lipizzan horse breed are reviewed. The contribution of several breeds, some of them already extinct, to the development of the Lipizzan horse, gives it a special status representing an important gene pool. This well-documented breed is a part of the common European natural and cultural heritage. Breeding practices establishing stallion and mare family lines as well as availability of pedigrees are described. Molecular analysis of mitochondrial DNA (mtDNA) and microsatellite data allowed us to analyse the structure of the Lipizzan population, to estimate genetic variability within the population and to test the reliability of the pedigree data. DNA sequence analysis of the mtDNA control region confirmed relative high variability of the gene pool, containing majority of mtDNA haplotypes found in horse populations worldwide. Microsatellite analysis showed that the level of heterozygosity in the Lipizzan population is comparable with the heterozygosity in other populations. The fact that majority of the Lipizzan population is bred on eight state studs in the Central and Eastern Europe contributes to the structuring of the population which results in three clusters: classical cluster, represented by studs Lipica, Piber and Monterotondo, transition cluster, represented by studs Szilvasvarad, Djakovo and Topolćianky and eastern cluster represented by studs Beclean and Fagaras. The molecular markers also allowed verification of pedigree data, and the rough estimation of pedigree errors was about 10%.
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Affiliation(s)
- P Dovc
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
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Genetic closeness of Zanskari and Spiti ponies of India inferred through microsatellite markers. J Equine Vet Sci 2006. [DOI: 10.1016/j.jevs.2006.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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46
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Analysis and Selection of Microsatellites Markers for Individual Traceability System in Hanwoo. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2005. [DOI: 10.5187/jast.2005.47.4.491] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Ibeagha-Awemu EM, Erhardt G. Genetic structure and differentiation of 12 African Bos indicus and Bos taurus cattle breeds, inferred from protein and microsatellite polymorphisms. J Anim Breed Genet 2005; 122:12-20. [PMID: 16130484 DOI: 10.1111/j.1439-0388.2004.00478.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Level of genetic differentiation, gene flow and genetic structuring of nine Bos indicus and three Bos taurus cattle breeds in Cameroon and Nigeria were estimated using the genetic information from 16 microsatellite, five blood protein and seven milk protein markers. The global heterozygote deficit across all populations (Fit) amounted to 11.7% (p < 0.001). The overall significant (p < 0.001) deficit of heterozygotes because of inbreeding within breeds (Fis) amounted to 6.1%. The breeds were moderately differentiated (Fst = 6%, p < 0.001) with all loci except CSN1S2 contributing significantly to the Fst value. The 12 populations belong to two genetic clusters, a zebu and a taurine cluster. While inferred sub-clusters within the taurine group corresponded extremely well to predefined breed categorizations, no real sub-clusters, corresponding to predefined breeds, existed within the zebu cluster. With the application of prior population information, cluster analysis achieved posterior probabilities from 0.962 to 0.994 of correctly assigning individuals to their rightful populations. High gene flow was evident between the zebu populations. Positive and negative implications of the observed genetic structure of the breeds on their development, improvement and conservation are discussed. The study shows that the breeds are threatened by uncontrolled breeding and therefore are at risk to become genetically uniform in the future. This situation can be avoided by putting in place effective breeding and management measures aimed at limiting uncontrolled mating between the breeds and to preserve special characteristics, genetic as well as breed biodiversity. The first step towards realizing these goals might be to geographically demarcate the breeds.
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Affiliation(s)
- E M Ibeagha-Awemu
- Institut für Tierzucht und Haustiergenetik, Justus-Liebig Universität Giessen, Giessen, Germany
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48
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