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Voronkova VN, Nikolaeva EA, Piskunov AK, Babayan OV, Takasu M, Tozaki T, Svishcheva GR, Stolpovsky YA. Assessment of Genetic Diversity and Structure of Russian and Mongolian Autochthonous Horse Breeds Using Nuclear and Mitochondrial DNA Markers. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422080105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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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Amano T, Tozaki T, Takasu M, Onogi A, Yamada F, Kawai M, Ueda J. Changes of sires in a breeding farm enables maintenance of DNA-level genetic variation in a produced herd of Hokkaido Native Horses. Anim Sci J 2019; 91:e13318. [PMID: 31755177 DOI: 10.1111/asj.13318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/06/2019] [Accepted: 10/23/2019] [Indexed: 11/29/2022]
Abstract
We investigated whether regular changes of the sire in a breeding farm of Hokkaido Native Horses (HKDs) enables the DNA-level genetic variation of the produced animals to be maintained. The genotypes of 31 microsatellite markers were identified and analyzed in 207 animals produced in a breeding farm in which the sire was replaced every 3 to 5 years. The mean allele number indicating the degree of genetic variation was 5.97 and was similar to those reported previously. The mean observed heterozygosity was 0.74 and was higher than the expected heterozygosity, 0.69; FIS was -0.07, indicating that the analyzed animals reflected frequent outbreeding and had maintained genetic variation. Based on genetic structural analysis, the number of genetic subpopulations of the animals was estimated to be as 6, and the majority (more than 50%) of each subpopulation corresponded to the progeny of one of the sires used in the breeding farm; these observations suggested that genetic variation in the analyzed animals reflected the genetic differences among sires. Pedigree records indicated that the average co-ancestry coefficient between sires used in the breeding farm was 0.015 corresponding to second cousin. This level of kinship among sires is acceptable for producing HKDs that maintain genetic variation.
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Affiliation(s)
- Tomoko Amano
- College of Agriculture, Food and Environment Sciences, Department of Sustainable Agriculture, Laboratory of Animal Genetics, Rakuno Gakuen University, Hokkaido, Japan
| | - Teruaki Tozaki
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi, Japan.,Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Masaki Takasu
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Akio Onogi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Fumihiro Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Masahito Kawai
- Field Science Center for Northern Biosphere, Hokkaido University, Hokkaido, Japan
| | - Junji Ueda
- College of Agriculture, Food and Environment Sciences, Department of Sustainable Agriculture, Laboratory of Animal Genetics, Rakuno Gakuen University, Hokkaido, Japan
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Genetic diversity of Estonian horse breeds and their genetic affinity to northern European and some Asian breeds. Livest Sci 2019. [DOI: 10.1016/j.livsci.2018.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Cosenza M, La Rosa V, Rosati R, Chiofalo V. Genetic diversity of the Italian thoroughbred horse population. ITALIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1080/1828051x.2018.1547128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Mario Cosenza
- Laboratorio di Genetica Forense Veterinaria, Unirelab srl, Settimo Milanese, Milano, Italy
| | - Valentina La Rosa
- Laboratorio di Genetica Forense Veterinaria, Unirelab srl, Settimo Milanese, Milano, Italy
| | - Raffaella Rosati
- Laboratorio di Genetica Forense Veterinaria, Unirelab srl, Settimo Milanese, Milano, Italy
| | - Vincenzo Chiofalo
- Laboratorio di Genetica Forense Veterinaria, Unirelab srl, Settimo Milanese, Milano, Italy
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Putnová L, Štohl R, Vrtková I. Genetic monitoring of horses in the Czech Republic: A large-scale study with a focus on the Czech autochthonous breeds. J Anim Breed Genet 2018; 135:73-83. [PMID: 29345072 DOI: 10.1111/jbg.12313] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 12/07/2017] [Indexed: 10/18/2022]
Abstract
We propose the first comprehensive in-depth study monitoring horses in the Czech Republic. We scanned 9,289 animals from 44 populations for 17 equine STRs. Other equids analysed involved Equus przewalskii and Equus asinus. The total of 228 different alleles were detected, with the mean number of 13.4 per locus. The highest allelic richness (AR) was found in the Welsh Part Bred (6.01), followed by the Camargue (5.93) and Czech Sport Pony (5.91), whereas the Friesian exhibited the lowest AR (3.06). Interpopulation differences explained approximately nine per cent of the total genetic diversity. Reynold's genetic distance ranged from 0.003 between the Czech Warmblood and the Slovak Warmblood to 0.404 between the Friesian and donkeys. Close genetic proximity between the Silesian Noriker and Noriker was revealed. The Moravian Warmblood was better differentiated and more distant from the Czech Warmblood than the Kinsky Horse and retained the original genes of the old Austro-Hungarian tribes. A high gene flow level and a lack of genetic structure were found in the seven studied populations. Despite the historical bottlenecks and previous inbreeding, the Czech-Moravian Belgian Horse, Hucul, Old Kladruber Horse and Silesian Noriker did not suffer a serious loss of genetic diversity due to genetic drift/low effective population size. A NeighborNet dendrogram revealed breeds not classified in their groups according to the nomenclature (the Friesian, Hafling and Merens).
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Affiliation(s)
- L Putnová
- Laboratory of Agrogenomics, Department of Morphology, Physiology and Animal Genetics, Faculty of Agronomy, Mendel University in Brno, Brno, Czech Republic
| | - R Štohl
- Department of Control and Instrumentation, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - I Vrtková
- Laboratory of Agrogenomics, Department of Morphology, Physiology and Animal Genetics, Faculty of Agronomy, Mendel University in Brno, Brno, Czech Republic
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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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Cortés O, Dunner S, Gama LT, Martínez AM, Delgado JV, Ginja C, Jiménez LM, Jordana J, Luis C, Oom MM, Sponenberg DP, Zaragoza P, Vega-Pla JL. The legacy of Columbus in American horse populations assessed by microsatellite markers. J Anim Breed Genet 2017; 134:340-350. [PMID: 28194814 DOI: 10.1111/jbg.12255] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 12/21/2016] [Indexed: 11/27/2022]
Abstract
Criollo horse populations descend from horses brought from the Iberian Peninsula over the period of colonization (15th to 17th century). They are spread throughout the Americas and have potentially undergone genetic hybridization with other breeds in the recent past. In this study, 25 autosomal microsatellites were genotyped in 50 horse breeds representing Criollo populations from 12 American countries (27 breeds), breeds from the Iberian Peninsula (19), one breed each from France and Morocco and two cosmopolitan horse breeds (Thoroughbred and Arabian). The genetic relationships among breeds identified five clusters: Celtic; Iberian; North American with Thoroughbred influence; most Colombian breeds; and nearly all other Criollo breeds. The group of "all other Criollo breeds" had the closest genetic relationship with breeds originating from the Iberian Peninsula, specifically with the Celtic group. For the whole set of Criollo breeds analysed, the estimated genetic contribution from other breeds was approximately 50%, 30% and 20% for the Celtic, Iberian and Arab-Thoroughbred groups, respectively. The spatial distribution of genetic diversity indicates that hotspots of genetic diversity are observed in populations from Colombia, Ecuador, Brazil, Paraguay and western United States, possibly indicating points of arrival and dispersion of Criollo horses in the American continent. These results indicate that Criollo breeds share a common ancestry, but that each breed has its own identity.
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Affiliation(s)
- O Cortés
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - S Dunner
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - L T Gama
- CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - A M Martínez
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - J V Delgado
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - C Ginja
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do Porto, Vairão, Portugal
| | - L M Jiménez
- Departamento de Producción Animal, Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia Sede Bogotá, Bogota, Columbia
| | - J Jordana
- Departamento de Ciencia Animal y de los Alimentos, Facultad de Veterinaria, Bellaterra, Spain
| | - C Luis
- Centro Interuniversitário de História das Ciências e da Tecnologia (CIUHCT), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.,Museu Nacional de História Natural e da Ciência (MUHNAC), Universidade de Lisboa, Lisboa, Portugal.,CIES-UL, Instituto Universitário de Lisboa (ISCTE-IUL), Lisboa, Portugal
| | - M M Oom
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - D P Sponenberg
- Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - P Zaragoza
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | | | - J L Vega-Pla
- Laboratorio de Investigación Aplicada, Crıa Caballar de las Fuerzas Armadas, Cordoba, Spain
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Seo JH, Park KD, Lee HK, Kong HS. Genetic diversity of Halla horses using microsatellite markers. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2016; 58:40. [PMID: 27891245 PMCID: PMC5114825 DOI: 10.1186/s40781-016-0120-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 10/17/2016] [Indexed: 12/04/2022]
Abstract
BACKGROUND Currently about 26,000 horses are breeding in Korea and 57.2% (14,776 horses) of them are breeding in Jeju island. According to the statistics published in 2010, the horses breeding in Jeju island are subdivided into Jeju horse (6.1%), Thoroughbred (18.8%) and Halla horse (75.1%). Halla horses are defined as a crossbreed between Jeju and Thoroughbred horses and are used for horse racing, horse riding and horse meat production. However, little research has been conducted on Halla horses because of the perception of crossbreed and people's weighted interest toward Jeju horses. METHOD Using 17 Microsatellite (MS) Markers recommended by International Society for Animal Genetics (ISAG), genomic DNAs were extracted from the hair roots of 3,880 Halla horses breeding in Korea and genetic diversity was identified by genotyping after PCR was performed. RESULTS AND CONCLUSION In average, 10.41 alleles (from 6 alleles in HTG7 to 17 alleles in ASB17) were identified after the analysis using 17 MS Markers. The mean value of Hobs was 0.749 with a range from 0.612(HMS1) to 0.857(ASB2). Also, it was found that Hexp and PIC values were lowest in HMS1 (0.607 and 0.548, respectively), and highest in LEX3(0.859 and 0.843, respectively), and the mean value of Hexp was 0.760 and that of PIC was 0.728. 17 MS markers used in this studies were considered as appropriate markers for the polymorphism analysis of Halla horses. The frequency for the appearance of identical individuals was 5.90 × 10-20 when assumed as random mating population and when assumed as half-sib and full-sib population, frequencies were 4.08 × 10-15 and 3.56 × 10-8, respectively. Based on these results, the 17 MS markers can be used adequately for the Individual Identification and Parentage Verification of Halla horses. Remarkably, allele M and Q of ASB23 marker, G of HMS2 marker, H and L of HTG6 marker, L of HTG7 marker, E of LEX3 marker were the specific alleles unique to Halla horses.
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Affiliation(s)
- Joo-Hee Seo
- Genomic Informatics Center, Hankyong National University, Anseong, 17579 Korea
- Department of Genomic Informatics, Graduate School of Future Convergence Technology, Hankyong National University, Anseong, 456-749 Korea
| | | | - Hak-Kyo Lee
- ChonBuk National University, Jeonju, 54896 Korea
| | - Hong-Sik Kong
- Genomic Informatics Center, Hankyong National University, Anseong, 17579 Korea
- Department of Genomic Informatics, Graduate School of Future Convergence Technology, Hankyong National University, Anseong, 456-749 Korea
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Pablo Gómez M, Landi V, Martínez AM, Gómez Carpio M, Nogales Baena S, Delgado Bermejo JV, Oom MDM, Luis C, Ouragh L, Vega-Pla JL. Genetic diversity of the semi-feral Marismeño horse breed assessed with microsatellites. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.1080/1828051x.2016.1241132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | - Vincenzo Landi
- Departamento de Genética, University of Cordoba, Córdoba, Spain
| | | | | | | | | | - María do Mar Oom
- Centro de Biologia Ambiental, University of Lisboa, Lisboa, Portugal
| | - Cristina Luis
- Centro Interuniversitário de História das Ciências e da Tecnologia, University of Lisboa, Lisboa, Portugal
- Museu Nacional de História Natural e da Ciência, University of Lisboa, Lisboa, Portugal
| | | | - José Luis Vega-Pla
- Laboratorio de Investigación Aplicada, Ministerio de Defensa, Cordoba, Spain
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Yaro M, Munyard KA, Stear MJ, Groth DM. Molecular identification of livestock breeds: a tool for modern conservation biology. Biol Rev Camb Philos Soc 2016; 92:993-1010. [DOI: 10.1111/brv.12265] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 02/14/2016] [Accepted: 02/18/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Mohammed Yaro
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
| | - Kylie A. Munyard
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
| | - Michael J. Stear
- Institute of Biodiversity, Animal Health and Comparative Medicine; University of Glasgow; Bearsden Road Glasgow G61 1QH U.K
| | - David M. Groth
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
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Dalvit C, Zanetti E, Cassandro M. Estimation of genetic diversity over time in an in-situ marker assisted conservation scheme of local chicken breeds. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2009.s2.63] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Chiara Dalvit
- Dipartimento di Scienze Animali, Università di Padova, Italy
| | - Enrico Zanetti
- Dipartimento di Scienze Animali, Università di Padova, Italy
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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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Ivanković A, Ramljak J, Dovč P, Kelava N, Konjačić M. Genetic structure of three Croatian horse breeds: implications for their conservation strategy. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2009.677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ciampolini R, Cecchi F, Bramante A, Casetti F, Presciuttini S. Genetic variability of the Bracco Italiano dog breed based on microsatellite polimorphism. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2011.e59] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Roberta Ciampolini
- Dipartimento di Patologia Animale Profilassi ed Igiene degli Alimenti, Università di Pisa, Italy
| | - Francesca Cecchi
- Dipartimento di Patologia Animale Profilassi ed Igiene degli Alimenti, Università di Pisa, Italy
| | - Assunta Bramante
- Dipartimento di Patologia Animale Profilassi ed Igiene degli Alimenti, Università di Pisa, Italy
| | - Fabio Casetti
- Società Amatori Bracco Italiano, Mirabello di Senna Lodigiana (LO), Italy
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Matassino D, Cecchi F, Ciani F, Incoronato C, Occidente M, Santoro L, Ciampolini R. Genetic Diversity and Variability in two Italian Autochthonous Donkey Genetic Types Assessed by Microsatellite Markers. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2014.3028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Al-Mamun HA, Clark SA, Kwan P, Gondro C. Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep. Genet Sel Evol 2015; 47:90. [PMID: 26602211 PMCID: PMC4659207 DOI: 10.1186/s12711-015-0169-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 11/02/2015] [Indexed: 01/23/2023] Open
Abstract
Background Knowledge of the genetic structure and overall diversity of livestock species is important to maximise the potential of genome-wide association studies and genomic prediction. Commonly used measures such as linkage disequilibrium (LD), effective population size (Ne), heterozygosity, fixation index (FST) and runs of homozygosity (ROH) are widely used and help to improve our knowledge about genetic diversity in animal populations. The development of high-density single nucleotide polymorphism (SNP) arrays and the subsequent genotyping of large numbers of animals have greatly increased the accuracy of these population-based estimates. Methods In this study, we used the Illumina OvineSNP50 BeadChip array to estimate and compare LD (measured by r2 and D′), Ne, heterozygosity, FST and ROH in five Australian sheep populations: three pure breeds, i.e., Merino (MER), Border Leicester (BL), Poll Dorset (PD) and two crossbred populations i.e. F1 crosses of Merino and Border Leicester (MxB) and MxB crossed to Poll Dorset (MxBxP). Results Compared to other livestock species, the sheep populations that were analysed in this study had low levels of LD and high levels of genetic diversity. The rate of LD decay was greater in Merino than in the other pure breeds. Over short distances (<10 kb), the levels of LD were higher in BL and PD than in MER. Similarly, BL and PD had comparatively smaller Ne than MER. Observed heterozygosity in the pure breeds ranged from 0.3 in BL to 0.38 in MER. Genetic distances between breeds were modest compared to other livestock species (highest FST = 0.063) but the genetic diversity within breeds was high. Based on ROH, two chromosomal regions showed evidence of strong recent selection. Conclusions This study shows that there is a large range of genome diversity in Australian sheep breeds, especially in Merino sheep. The observed range of diversity will influence the design of genome-wide association studies and the results that can be obtained from them. This knowledge will also be useful to design reference populations for genomic prediction of breeding values in sheep. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0169-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Samuel A Clark
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.
| | - Paul Kwan
- School of Science and Technology, University of New England, Armidale, NSW, 2351, Australia.
| | - Cedric Gondro
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.
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Abstract
Salernitano (SAL) is an ancient Italian horse breed developed over the course of the ages together with Napoletano and, during the 20th century, by crossing with Thoroughbred horse lines. Excellent in hurdle jumping, this breed is currently facing a concrete risk of extinction due to the lack of appropriate management strategies. This research is the first SAL genetic characterization that aims to set up the basic knowledge for a conservation plan. A representative sample of 61 SALs was analyzed by means of a set of 16 microsatellites markers (short tandem repeats (STRs)). The sequence of hypervariable D-loop mtDNA region was also performed on a subset of 24 mares in order to study the maternal diversity and obtain a complete picture of the internal genetic variation. All the molecular data were analyzed together with those obtained from three Sicilian horse breeds investigated in a previous research (Siciliano, Sanfratellano and Sicilian Oriental Purebred). STRs markers revealed a moderate level of genetic diversity in SAL (alleles/locus 5.1, He 0.67) and confirmed the hunch of genetic erosion. Autosomal variability highlighted a very light deficit of homozygotes (FIS=-0.067). Experimental D-loop sequences were compared by multiple alignments with those retrieved from biological databases and revealed two unreported haplotypes. The phylogenetic network, which was built on mtDNA sequences, included various cosmopolitan and European horses and showed SAL haplotypes distributed among different mtDNA lineages.
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Ciampolini R, Cecchi F, Paci G, Policardo C, Spaterna A. Investigation on the genetic variability of the american Pit Bull Terrier dogs belonging to an Italian breeder using microsatellite markers and genealogical data. CYTOL GENET+ 2013. [DOI: 10.3103/s009545271304004x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Khanshour A, Conant E, Juras R, Cothran EG. Microsatellite Analysis of Genetic Diversity and Population Structure of Arabian Horse Populations. J Hered 2013; 104:386-98. [DOI: 10.1093/jhered/est003] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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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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22
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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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23
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Bigi D, Perrotta G. Genetic structure and differentiation of the Italian catria horse. ACTA ACUST UNITED AC 2012; 103:134-9. [PMID: 22156056 DOI: 10.1093/jhered/esr121] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Catria is 1 of the 22 native Italian horse breeds that now survive from a larger number. Thirty individuals, representative of the Catria horse, were analyzed for 11 microsatellites and compared with data of 10 breeds reared in Italy. Three different approaches, genetic distances, correspondence analysis, and clustering methods, were considered to study genetic relationships among Catria and the other horse populations. Genetic differentiation among breeds was highly significant (P < 0.01) for all loci. Average F(ST) values indicate that around 10% of the total genetic variation was explained by the between-breed differences and the 3 approaches utilized gave similar results. Italian native breeds are clearly separated from the other examined breeds. However, by the correspondence analysis, the Catria appears closer to Maremmano and Murgese. The results of Bayesian approaches give further information showing for Catria a common origin with Maremmano and Italian Heavy Draught. Genetic relationships among Catria and the other breeds are consistent with the breed's documented history. The data and information found here can be utilized in the organization of conservation programmes planned to reduce inbreeding and to minimize loss of genetic variability.
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Affiliation(s)
- Daniele Bigi
- Dipartimento di Protezione e Valorizzazione Agroalimentare(DIPROVAL)-Sezione Allevamenti Zootecnici, Faculty of Agriculture, University of Bologna, Via F.lli Rosselli 107, 42123 Reggio Emilia, Italy.
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24
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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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25
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Koban E, Denizci M, Aslan O, Aktoprakligil D, Aksu S, Bower M, Balcioglu BK, Ozdemir Bahadir A, Bilgin R, Erdag B, Bagis H, Arat S. High microsatellite and mitochondrial diversity in Anatolian native horse breeds shows Anatolia as a genetic conduit between Europe and Asia. Anim Genet 2011; 43:401-9. [PMID: 22497212 DOI: 10.1111/j.1365-2052.2011.02285.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The horse has been a food source, but more importantly, it has been a means for transport. Its domestication was one of the crucial steps in the history of human civilization. Despite the archaeological and molecular studies carried out on the history of horse domestication, which would contribute to conservation of the breeds, the details of the domestication of horses still remain to be resolved. We employed 21 microsatellite loci and mitochondrial control region partial sequences to analyse genetic variability within and among four Anatolian native horse breeds, Ayvacık Pony, Malakan Horse, Hınıs Horse and Canik Horse, as well as samples from indigenous horses of unknown breed ancestry. The aims of the study were twofold: first, to produce data from the prehistorically and historically important land bridge, Anatolia, in order to assess its role in horse domestication and second, to analyse the data from a conservation perspective to help the ministry improve conservation and management strategies regarding native horse breeds. Even though the microsatellite data revealed a high allelic diversity, 98% of the genetic variation partitioned within groups. Genetic structure did not correlate with a breed or geographic origin. High diversity was also detected in mtDNA control region sequence analysis. Frequencies of two haplogroups (HC and HF) revealed a cline between Asia and Europe, suggesting Anatolia as a probable connection route between the two continents. This first detailed genetic study on Anatolian horse breeds revealed high diversity among horse mtDNA haplogroups in Anatolia and suggested Anatolia's role as a conduit between the two continents. The study also provides an important basis for conservation practices in Turkey.
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Affiliation(s)
- E Koban
- TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Institute, Kocaeli, Turkey
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26
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Zanetti E, De Marchi M, Abbadi M, Cassandro M. Variation of genetic diversity over time in local Italian chicken breeds undergoing in situ conservation. Poult Sci 2011; 90:2195-201. [DOI: 10.3382/ps.2011-01527] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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27
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Guastella AM, Zuccaro A, Criscione A, Marletta D, Bordonaro S. Genetic analysis of Sicilian autochthonous horse breeds using nuclear and mitochondrial DNA markers. ACTA ACUST UNITED AC 2011; 102:753-8. [PMID: 21914666 DOI: 10.1093/jhered/esr091] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Genetic diversity and relationship among 3 Sicilian horse breeds were investigated using 16 microsatellite markers and a 397-bp length mitochondrial D-loop sequence. The analysis of autosomal DNA was performed on 191 horses (80 Siciliano [SIC], 61 Sanfratellano [SAN], and 50 Sicilian Oriental Purebred [SOP]). SIC and SAN breeds were notably higher in genetic variability than the SOP. Genetic distances and cluster analysis showed a close relationship between SIC and SAN breeds, as expected according to the breeds' history. Sequencing of hypervariable mitochondrial DNA region was performed on a subset of 60 mares (20 for each breed). Overall, 20 haplotypes with 31 polymorphic sites were identified: A higher haplotype diversity was detected in SIC and SAN breeds, with 13 and 11 haplotypes respectively, whereas only one haplotype was found in SOP. These were compared with 118 sequences from GenBank. BLAST showed that 17 of the 20 haplotypes had been reported previously in other breeds. One haplotype, found in SIC, traces back to a Bronze Age archaeological site (Inner Mongolia). The 3 Sicilian breeds are now rare, and 2 of them are officially endangered. Our results represent a valuable tool for management strategies as well as for conservation purposes.
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Affiliation(s)
- Anna Maria Guastella
- DISPA Sezione di Scienze delle Produzioni Animali, Università degli Studi di Catania, via Valdisavoia, 5, 95123 Catania, Italy
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28
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Ling YH, Ma YH, Guan WJ, Cheng YJ, Wang YP, Han JL, Mang L, Zhao QJ, He XH, Pu YB, Fu BL. Evaluation of the genetic diversity and population structure of Chinese indigenous horse breeds using 27 microsatellite markers. Anim Genet 2011; 42:56-65. [PMID: 20477800 DOI: 10.1111/j.1365-2052.2010.02067.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We determined the genetic diversity and evolutionary relationships among 26 Chinese indigenous horse breeds and two introduced horse breeds by genotyping these animals for 27 microsatellite loci. The 26 Chinese horse breeds come from 12 different provinces. Two introduced horse breeds were the Mongolia B Horse from Mongolia and the Thoroughbred Horse from the UK. A total of 330 alleles were detected, and the expected heterozygosity ranged from 0.719 (Elenchuns) to 0.780 (Dali). The mean number of alleles among the horse breeds ranged from 6.74 (Hequ) to 8.81 (Debao). Although there were abundant genetic variations found, the genetic differentiation was low between the Chinese horses, which displayed only 2.4% of the total genetic variance among the different breeds. However, genetic differentiation (pairwise FST) among Chinese horses, although moderate, was still apparent and varied from 0.001 for the Guizou-Luoping pair to 0.064 for the Jingjiang-Elenchuns pair. The genetic differentiation patterns and genetic relationships among Chinese horse breeds were also consistent with their geographical distribution. The Thoroughbred and Mongolia B breeds could be discerned as two distinct breeds, but the Mongolia B horse in particular suffered genetic admixture with Chinese horses. The Chinese breeds could be divided into five major groups, i.e. the south or along the Yangtze river group (Bose, Debao, Wenshan, Lichuan, Jianchang, Guizhou, Luoping, Jinjiang and Dali), the Qinghai-Tibet Plateau group (Chaidamu, Hequ, Datong, Yushu, Tibet Grassland and Tibet Valley), the Northeast of China group (Elenchuns, Jilin and Heihe), the Northwest of China group (Kazakh, Yili and Yanqi) and the Inner Mongolia group (Mongolia A, Sanhe, Xinihe,Wuzhumuqin and Sengeng). This grouping pattern was further supported by principal component analysis and structure analysis.
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Affiliation(s)
- Y H Ling
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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29
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Zanetti E, De Marchi M, Dalvit C, Cassandro M. Genetic characterization of local Italian breeds of chickens undergoing in situ conservation. Poult Sci 2010; 89:420-7. [PMID: 20181856 DOI: 10.3382/ps.2009-00324] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The objectives of this study were to determine genetic variation and to analyze population structure of 6 Italian local chicken breeds involved in a conservation program. Twenty microsatellite markers were investigated in 337 birds belonging to 6 breeds: Ermellinata di Rovigo, Robusta Maculata, Robusta Lionata, Pépoi, Padovana, and Polverara; a commercial layer cross was used as reference. One hundred twelve alleles were detected in the overall population, with a mean number of 5.6 +/- 2.1 alleles per locus. For the local breeds, the observed and expected heterozygosity ranged from a minimum of 0.240 to a maximum of 0.413 and from 0.243 to 0.463 for the Pépoi and Polverara breeds, respectively. Deviation from Hardy-Weinberg equilibrium was observed in 5 breeds and in the commercial cross. The overall population heterozygote deficiency was 0.427, the average inbreeding coefficient was 0.097, and the heterozygote deficiency due to breed subdivisions was 0.437. Reynolds' distances were used to draw an unrooted neighbor-joining tree, which topology gave information on the genetic origin of these breeds and confirmed their known history. The estimated molecular kinship within a breed ranged from 0.559 to 0.769, evidencing high coancestry. Structure analysis was performed to detect the presence of population substructures. Inferred clusters corresponded to the different breeds, without presence of admixture. The exception was the Polverara breed, for which a more complex genetic structure was found. The results supported the decision of safeguarding these breeds as an important reservoir of genetic diversity and confirmed the usefulness of microsatellite markers to characterize and to monitor genetic variability in local chicken breeds.
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Affiliation(s)
- E Zanetti
- Department of Animal Science, University of Padova, Viale dell'Università, Legnaro (PD), Italy
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30
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van de Goor LHP, Panneman H, van Haeringen WA. A proposal for standardization in forensic equine DNA typing: allele nomenclature for 17 equine-specific STR loci. Anim Genet 2010; 41:122-7. [DOI: 10.1111/j.1365-2052.2009.01975.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Toro MA, Fernández J, Caballero A. Molecular characterization of breeds and its use in conservation. Livest Sci 2009. [DOI: 10.1016/j.livsci.2008.07.003] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Leroy G, Callède L, Verrier E, Mériaux JC, Ricard A, Danchin-Burge C, Rognon X. Genetic diversity of a large set of horse breeds raised in France assessed by microsatellite polymorphism. Genet Sel Evol 2009; 41:5. [PMID: 19284689 PMCID: PMC3225878 DOI: 10.1186/1297-9686-41-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Accepted: 01/05/2009] [Indexed: 11/10/2022] Open
Abstract
The genetic diversity and structure of horses raised in France were investigated using 11 microsatellite markers and 1679 animals belonging to 34 breeds. Between-breed differences explained about ten per cent of the total genetic diversity (Fst = 0.099). Values of expected heterozygosity ranged from 0.43 to 0.79 depending on the breed. According to genetic relationships, multivariate and structure analyses, breeds could be classified into four genetic differentiated groups: warm-blooded, draught, Nordic and pony breeds. Using complementary maximisation of diversity and aggregate diversity approaches, we conclude that particular efforts should be made to conserve five local breeds, namely the Boulonnais, Landais, Merens, Poitevin and Pottok breeds.
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Affiliation(s)
- Grégoire Leroy
- AgroParisTech, UMR1236 Génétique et Diversité Animales, 16 rue Claude Bernard, Paris, France.
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33
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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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34
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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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35
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Laloë D, Jombart T, Dufour AB, Moazami-Goudarzi K. Consensus genetic structuring and typological value of markers using multiple co-inertia analysis. Genet Sel Evol 2007. [DOI: 10.1051/gse:2007021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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