1
|
Radhika G, Aravindakshan TV, Anilkumar K, Manoj M, Thomas S. Genetic diversity analysis of cattle genetic groups of Kerala state using microsatellite data. Anim Biotechnol 2023; 34:1154-1162. [PMID: 34955081 DOI: 10.1080/10495398.2021.2014857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Cattle belonging to seven different genetic groups in Kerala state, India were chosen for the study to find out the genetic diversity between the groups, which would aid in their sustainable improvement and conservation of native cattle. They included the native groups namely, Vechur, Kasaragod, Vadakara dwarf and Vilwadri, along with three different grades of crossbred cattle, based on milk production. Genomic DNA was isolated from 20 to 30 unrelated animals of each group and a panel of 25 microsatellite markers as suggested by FAO-ISAG, were amplified by multiplex PCR. The PCR amplicons were genotyped and the allelic data analyzed using suitable Bioinformatics softwares. The present study showed that the observed number of alleles was much more than the expected, in all populations. The mean PIC value obtained for the present study was 0.8912 and increased number of private alleles were observed, especially in Vilwadri and Kasaragod groups. Negative value of FIS (-0.055) indicated that the level of inbreeding was less. The FST value was 0.1442 indicating that the populations showed good genetic differentiation. The results of Structure analysis revealed admixture only in Vadakara population. The results obtained from the present study showed that Vilwadri and Kasaragod cattle showed distinct differences from other groups.
Collapse
Affiliation(s)
- G Radhika
- College of Veterinary and Animal Sciences, KVASU, Pookode, Wayanad, India
| | - T V Aravindakshan
- Centre for Advanced Studies in Animal Genetics and Breeding, Mannuthy, KVASU, Wayanad, India
| | - K Anilkumar
- College of Veterinary and Animal Sciences, Mannuthy, KVASU, Pookode, Wayanad, India
| | - M Manoj
- College of Veterinary and Animal Sciences, Mannuthy, KVASU, Pookode, Wayanad, India
| | - Stephy Thomas
- Centre for Advanced Studies in Animal Genetics and Breeding, Mannuthy, KVASU, Wayanad, India
| |
Collapse
|
2
|
Orazymbetova Z, Ualiyeva D, Dossybayev K, Torekhanov A, Sydykov D, Mussayeva A, Baktybayev G. Genetic Diversity of Kazakhstani Equus caballus (Linnaeus, 1758) Horse Breeds Inferred from Microsatellite Markers. Vet Sci 2023; 10:598. [PMID: 37888550 PMCID: PMC10611244 DOI: 10.3390/vetsci10100598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Understanding the genetic diversity and structure of domesticated horse (Equus caballus) populations is critical for long-term herd management and breeding programs. This study examines 435 horses from Kazakhstan, covering seven groups in three geographic areas using 11 STR markers. Identified are 136 alleles, with the mean number of alleles per locus ranging from 9 to 19. VHL20 is the most variable locus across groups, while loci HTG4, AHT4, AHT5, HTG7, and HMS3 are variable in most populations. The locus AHT5 in the Emba population shows the highest frequency of rare alleles, while the lowest frequency, 0.005, is observed in the Kulandy population. All loci were highly informative for the Kazakhstani populations of E. caballus, with PIC values higher than 0.5. Pairwise variations in Wright's FST distances show that the examined varieties have little genetic differentiation (0.05%), indicating a high degree of admixture and a continuing lineage sorting process. Phylogenetic and population structure analyses reveal three major clusters of Kazakh horses, representing (I) the Uralsk population of the Kushum breed and the monophyly of two groups: (II) the Kozhamberdy population of the Mugalzhar breed, and (III) the Mugalzhar-Kushum breed populations. Kazakhstani horse populations, while being regionally isolated, were recently in contact with each other.
Collapse
Affiliation(s)
- Zarina Orazymbetova
- Kazakh Research Institute of Livestock and Fodder Production, Almaty 050035, Kazakhstan; (Z.O.); (D.S.)
- Institute of Genetics and Physiology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty 050060, Kazakhstan
| | - Daniya Ualiyeva
- Institute of Genetics and Physiology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty 050060, Kazakhstan
- Institute of Zoology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty 050060, Kazakhstan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Kairat Dossybayev
- Kazakh Research Institute of Livestock and Fodder Production, Almaty 050035, Kazakhstan; (Z.O.); (D.S.)
- Institute of Genetics and Physiology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty 050060, Kazakhstan
| | - Aibyn Torekhanov
- Kazakh Research Institute of Livestock and Fodder Production, Almaty 050035, Kazakhstan; (Z.O.); (D.S.)
| | - Dauren Sydykov
- Kazakh Research Institute of Livestock and Fodder Production, Almaty 050035, Kazakhstan; (Z.O.); (D.S.)
| | - Aizhan Mussayeva
- Institute of Genetics and Physiology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty 050060, Kazakhstan
| | - Gabiden Baktybayev
- Kazakh Research Institute of Livestock and Fodder Production, Almaty 050035, Kazakhstan; (Z.O.); (D.S.)
| |
Collapse
|
3
|
Vincelette A. The Characteristics, Distribution, Function, and Origin of Alternative Lateral Horse Gaits. Animals (Basel) 2023; 13:2557. [PMID: 37627349 PMCID: PMC10451235 DOI: 10.3390/ani13162557] [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: 06/15/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
This article traces the characteristics, origin, distribution, and function of alternative lateral horse gaits, i.e., intermediate speed lateral-sequence gaits. Such alternative lateral gaits (running walk, rack, broken pace, hard pace, and broken trot) are prized by equestrians today for their comfort and have been found in select horse breeds for hundreds of years and even exhibited in fossil equid trackways. After exploring the evolution and development of alternative lateral gaits via fossil equid trackways, human art, and historical writings, the functional and genetic factors that led to the genesis of these gaits are discussed. Such gaited breeds were particularly favored and spread by the Scythians, Celts, Turks, and Spaniards. Fast and low-swinging hard pacing gaits are common in several horse breeds of mountainous areas of East and North Asia; high-stepping rack and running walk gaits are often displayed in European and North and South American breeds; the broken pace is found in breeds of Central Asia, Southeast Asia, West Asia, Western North America, and Brazil in South America; and the broken trot occurs in breeds of North Asia, South Asia, the Southern United States, and Brazil in South America, inhabiting desert or marshy areas.
Collapse
Affiliation(s)
- Alan Vincelette
- Department of Pretheology, St. John's Seminary, 5012 Seminary Road, Camarillo, CA 93021, USA
| |
Collapse
|
4
|
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]
|
5
|
Hernández-Quiroz F, Murugesan S, Flores-Rivas C, Piña-Escobedo A, Juárez-Hernández JI, García-Espitia M, Chávez-Carbajal A, Nirmalkar K, García-Mena J. A high-throughput DNA sequencing study of fecal bacteria of seven Mexican horse breeds. Arch Microbiol 2022; 204:382. [PMID: 35687150 DOI: 10.1007/s00203-022-03009-2] [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: 02/15/2022] [Revised: 05/13/2022] [Accepted: 05/19/2022] [Indexed: 11/02/2022]
Abstract
Horses are non-ruminant, herbivorous mammals, been used through history for various purposes, with a gut microbiota from cecum to the colon, possessing remarkable fermentative capacity. We studied the fecal microbiota of Azteca, Criollo, Frisian, Iberian, Pinto, Quarter and Spanish horse breeds living in Mexico by next-generation DNA sequencing of 16S rRNA gene libraries. Dominant phyla Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes, Fibrobacteres, Actinobacteria and Verrucomicrobia have different relative abundances among breeds, with contrasted alpha and beta diversities as well. Heatmap analysis revealed that Ruminococcaceae, Lachnospiraceae, Mogibacteriaceae families, and order Clostridiales are more abundant in Spanish, Azteca, Quarter and Criollo breeds. The LEfSe analysis displayed higher abundance of order Bacteroidales, family BS11, and genera Faecalibacterium, Comamonas, Collinsella, Acetobacter, and Treponema in Criollo, Azteca, Iberian, Spanish, Frisian, Pinto, and Quarter horse breeds. The conclusion is that dominant bacterial taxa, found in fecal samples of horse breeds living in Mexico, have different relative abundances.
Collapse
Affiliation(s)
- Fernando Hernández-Quiroz
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av IPN 2508 Col Zacatenco, CDMX, 07360, Ciudad de México, Mexico.,Computer Science Department, University of Nebraska-Lincoln (UNL), Lincoln, NE, USA
| | - Selvasankar Murugesan
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av IPN 2508 Col Zacatenco, CDMX, 07360, Ciudad de México, Mexico.,Division of Translational Medicine, Research Department, Sidra Medicine, 26999, Doha, Qatar
| | - Cintia Flores-Rivas
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av IPN 2508 Col Zacatenco, CDMX, 07360, Ciudad de México, Mexico
| | - Alberto Piña-Escobedo
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av IPN 2508 Col Zacatenco, CDMX, 07360, Ciudad de México, Mexico
| | - Josué Isaac Juárez-Hernández
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av IPN 2508 Col Zacatenco, CDMX, 07360, Ciudad de México, Mexico
| | - Matilde García-Espitia
- Escuela Nacional de Medicina y Homeopatía del Instituto Politécnico Nacional, Guillermo Massieu Helguera 239, CDMX, 07320, Ciudad de México, Mexico
| | - Alejandra Chávez-Carbajal
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av IPN 2508 Col Zacatenco, CDMX, 07360, Ciudad de México, Mexico.,Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Khemlal Nirmalkar
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av IPN 2508 Col Zacatenco, CDMX, 07360, Ciudad de México, Mexico.,Biodesign Center for Health through Microbiomes, Arizona State 16 University, Tempe, AZ, USA
| | - Jaime García-Mena
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av IPN 2508 Col Zacatenco, CDMX, 07360, Ciudad de México, Mexico.
| |
Collapse
|
6
|
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.
Collapse
|
7
|
Marín Navas C, Delgado Bermejo JV, McLean AK, León Jurado JM, Rodriguez de la Borbolla y Ruiberriz de Torres A, Navas González FJ. Discriminant Canonical Analysis of the Contribution of Spanish and Arabian Purebred Horses to the Genetic Diversity and Population Structure of Hispano-Arabian Horses. Animals (Basel) 2021; 11:ani11020269. [PMID: 33494478 PMCID: PMC7912545 DOI: 10.3390/ani11020269] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The demographic and genetic diversity structure and the contributions of Spanish (PRE) and Arabian Purebred (PRá) horses to the process of conformation of the Hispano-Arabian (Há) horse breed were evaluated. Genetic diversity parameters (inbreeding coefficient, genetic conservation index, coancestry coefficient, non-random mating degree, relatedness coefficient, maximum, complete, and equivalent generations, and number of offspring) were evaluated using a discriminant canonical analysis to determine the partial contributions of each founder breed to the development of Há horse breed. The calculation of Nei genetic distances suggests the overlapping could be estimated in 29.55% of the gene pool of the Há having a PRE origin while 70.45% of the gene pool of the breed may derive from a PRá origin. Although a progressive loss of founder representation may have occurred, breeding strategies implemented considering mating between animals with the highest genetic conservation indices (GCI) may compensate for its effects. Abstract Genetic diversity and population structure were analyzed using the historical and current pedigree information of the Arabian (PRá), Spanish Purebred (PRE), and Hispano-Arabian (Há) horse breeds. Genetic diversity parameters were computed and a canonical discriminant analysis was used to determine the contributions of ancestor breeds to the genetic diversity of the Há horse. Pedigree records were available for 207,100 animals born between 1884 and 2019. Nei’s distances and the equivalent subpopulations number indicated the existence of a highly structured, integrated population for the Há breed, which is more closely genetically related to PRá than PRE horses. An increase in the length of the generation interval might be an effective solution to reduce the increase in inbreeding found in the studied breeds (8.44%, 8.50%, and 2.89%, for PRá, PRE, and Há, respectively). Wright’s fixation statistics indicated slight interherd inbreeding. Pedigree completeness suggested genetic parameters were highly reliable. High GCI levels found for number of founders and non-founders and their relationship to the evolution of inbreeding permit controlling potential deleterious negative effects from excessively frequent mating between interrelated individuals. For instance, the use of individuals presenting high GCI may balance founders’ gene contributions and consequently preserve genetic diversity levels (current genetic diversity loss in PRá, PRE, and Há is 6%, 7%, and 4%, respectively).
Collapse
Affiliation(s)
- Carmen Marín Navas
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (C.M.N.); (J.V.D.B.)
| | - Juan Vicente Delgado Bermejo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (C.M.N.); (J.V.D.B.)
| | - Amy Katherine McLean
- Department of Animal Science, University of California Davis, Davis, CA 95617, USA;
| | - José Manuel León Jurado
- Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, 14071 Córdoba, Spain;
| | | | - Francisco Javier Navas González
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14071 Córdoba, Spain; (C.M.N.); (J.V.D.B.)
- Correspondence: ; Tel.: +34-957-21-87-06
| |
Collapse
|
8
|
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.
Collapse
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)
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
BEHL RAHUL, NIRANJAN SK, BEHL JYOTSNA, VIJH RK. Individual identification and population assignment with microsatellite markers in three Indian donkey populations. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2020. [DOI: 10.56093/ijans.v90i4.104204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ability of the microsatellite markers for individual identification and their potential for breed assignment of individuals was evaluated in three Indian donkey populations. The probability of identity of two random individuals within a population (G1), taking into consideration all eleven loci was 5.91×10–13, 1.06×10–12 and 3.67×10–14 in Ladakhi, Spiti and Andhra-brown donkeys, respectively. Similarly, the probability of identity of two random individuals from two different populations (G2) between Spiti and Ladakhi donkeys, the two most closely related populations, was only 8.05×10–21 . However, the population assignment precision using this set of 11 loci, the correct assignments ranged between 73.08 (Andhra-brown) to 96% (Ladakhi) with frequency method and between 88.46 (Andhra-brown) to 100% (Ladakhi) with Baysian approach. These results suggest that this set of markers can be a promising tool for identification of individuals and their products. Although G2 values were higher than the G1 values but when this set was specifically evaluated for breed allocation purposes, our results indicated that it may require further substantiation before this set can be safely employed for breed/population allocation of individuals in Indian donkey populations.
Collapse
|
11
|
Kalashnikov V, Khrabrova L, Blohina N, Zaitcev A, Kalashnikova T. Dynamics of the Inbreeding Coefficient and Homozygosity in Thoroughbred Horses in Russia. Animals (Basel) 2020; 10:ani10071217. [PMID: 32708952 PMCID: PMC7401591 DOI: 10.3390/ani10071217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/09/2020] [Accepted: 07/14/2020] [Indexed: 11/16/2022] Open
Abstract
The Thoroughbred (TB) horse has hugely impacted the development of horse breeding around the world. This breed has unique genetic qualities due to having had a closed studbook for approximately 300 years. In Russia, TBs have been bred since the second half of the 18th century. Here, we analyzed the genetic diversity and the inbreeding level in TB horses (n = 9680) for the period from 1990 to 2018 using polymorphisms of 17 microsatellite loci. We found that the genetic structure of the TB breed in Russia is represented by 100 alleles of panel STR (short tandem repeat) loci and has been stable for the past three decades. The conducted monitoring revealed a slight increase in the Wright's inbreeding coefficient in all age and sex groups of TB horses (stallions, broodmares, and foals) from 0.68% to 0.90%, which was followed by a decrease in the degree of heterozygosity, Ho, from 68.5% to 67.6%. The Spearman's rank correlation coefficient between the level of inbreeding and the degree of homozygosity was estimated (r = 0.022; p > 0.05). The obtained data on the DNA genotypes of horses of different breeds provide a unique base for the evaluation of genetic variability and the control of genetic variability of horses in selection programs.
Collapse
|
12
|
Koseman A, Ozsensoy Y, Erdogan M, Yarali C, Toprak B, Zengin K, Seker I. Investigation of Genetic Variations using Microsatellite Markers in Colored Horses in Turkey. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420050075] [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]
|
13
|
Winton CL, McMahon R, Hegarty MJ, McEwan NR, Davies‐Morel MCG, Morgan C, Nash DM. Genetic diversity within and between British and Irish breeds: The maternal and paternal history of native ponies. Ecol Evol 2020; 10:1352-1367. [PMID: 32076519 PMCID: PMC7029099 DOI: 10.1002/ece3.5989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 11/09/2022] Open
Abstract
The UK and Ireland have many native pony breeds with historical and cultural importance as well as being a source of uncharacterized genetic diversity. However, there is a lack of comprehensive research investigating their genetic diversity and phylogenetic interrelationships. Many studies contain a limited number of pony breeds or small sample sizes for these breeds. This may result in erroneous grouping of pony breeds that otherwise have intricate interrelationships with each other and are not evaluated correctly when placed as a token subset of a larger dataset. This is the first study that specifically investigates the genetic diversity within and between British and Irish native pony breeds using large sample numbers from locations of their native origin. This study used a panel of microsatellite markers and sequence analysis of the mitochondrial control region to analyze the genetic diversity within and between 11 pony breeds from Britain and Ireland. A large dataset was collected (a total of 485 animals were used for mtDNA analysis and 450 for microsatellite analysis), and previously published data were used to place the British and Irish ponies in a global context. The native ponies of Britain and Ireland were found to have had a complex history, and the interrelationships between the breeds were revealed. Overall, high levels of genetic diversity were maintained in native breeds, although some reduction was evident in small or isolated populations (Shetland, Carneddau, and Section C). Unusual mitochondrial diversity distribution patterns were apparent for the Carneddau and Dartmoor, although among breeds and global haplogroups there was a high degree of haplotype sharing evident, well-represented within British and Irish ponies. Ancestral maternal diversity was maintained by most populations, particularly the Fells and Welsh ponies, which exhibited rare and ancient lineages. The maternal and paternal histories of the breeds are distinct, with male-biased crossings between native breeds, and other shared influences, likely Arabs and Thoroughbreds, are apparent. The data generated herein provide valuable information to guide and implement the conservation of increasingly rare native genetic resources.
Collapse
Affiliation(s)
- Clare L. Winton
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Robert McMahon
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
- Molecular HaematologyHaematology LaboratoryRoyal Infirmary of EdinburghEdinburghUK
| | - Matthew J. Hegarty
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Neil R. McEwan
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
- School of Pharmacy and Life SciencesRobert Gordon UniversityAberdeenUK
| | | | - Charly Morgan
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Deborah M. Nash
- Institute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| |
Collapse
|
14
|
First report of zoonotic Cryptosporidium parvum GP60 subtypes IIaA15G2R1 and IIaA16G3R1 in wild ponies from the northern Iberian Peninsula. Parasitol Res 2019; 119:249-254. [PMID: 31758296 DOI: 10.1007/s00436-019-06529-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 10/28/2019] [Indexed: 01/25/2023]
Abstract
Studies on the prevalence and molecular characterization of Cryptosporidium spp. affecting feral horses are scarce. The highland areas of the northern Iberian Peninsula are home to a large population of wild ponies which generally roam free in the ancient natural range and are subjected to a traditional exploitation regime. In the present study, a total of 79 non-diarrhoeal faecal samples from the wild ponies were collected from the ground immediately after defecation. Cryptosporidium was detected in 10 of the samples (12.6%) by a direct immunofluorescence antibody test and DNA amplification and sequencing. Analysis of partial sequences of the small subunit ribosomal RNA (SSU-rRNA) and heat shock protein (hsp70) loci revealed the presence of Cryptosporidium parvum. In addition, amplification and sequencing of a fragment of the 60-kDa glycoprotein (GP60) locus identified C. parvum subtypes IIaA15G2R1 and IIaA16G3R1. This study reports, for the first time, the occurrence of C. parvum in wild ponies in Europe, specifically in the northern Iberian Peninsula. Identification of the common subtype IIaA15G2R1 and also subtype IIaA16G3R1 (first description) indicates that these hosts may play a role in the sylvatic transmission of C. parvum and that they may act as a reservoir of zoonotic cryptosporidiosis.
Collapse
|
15
|
Deshpande K, Perez E, Leyva N, Suarez M, Mills DK. Genetic Structure of the Big Summit Herd and Neighboring Wild Horse Populations Inhabiting Herd Management Areas of Oregon. WEST N AM NATURALIST 2019. [DOI: 10.3398/064.079.0109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Ketaki Deshpande
- International Forensic Research Institute, Florida International University, Miami, FL 33199
| | - Evelyn Perez
- International Forensic Research Institute, Florida International University, Miami, FL 33199
| | - Natalie Leyva
- International Forensic Research Institute, Florida International University, Miami, FL 33199
| | - Merly Suarez
- Department of Biological Sciences, Florida International University, Miami, FL 33199
| | - DeEtta K. Mills
- International Forensic Research Institute, Florida International University, Miami, FL 33199
| |
Collapse
|
16
|
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]
|
17
|
Dorji J, Tamang S, Tshewang T, Dorji T, Dorji TY. Genetic diversity and population structure of three traditional horse breeds of Bhutan based on 29 DNA microsatellite markers. PLoS One 2018; 13:e0199376. [PMID: 29949614 PMCID: PMC6021118 DOI: 10.1371/journal.pone.0199376] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 06/06/2018] [Indexed: 11/19/2022] Open
Abstract
The genetic variability and population structure of three Bhutanese traditional horse breeds were assessed through genotyping of 74 horses (Boeta 25, Sharta 14 and Yuta 35) for 29 microsatellite DNA loci. Altogether, 282 alleles were detected across 29 polymorphic loci. The allelic diversity (NE) (Boeta 4.94; Sharta 4.65; Yuta 5.30) and gene diversities (HE) (Boeta 0.78; Sharta 0.77; Yuta 0.79) were high. None of the breeds deviated significantly from the Hardy-Weinberg equilibrium. There was no sign of significant population bottleneck for all the breeds. The inbreeding estimates (FIS) of the breeds were low (Boeta 0.023; Sharta 0.001; Yuta 0.021). Analysis of molecular variance showed 0.6% of the total genetic variation among breeds, 1.9% among individuals and 97.5% within individuals. The global FIT, FST, and FIS estimates for the population were 0.025, 0.006 and 0.019 respectively. The analysis of population structure failed to distinguish subpopulations in traditional horses and this was supported by a high genetic exchange among the breeds. Overall, the results of this study suggest a rich genetic diversity in the traditional horse despite a very low genetic differentiation among the breeds in Bhutan.
Collapse
Affiliation(s)
- Jigme Dorji
- National Biodiversity Centre, Serbithang, Ministry of Agriculture and Forests, Thimphu, Bhutan
- * E-mail:
| | - Sonam Tamang
- National Biodiversity Centre, Serbithang, Ministry of Agriculture and Forests, Thimphu, Bhutan
| | - Tshewang Tshewang
- National Biodiversity Centre, Serbithang, Ministry of Agriculture and Forests, Thimphu, Bhutan
| | - Tshering Dorji
- National Biodiversity Centre, Serbithang, Ministry of Agriculture and Forests, Thimphu, Bhutan
| | - Tashi Yangzome Dorji
- National Biodiversity Centre, Serbithang, Ministry of Agriculture and Forests, Thimphu, Bhutan
| |
Collapse
|
18
|
Colino-Rabanal VJ, Rodríguez-Díaz R, Blanco-Villegas MJ, Peris SJ, Lizana M. Human and ecological determinants of the spatial structure of local breed diversity. Sci Rep 2018; 8:6452. [PMID: 29691460 PMCID: PMC5915451 DOI: 10.1038/s41598-018-24641-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 03/26/2018] [Indexed: 02/01/2023] Open
Abstract
Since domestication, a large number of livestock breeds adapted to local conditions have been created by natural and artificial selection, representing one of the most powerful ways in which human groups have constructed niches to meet their need. Although many authors have described local breeds as the result of culturally and environmentally mediated processes, this study, located in mainland Spain, is the first aimed at identifying and quantifying the environmental and human contributions to the spatial structure of local breed diversity, which we refer to as livestock niche. We found that the more similar two provinces were in terms of human population, ecological characteristics, historical ties, and geographic distance, the more similar the composition of local breeds in their territories. Isolation by human population distance showed the strongest effect, followed by isolation by the environment, thus supporting the view of livestock niche as a socio-cultural product adapted to the local environment, in whose construction humans make good use of their ecological and cultural inheritances. These findings provide a useful framework to understand and to envisage the effects of climate change and globalization on local breeds and their livestock niches.
Collapse
Affiliation(s)
- Victor J Colino-Rabanal
- Area of Zoology, Department of Animal Biology, Parasitology, Ecology, Edaphology and Agronomic Chemistry, University of Salamanca, Campus Miguel de Unamuno, 37071, Salamanca, Spain.
| | - Roberto Rodríguez-Díaz
- Area of Physical Anthropology, Department of Animal Biology, Parasitology, Ecology, Edaphology and Agronomic Chemistry, University of Salamanca, Campus Miguel de Unamuno, 37071, Salamanca, Spain
| | - María José Blanco-Villegas
- Area of Physical Anthropology, Department of Animal Biology, Parasitology, Ecology, Edaphology and Agronomic Chemistry, University of Salamanca, Campus Miguel de Unamuno, 37071, Salamanca, Spain
| | - Salvador J Peris
- Area of Zoology, Department of Animal Biology, Parasitology, Ecology, Edaphology and Agronomic Chemistry, University of Salamanca, Campus Miguel de Unamuno, 37071, Salamanca, Spain
| | - Miguel Lizana
- Area of Zoology, Department of Animal Biology, Parasitology, Ecology, Edaphology and Agronomic Chemistry, University of Salamanca, Campus Miguel de Unamuno, 37071, Salamanca, Spain
| |
Collapse
|
19
|
Jemmali B, Haddad MM, Barhoumi N, Tounsi S, Lasfer F, Trabelsi A, Ben Aoun B, Gritli I, Ezzar S, Ben Younes A, Ezzaouia MH, Rekik B, Ouled Ahmed H. Genetic diversity in Tunisian horse breeds. Arch Anim Breed 2017. [DOI: 10.5194/aab-60-153-2017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. This study aimed at screening genetic diversity and differentiation in four horse breeds raised in Tunisia, the Barb, Arab-Barb, Arabian, and English Thoroughbred breeds. A total of 200 blood samples (50 for each breed) were collected from the jugular veins of animals, and genomic DNA was extracted. The analysis of the genetic structure was carried out using a panel of 16 microsatellite loci. Results showed that all studied microsatellite markers were highly polymorphic in all breeds. Overall, a total of 147 alleles were detected using the 16 microsatellite loci. The average number of alleles per locus was 7.52 (0.49), 7.35 (0.54), 6.3 (0.44), and 6 (0.38) for the Arab-Barb, Barb, Arabian, and English Thoroughbred breeds, respectively. The observed heterozygosities ranged from 0.63 (0.03) in the English Thoroughbred to 0.72 in the Arab-Barb breeds, whereas the expected heterozygosities were between 0.68 (0.02) in the English Thoroughbred and 0.73 in the Barb breeds. All FST values calculated by pairwise breed combinations were significantly different from zero (p < 0.05) and an important genetic differentiation among breeds was revealed. Genetic distances, the factorial correspondence, and principal coordinate analyses showed that the important amount of genetic variation was within population. These results may facilitate conservation programs for the studied breeds and enhance preserve their genetic diversity.
Collapse
|
20
|
Mathematical Constraints on FST: Biallelic Markers in Arbitrarily Many Populations. Genetics 2017; 206:1581-1600. [PMID: 28476869 DOI: 10.1534/genetics.116.199141] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 05/03/2017] [Indexed: 02/01/2023] Open
Abstract
[Formula: see text] is one of the most widely used statistics in population genetics. Recent mathematical studies have identified constraints that challenge interpretations of [Formula: see text] as a measure with potential to range from 0 for genetically similar populations to 1 for divergent populations. We generalize results obtained for population pairs to arbitrarily many populations, characterizing the mathematical relationship between [Formula: see text] the frequency M of the more frequent allele at a polymorphic biallelic marker, and the number of subpopulations K We show that for fixed K, [Formula: see text] has a peculiar constraint as a function of M, with a maximum of 1 only if [Formula: see text] for integers i with [Formula: see text] For fixed M, as K grows large, the range of [Formula: see text] becomes the closed or half-open unit interval. For fixed K, however, some [Formula: see text] always exists at which the upper bound on [Formula: see text] lies below [Formula: see text] We use coalescent simulations to show that under weak migration, [Formula: see text] depends strongly on M when K is small, but not when K is large. Finally, examining data on human genetic variation, we use our results to explain the generally smaller [Formula: see text] values between pairs of continents relative to global [Formula: see text] values. We discuss implications for the interpretation and use of [Formula: see text].
Collapse
|
21
|
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
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
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
| |
Collapse
|
25
|
Bruzzone A, Iamartino D, Blasi M, Pilla F. The Pentro horse: genetic characterization by microsatellite markers. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2003.223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | | | | | - Fabio Pilla
- Dipartimento siva. Università del Molise, Campobasso, Italy
| |
Collapse
|
26
|
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]
|
27
|
Alves JM, Carneiro M, Afonso S, Lopes S, Garreau H, Boucher S, Allain D, Queney G, Esteves PJ, Bolet G, Ferrand N. Levels and Patterns of Genetic Diversity and Population Structure in Domestic Rabbits. PLoS One 2015; 10:e0144687. [PMID: 26689909 PMCID: PMC4686922 DOI: 10.1371/journal.pone.0144687] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 11/23/2015] [Indexed: 11/23/2022] Open
Abstract
Over thousands of years humans changed the genetic and phenotypic composition of several organisms and in the process transformed wild species into domesticated forms. From this close association, domestic animals emerged as important models in biomedical and fundamental research, in addition to their intrinsic economical and cultural value. The domestic rabbit is no exception but few studies have investigated the impact of domestication on its genetic variability. In order to study patterns of genetic structure in domestic rabbits and to quantify the genetic diversity lost with the domestication process, we genotyped 45 microsatellites for 471 individuals belonging to 16 breeds and 13 wild localities. We found that both the initial domestication and the subsequent process of breed formation, when averaged across breeds, culminated in losses of ~20% of genetic diversity present in the ancestral wild population and domestic rabbits as a whole, respectively. Despite the short time elapsed since breed diversification we uncovered a well-defined structure in domestic rabbits where the FST between breeds was 22%. However, we failed to detect deeper levels of structure, probably consequence of a recent and single geographic origin of domestication together with a non-bifurcating process of breed formation, which were often derived from crosses between two or more breeds. Finally, we found evidence for intrabreed stratification that is associated with demographic and selective causes such as formation of strains, colour morphs within the same breed, or country/breeder of origin. These additional layers of population structure within breeds should be taken into account in future mapping studies.
Collapse
Affiliation(s)
- Joel M. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- * E-mail:
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
| | - Susana Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
| | - Hervé Garreau
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
| | | | - Daniel Allain
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
| | | | - Pedro J. Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
- CITS, Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra, Portugal
| | - Gerard Bolet
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
| | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| |
Collapse
|
28
|
Genetic diversity and population structure analysis of native and crossbred goat genetic groups of Kerala, India. Small Rumin Res 2015. [DOI: 10.1016/j.smallrumres.2015.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
29
|
Burócziová M, Říha J, Židek R, Trandžík J, Jakabová D. Genetic structure of nine horse populations. ACTA UNIVERSITATIS AGRICULTURAE ET SILVICULTURAE MENDELIANAE BRUNENSIS 2014. [DOI: 10.11118/actaun200856020057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
30
|
Martínez-Camblor P, Carleos C, Baro JÁ, Cañón J. Standard statistical tools for the breed allocation problem. J Appl Stat 2014. [DOI: 10.1080/02664763.2014.898136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
31
|
Berber N, Gaouar S, Leroy G, Kdidi S, Tabet Aouel N, Saïdi Mehtar N. Molecular characterization and differentiation of five horse breeds raised in Algeria using polymorphic microsatellite markers. J Anim Breed Genet 2014; 131:387-94. [DOI: 10.1111/jbg.12092] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/16/2014] [Indexed: 12/01/2022]
Affiliation(s)
- N. Berber
- Laboratoire de Génétique Moléculaire et cellulaire; Université des sciences et de la technologie d'Oran - mohamed Boudiaf- USTOMB, BP 1505 El M'naouer; Oran Algeria
| | - S. Gaouar
- Département de biologie; Université de Tlemcen; Telemcen Algeria
| | - G. Leroy
- AgroParisTech; UMR1236 Génétique et Diversité Animales; Paris France
- INRA; UMR1236 Génétique et Diversité Animales; Jouy-en-Josas France
| | - S. Kdidi
- Livestock & Wildlife Laboratory; Arid Lands Institute; Medenine Tunisia
- Laboratory of Genetics; Immunology and Human Pathology; Faculty of Sciences; Tunis-El Manar University; Tunisia Tunisia
| | - N. Tabet Aouel
- Département de biotechnologie; Université d'Oran Es-sénia; Oran Algeria
| | - N. Saïdi Mehtar
- Laboratoire de Génétique Moléculaire et cellulaire; Université des sciences et de la technologie d'Oran - mohamed Boudiaf- USTOMB, BP 1505 El M'naouer; Oran Algeria
| |
Collapse
|
32
|
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.
Collapse
|
33
|
Winton CL, Hegarty MJ, McMahon R, Slavov GT, McEwan NR, Davies-Morel MC, Morgan CM, Powell W, Nash DM. Genetic diversity and phylogenetic analysis of native mountain ponies of Britain and Ireland reveals a novel rare population. Ecol Evol 2013; 3:934-47. [PMID: 23610635 PMCID: PMC3631405 DOI: 10.1002/ece3.507] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 01/22/2013] [Accepted: 01/23/2013] [Indexed: 11/08/2022] Open
Abstract
The conservation of unique populations of animals is critical in order to preserve valuable genetic diversity and, where populations are free-living, maintain their irreplaceable influence upon habitat ecology. An accurate assessment of genetic diversity and structure within and between populations is crucial in order to design and implement conservation strategies in natural and domesticated species. Moreover, where it is possible to identify relic populations that are related to a structured breed an ideal opportunity presents itself to model processes that reveal historical factors that have shaped genetic diversity. The origins of native UK mountain and moorland ponies are uncertain, but they may have directly descended from prehistoric populations and potentially harbour specific adaptations to the uplands of Britain and Ireland. To date, there have been no studies of population structure and genetic diversity present within a free-living group of ponies in the Carneddau mountain range of North Wales. Herein, we describe the use of microsatellites and SNPs together with analysis of the mitochondrial control region to quantify the extent and magnitude of genetic diversity present in the feral Carneddau pony and relate this to several recognised British and Irish pony breeds. Our results establish that the feral Carneddau ponies represent a unique and distinctive population that merits recognition as a defined population and conservation priority. We discuss the implications for conservation of this population as a unique pool of genetic diversity adapted to the British uplands and potentially of particular value in maintaining the biodiversity of these habitats.
Collapse
Affiliation(s)
- Clare L Winton
- IBERS, Aberystwyth University Aberystwyth, Ceredigion, SY23 3DA, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
34
|
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]
|
35
|
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.
Collapse
Affiliation(s)
- Jessica L Petersen
- University of Minnesota, College of Veterinary Medicine, St Paul, MN, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Xu LX, Yang SL, Lin RY, Yang HB, Li AP, Wan QS. Genetic diversity and population structure of Chinese pony breeds using microsatellite markers. GENETICS AND MOLECULAR RESEARCH 2012; 11:2629-40. [PMID: 22782636 DOI: 10.4238/2012.june.25.4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
China is one of the principal origins of ponies in the world. We made a comprehensive analysis of genetic diversity and population structure of Chinese ponies based on 174 animals of five indigenous Chinese pony breeds from five provinces using 13 microsatellite markers. One hundred and forty-four alleles were detected; the mean number of effective alleles among the pony breeds ranged from 5.38 (Guizhou) to 6.78 (Sichuan); the expected heterozygosity ranged from 0.82 (Guizhou) to 0.85 (Debao, Sichuan). Although abundant genetic variation was found, the genetic differentiation was low between the ponies, with 6% total genetic variance among the different breeds. All the pairwise F(ST) values were significant; they varied from 0.0424 for the Sichuan-Yunnan pair to 0.0833 for the Guizhou-Sichuan pair. All five pony breeds deviated from Hardy-Weinberg equilibrium, except the Yunnan pony. Phylogenetic trees of the five pony breeds based on genetic distances were constructed using a neighbor-joining method. The Sichuan and Yunnan ponies were grouped into the same branch, with a high bootstrap support value (97%). Guizhou and Ningqiang ponies were clustered into the same branch with a bootstrap value of 56%, whereas the Debao pony was placed in a separate group, with a bootstrap value of 56%. This grouping pattern was supported by genetic structure analysis.
Collapse
Affiliation(s)
- L X Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction for Mountainous Areas, Chinese Educational Ministry, Guizhou University, Guiyang, China
| | | | | | | | | | | |
Collapse
|
37
|
Warmuth V, Manica A, Eriksson A, Barker G, Bower M. Autosomal genetic diversity in non-breed horses from eastern Eurasia provides insights into historical population movements. Anim Genet 2012; 44:53-61. [PMID: 22607477 DOI: 10.1111/j.1365-2052.2012.02371.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2012] [Indexed: 12/22/2022]
Abstract
Many events in the history of eastern Eurasia, including the process of domestication itself, the initial spread of domestic horses and subsequent movements, are believed to have affected the genetic structure of domestic horse populations in this area. We investigated levels of within- and between-population genetic diversity in 'non-breed horses' (working horses sampled in remote areas) from 17 locations in Asia and parts of Eastern Europe, using 26 autosomal microsatellite loci. Non-breed horses have not been subject to the same intensity of artificial selection and closed breeding as have most breed animals and are thus expected to better reflect the population history of domestic horses. Despite geographic distances of between 300 and 7000 km between sampling locations, pairwise F (ST) was very low (range: <0.001 to -0.033), suggesting historically high levels of gene flow. Our analyses of non-breed horses revealed a pattern of isolation by distance and a significant decline in genetic diversity (expected heterozygosity and allelic richness) from east to west, consistent with a westward expansion of horses out of East Asia. Although the timing of this putative expansion is unclear, our results highlight the benefit of studying animals that do not belong to particular breeds when investigating aspects of a population's history.
Collapse
Affiliation(s)
- Vera Warmuth
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK.
| | | | | | | | | |
Collapse
|
38
|
Colli L, Perrotta G, Negrini R, Bomba L, Bigi D, Zambonelli P, Verini Supplizi A, Liotta L, Ajmone-Marsan P. Detecting population structure and recent demographic history in endangered livestock breeds: the case of the Italian autochthonous donkeys. Anim Genet 2012; 44:69-78. [DOI: 10.1111/j.1365-2052.2012.02356.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2012] [Indexed: 11/29/2022]
Affiliation(s)
- L. Colli
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e il DNA Antico; Facoltà di Agraria; Università Cattolica del S. Cuore di Piacenza; I-29122; Piacenza; Italy
| | - G. Perrotta
- Laboratorio di Genetica e Servizi L.G.S.; I-26100; Cremona; Italy
| | - R. Negrini
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e il DNA Antico; Facoltà di Agraria; Università Cattolica del S. Cuore di Piacenza; I-29122; Piacenza; Italy
| | - L. Bomba
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e il DNA Antico; Facoltà di Agraria; Università Cattolica del S. Cuore di Piacenza; I-29122; Piacenza; Italy
| | - D. Bigi
- Dipartimento di Protezione e Valorizzazione Agro-Alimentare; Università di Bologna - Sede di Reggio Emilia; I-42123; Reggio Emilia; Italy
| | - P. Zambonelli
- Dipartimento di Protezione e Valorizzazione Agro-Alimentare; Università di Bologna - Sede di Reggio Emilia; I-42123; Reggio Emilia; Italy
| | - A. Verini Supplizi
- Dipartimento di Patologia; Diagnostica e Clinica Veterinaria; Università di Perugia; I-06126; Perugia; Italy
| | - L. Liotta
- Dipartimento di Morfologia, Biochimica; Fisiologia e Produzioni Animali; Università di Messina; I-98168; Messina; Italy
| | - P. Ajmone-Marsan
- Istituto di Zootecnica e BioDNA Centro di Ricerca sulla Biodiversità e il DNA Antico; Facoltà di Agraria; Università Cattolica del S. Cuore di Piacenza; I-29122; Piacenza; Italy
| |
Collapse
|
39
|
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.
Collapse
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.
| | | |
Collapse
|
40
|
Doan R, Cohen N, Harrington J, Veazey K, Veazy K, Juras R, Cothran G, McCue ME, Skow L, Dindot SV. Identification of copy number variants in horses. Genome Res 2012; 22:899-907. [PMID: 22383489 PMCID: PMC3337435 DOI: 10.1101/gr.128991.111] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Copy number variants (CNVs) represent a substantial source of genetic variation in mammals. However, the occurrence of CNVs in horses and their subsequent impact on phenotypic variation is unknown. We performed a study to identify CNVs in 16 horses representing 15 distinct breeds (Equus caballus) and an individual gray donkey (Equus asinus) using a whole-exome tiling array and the array comparative genomic hybridization methodology. We identified 2368 CNVs ranging in size from 197 bp to 3.5 Mb. Merging identical CNVs from each animal yielded 775 CNV regions (CNVRs), involving 1707 protein- and RNA-coding genes. The number of CNVs per animal ranged from 55 to 347, with median and mean sizes of CNVs of 5.3 kb and 99.4 kb, respectively. Approximately 6% of the genes investigated were affected by a CNV. Biological process enrichment analysis indicated CNVs primarily affected genes involved in sensory perception, signal transduction, and metabolism. CNVs also were identified in genes regulating blood group antigens, coat color, fecundity, lactation, keratin formation, neuronal homeostasis, and height in other species. Collectively, these data are the first report of copy number variation in horses and suggest that CNVs are common in the horse genome and may modulate biological processes underlying different traits observed among horses and horse breeds.
Collapse
Affiliation(s)
- Ryan Doan
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Mahrous KF, Hassanane M, Abdel Mordy M, Shafey HI, Hassan N. Genetic variations in horse using microsatellite markers. JOURNAL OF GENETIC ENGINEERING AND BIOTECHNOLOGY 2011. [DOI: 10.1016/j.jgeb.2011.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
42
|
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]
|
43
|
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.
Collapse
Affiliation(s)
- E Koban
- TUBITAK Marmara Research Center, Genetic Engineering and Biotechnology Institute, Kocaeli, Turkey
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Rendo F, Iriondo M, Manzano C, Estonba A. Effects of a 10-year conservation programme on the genetic diversity of the Pottoka pony--new clues regarding their origin. J Anim Breed Genet 2011; 129:234-43. [PMID: 22583328 DOI: 10.1111/j.1439-0388.2011.00955.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we present the results of a genetic analysis of 463 Pottoka ponies corresponding to four generations, using 17 microsatellite markers. Ten years after the beginning of the Pottoka conservation programme, the values for the genetic diversity of the breed are still high and stable, indicating the success of the programme. We found null alleles in Pottoka for the ASB23, HMS3 and HTG10 microsatellites. Together with information obtained from other pony breeds from the Iberian Peninsula, this finding indicates that these microsatellites should not be used for phylogenetic analyses or parentage tests, at least for these breeds. The high heterozygosity exhibited by this breed in comparison to other ponies, together with its genetic proximity to the centroid of the allele frequencies, suggest that Pottoka allele frequencies are close to those initially exhibited by the ancestors of current European ponies. The results obtained in the current work, together with results from previous studies of ponies and horses from the Iberian Peninsula, corroborate the idea of a unique origin of all ponies from the European Atlantic Area. In contrast, our results do not corroborate the idea that these are derived from a domestication event in the Iberian Peninsula, nor that they have incorporated ancient Iberian horse genes into their genetic pool to a larger extent than other horse breeds.
Collapse
Affiliation(s)
- F Rendo
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country, Bilbao, Spain
| | | | | | | |
Collapse
|
45
|
Conant EK, Juras R, Cothran EG. A microsatellite analysis of five Colonial Spanish horse populations of the southeastern United States. Anim Genet 2011; 43:53-62. [PMID: 22221025 DOI: 10.1111/j.1365-2052.2011.02210.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The domestic horse (Equus caballus) was re-introduced to the Americas by Spanish explorers. Although horses from other parts of Europe were subsequently introduced, some New World populations maintain characteristics ascribed to their Spanish heritage. The southeastern United States has a history of Spanish invasion and settlement, and this influence on local feral horse populations includes two feral-recaptured breeds: the Florida Cracker and the Marsh Tacky, both of which are classified as Colonial Spanish horses. The feral Banker horses found on islands off the coast of North Carolina, which include, among others, the Shackleford Banks, the Corolla and the Ocracoke, are also Colonial Spanish horses. Herein we analyse 15 microsatellite loci from 532 feral and 2583 domestic horses in order to compare the genetic variation of these five Colonial Spanish Horse populations to 40 modern horse breeds. We find that the Corolla horse has very low heterozygosity and that both the Corolla and Ocracoke populations have a low mean number of alleles. We also find that the Florida Cracker population has a heterozygosity deficit. In addition, we find evidence of similarity of the Shackleford Banks, Marsh Tacky and Florida Cracker populations to New World Iberian horse breeds, while the origins of the other two populations are less clear.
Collapse
Affiliation(s)
- E K Conant
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA
| | | | | |
Collapse
|
46
|
European domestic horses originated in two holocene refugia. PLoS One 2011; 6:e18194. [PMID: 21479181 PMCID: PMC3068172 DOI: 10.1371/journal.pone.0018194] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 02/28/2011] [Indexed: 12/01/2022] Open
Abstract
The role of European wild horses in horse domestication is poorly understood. While the fossil record for wild horses in Europe prior to horse domestication is scarce, there have been suggestions that wild populations from various European regions might have contributed to the gene pool of domestic horses. To distinguish between regions where domestic populations are mainly descended from local wild stock and those where horses were largely imported, we investigated patterns of genetic diversity in 24 European horse breeds typed at 12 microsatellite loci. The distribution of high levels of genetic diversity in Europe coincides with the distribution of predominantly open landscapes prior to domestication, as suggested by simulation-based vegetation reconstructions, with breeds from Iberia and the Caspian Sea region having significantly higher genetic diversity than breeds from central Europe and the UK, which were largely forested at the time the first domestic horses appear there. Our results suggest that not only the Eastern steppes, but also the Iberian Peninsula provided refugia for wild horses in the Holocene, and that the genetic contribution of these wild populations to local domestic stock may have been considerable. In contrast, the consistently low levels of diversity in central Europe and the UK suggest that domestic horses in these regions largely derive from horses that were imported from the Eastern refugium, the Iberian refugium, or both.
Collapse
|
47
|
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.
Collapse
Affiliation(s)
- Y H Ling
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Bömcke E, Gengler N, Cothran EG. Genetic variability in the Skyros pony and its relationship with other Greek and foreign horse breeds. Genet Mol Biol 2011; 34:68-76. [PMID: 21637546 PMCID: PMC3085377 DOI: 10.1590/s1415-47572010005000113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 11/26/2010] [Indexed: 11/22/2022] Open
Abstract
In Greece, seven native horse breeds have been identified so far. Among these, the Skyros pony is outstanding through having a distinct phenotype. In the present study, the aim was to assess genetic diversity in this breed, by using different types of genetic loci and available genealogical information. Its relationships with the other Greek, as well as foreign, domestic breeds were also investigated. Through microsatellite and pedigree analysis it appeared that the Skyros presented a similar level of genetic diversity to the other European breeds. Nevertheless, comparisons between DNA-based and pedigree-based results revealed that a loss of genetic diversity had probably already occurred before the beginning of breed registration. Tests indicated the possible existence of a recent bottleneck in two of the three main herds of Skyros pony. Nonetheless, relatively high levels of heterozygosity and Polymorphism Information Content indicated sufficient residual genetic variability, probably useful in planning future strategies for breed conservation. Three other Greek breeds were also analyzed. A comparison of these with domestic breeds elsewhere, revealed the closest relationships to be with the Middle Eastern types, whereas the Skyros itself remained isolated, without any close relationship, whatsoever.
Collapse
Affiliation(s)
- Elisabeth Bömcke
- Animal Science Unit, Gembloux Agricultural University, Gembloux, Belgium
| | | | | |
Collapse
|
49
|
Genetic diversity in Tunisian dromedary (Camelus dromedarius) populations using microsatellite markers. Livest Sci 2010. [DOI: 10.1016/j.livsci.2010.05.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
50
|
Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S. Genetic diversity in farm animals--a review. Anim Genet 2010; 41 Suppl 1:6-31. [PMID: 20500753 DOI: 10.1111/j.1365-2052.2010.02038.x] [Citation(s) in RCA: 285] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology.
Collapse
Affiliation(s)
- L F Groeneveld
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Hoeltystr. 10, 31535 Neustadt, Germany
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|