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Alanzor Puente JM, Pons Barro ÁL, González Ariza A, Martínez Martínez MDA, Delgado Bermejo JV, Navas González FJ. Integrated Discriminant Evaluation of Molecular Genetic Markers and Genetic Diversity Parameters of Endangered Balearic Dog Breeds. Int J Mol Sci 2024; 25:2706. [PMID: 38473952 DOI: 10.3390/ijms25052706] [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: 01/27/2024] [Revised: 02/15/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
The genetic diversity analysis of six dog breeds, including Ca de Bestiar (CB), Ca de Bou (CBOU), Podenco Ibicenco (PI), Ca Rater (CR), Ca Mè (CM), and Ca de Conills (CC), reveals insightful findings. CB showcases the highest mean number of alleles (6.17) and heterozygosity values, with significant deviations from Hardy-Weinberg equilibrium (HWE) observed in five markers, indicating high intra-racial genetic diversity (average observed heterozygosity (Ho) = 0.754, expected heterozygosity (He) = 0.761). In contrast, CBOU presents the lowest mean number of alleles (5.05) and heterozygosity values, coupled with moderate polymorphic information content (PIC) values and a moderate level of intra-racial genetic diversity (average Ho = 0.313, He = 0.394). PI demonstrates moderate genetic diversity with an average of 5.75 alleles and highly informative PIC values, while CR displays robust genetic diversity with an average of 6.61 alleles and deviations from equilibrium, indicating potential risks of inbreeding (average Ho = 0.563, He = 0.658). CM exhibits moderate genetic diversity and deviations from equilibrium, similar to CBOU, with an average of 6.5 alleles and moderate PIC values (average Ho = 0.598, He = 0.676). Conversely, CC shows a wider range of allelic diversity and deviations from equilibrium (average Ho = 0.611, He = 0.706), suggesting a more diverse genetic background. Inter-racial analysis underscores distinct genetic differentiation between breeds, emphasizing the importance of informed breeding decisions and proactive genetic management strategies to preserve diversity, promote breed health, and ensure long-term sustainability across all breeds studied.
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Affiliation(s)
- José Manuel Alanzor Puente
- Institut de Reserca i Formaciò Agroalimentaria de les Illes Balears IRFAP, Conselleria d'Agricultura, Pesca i Alimentació, Govern Illes Balears, 07009 Palma, Spain
| | - Águeda Laura Pons Barro
- Institut de Reserca i Formaciò Agroalimentaria de les Illes Balears IRFAP, Conselleria d'Agricultura, Pesca i Alimentació, Govern Illes Balears, 07009 Palma, Spain
| | - Antonio González Ariza
- Centro Agropecuario Provincial de Córdoba, Diputación Provincial de Córdoba, 14014 Córdoba, Spain
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Nikitović J, Pojskić N, Kalajdžić A, Ušanović L, Maletić Z, Stroil BK. Genetic Diversity of Bosnian and Herzegovinian Autochthonous Dog Breed Bosnian Broken-Haired Hound-Barak. Biochem Genet 2022; 61:901-915. [PMID: 36229562 DOI: 10.1007/s10528-022-10291-8] [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: 04/19/2022] [Accepted: 10/02/2022] [Indexed: 11/02/2022]
Abstract
Fédération Cynologique Internationale (FCI) classifies a group of hound dogs in the sixth FCI group divided into three sections and three subsections that include 76 dog breeds. With the Istrian wire-haired hound, the Bosnian broken-haired hound-Barak is one of the two internationally recognized and standardized broken-haired hound breeds from the Balkans. However, genotyping of this breed has not been the subject of study so far. A total of 30 dogs (22 males and eight females) from different breeders from 17 locations in Bosnia and Herzegovina were selected for genotyping. All selected individuals had a valid pedigree issued by the Kennel Club in Bosnia and Herzegovina to ensure dogs were unrelated. Hairs with follicles were used for DNA extraction. Ten microsatellite loci from the commercial StockMarks® for Canine Genotyping Kit were amplified. Estimated genetic indices showed that Bosnian broken-haired hound-Barak harbors a high genetic variability. Phylogenetic relationships between Barak and the other 15 dog breeds, including Tornjak, another indigenous breed from Bosnia and Herzegovina, were assessed. An analysis showed clear differentiation of Barak, with Tornjak as the closest one among analyzed breeds. The results suggest that Barak, as we know it today, was developed during the formation of most modern breeds. Although Barak cannot yet be considered an endangered breed thanks to enthusiasts and hunters, the declining population trends impose the urgent need to establish an animal gene bank and programs for in situ conservation to protect and preserve this autochthonous breed of hound dog for future generations.
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Affiliation(s)
- Jelena Nikitović
- Institute for Genetic Resources, University of Banja Luka, Bulevar vojvode Petra Bojovica 1a, 78000, Banja Luka, Bosnia and Herzegovina.
| | - Naris Pojskić
- University of Sarajevo-Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, 71000, Sarajevo, Bosnia and Herzegovina
| | - Abdurahim Kalajdžić
- University of Sarajevo-Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, 71000, Sarajevo, Bosnia and Herzegovina
| | - Lejla Ušanović
- University of Sarajevo-Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, 71000, Sarajevo, Bosnia and Herzegovina
| | - Zoran Maletić
- Ministry of Agriculture, Forestry and Water Management, Trg Republike Srpske 1, 78000, Banja Luka, Bosnia and Herzegovina
| | - Belma Kalamujić Stroil
- University of Sarajevo-Institute for Genetic Engineering and Biotechnology, Zmaja od Bosne 8, 71000, Sarajevo, Bosnia and Herzegovina
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Kriangwanich W, Nganvongpanit K, Buddhachat K, Siengdee P, Chomdej S, Ponsuksili S, Thitaram C. Genetic variations and dog breed identification using inter-simple sequence repeat markers coupled with high resolution melting analysis. PeerJ 2020; 8:e10215. [PMID: 33194413 PMCID: PMC7605226 DOI: 10.7717/peerj.10215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/28/2020] [Indexed: 12/28/2022] Open
Abstract
The identification of differing physical characteristics of dogs is an uncomplicated and straightforward way to categorize dog breeds. However, many dog owners and veterinarians still struggle to distinguish between pure breed and mixed variations in certain breeds of dogs. Presently, the absence of the tools and methods needed to confirm a pure breed dog is a significant problem since the only method available to validate pure or mongrel breeds is the official pedigree system. Inter-simple sequence repeat markers have been successfully used to assess genetic variations and differentiations. Notably, inter-simple sequence repeat markers coupled with high resolution melting analysis were effectively used for the breed identification of 43 breeds of dogs (total 463 dogs). The 10 primers chosen for analysis resulted in a range of 31-78.6% of breed discrimination when using one primer, while a combination of two primers was able to successfully discriminate between all of the 43 dog breeds (100%). Shannon's index information (I = 2.586 ± 0.034) and expected heterozygosity (H e = 0.908 ± 0.003) indicated a high level of genetic diversity among breeds. The fixation index (F st ) revealed a value of 10.4%, demonstrating that there was a high level of genetic subdivision between populations. This study showed that inter-simple sequence repeat marker analysis was effective in demonstrating high genetic diversity among varying breeds of dogs, while a combination of Inter-simple sequence repeat marker analysis and high resolution melting analysis could provide an optional technique for researchers to effectively identify breeds through genetic variations.
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Affiliation(s)
- Wannapimol Kriangwanich
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Korakot Nganvongpanit
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand
| | - Kittisak Buddhachat
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Puntita Siengdee
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand
- Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Siriwadee Chomdej
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | | | - Chatchote Thitaram
- Center of Excellence in Elephant and Wildlife Research, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
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Talenti A, Dreger DL, Frattini S, Polli M, Marelli S, Harris AC, Liotta L, Cocco R, Hogan AN, Bigi D, Caniglia R, Parker HG, Pagnacco G, Ostrander EA, Crepaldi P. Studies of modern Italian dog populations reveal multiple patterns for domestic breed evolution. Ecol Evol 2018; 8:2911-2925. [PMID: 29531705 PMCID: PMC5838073 DOI: 10.1002/ece3.3842] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/27/2017] [Indexed: 01/16/2023] Open
Abstract
Through thousands of years of breeding and strong human selection, the dog (Canis lupus familiaris) exists today within hundreds of closed populations throughout the world, each with defined phenotypes. A singular geographic region with broad diversity in dog breeds presents an interesting opportunity to observe potential mechanisms of breed formation. Italy claims 14 internationally recognized dog breeds, with numerous additional local varieties. To determine the relationship among Italian dog populations, we integrated genetic data from 263 dogs representing 23 closed dog populations from Italy, seven Apennine gray wolves, and an established dataset of 161 globally recognized dog breeds, applying multiple genetic methods to characterize the modes by which breeds are formed within a single geographic region. Our consideration of each of five genetic analyses reveals a series of development events that mirror historical modes of breed formation, but with variations unique to the codevelopment of early dog and human populations. Using 142,840 genome-wide SNPs and a dataset of 1,609 canines, representing 182 breeds and 16 wild canids, we identified breed development routes for the Italian breeds that included divergence from common populations for a specific purpose, admixture of regional stock with that from other regions, and isolated selection of local stock with specific attributes.
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Affiliation(s)
- Andrea Talenti
- Dipartimento di Medicina VeterinariaUniversità di MilanoMilanoItaly
| | - Dayna L. Dreger
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Stefano Frattini
- Dipartimento di Medicina VeterinariaUniversità di MilanoMilanoItaly
| | - Michele Polli
- Dipartimento di Medicina VeterinariaUniversità di MilanoMilanoItaly
| | - Stefano Marelli
- Dipartimento di Medicina VeterinariaUniversità di MilanoMilanoItaly
| | - Alexander C. Harris
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Luigi Liotta
- Dipartimento di Scienze VeterinarieUniversity of MessinaMessinaItaly
| | - Raffaella Cocco
- Dipartimento di Medicina VeterinariaUniversity of SassariSassariItaly
| | - Andrew N. Hogan
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Daniele Bigi
- Dipartimento di Scienza e Tecnologie Agro‐AlimentariAlma Mater Studiorum University of BolognaBolognaItaly
| | - Romolo Caniglia
- Area per la Genetica della ConservazioneIstituto Superiore per la Protezione e la Ricerca AmbientaleOzzano dell'EmiliaBolognaItaly
| | - Heidi G. Parker
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Giulio Pagnacco
- Dipartimento di Medicina VeterinariaUniversità di MilanoMilanoItaly
| | - Elaine A. Ostrander
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Paola Crepaldi
- Dipartimento di Medicina VeterinariaUniversità di MilanoMilanoItaly
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Radko A, Rubiś D, Szumiec A. Analysis of microsatellite DNA polymorphism in the Tatra Shepherd Dog. JOURNAL OF APPLIED ANIMAL RESEARCH 2017. [DOI: 10.1080/09712119.2017.1292912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Anna Radko
- Department of Genomics and Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - Dominika Rubiś
- Department of Genomics and Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - Agnieszka Szumiec
- Department of Genomics and Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
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Ciampolini R, Cecchi F, Bramante A, Casetti F, Presciuttini S. Genetic variability of the Bracco Italiano dog breed based on microsatellite polimorphism. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2011.e59] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Roberta Ciampolini
- Dipartimento di Patologia Animale Profilassi ed Igiene degli Alimenti, Università di Pisa, Italy
| | - Francesca Cecchi
- Dipartimento di Patologia Animale Profilassi ed Igiene degli Alimenti, Università di Pisa, Italy
| | - Assunta Bramante
- Dipartimento di Patologia Animale Profilassi ed Igiene degli Alimenti, Università di Pisa, Italy
| | - Fabio Casetti
- Società Amatori Bracco Italiano, Mirabello di Senna Lodigiana (LO), Italy
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Cecchi F, Paci G, Spaterna A, Ragatzu M, Ciampolini R. Demographic approach on the study of genetic parameters in the dogBraque FrançaistypePyrénéesItalian population. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.1080/1828051x.2015.1128689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Cecchi F, Paci G, Spaterna A, Ciampolini R. Genetic Variability inBracco ItalianoDog Breed Assessed by Pedigree Data. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2013.e54] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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La Manna V, Lasagna E, Ceccobelli S, Di Lorenzo P, De Cosmo AM, Attard G, Sarti FM, Panella F, Renieri C. Genetic Differentiation Between Segugio Dell’Appeinnino and Segugio Maremmano Dog Breeds Assessed by Microsatellite Markers. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2015.3809] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Vincenzo La Manna
- Scuola del Farmaco e dei Prodotti della Salute, University of Camerino, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Italy
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Italy
| | - Piera Di Lorenzo
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Italy
| | - Attilio M. De Cosmo
- Scuola del Farmaco e dei Prodotti della Salute, University of Camerino, Italy
| | - George Attard
- Institute of Earth Systems, University of Malta, Msida, Malta
| | - Francesca M. Sarti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Italy
| | - Francesco Panella
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Italy
| | - Carlo Renieri
- Scuola di Bioscienze e Medicina Veterinaria, University of Camerino, Italy
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Parker HG, Gilbert SF. From caveman companion to medical innovator: genomic insights into the origin and evolution of domestic dogs. ACTA ACUST UNITED AC 2015; 5:239-255. [PMID: 28490917 DOI: 10.2147/agg.s57678] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The phenotypic and behavioral diversity of the domestic dog has yet to be matched by any other mammalian species. In their current form, which comprises more than 350 populations known as breeds, there is a size range of two orders of magnitude and morphological features reminiscent of not only different species but also different phylogenetic families. The range of both appearance and behavior found in the dog is the product of millennia of human interference, and though humans created the diversity it remains a point of fascination to both lay and scientific communities. In this review we summarize the current understanding of the history of dog domestication based on molecular data. We will examine the ways that canine genetic and genomic studies have evolved and look at examples of dog genetics in the light of human disease.
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Affiliation(s)
- Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, Bethesda MD, 20892 USA
| | - Samuel F Gilbert
- National Human Genome Research Institute, National Institutes of Health, Bethesda MD, 20892 USA
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11
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Statistical analysis and genetic diversity of three dog breeds using simple sequence repeats. Genes Genomics 2014. [DOI: 10.1007/s13258-014-0237-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Abstract
A rose may be a rose by any other name, but when you call a dog a poodle it becomes a very different animal than if you call it a bulldog. Both the poodle and the bulldog are examples of dog breeds of which there are >400 recognized worldwide. Breed creation has played a significant role in shaping the modern dog from the length of his leg to the cadence of his bark. The selection and line-breeding required to maintain a breed has also reshaped the genome of the dog, resulting in a unique genetic pattern for each breed. The breed-based population structure combined with extensive morphologic variation and shared human environments have made the dog a popular model for mapping both simple and complex traits and diseases. In order to obtain the most benefit from the dog as a genetic system, it is necessary to understand the effect structured breeding has had on the genome of the species. That is best achieved by looking at genomic analyses of the breeds, their histories, and their relationships to each other.
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Affiliation(s)
- Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50, Room 5347, Bethesda, MD 20892, USA.
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13
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Streitberger K, Schweizer M, Kropatsch R, Dekomien G, Distl O, Fischer MS, Epplen JT, Hertwig ST. Rapid genetic diversification within dog breeds as evidenced by a case study on Schnauzers. Anim Genet 2011; 43:577-86. [DOI: 10.1111/j.1365-2052.2011.02300.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2011] [Indexed: 11/28/2022]
Affiliation(s)
| | - M. Schweizer
- Naturhistorisches Museum der Burgergemeinde Bern; Bernastrasse 15; CH 3005; Bern; Switzerland
| | - R. Kropatsch
- Humangenetik; Ruhr-Universität; Universitätsstr. 150; 44801; Bochum; Germany
| | - G. Dekomien
- Humangenetik; Ruhr-Universität; Universitätsstr. 150; 44801; Bochum; Germany
| | - O. Distl
- Institut für Tierzucht und Vererbungsforschung; Stiftug Tierärztliche Hochschule Hannover; Bünteweg 17p; 30559; Hannover; Germany
| | - M. S. Fischer
- Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum; Friedrich-Schiller-Universität; Erbertstr. 1; 07743; Jena; Germany
| | - J. T. Epplen
- Humangenetik; Ruhr-Universität; Universitätsstr. 150; 44801; Bochum; Germany
| | - S. T. Hertwig
- Naturhistorisches Museum der Burgergemeinde Bern; Bernastrasse 15; CH 3005; Bern; Switzerland
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Gagliardi R, Llambí S, García C, Arruga MV. Microsatellite characterization of Cimarron Uruguayo dogs. Genet Mol Biol 2011; 34:165-8. [PMID: 21637561 PMCID: PMC3085364 DOI: 10.1590/s1415-47572010005000101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 07/29/2010] [Indexed: 11/28/2022] Open
Abstract
Various genetic markers, including microsatellites, have been used to analyze the genetic polymorphism and heterozygosity in canine breeds. In this work, we used nine microsatellite markers to investigate the genetic variability in Cimarron Uruguayo dogs, the only officially recognized native canine breed in Uruguay. DNA from 30 Cimarron Uruguayo dogs from northeastern and southern Uruguay was analyzed. The allelic frequencies for each microsatellite, the genetic variability and the consanguinity were calculated, as were the polymorphic information content (PIC) and the probability of exclusion (PE). All of the microsatellites studied were polymorphic. FH 2361, FH 2305 and PEZ 03 were the most informative, with PIC values > 0.7, in agreement with results for other canine breeds. The PE values for the markers were within the ranges previously described and were generally greater for microsatellites with higher PIC values. The heterozygosity value (0.649) was considered high since only nine microsatellites were analyzed. Compared with data for other breeds, the results obtained here indicate that Cimarron Uruguayo dogs have high genetic diversity.
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Affiliation(s)
- Rosa Gagliardi
- Área Genética, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
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15
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Shinkarenko LN, Guliakova OG, Malienko VA, Melnychuk SD, Spyrydonov VG. Analysis of genetic variability in American Pit Bull Terrier breed of dogs with a high inbreeding level using microsatellite markers. CYTOL GENET+ 2010. [DOI: 10.3103/s0095452710040031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Pires AE, Amorim IR, Ginja C, Gomes M, Godinho I, Simões F, Oom M, Petrucci-Fonseca F, Matos J, Bruford MW. Molecular structure in peripheral dog breeds: Portuguese native breeds as a case study. Anim Genet 2009; 40:383-92. [DOI: 10.1111/j.1365-2052.2009.01849.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Mukesh M, Sodhi M, Kataria R, Mishra B. Use of microsatellite multilocus genotypic data for individual assignment assay in six native cattle breeds from north-western region of India. Livest Sci 2009. [DOI: 10.1016/j.livsci.2008.05.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Kang BT, Kim KS, Min MS, Chae YJ, Kang JW, Yoon J, Choi J, Seong JK, Park HC, An J, Lee MH, Park HM, Lee H. Microsatellite loci analysis for the genetic variability and the parentage test of five dog breeds in South Korea. Genes Genet Syst 2009; 84:245-51. [DOI: 10.1266/ggs.84.245] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Byeong-Teck Kang
- BK21 Program of Basic and Diagnostic Veterinary Specialist Program for Animal Diseases and Department of Veterinary Internal Medicine, College of Veterinary Medicine, Konkuk University
| | | | - Mi-Sook Min
- Conservation Genome Resource Bank for Korean Wildlife
| | | | | | | | - Jihye Choi
- Department of Veterinary Medical Imaging
| | - Je-Kyung Seong
- Laboratory of Developmental Biology and Genomics, BK21 Program for Veterinary Science and College of Veterinary Medicine, Seoul National University
| | - Han-Chan Park
- Conservation Genome Resource Bank for Korean Wildlife
| | - Junghwa An
- Conservation Genome Resource Bank for Korean Wildlife
| | - Mun-Han Lee
- Conservation Genome Resource Bank for Korean Wildlife
| | - Hee-Myung Park
- BK21 Program of Basic and Diagnostic Veterinary Specialist Program for Animal Diseases and Department of Veterinary Internal Medicine, College of Veterinary Medicine, Konkuk University
| | - Hang Lee
- Conservation Genome Resource Bank for Korean Wildlife
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Parra D, Méndez S, Cañón J, Dunner S. Genetic differentiation in pointing dog breeds inferred from microsatellites and mitochondrial DNA sequence. Anim Genet 2008; 39:1-7. [PMID: 18254732 DOI: 10.1111/j.1365-2052.2007.01658.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent studies presenting genetic analysis of dog breeds do not focus specifically on genetic relationships among pointing dog breeds, although hunting was among the first traits of interest when dogs were domesticated. This report compares histories with genetic relationships among five modern breeds of pointing dogs (English Setter, English Pointer, Epagneul Breton, Deutsch Drahthaar and German Shorthaired Pointer) collected in Spain using mitochondrial, autosomal and Y-chromosome information. We identified 236 alleles in autosomal microsatellites, four Y-chromosome haplotypes and 18 mitochondrial haplotypes. Average F(ST) values were 11.2, 14.4 and 13.1 for autosomal, Y-chromosome microsatellite markers and mtDNA sequence respectively, reflecting relatively high genetic differentiation among breeds. The high gene diversity observed in the pointing breeds (61.7-68.2) suggests contributions from genetically different individuals, but that these individuals originated from the same ancestors. The modern English Setter, thought to have arisen from the Old Spanish Pointer, was the first breed to cluster independently when using autosomal markers and seems to share a common maternal origin with the English Pointer and German Shorthaired Pointer, either via common domestic breed females in the British Isles or through the Old Spanish Pointer females taken to the British Isles in the 14th and 16th centuries. Analysis of mitochondrial DNA sequence indicates the isolation of the Epagneul Breton, which has been formally documented, and shows Deutsch Drahthaar as the result of crossing the German Shorthaired Pointer with other breeds. Our molecular data are consistent with historical documents.
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Affiliation(s)
- D Parra
- Department of Animal Production, Veterinary Faculty, Universidad Complutense, 28040 Madrid, Spain
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Onogi A, Nurimoto M, Sato Y, Morita M. A chromosomal duplication that includes the canine microsatellite INRA21 in Labrador Retrievers. Anim Genet 2008; 39:241-8. [PMID: 18355398 DOI: 10.1111/j.1365-2052.2008.01705.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
INRA21 is one of the canine microsatellites recommended for parentage verification by the International Society for Animal Genetics. In Labrador Retrievers, abnormal peak patterns such as three-peak patterns during capillary electrophoresis were frequently observed at INRA21. Pedigree analysis indicated that the abnormal peak patterns were due to inheritable causes, and semiquantitative multiplex (SQM) PCR analysis showed that the abnormal peak patterns were caused by chromosomal duplication. Walking SQM-PCR analysis revealed that the size of the duplicated segment was approximately 1.58 Mb. Genotypes of microsatellites within the duplicated segment indicated that the duplication was an identical-by-descent mutation. This duplication is probably carried by more than half of the dogs in the Japanese population of Labrador Retrievers. The abnormal peak patterns at INRA21 were also observed in German Shorthaired Pointers and Flat-Coated Retrievers. Genotyping analysis of the microsatellites within the duplicated segment in Labrador Retrievers suggested that the abnormal peak patterns observed in the two breeds were due to the duplication inherited from the same ancestor as the duplication of Labrador Retrievers. This study urges attention to the use of INRA21 and shows an example of copy number polymorphisms that are characteristic to dog breeds or lineages.
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Affiliation(s)
- A Onogi
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi 371-0121, Japan.
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21
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Björnerfeldt S, Hailer F, Nord M, Vilà C. Assortative mating and fragmentation within dog breeds. BMC Evol Biol 2008; 8:28. [PMID: 18226210 PMCID: PMC2266708 DOI: 10.1186/1471-2148-8-28] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Accepted: 01/28/2008] [Indexed: 11/10/2022] Open
Abstract
Background There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. Results Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. Conclusion The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic population structure. The same processes which have historically created dog breeds are still ongoing, and create further subdivision within current dog breeds.
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Affiliation(s)
- Susanne Björnerfeldt
- Department of Evolutionary Biology, Uppsala University, S-752 36 Uppsala, Sweden.
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Parker HG, Kukekova AV, Akey DT, Goldstein O, Kirkness EF, Baysac KC, Mosher DS, Aguirre GD, Acland GM, Ostrander EA. Breed relationships facilitate fine-mapping studies: a 7.8-kb deletion cosegregates with Collie eye anomaly across multiple dog breeds. Genome Res 2007; 17:1562-71. [PMID: 17916641 DOI: 10.1101/gr.6772807] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The features of modern dog breeds that increase the ease of mapping common diseases, such as reduced heterogeneity and extensive linkage disequilibrium, may also increase the difficulty associated with fine mapping and identifying causative mutations. One way to address this problem is by combining data from multiple breeds segregating the same trait after initial linkage has been determined. The multibreed approach increases the number of potentially informative recombination events and reduces the size of the critical haplotype by taking advantage of shortened linkage disequilibrium distances found across breeds. In order to identify breeds that likely share a trait inherited from the same ancestral source, we have used cluster analysis to divide 132 breeds of dog into five primary breed groups. We then use the multibreed approach to fine-map Collie eye anomaly (cea), a complex disorder of ocular development that was initially mapped to a 3.9-cM region on canine chromosome 37. Combined genotypes from affected individuals from four breeds of a single breed group significantly narrowed the candidate gene region to a 103-kb interval spanning only four genes. Sequence analysis revealed that all affected dogs share a homozygous deletion of 7.8 kb in the NHEJ1 gene. This intronic deletion spans a highly conserved binding domain to which several developmentally important proteins bind. This work both establishes that the primary cea mutation arose as a single disease allele in a common ancestor of herding breeds as well as highlights the value of comparative population analysis for refining regions of linkage.
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Affiliation(s)
- Heidi G Parker
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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23
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Veit-Kensch CE, Medugorac I, Jedrzejewski W, Bunevich AN, Foerster M. A heuristic two-dimensional presentation of microsatellite-based data applied to dogs and wolves. Genet Sel Evol 2007. [DOI: 10.1051/gse:2007014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Short AD, Kennedy LJ, Barnes A, Fretwell N, Jones C, Thomson W, Ollier WER. Hardy–Weinberg Expectations in Canine Breeds: Implications for Genetic Studies. J Hered 2007; 98:445-51. [PMID: 17526918 DOI: 10.1093/jhered/esm020] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hardy-Weinberg equilibrium (HWE) is a useful indicator of genotype frequencies within a population and whether they are based on a valid definition of alleles and a randomly mating sample. HWE assumes a stable population of adequate size without selective pressures and is used in human genetic studies as a guide to data quality by comparing observed genotype frequencies to those expected within a population. The calculation of genetic associations in case-control studies assume that the population is "in HWE." Canine breed populations deviate away from many of the criteria for HWE, and if genetic markers are not in HWE, conventional statistical analysis cannot be performed. To date, little attention has been paid as to whether genetic markers in dog breeds are distributed in compliance to HWE. In this study, 109 single-nucleotide polymorphisms (SNPs) were genotyped from 13 genes in a cohort of 894 dogs encompassing 33 breeds. Analysis of the entire cohort of dogs revealed a significant deviation away from HWE for all SNPs tested (P < 0.00001); analysis of the cohort stratified by breed and subbreed indicated that the majority of the markers complied with HWE expectation. This suggests that canine case-control association studies will be valid if performed within defined breeds.
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Affiliation(s)
- Andrea D Short
- Centre for Integrated Genomic Medical Research, Stopford Building, The University of Manchester, Manchester M13 9PT, UK.
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Abstract
The domestication of the dog from its wolf ancestors is perhaps the most complex genetic experiment in history, and certainly the most extensive. Beginning with the wolf, man has created dog breeds that are hunters or herders, big or small, lean or squat, and independent or loyal. Most breeds were established in the 1800s by dog fanciers, using a small number of founders that featured traits of particular interest. Popular sire effects, population bottlenecks, and strict breeding programs designed to expand populations with desirable traits led to the development of what are now closed breeding populations, with limited phenotypic and genetic heterogeneity, but which are ideal for genetic dissection of complex traits. In this review, we first discuss the advances in mapping and sequencing that accelerated the field in recent years. We then highlight findings of interest related to disease gene mapping and population structure. Finally, we summarize novel results on the genetics of morphologic variation.
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26
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Abstract
The dog has emerged as a premier species for the study of morphology, behavior, and disease. The recent availability of a high-quality draft sequence lifts the dog system to a new threshold. We provide a primer to use the dog genome by first focusing on its evolutionary history. We overview the relationship of dogs to wild canids and discuss their origin and domestication. Dogs clearly originated from a substantial number of gray wolves and dog breeds define distinct genetic units that can be divided into at least four hierarchical groupings. We review evidence showing that dogs have high levels of linkage disequilibrium. Consequently, given that dog breeds express specific phenotypic traits and vary in behavior and the incidence of genetic disease, genomic-wide scans for linkage disequilibrium may allow the discovery of genes influencing breed-specific characteristics. Finally, we review studies that have utilized the dog to understand the genetic underpinning of several traits, and we summarize genomic resources that can be used to advance such studies. We suggest that given these resources and the unique characteristics of breeds, that the dog is a uniquely valuable resource for studying the genetic basis of complex traits.
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Affiliation(s)
- Elaine A Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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27
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Abstract
Genetic variability of the dog breed Hanoverian Hound was analysed using a set of 16 microsatellites. The sample of 92 dogs was representative for the total current population [n=334, inbreeding coefficient 9.2%, relationship coefficient 11.2%] with respect to the level and distribution of the inbreeding and relationship coefficients. All microsatellites used were in Hardy-Weinberg equilibrium. The average number of alleles was 6.4. The average observed heterozygosity (H(O)) was slightly higher than the expected heterozygosity (H(E)). Dinucleotide microsatellites exhibited lower polymorphism information content (PIC) than tetranucleotide microsatellites (0.52 versus 0.66). The average PIC was 0.61. The individual inbreeding coefficient was negatively related to the average H(O) of all microsatellites, whereas the proportion of genes from introducing of Hanoverian Hounds from abroad showed no relationships to H(O). We found that the genetic variability in the Hanoverian Hounds analysed here was unexpectedly higher than that previously published for dog breeds of similar population size. Even in dog breeds of larger population size heterogyzosity was seldom higher than that observed here. The rather high genetic variability as quantified by polymorphic microsatellites in Hanoverian Hounds may be due to a large genetic variation in the founder animals of this breed and to the fact that this genetic diversity could be maintained despite genetic bottlenecks experienced by this breed in the 1920s and 1950s and despite the presence of high inbreeding and relationship coefficients for more than 50 years.
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Affiliation(s)
- L Lüpke
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
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Puja IK, Irion DN, Schaffer AL, Pedersen NC. The Kintamani Dog: Genetic Profile of an Emerging Breed from Bali, Indonesia. J Hered 2005; 96:854-9. [PMID: 16014810 DOI: 10.1093/jhered/esi067] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Kintamani dog is an evolving breed indigenous to the Kintamani region of Bali. Kintamani dogs cohabitate with feral Bali street dogs, although folklore has the breed originating 600 years ago from a Chinese Chow Chow. The physical and personality characteristics of the Kintamani dog make it a popular pet for the Balinese, and efforts are currently under way to have the dog accepted by the Federation Cynologique Internationale as a recognized breed. To study the genetic background of the Kintamani dog, 31 highly polymorphic short tandem repeat markers were analyzed in Kintamani dogs, Bali street dogs, Australian dingoes, and nine American Kennel Club (AKC) recognized breeds of Asian or European origin. The Kintamani dog was identical to the Bali street dog at all but three loci. The Bali street dog and Kintamani dog were most closely aligned with the Australian dingo and distantly related to AKC recognized breeds of Asian but not European origin. Therefore, the Kintamani dog has evolved from Balinese feral dogs with little loss of genetic diversity.
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Affiliation(s)
- I K Puja
- School of Veterinary Medicine, University of Udyana, Denpasar, 80114 Bali, Indonesia
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29
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Stai SM, Hughes CR. Characterization of microsatellite loci in wild and domestic Muscovy ducks (Cairina moschata). Anim Genet 2004; 34:387-9. [PMID: 14510679 DOI: 10.1046/j.1365-2052.2003.01038.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- S M Stai
- Department of Biology, University of Miami, Coral Gables, FL 33124-0421, USA.
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Koskinen MT. Individual assignment using microsatellite DNA reveals unambiguous breed identification in the domestic dog. Anim Genet 2003; 34:297-301. [PMID: 12873219 DOI: 10.1046/j.1365-2052.2003.01005.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Modern individual clustering methods utilising hypervariable nuclear microsatellite DNA polymorphisms are being increasingly applied in the field of population genetics. This study explores the efficiency of the clustering methods in identifying the breeds of origin of 250 domestic dog (Canis familiaris) individuals based on 10 microsatellite loci. An allele sharing distance (DAS) matrix and the corresponding neighbour-joining tree of individuals revealed monophyletic assemblages that corresponded perfectly with the breeds of origin of the dogs. Individual assignment tests using a Bayesian statistical approach, an allele frequency based method, and a DCE genetic distance based method were all extremely powerful. Most strikingly, the Bayesian method provided 100% assignment success of individuals into their correct breeds of origin and 100% exclusion success of individuals from all alternate reference populations with a high level of statistical confidence (P < 0.0001). A Bayesian Markov Chain Monte Carlo clustering approach revealed clear distinction of individuals into groups according to their breeds of origin, with a near-zero level of 'genetic admixture' among breeds. The results demonstrate that an FST of 0.18, mean expected gene diversity of 0.6 across 10 loci, and approximately 50 individuals per reference population suffice to provide maximum individual assignment success in C. familiaris. This refutes the traditional view that DNA based dog breed identification is not feasible at the individual level of resolution.
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Affiliation(s)
- M T Koskinen
- Department of Ecology and Systematics, Division of Population Biology, University of Helsinki, Helsinki, Finland.
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Proschowsky HF, Olsen JB, Jepsen B, Fredholm M. Evaluation of the present breeding programme against copper toxicosis in Danish Bedlington terriers. Anim Genet 2003; 34:142-5. [PMID: 12648098 DOI: 10.1046/j.1365-2052.2003.00964.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A breeding programme to eradicate copper toxicosis in Danish Bedlington terriers has been established based on a DNA marker test. Genotyping of both parents is compulsory and after 1 January 2000, only homozygous non-carriers are used for breeding. In this study, two groups of Bedlington terriers were genotyped at 18 microsatellite loci. One group represented the original population of Bedlington terriers before introducing the breeding programme (n = 23); the other represented a group of homozygous non-carriers (n = 24) available for breeding after year 2000. Allele numbers, allele frequencies, observed heterozygosities (Ho), expected heterozygosities (He), locus-specific coefficients of inbreeding (Fl) and Nei's genetic distance (D) was calculated. Individual coefficients of inbreeding (Fi) were calculated from the pedigrees and an assignment test was performed. Four rare alleles were lost in the group of homozygous non-carriers. No significant differences were observed between the mean values of allele numbers, Ho, He, Fl and Fi of the two populations of dogs. Nei's genetic distance between the two populations was 0.06 and 88% of the homozygous non-carriers were assigned correctly in the assignment test. The overall diversity of the breed was low (Ho = 0.41) and the breeders were advised to include the heterozygous carriers again.
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Affiliation(s)
- H F Proschowsky
- Division of Animal Genetics, Department of Animal Science and Animal Health, The Royal Veterinary and Agricultural University, Frederiksberg C, Denmark.
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32
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Klukowska J, Strabel T, Mackowski M, Switonski M. Microsatellite polymorphism and genetic distances between the dog, red fox and arctic fox. J Anim Breed Genet 2003. [DOI: 10.1046/j.1439-0388.2003.00375.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Gilmore S, Peakall R, Robertson J. Short tandem repeat (STR) DNA markers are hypervariable and informative in Cannabis sativa: implications for forensic investigations. Forensic Sci Int 2003; 131:65-74. [PMID: 12505473 DOI: 10.1016/s0379-0738(02)00397-3] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Short tandem repeat (STR) markers are the DNA marker of choice in forensic analysis of human DNA. Here we extend the application of STR markers to Cannabis sativa and demonstrate their potential for forensic investigations. Ninety-three individual cannabis plants, representing drug and fibre accessions of widespread origin were profiled with five STR makers. A total of 79 alleles were detected across the five loci. All but four individuals from a single drug-type accession had a unique multilocus genotype. An analysis of molecular variance (AMOVA) revealed significant genetic variation among accessions, with an average of 25% genetic differentiation. By contrast, only 6% genetic difference was detected between drug and fibre crop accessions and it was not possible to unequivocally assign plants as either drug or fibre type. However, our results suggest that drug strains may typically possess lower genetic diversity than fibre strains, which may ultimately provide a means of genetic delineation. Our findings demonstrate the promise of cannabis STR markers to provide information on: (1) agronomic type, (2) the geographical origin of drug seizures, and (3) evidence of conspiracy in production of clonally propagated drug crops.
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Affiliation(s)
- Simon Gilmore
- Centre for Forensic Science, Canberra Institute of Technology, G.P.O. Box 826, Canberra ACT 2601, Australia.
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Brouillette JA, Venta PJ. Within-breed heterozygosity of canine single nucleotide polymorphisms identified by across-breed comparison. Anim Genet 2002; 33:464-7. [PMID: 12464024 DOI: 10.1046/j.1365-2052.2002.00918.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Identification of single nucleotide polymorphisms (SNPs) by DNA sequence comparison across breeds is a strategy for developing genetic markers that are useful for many breeds. However, the heterozygosity of SNPs identified in this way might be severely reduced within breeds by inbreeding or genetic drift in the small effective population size of a breed (population subdivision). The effect of inbreeding and population subdivision on heterozygosity of SNPs in dog breeds has never been investigated in a systematic way. We determined the genotypes of dogs from three divergent breeds for SNPs in four canine genes (ACTC, LMNA, SCGB, and TYMS) identified by across-breed DNA sequence comparison, and compared the genotype frequencies to those expected under Hardy-Weinberg equilibrium (HWE). Although population subdivision significantly skewed allele frequencies across breeds for two of the SNPs, the deviations of observed heterozygosities compared with those expected within breeds were minimal. These results indicate that across-breed DNA sequence comparison is a reasonable strategy for identifying SNPs that are useful within many canine breeds.
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Affiliation(s)
- J A Brouillette
- Microbiology and Molecular Genetics, Genetics Program, College of Human Medicine, Michigan State University, East Lansing 48824-1314, USA
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35
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Oliveira P, Oliveira D, Teixeira C, Velloso A, Coelho E, Rodrigues S, Alves C. Teste de DNA para verificação de parentesco em cães: avaliação do método não automatizado com o auxílio do primer CMR S. ARQ BRAS MED VET ZOO 2002. [DOI: 10.1590/s0102-09352002000500018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Moazami-Goudarzi K, Laloë D. Is a Multivariate Consensus Representation of Genetic Relationships Among Populations Always Meaningful? Genetics 2002; 162:473-84. [PMID: 12242255 PMCID: PMC1462258 DOI: 10.1093/genetics/162.1.473] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
To determine the relationships among closely related populations or species, two methods are commonly used in the literature: phylogenetic reconstruction or multivariate analysis. The aim of this article is to assess the reliability of multivariate analysis. We describe a method that is based on principal component analysis and Mantel correlations, using a two-step process: The first step consists of a single-marker analysis and the second step tests if each marker reveals the same typology concerning population differentiation. We conclude that if single markers are not congruent, the compromise structure is not meaningful. Our model is not based on any particular mutation process and it can be applied to most of the commonly used genetic markers. This method is also useful to determine the contribution of each marker to the typology of populations. We test whether our method is efficient with two real data sets based on microsatellite markers. Our analysis suggests that for closely related populations, it is not always possible to accept the hypothesis that an increase in the number of markers will increase the reliability of the typology analysis.
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Affiliation(s)
- K Moazami-Goudarzi
- Laboratoire de Génétique Biochimique et de Cytogénétique, INRA, 78352 Jouy-en-Josas, France
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