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Varga L, Edviné EM, Hudák P, Anton I, Pálinkás-Bodzsár N, Zsolnai A. Balancing at the Borderline of a Breed: A Case Study of the Hungarian Short-Haired Vizsla Dog Breed, Definition of the Breed Profile Using Simple SNP-Based Methods. Genes (Basel) 2022; 13:2022. [PMID: 36360261 PMCID: PMC9690546 DOI: 10.3390/genes13112022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/30/2022] [Accepted: 10/31/2022] [Indexed: 09/16/2023] Open
Abstract
The aim of this study was to determine the breed boundary of the Hungarian Short-haired Vizsla (HSV) dog breed. Seventy registered purebred HSV dogs were genotyped on approximately 145,000 SNPs. Principal Component Analysis (PCA) and Admixture analysis certified that they belong to the same population. The outer point of the breed demarcation was a single Hungarian Wire-haired Vizsla (HWV) individual, which was the closest animal genetically to the HSV population in the PCA analysis. Three programs were used for the breed assignment calculations, including the widely used GeneClass2.0 software and two additional approaches developed here: the 'PCA-distance' and 'IBS-central' methods. Both new methods calculate a single number that represents how closely a dog fits into the actual reference population. The former approach calculates this number based on the PCA distances from the median of HSV animals. The latter calculates it from identity by state (IBS) data, measuring the distance from a central animal that is the best representative of the breed. Having no mixed-breed dogs with known HSV genome proportion, admixture animals were simulated by using data of HSV and HWV individuals to calibrate the inclusion/exclusion probabilities for the assignment. The numbers generated from these relatively simple calculations can be used by breeders and clubs to keep their populations under genetic supervision.
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Affiliation(s)
- László Varga
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent István Campus, 2100 Gödöllő, Hungary
- Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, 2100 Gödöllő, Hungary
| | - Erika Meleg Edviné
- Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, 2100 Gödöllő, Hungary
| | - Péter Hudák
- Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, 2100 Gödöllő, Hungary
| | - István Anton
- Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, 2053 Herceghalom, Hungary
| | - Nóra Pálinkás-Bodzsár
- Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, 2100 Gödöllő, Hungary
| | - Attila Zsolnai
- Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, 2100 Gödöllő, Hungary
- Department of Animal Breeding, Institute of Animal Science, Hungarian University of Agriculture and Life Sciences, Kaposvár Campus, 2053 Herceghalom, Hungary
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2
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Raymond PW, Velie BD, Wade CM. Forensic DNA phenotyping: Canis familiaris breed classification and skeletal phenotype prediction using functionally significant skeletal SNPs and indels. Anim Genet 2021; 53:247-263. [PMID: 34963196 DOI: 10.1111/age.13165] [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: 10/21/2020] [Revised: 11/30/2021] [Accepted: 12/12/2021] [Indexed: 11/29/2022]
Abstract
This review highlights a novel application of breed identification and prediction of skeletal traits in forensic investigations using canine DNA evidence. Currently, genotyping methods used for canine breed classification involve the application of highly polymorphic short tandem repeats in addition to larger commercially available SNP arrays. Both applications face technical challenges. An additional approach to breed identification could be through genotyping SNPs and indels that characterise the array of skeletal differences displayed across domestic dog populations. Research has shown that a small number of genetic variants of large effect drive differences in skeletal phenotypes among domestic dog breeds. This feature makes functionally significant canine skeletal variants a cost-effective target for forensic investigators to classify individuals according to their breed. Further analysis of these skeletal variants would enable the prediction of external appearance. To date, functionally significant genes with genetic variants associated with differences in size, bulk, skull shape, ear shape, limb length, digit type, and tail morphology have been uncovered. Recommendations of a cost-effective genotyping method that can be readily designed and applied by forensic investigators have been given. Further advances to improve the field of canine skeletal forensic DNA phenotyping include the refinement of phenotyping methods, further biological validation of the skeletal genetic variants and establishing a publicly available database for storage of allele frequencies of the skeletal genetic variants in the wider domestic dog population.
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Affiliation(s)
- Patrick W Raymond
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Brandon D Velie
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Claire M Wade
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
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Chibuk J, Flory A, Kruglyak KM, Leibman N, Nahama A, Dharajiya N, van den Boom D, Jensen TJ, Friedman JS, Shen MR, Clemente-Vicario F, Chorny I, Tynan JA, Lytle KM, Holtvoigt LE, Murtaza M, Diaz LA, Tsui DWY, Grosu DS. Horizons in Veterinary Precision Oncology: Fundamentals of Cancer Genomics and Applications of Liquid Biopsy for the Detection, Characterization, and Management of Cancer in Dogs. Front Vet Sci 2021; 8:664718. [PMID: 33834049 PMCID: PMC8021921 DOI: 10.3389/fvets.2021.664718] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 02/23/2021] [Indexed: 12/14/2022] Open
Abstract
Cancer is the leading cause of death in dogs, in part because many cases are identified at an advanced stage when clinical signs have developed, and prognosis is poor. Increased understanding of cancer as a disease of the genome has led to the introduction of liquid biopsy testing, allowing for detection of genomic alterations in cell-free DNA fragments in blood to facilitate earlier detection, characterization, and management of cancer through non-invasive means. Recent discoveries in the areas of genomics and oncology have provided a deeper understanding of the molecular origins and evolution of cancer, and of the "one health" similarities between humans and dogs that underlie the field of comparative oncology. These discoveries, combined with technological advances in DNA profiling, are shifting the paradigm for cancer diagnosis toward earlier detection with the goal of improving outcomes. Liquid biopsy testing has already revolutionized the way cancer is managed in human medicine - and it is poised to make a similar impact in veterinary medicine. Multiple clinical use cases for liquid biopsy are emerging, including screening, aid in diagnosis, targeted treatment selection, treatment response monitoring, minimal residual disease detection, and recurrence monitoring. This review article highlights key scientific advances in genomics and their relevance for veterinary oncology, with the goal of providing a foundational introduction to this important topic for veterinarians. As these technologies migrate from human medicine into veterinary medicine, improved awareness and understanding will facilitate their rapid adoption, for the benefit of veterinary patients.
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Affiliation(s)
| | | | | | - Nicole Leibman
- The Cancer Institute, Animal Medical Center, New York, NY, United States
| | | | | | | | | | | | - M. Richard Shen
- RS Technology Ventures LLC., Rancho Santa Fe, CA, United States
| | | | | | | | | | | | - Muhammed Murtaza
- Department of Surgery and Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Luis A. Diaz
- Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
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4
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Guldbrandtsen B, Nielsen VH, Schönherz AA. Genomic assessment of suitability of pigs for inclusion in the Pied Danish Pig conservation program – A case study. ACTA AGR SCAND A-AN 2020. [DOI: 10.1080/09064702.2020.1732455] [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]
Affiliation(s)
- Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Vivi H. Nielsen
- Danish Center for Agriculture, Aarhus University, Tjele, Denmark
| | - Anna A. Schönherz
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
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Janeš M, Zorc M, Cubric-Curik V, Curik I, Dovc P. Population structure and genetic history of Tibetan Terriers. Genet Sel Evol 2019; 51:79. [PMID: 31881816 PMCID: PMC6935067 DOI: 10.1186/s12711-019-0520-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/17/2019] [Indexed: 01/08/2023] Open
Abstract
Background Tibetan Terrier is a popular medium-sized companion dog breed. According to the history of the breed, the western population of Tibetan Terriers includes two lineages, Lamleh and Luneville. These two lineages derive from a small number of founder animals from the native Tibetan Terrier population, which were brought to Europe in the 1920s. For almost a century, the western population of Tibetan Terriers and the native population in Tibet were reproductively isolated. In this study, we analysed the structure of the western population of Tibetan Terriers, the original native population from Tibet and of different crosses between these two populations. We also examined the genetic relationships of Tibetan Terriers with other dog breeds, especially terriers and some Asian breeds, and the within-breed structure of both Tibetan Terrier populations. Results Our analyses were based on high-density single nucleotide polymorphism (SNP) array (Illumina HD Canine 170 K) and microsatellite (18 loci) genotypes of 64 Tibetan Terriers belonging to different populations and lineages. For the comparative analysis, we used 348 publicly available SNP array genotypes of dogs from other breeds. We found that the western population of Tibetan Terriers and the native Tibetan Terriers clustered together with other Asian dog breeds, whereas all other terrier breeds were grouped into a separate group. We were also able to differentiate the western Tibetan Terrier lineages (Lamleh and Luneville) from the native Tibetan Terrier population. Conclusions Our results reveal the relationships between the western and native populations of Tibetan Terriers and support the hypothesis that Tibetan Terrier belongs to the group of ancient dog breeds of Asian origin, which are close to the ancestors of the modern dog that were involved in the early domestication process. Thus, we were able to reject the initial hypothesis that Tibetan Terriers belong to the group of terrier breeds. The existence of this native population of Tibetan Terriers at its original location represents an exceptional and valuable genetic resource.
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Affiliation(s)
- Mateja Janeš
- Department of Animal Science, University of Zagreb, Faculty of Agriculture, Zagreb, Croatia
| | - Minja Zorc
- Department of Animal Science, University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Vlatka Cubric-Curik
- Department of Animal Science, University of Zagreb, Faculty of Agriculture, Zagreb, Croatia
| | - Ino Curik
- Department of Animal Science, University of Zagreb, Faculty of Agriculture, Zagreb, Croatia
| | - Peter Dovc
- Department of Animal Science, University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia.
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Berger B, Heinrich J, Niederstätter H, Hecht W, Morf N, Hellmann A, Rohleder U, Schleenbecker U, Berger C, Parson W. Forensic characterization and statistical considerations of the CaDNAP 13-STR panel in 1,184 domestic dogs from Germany, Austria, and Switzerland. Forensic Sci Int Genet 2019; 42:90-98. [PMID: 31277051 DOI: 10.1016/j.fsigen.2019.06.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/21/2019] [Accepted: 06/22/2019] [Indexed: 12/13/2022]
Abstract
Crime scene samples originating from domestic dogs such as hair, blood, or saliva can be probative as possible transfer evidence in human crime and in dog attack cases. In the majority of such cases canine DNA identification using short tandem repeat (STR) analysis is the method of choice, which demands, among others, a systematic survey of allele frequency data in the relevant dog populations. A set of 13 highly polymorphic canine STR markers was used to analyze samples of 1,184 dogs (including 967 purebred dogs) from the so-called DACH countries (Germany, Austria, Switzerland). This CaDNAP 13-STR panel has previously been validated for canine identification in a forensic context. Here, we present robust estimates of allele frequencies, which are essential to assess the weight of the evidence by estimating the probability of a matching DNA profile within the dog population under question, e.g. in the form of a random match probability (RMP). The geographical provenance of the tested dogs showed a negligible influence on the observed genotype variation. Therefore, we combined the STR data from all three countries into a single dog population sample (DPS). In contrast, pronounced genetic differentiation between dog breeds was found by principal component analysis and sub-structure analysis with the STRUCTURE software. These findings entailed the need to account for the effects of DPS breed composition on allele frequency estimates. A possible strategy, which was favored here, relies on collecting a DPS that is guided by the breed composition of the relevant dog population. In total, dogs from 166 different breeds were included in our DPS, 64 of them including at least 5 individuals (n = 771 dogs). Sampling reflected the abundance of breeds in the DACH countries with the following being the most common ones: German Shepherds (population frequency: 14.3%), Dachshunds (5.9%), Labrador Retrievers (3.9%), and Golden Retrievers (3.2%). The pedigree listing of the purebred dogs in our DPS ranked German Shepherds (DPS frequency 8.5%) first, followed by Labrador Retrievers (3.9%), Golden Retrievers (3%), and Dachshunds (2.5%). RMP values based on overall allele frequencies and accounting for substructure using FST between breeds ranged between 10-13 and 10-14 and represent a conservative approach of RMP assessment.
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Affiliation(s)
- Burkhard Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
| | - Josephin Heinrich
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Werner Hecht
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Nadja Morf
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Andreas Hellmann
- Bundeskriminalamt, Kriminaltechnisches Institut, Wiesbaden, Germany
| | - Udo Rohleder
- Bundeskriminalamt, Kriminaltechnisches Institut, Wiesbaden, Germany
| | | | - Cordula Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
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Putnová L, Štohl R. Comparing assignment-based approaches to breed identification within a large set of horses. J Appl Genet 2019; 60:187-198. [PMID: 30963515 DOI: 10.1007/s13353-019-00495-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/25/2019] [Indexed: 10/27/2022]
Abstract
Considering the extensive data sets and statistical techniques, animal breeding embodies a branch of machine learning that has a constantly increasing impact on breeding. In our study, information regarding the potential of machine learning and data mining within a large set of horses and breeds is presented. The individual assignment methods and factors influencing the success rate of the procedure are compared at the Czech population scale. The fixation index values ranged from 0.057 (HMS1) to 0.144 (HTG6), and the overall genetic differentiation amounted to 8.9% among the breeds. The highest genetic divergence (FST = 0.378) was established between the Friesian and Equus przewalskii; the highest degree of gene migration was obtained between the Czech and Bavarian Warmblood (Nm = 14,302); and the overall global heterozygote deficit across the populations was 10.4%. The eight standard methods (Bayesian, frequency, and distance) using GeneClass software and almost all mainstream classification algorithms (Bayes Net, Naive Bayes, IB1, IB5, KStar, JRip, J48, Random Forest, Random Tree, PART, MLP, and SVM) from the WEKA machine learning workbench were compared by utilizing 314,874 real allelic data sets. The Bayesian method (GeneClass, 89.9%) and Bayesian network algorithm (WEKA, 84.8%) outperformed the other techniques. The breed genomic prediction accuracy reached the highest value in the cold-blooded horses. The overall proportion of individuals correctly assigned to a population depended mainly on the breed number and genetic divergence. These statistical tools could be used to assess breed traceability systems, and they exhibit the potential to assist managers in decision-making as regards breeding and registration.
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Affiliation(s)
- Lenka Putnová
- Laboratory of Agrogenomics, Department of Morphology, Physiology and Animal Genetics, Faculty of Agronomy, Mendel University in Brno, Zemědělská 1665/1, 613 00, Brno, Czech Republic.
| | - Radek Štohl
- Department of Control and Instrumentation, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technická 3082/12, 616 00, Brno, Czech Republic
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Abstract
Dogs are second only to humans in medical surveillance and preventative health care, leading to a recent perception of increased cancer incidence. Scientific priorities in veterinary oncology have thus shifted, with a demand for cancer genetic screens, better diagnostics, and more effective therapies. Most dog breeds came into existence within the last 300 years, and many are derived from small numbers of founders. Each has undergone strong artificial selection, in which dog fanciers selected for many traits, including body size, fur type, color, skull shape, and behavior, to create novel breeds. The adoption of the breed barrier rule-no dog may become a registered member of a breed unless both its dam and its sire are registered members-ensures a relatively closed genetic pool within each breed. As a result, there is strong phenotypic homogeneity within breeds but extraordinary phenotypic variation between breeds. One consequence of this is the high level of breed-associated genetic disease. We and others have taken advantage of this to identify genes for a large number of canine maladies for which mouse models do not exist, particularly with regard to cancer.
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Affiliation(s)
- Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Dayna L Dreger
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA; .,Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jacquelyn M Evans
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
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Malik M, Moaeen-ud-Din M, Bilal G, Ghaffar A, Muner R, Raja G, Khan W. Development of amplified fragment length polymorphism (AFLP) markers for the identification of Cholistani cattle. Arch Anim Breed 2018; 61:387-394. [PMID: 32175445 PMCID: PMC7065403 DOI: 10.5194/aab-61-387-2018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 09/27/2018] [Indexed: 11/17/2022] Open
Abstract
The identification issue of livestock can be resolved by using molecular identification tools that are acceptable to preserve and maintain pure breeds worldwide. The application of a molecular identification methodology is more important for developing nations, e.g., Pakistan, where uncontrolled crossbreeding has become a common practice and the import of exotic animals and germplasm is ever increasing. This presents a risk to local breeds as also stated by the FAO. Therefore, the current study was designed to develop standard molecular markers for Cholistani cattle to ascertain their purity for breeding purpose. In this study 50 and 48 unrelated males were sampled for Cholistani and each crossbred cattle, respectively. Candidate molecular markers present in Cholistani but absent in crossbred cattle and vice versa were detected using the amplified fragment length polymorphism (AFLP) method. Eleven markers were developed and were converted to single nucleotide polymorphism (SNP) markers for genotyping. The allele frequencies in both breeds were determined for discrimination ability using polymerase-chain-reaction-restriction-fragment-polymorphism (PCR-AFLP). The probability of identifying the Cholistani breed was 0.905 and the probability of misjudgment was 0.073 using a panel of markers. The identified markers can ascertain the breed purity and are likely to extend the facility for breed purity testing before entering into a genetic improvement program in the country.
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Affiliation(s)
- Muhammad Haseeb Malik
- University Institute of Biochemistry & Biotechnology, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan
- These authors contributed equally to this work
| | - Muhammad Moaeen-ud-Din
- National Center for Livestock Breeding, Genetics & Genomics, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan
- Department of Animal Breeding & Genetics, Faculty of Veterinary & Animal Sciences, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan
- These authors contributed equally to this work
| | - Ghulam Bilal
- Department of Animal Breeding & Genetics, Faculty of Veterinary & Animal Sciences, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan
| | - Abdul Ghaffar
- Animal Science Institute, National Agriculture Research Council, Islamabad, Pakistan
| | - Raja Danish Muner
- Department of Animal Breeding & Genetics, Faculty of Veterinary & Animal Sciences, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan
| | - Ghazala Kaukab Raja
- University Institute of Biochemistry & Biotechnology, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan
| | - Waqas Ahmad Khan
- Department of Biotechnology, Faculty of Sciences, University of Sargodha, Sargodha, Pakistan
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Gunter LM, Barber RT, Wynne CDL. A canine identity crisis: Genetic breed heritage testing of shelter dogs. PLoS One 2018; 13:e0202633. [PMID: 30138476 PMCID: PMC6107223 DOI: 10.1371/journal.pone.0202633] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 08/07/2018] [Indexed: 11/19/2022] Open
Abstract
Previous research in animal shelters has determined the breeds of dogs living in shelters by their visual appearance; however the genetic breed testing of such dogs is seldom conducted, and few studies have compared the breed labels assigned by shelter staff to the results of this testing. In the largest sampling of shelter dogs’ breed identities to-date, 459 dogs at Arizona Animal Welfare League & SPCA (AAWL) in Phoenix, Arizona, and 460 dogs at San Diego Humane Society & SPCA (SDHS) in San Diego, California, were genetically tested using a commercially available product to determine their breed heritage. In our sample, genetic analyses identified 125 distinct breeds with 91 breeds present at both shelters, and 4.9% of the dogs identified as purebreds. The three most common breed signatures, in order of prevalence, American Staffordshire Terrier, Chihuahua, and Poodle, accounted for 42.5% or all breed identifications at the great grandparent level. During their stay at the shelter, dogs with pit bull-type ancestries waited longer to be adopted than other dogs. When we compared shelter breed assignment as determined by visual appearance to that of genetic testing, staff at SDHS was able to successfully match at least one breed in the genetic heritage of 67.7% of dogs tested; however their agreement fell to 10.4% when asked to identify more than one breed. Lastly, we found that as the number of pit bull-type relatives in a dog’s heritage increased, so did the shelter’s ability to match the results of DNA analysis. In total when we consider the complexity of shelter dog breed heritage and the failure to identify multiple breeds based on visual identification coupled with our inability to predict how these breeds then interact within an individual dog, we believe that focusing resources on communicating the physical and behavioral characteristics of shelter dogs would best support adoption efforts.
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Affiliation(s)
- Lisa M. Gunter
- Department of Psychology, Arizona State University, Tempe, Arizona, United States of America
- * E-mail:
| | - Rebecca T. Barber
- Mary Lou Fulton Teachers College, Arizona State University, Tempe, Arizona, United States of America
| | - Clive D. L. Wynne
- Department of Psychology, Arizona State University, Tempe, Arizona, United States of America
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11
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Berger B, Berger C, Heinrich J, Niederstätter H, Hecht W, Hellmann A, Rohleder U, Schleenbecker U, Morf N, Freire-Aradas A, McNevin D, Phillips C, Parson W. Dog breed affiliation with a forensically validated canine STR set. Forensic Sci Int Genet 2018; 37:126-134. [PMID: 30149287 DOI: 10.1016/j.fsigen.2018.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/23/2018] [Accepted: 08/11/2018] [Indexed: 11/28/2022]
Abstract
We tested a panel of 13 highly polymorphic canine short tandem repeat (STR) markers for dog breed assignment using 392 dog samples from the 23 most popular breeds in Austria, Germany, and Switzerland. This STR panel had originally been selected for canine identification. The dog breeds sampled in this study featured a population frequency ≥1% and accounted for nearly 57% of the entire pedigree dog population in these three countries. Breed selection was based on a survey comprising records for nearly 1.9 million purebred dogs belonging to more than 500 different breeds. To derive breed membership from STR genotypes, a range of algorithms were used. These methods included discriminant analysis of principal components (DAPC), STRUCTURE, GeneClass2, and the adegenet package for R. STRUCTURE analyses suggested 21 distinct genetic clusters. Differentiation between most breeds was clearly discernable. Fourteen of 23 breeds (61%) exhibited maximum mean cluster membership proportions of more than 0.70 with a highest value of 0.90 found for Cavalier King Charles Spaniels. Dogs of only 6 breeds (26%) failed to consistently show only one major cluster. The DAPC method yielded the best assignment results in all 23 declared breeds with 97.5% assignment success. The frequency-based assignment test also provided a high success rate of 87%. These results indicate the potential viability of dog breed prediction using a well-established and sensitive set of 13 canine STR markers intended for forensic routine use.
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Affiliation(s)
- Burkhard Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Cordula Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Josephin Heinrich
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Werner Hecht
- Institute of Veterinary Pathology, Justus-Liebig-University, Giessen, Germany
| | - Andreas Hellmann
- Bundeskriminalamt, Kriminaltechnisches Institut, Wiesbaden, Germany
| | - Udo Rohleder
- Bundeskriminalamt, Kriminaltechnisches Institut, Wiesbaden, Germany
| | | | - Nadja Morf
- Institute of Legal Medicine, University of Zürich, Switzerland
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Dennis McNevin
- Centre for Forensic Science, School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Australia
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA.
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12
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Parker HG, Dreger DL, Rimbault M, Davis BW, Mullen AB, Carpintero-Ramirez G, Ostrander EA. Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development. Cell Rep 2018; 19:697-708. [PMID: 28445722 DOI: 10.1016/j.celrep.2017.03.079] [Citation(s) in RCA: 223] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/10/2017] [Accepted: 03/28/2017] [Indexed: 11/30/2022] Open
Abstract
There are nearly 400 modern domestic dog breeds with a unique histories and genetic profiles. To track the genetic signatures of breed development, we have assembled the most diverse dataset of dog breeds, reflecting their extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses, we uncover geographic patterns of development and independent origins of common traits. Our analyses reveal the hybrid history of breeds and elucidate the effects of immigration, revealing for the first time a suggestion of New World dog within some modern breeds. Finally, we used cladistics and haplotype sharing to show that some common traits have arisen more than once in the history of the dog. These analyses characterize the complexities of breed development, resolving longstanding questions regarding individual breed origination, the effect of migration on geographically distinct breeds, and, by inference, transfer of trait and disease alleles among dog breeds.
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Affiliation(s)
- Heidi G Parker
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dayna L Dreger
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maud Rimbault
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brian W Davis
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra B Mullen
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gretchen Carpintero-Ramirez
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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13
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Molekulargenetische Identifikation von Canidae in der forensischen Praxis. Rechtsmedizin (Berl) 2015. [DOI: 10.1007/s00194-015-0036-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Genetic characterization of four native Italian shepherd dog breeds and analysis of their relationship to cosmopolitan dog breeds using microsatellite markers. Animal 2015; 9:1921-8. [PMID: 26245492 DOI: 10.1017/s1751731115001561] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Very little research into genetic diversity of Italian native dog breeds has been carried out so far. In this study we aimed to estimate and compare the genetic diversity of four native Italian shepherd dog breeds: the Maremma, Bergamasco, Lupino del Gigante and Oropa shepherds. Therefore, some cosmopolitan dog breeds, which have been widely raised in Italy for a long time past, have also been considered to check possible influence of these dog populations on the Italian autochthonous breeds considered here. A total of 212 individuals, belonging to 10 different dog breeds, were sampled and genotyped using 18 autosomal microsatellite loci. We analyzed the genetic diversity of these breeds, within breed diversity, breed relationship and population structure. The 10 breeds considered in this study were clearly genetically differentiated from each other, regardless of current population sizes and the onset of separate breeding history. The level of genetic diversity explained 20% of the total genetic variation. The level of H E found here is in agreement with that found by other studies. The native Italian breeds showed generally higher genetic diversity compared with the long established, well-defined cosmopolitan dog breeds. As the Border Collie seems closer to the Italian breeds than the other cosmopolitan shepherd dogs considered here, a possible utilization of this breed to improve working performance in Italian traditional working shepherd dogs cannot be ignored. The data and information found here can be utilized in the organization of conservation programs planned to reduce inbreeding and to minimize loss of genetic variability.
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15
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Iquebal MA, Ansari MS, Sarika, Dixit SP, Verma NK, Aggarwal RAK, Jayakumar S, Rai A, Kumar D. Locus minimization in breed prediction using artificial neural network approach. Anim Genet 2014; 45:898-902. [PMID: 25183434 DOI: 10.1111/age.12208] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2014] [Indexed: 11/26/2022]
Abstract
Molecular markers, viz. microsatellites and single nucleotide polymorphisms, have revolutionized breed identification through the use of small samples of biological tissue or germplasm, such as blood, carcass samples, embryos, ova and semen, that show no evident phenotype. Classical tools of molecular data analysis for breed identification have limitations, such as the unavailability of referral breed data, causing increased cost of collection each time, compromised computational accuracy and complexity of the methodology used. We report here the successful use of an artificial neural network (ANN) in background to decrease the cost of genotyping by locus minimization. The webserver is freely accessible (http://nabg.iasri.res.in/bisgoat) to the research community. We demonstrate that the machine learning (ANN) approach for breed identification is capable of multifold advantages such as locus minimization, leading to a drastic reduction in cost, and web availability of reference breed data, alleviating the need for repeated genotyping each time one investigates the identity of an unknown breed. To develop this model web implementation based on ANN, we used 51,850 samples of allelic data of microsatellite-marker-based DNA fingerprinting on 25 loci covering 22 registered goat breeds of India for training. Minimizing loci to up to nine loci through the use of a multilayer perceptron model, we achieved 96.63% training accuracy. This server can be an indispensable tool for identification of existing breeds and new synthetic commercial breeds, leading to protection of intellectual property in case of sovereignty and bio-piracy disputes. This server can be widely used as a model for cost reduction by locus minimization for various other flora and fauna in terms of variety, breed and/or line identification, especially in conservation and improvement programs.
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Affiliation(s)
- M A Iquebal
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
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16
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Li YH, Chu HP, Jiang YN, Lin CY, Li SH, Li KT, Weng GJ, Cheng CC, Lu DJ, Ju YT. Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 27:616-27. [PMID: 25049996 PMCID: PMC4093195 DOI: 10.5713/ajas.2013.13365] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/12/2013] [Accepted: 12/12/2013] [Indexed: 11/27/2022]
Abstract
The Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to track the genetic qualities of laboratory animals and stud stock is an important function of genetic databases. For more than two decades, Lanyu derived breeds of common ancestry and crossbreeds have been used to examine the effectiveness of genetic marker selection and optimal approaches for individual assignment. In this paper, these pigs and the following breeds: Berkshire, Duroc, Landrace and Yorkshire, Meishan and Taoyuan, TLRI Black Pig No. 1, and Kaohsiung Animal Propagation Station Black pig are studied to build a genetic reference database. Nineteen microsatellite markers (loci) provide information on genetic variation and differentiation among studied breeds. High differentiation index (FST) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu's inbred populations. Inbreeding values (FIS) show that Lanyu and its derived inbred breeds have significant loss of heterozygosity. Individual assignment testing of 352 animals was done with different numbers of microsatellite markers in this study. The testing assigned 99% of the animals successfully into their correct reference populations based on 9 to 14 markers ranking D-scores, allelic number, expected heterozygosity (HE) or FST, respectively. All miss-assigned individuals came from close lineage Lanyu breeds. To improve individual assignment among close lineage breeds, microsatellite markers selected from Lanyu populations with high polymorphic, heterozygosity, FST and D-scores were used. Only 6 to 8 markers ranking HE, FST or allelic number were required to obtain 99% assignment accuracy. This result suggests empirical examination of assignment-error rates is required if discernible levels of co-ancestry exist. In the reference group, optimum assignment accuracy was achievable achieved through a combination of different markers by ranking the heterozygosity, FST and allelic number of close lineage populations.
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Affiliation(s)
- Y H Li
- Taitung Animal Propagation Station, Livestock Research Institute, Taitung, Taiwan
| | - H P Chu
- Taitung Animal Propagation Station, Livestock Research Institute, Taitung, Taiwan
| | - Y N Jiang
- Taitung Animal Propagation Station, Livestock Research Institute, Taitung, Taiwan
| | - C Y Lin
- Taitung Animal Propagation Station, Livestock Research Institute, Taitung, Taiwan
| | - S H Li
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - K T Li
- Institute of History and Philology, Academia Sinica, Taipei, Taiwan
| | - G J Weng
- Institute of Wildlife Conservation, National Pingtung University of Science and Technology, Pintung, Taiwan
| | - C C Cheng
- Graduate Institute of Hakka Cultural Industry, National Pingtung University of Science and Technology, Pintung, Taiwan
| | - D J Lu
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Y T Ju
- Taitung Animal Propagation Station, Livestock Research Institute, Taitung, Taiwan
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17
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Iquebal MA, Sarika, Dhanda SK, Arora V, Dixit SP, Raghava GPS, Rai A, Kumar D. Development of a model webserver for breed identification using microsatellite DNA marker. BMC Genet 2013; 14:118. [PMID: 24320218 PMCID: PMC3890620 DOI: 10.1186/1471-2156-14-118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/04/2013] [Indexed: 11/10/2022] Open
Abstract
Background Identification of true to breed type animal for conservation purpose is imperative. Breed dilution is one of the major problems in sustainability except cases of commercial crossbreeding under controlled condition. Breed descriptor has been developed to identify breed but such descriptors cover only “pure breed” or true to the breed type animals excluding undefined or admixture population. Moreover, in case of semen, ova, embryo and breed product, the breed cannot be identified due to lack of visible phenotypic descriptors. Advent of molecular markers like microsatellite and SNP have revolutionized breed identification from even small biological tissue or germplasm. Microsatellite DNA marker based breed assignments has been reported in various domestic animals. Such methods have limitations viz. non availability of allele data in public domain, thus each time all reference breed has to be genotyped which is neither logical nor economical. Even if such data is available but computational methods needs expertise of data analysis and interpretation. Results We found Bayesian Networks as best classifier with highest accuracy of 98.7% using 51850 reference allele data generated by 25 microsatellite loci on 22 goat breed population of India. The FST values in the study were seen to be low ranging from 0.051 to 0.297 and overall genetic differentiation of 13.8%, suggesting more number of loci needed for higher accuracy. We report here world’s first model webserver for breed identification using microsatellite DNA markers freely accessible at http://cabin.iasri.res.in/gomi/. Conclusion Higher number of loci is required due to less differentiable population and large number of breeds taken in this study. This server will reduce the cost with computational ease. This methodology can be a model for various other domestic animal species as a valuable tool for conservation and breed improvement programmes.
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Affiliation(s)
| | | | | | | | | | | | | | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India.
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18
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Suárez NM, Betancor E, Fregel R, Pestano J. Genetic characterization, at the mitochondrial and nuclear DNA levels, of five Canary Island dog breeds. Anim Genet 2013; 44:432-41. [PMID: 23384391 DOI: 10.1111/age.12024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2012] [Indexed: 11/30/2022]
Abstract
Many studies presenting genetic analysis of dog breeds have been conducted without the inclusion of island dog breeds, although isolation can be one of the main factors in their origin. Here we report the genetic analysis at the nuclear and mitochondrial DNA levels of five Canary Island dog breeds (Canarian Warren Hound, Canary Island Mastiff, Garafiano Shepherd, La Palma Rat-Hunter and El Hierro Wolfhound) to fill this gap and, at the same time, genetically characterize these breeds. We identified 168 alleles in autosomal microsatellites and 16 mitochondrial haplotypes. Observed and expected heterozygosities ranged from 0.556 to 0.783 and from 0.737 to 0.943 respectively. Furthermore, three haplotypes were newly described and exclusive to a particular breed (A17+ in the Canary Island Mastiff; A33+ in the Canarian Warren Hound; Bi in the La Palma Rat-Hunter). The outcome of our analyses also revealed different breed histories consistent with historical documents and hypothetical origin designations. Although mtDNA haplotypes showed poor breed discriminating power, autosomal markers allowed a clear clustering of each single population. We expect that our results, together with further analyses, will help to make the population histories of island dog breeds clearer.
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Affiliation(s)
- N M Suárez
- Department of Genetics, Faculty of Medicine, Universidad de Las Palmas de Gran Canaria, 35080, Las Palmas de Gran Canaria, Spain.
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19
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Mellanby RJ, Ogden R, Clements DN, French AT, Gow AG, Powell R, Corcoran B, Schoeman JP, Summers KM. Population structure and genetic heterogeneity in popular dog breeds in the UK. Vet J 2012; 196:92-7. [PMID: 23084740 DOI: 10.1016/j.tvjl.2012.08.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 08/09/2012] [Accepted: 08/12/2012] [Indexed: 10/27/2022]
Abstract
There is increasing concern that reproductive isolation related to breed specifications in dogs, while maintaining genetic differences among breeds, is likely to promote breed-specific genetic disorders. This study examined genetic diversity among 13 popular dog breed groups in the UK. Most breeds showed high levels of homozygosity when compared with crossbred animals. The Boxer and West Highland white terrier showed the lowest heterozygosity, while the Jack Russell terrier group (not a registered breed in the UK) had a level of heterozygosity comparable to crossbred dogs. Analysis of genetic distance between breeds showed significantly different inbreeding coefficients for pairwise comparisons among registered breeds, with the most divergent breeds being the Boxer and West Highland white terrier. The Rottweiler and Golden retriever showed the highest levels of inbreeding. The least distinct group contained crossbred dogs. The results show that the registered breeds are subject to a 'breed barrier' which promotes reduction in genetic diversity.
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Affiliation(s)
- Richard J Mellanby
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
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20
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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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21
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Pant SD, Schenkel FS, Verschoor CP, Karrow NA. Use of Breed-Specific Single Nucleotide Polymorphisms to Discriminate Between Holstein and Jersey Dairy Cattle Breeds. Anim Biotechnol 2012; 23:1-10. [DOI: 10.1080/10495398.2012.636224] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Sameer D. Pant
- a Department of Animal and Poultry Science , Centre for Genetic Improvement of Livestock , Guelph , Ontario , Canada
| | - Flavio S. Schenkel
- a Department of Animal and Poultry Science , Centre for Genetic Improvement of Livestock , Guelph , Ontario , Canada
| | - Chris P. Verschoor
- a Department of Animal and Poultry Science , Centre for Genetic Improvement of Livestock , Guelph , Ontario , Canada
| | - Niel A. Karrow
- a Department of Animal and Poultry Science , Centre for Genetic Improvement of Livestock , Guelph , Ontario , Canada
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22
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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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23
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van Asch B, Pereira R, Carneiro J, Amorim A. Population assignment in seven Portuguese dog breeds and Iberian wolves. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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24
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Withen KB, Brüniche-Olsen A, Pedersen BV, Gravlund P. The Agersoe cattle: the last remnants of the Danish island cattle (Bos taurus)? J Anim Breed Genet 2011; 128:141-52. [PMID: 21385229 DOI: 10.1111/j.1439-0388.2010.00883.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A phenotypically interesting strain of cattle existed on the small island of Agersoe, on the west coast of Zealand, Denmark, in the beginning of the last decade. The cattle share a great resemblance to the extinct Danish breed, the Island cattle. The objective of this study was to genetically characterize the Agersoe cattle, using microsatellites, amplified fragment length polymorphism (AFLP) and mtDNA markers, and analyse the genetic variability within the breed and the genetic relationship to 14 European breeds with focus on the Red Danish and Jutland breed. The results show diversity in nuclear markers comparable to that of modern breeds and that the Agersoe cattle are separable from the two native breeds. The absence of inbreeding and the degree of genetic diversity are taken as a sign of recent admixture. The Agersoe cattle did not exhibit a consistent association with any of the European breeds. Several arguments based on this survey have been put forward in favour of characterizing the Agersoe cattle as being the last remnants of the Danish Island Cattle.
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Affiliation(s)
- K B Withen
- Department of Biology, University of Copenhagen, Copenhagen Ø, Denmark
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25
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Kim YK, Hong YJ, Min MS, Kim KS, Kim YJ, Voloshina I, Myslenkov A, Smith GJD, Cuong ND, Tho HH, Han SH, Yang DH, Kim CB, Lee H. Genetic status of Asiatic black bear (Ursus thibetanus) reintroduced into South Korea based on mitochondrial DNA and microsatellite loci analysis. ACTA ACUST UNITED AC 2011; 102:165-74. [PMID: 21325020 DOI: 10.1093/jhered/esq121] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Asiatic black bear is one of the most endangered mammals in South Korea owing to population declines resulting from human exploitation and habitat fragmentation. To restore the black bear population in South Korea, 27 bear cubs from North Korea and Russian Far East (Primorsky Krai) were imported and released into Jirisan National Park, a reservoir of the largest wild population in South Korea, in 2004. To monitor the success of this reintroduction, the genetic diversity and population structure of the reintroduced black bears were measured using both mitochondrial and nuclear DNA markers. Mitochondrial D-loop region DNA sequences (615 bp) of 43 Japanese black bears from previous study and 14 Southeast Asian black bears in this study were employed to obtain phylogenetic inference of the reintroduced black bears. The mitochondrial phylogeny indicated Asiatic black bear populations from Russian Far East and North Korea form a single evolutionary unit distinct from populations from Japan and Southeast Asia. Mean expected heterozygosity (H(E)) across 16 microsatellite loci was 0.648 for Russian and 0.676 for North Korean populations. There was a moderate but significant level of microsatellite differentiation (F(ST) = 0.063) between black bears from the 2 source areas. In addition, genetic evidences revealed that 2 populations are represented as diverging groups, with lingering genetic admixture among individuals of 2 source populations. Relatedness analysis based on genetic markers indicated several discrepancies with the pedigree records. Implication of the phylogenetic and genetic evidences on long-term management of Asiatic black bears in South Korea is discussed.
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Affiliation(s)
- Yung-Kun Kim
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 151-742, Korea
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Wildlife forensics: “Supervised” assignment testing can complicate the association of suspect cases to source populations. Forensic Sci Int Genet 2011; 5:50-6. [DOI: 10.1016/j.fsigen.2010.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 01/28/2010] [Accepted: 02/05/2010] [Indexed: 11/18/2022]
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27
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Yuan YH, Hou BW, Xu HJ, Luo J, Ding XY. Identification of the Geographic Origin of Dendrobium thyrsiflorum on Chinese Herbal Medicine Market Using Trinucleotide Microsatellite Markers. Biol Pharm Bull 2011; 34:1794-800. [DOI: 10.1248/bpb.34.1794] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Bei Wei Hou
- College of Life Sciences, Nanjing Normal University
| | - Hui Jun Xu
- College of Life Sciences, Nanjing Normal University
| | - Jing Luo
- College of Life Sciences, Nanjing Normal University
| | - Xiao Yu Ding
- College of Life Sciences, Nanjing Normal University
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28
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Kropatsch R, Streitberger K, Schulte-Middelmann T, Dekomien G, Epplen J. On ancestors of dog breeds with focus on Weimaraner hunting dogs. J Anim Breed Genet 2010; 128:64-72. [DOI: 10.1111/j.1439-0388.2010.00874.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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29
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An empirical assessment of individual-based population genetic statistical techniques: application to British pig breeds. Heredity (Edinb) 2010; 106:261-9. [PMID: 20551978 DOI: 10.1038/hdy.2010.80] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Recently developed Bayesian genotypic clustering methods for analysing genetic data offer a powerful tool to evaluate the genetic structure of domestic farm animal breeds. The unit of study with these approaches is the individual instead of the population. We aimed to empirically evaluate various individual-based population genetic statistical methods for characterization of genetic diversity and structure of livestock breeds. Eighteen British pig populations, comprising 819 individuals, were genotyped at 46 microsatellite markers. Three Bayesian genotypic clustering approaches, principle component analysis (PCA) and phylogenetic reconstruction were applied to individual multilocus genotypes to infer the genetic structure and diversity of the British pig breeds. Comparisons of the three Bayesian genotypic clustering methods (STRUCTURE, BAPS and STRUCTURAMA) revealed some broad similarities but also some notable differences. Overall, the methods agreed that majority of the British pig breeds are independent genetic units with little evidence of admixture. The three Bayesian genotypic clustering methods provided complementary, biologically credible clustering solutions but at different levels of resolution. BAPS detected finer genetic differentiation and in some cases, populations within breeds. Consequently, it estimated a greater number of underlying genetic populations (K, in the notation of Bayesian clustering methods). Two of the Bayesian methods (STRUCTURE and BAPS) and phylogenetic reconstruction provided similar success in assignment of individuals, supporting the use of these methods for breed assignment.
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30
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Ginja C, Telo Da Gama L, Penedo MCT. Analysis of STR markers reveals high genetic structure in Portuguese native cattle. ACTA ACUST UNITED AC 2009; 101:201-10. [PMID: 19965912 DOI: 10.1093/jhered/esp104] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Genetic structure and diversity of 13 Portuguese native and 3 imported cattle breeds were assessed with 39 microsatellites. Allelic richness per locus was high, with an overall average of 8.3 +/- 2.5. The mean observed and expected heterozygosities were 0.673 +/- 0.043 and 0.691 +/- 0.034, respectively. The mean number of alleles per breed ranged between 5.36 +/- 1.27 and 7.87 +/- 2.66. Brava de Lide and Mirandesa breeds had the lowest genetic diversity, whereas Minhota, Arouquesa, and Mertolenga had the highest. Significant (P < 0.05) heterozygote deficit was detected in all breeds except Garvonesa, Marinhoa, Minhota, and Limousin. Hardy-Weinberg deviations are most probably due to inbreeding, particularly in Alentejana, Brava de Lide, Mertolenga, and Ramo Grande (F(is) > 0, P < 0.0001). Based on the principal component and the Neighbor-Net analyses, Mirandesa was the most genetically distinct breed. Even though admixture was detected across all breeds (6.7%, q < 0.800), the molecular structure was consistent with original breed designations, with the exception of Cachena that had a clear influence of Barrosã (K = 15). Mertolenga showed substructure with independent clustering of red speckled animals. The percentage animals correctly assigned was >or=90 in all breeds except Cachena, Garvonesa, and Preta (q >or= 0.800). The results obtained here confirmed that high levels of genetic diversity exist within Portuguese native cattle and that the breeds are highly structured. Conservation measures should be implemented for all native breeds to minimize inbreeding.
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Affiliation(s)
- Catarina Ginja
- Instituto Superior de Agronomia, Tapada da Ajuda, 1349-017 Lisboa, Portugal.
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31
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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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32
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Pribánová M, Horák P, Schröffelová D, Urban T, Bechynová R, Musilová L. Analysis of genetic variability in the Czech Dachshund population using microsatellite markers. J Anim Breed Genet 2009; 126:311-8. [PMID: 19630882 DOI: 10.1111/j.1439-0388.2008.00772.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The primary goal of this study was to analyse genetic variation within and among six Dachshund varieties in the Czech Republic using 10 microsatellites from StockMarks Paternity Polymerase Chain Reaction (PCR) Typing kit. A total of 632 Dachshunds were sampled - 99 Standard Smooth-haired, 72 Standard Long-haired, 272 Standard Wire-haired, 42 Miniature Smooth-haired, 73 Miniature Long-haired and 74 Miniature Wire-haired. Average observed heterozygosity and polymorphic information content ranged in particular Dachshund varieties between 0.58-0.70 and 0.57-0.64, respectively. Subsequent analysis of the population structure (F-statistics; Nei's genetic identity) showed that Standard Dachshunds shared allele frequencies most closely with their miniature equivalents, and smooth coat type is closer to Wire-haired coat type than to the Long-haired one. Analysis of molecular variance revealed that 11.81% of the total variance occurred among varieties. The value of combined exclusion probability (0.9955) validated usefulness of this panel of microsatellites for parentage verification in all analysed populations. We carried out 234 parentage verifications with 1.28% cases where parentage did not match.
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Affiliation(s)
- M Pribánová
- Laboratory of Immunogenetics, Czech Moravian Breeders Corporation, Hradistko, Czech Republic
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Leroy G, Verrier E, Meriaux JC, Rognon X. Genetic diversity of dog breeds: between-breed diversity, breed assignation and conservation approaches. Anim Genet 2009; 40:333-43. [DOI: 10.1111/j.1365-2052.2008.01843.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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34
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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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35
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Negrini R, Nicoloso L, Crepaldi P, Milanesi E, Colli L, Chegdani F, Pariset L, Dunner S, Leveziel H, Williams JL, Ajmone Marsan P. Assessing SNP markers for assigning individuals to cattle populations. Anim Genet 2009; 40:18-26. [PMID: 19016674 DOI: 10.1111/j.1365-2052.2008.01800.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- R Negrini
- Istituto di Zootecnica, Università Cattolica del S. Cuore, Piacenza, Italy.
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36
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Kotze A, Ehlers K, Cilliers D, Grobler J. The power of resolution of microsatellite markers and assignment tests to determine the geographic origin of cheetah (Acinonyx jubatus) in Southern Africa. Mamm Biol 2008. [DOI: 10.1016/j.mambio.2007.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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37
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Dalvit C, De Marchi M, Dal Zotto R, Gervaso M, Meuwissen T, Cassandro M. Breed assignment test in four Italian beef cattle breeds. Meat Sci 2008; 80:389-95. [PMID: 22063344 DOI: 10.1016/j.meatsci.2008.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2007] [Revised: 12/19/2007] [Accepted: 01/13/2008] [Indexed: 11/28/2022]
Affiliation(s)
- C Dalvit
- Department of Animal Science, University of Padova, 35020 Legnaro (PD), Italy
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38
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Tadano R, Nishibori M, Tsudzuki M. High accuracy of genetic discrimination among chicken lines obtained through an individual assignment test. Anim Genet 2008; 39:567-71. [PMID: 18699831 DOI: 10.1111/j.1365-2052.2008.01770.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the current study, we carried out assignment tests applying the Bayesian and distance-based methods, using 20 microsatellite genotypes in four chicken lines. The Bayesian method showed slightly higher performance of assignment than the distance-based method. In the assignment using the Bayesian method, >or=90% accuracy of assignment was attained by using only two of the most heterozygous markers, whereas in the case of the least heterozygous markers, six were needed to reach the same level of accuracy. In the assignment of the most closely related line pair (F(ST) = 0.1736), at least 12 markers selected by random ordering and at least 15 individuals per line were needed to stably obtain high accuracy of assignment (>or=97%), whereas using only six random markers achieved 97-100% of accuracy between the two most distinct lines (F(ST) = 0.3651) without reference to the sample size per line.
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Affiliation(s)
- R Tadano
- Laboratory of Animal Breeding and Genetics, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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39
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Kim TH, Kim KS, Choi BH, Yoon DH, Jang GW, Lee KT, Chung HY, Lee HY, Park HS, Lee JW. Genetic structure of pig breeds from Korea and China using microsatellite loci analysis. J Anim Sci 2008; 83:2255-63. [PMID: 16160034 DOI: 10.2527/2005.83102255x] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To understand molecular genetic characteristics of Korean pigs, the genetic relationships of nine pig breeds including two Korean pigs (Korean native pig and Korean wild pig), three Chinese pigs (Min pig, Xiang pig, and Wuzhishan pig), and four European breeds (Berkshire, Duroc, Landrace, and Yorkshire) were characterized from a 16-microsatellite loci analysis. The mean heterozygosity within breeds ranged from 0.494 to 0.703. Across multiple loci, significant deviation from Hardy-Weinberg equilibrium was observed in most pig breeds, except for two Chinese pigs (Min pig and Wuzhishan pig). This deviation was in the direction of heterozygote deficit. Across population loci, 36 of 144 significantly deviated (P < 0.05) from Hardy-Weinberg equilibrium. The mean FST, a measure of genetic divergence among subpopulations, of all loci indicated that 26.1% of total variation could be attributed to the breed difference. Relationship trees based on the Nei's DA genetic distance and scatter diagram from principal component analysis consistently displayed pronounced genetic differentiation among the Korean wild pig, Xiang pig, and Wuzhishan pig. Individual assignment test using a Bayesian method showed 100% success in assigning Korean and Chinese individual pigs into their correct breeds of origin and 100% exclusion success from all alternative reference populations at P < 0.001. These findings indicate that the Korean native pig has been experiencing progressive interbreeding with Western pig breeds after originating from a North China pig breed with a black coat color. Considering the close genetic relationship of Korean pigs to the Western breeds such as Berkshire and Landrace, our findings can be used as valuable genetic information for the preservation and further genetic improvement of the Korean native pig.
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Affiliation(s)
- T H Kim
- Animal Genomics and Bioinformatics Division, National Livestock Research Institute, RDA, Suwon, Gyeonggi 441-706, Republic of Korea.
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40
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41
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Lessons learned from the dog genome. Trends Genet 2007; 23:557-67. [DOI: 10.1016/j.tig.2007.08.013] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 08/23/2007] [Accepted: 08/23/2007] [Indexed: 12/11/2022]
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Stella A, Panzitta F, Gandini G, Boettcher PJ. Use of linked loci as individuals or haplotypes for marker-assisted breed assignment. Anim Genet 2007; 39:8-14. [PMID: 17956592 DOI: 10.1111/j.1365-2052.2007.01662.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The objective of this study was to use simulation to evaluate the benefits of considering haplotypes of loci when linked single nucleotide polymorphisms are used for breed assignment. Three breeds of 10,000 females each were simulated under eight scenarios that differed according to the number of generations separating the breeds, size of breed founder populations and recombination rate between linked loci. Molecular genotypes consisted of 20 groups of three linked loci each. Breed assignment was performed in the final generation and was based on the frequency method. Haplotypes were reconstructed using the expectation-maximization algorithm. Accuracy of breed assignment was based on the frequency of correct breed assignment. Assignment accuracy increased as more genotypes (loci or haplotypes) were considered and more animals were used to estimate genotypic frequencies within breed. For most scenarios, use of haplotypes yielded equal or greater accuracies than when loci were considered independent. The advantage of haplotypes tended to increase as linkage disequilibrium between adjacent loci increased. The greatest advantage for using haplotypes was observed when recombination rate was low (0.001), breeds were separated by few generations (100), and a relatively large number of founder animals (110) was used to form new breeds. In this situation, 90% accuracy of breed assignment was achieved using nine to 14 haplotypes (i.e. 27-42 loci) depending on breed, vs. 39-57 individual loci.
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Affiliation(s)
- A Stella
- Parco Tecnologico Padano, 26900 Lodi, Italy
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43
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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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Negrini R, Milanesi E, Colli L, Pellecchia M, Nicoloso L, Crepaldi P, Lenstra JA, Ajmone-Marsan P. Breed assignment of Italian cattle using biallelic AFLP markers. Anim Genet 2007; 38:147-53. [PMID: 17326802 DOI: 10.1111/j.1365-2052.2007.01573.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The verification of the breed origin of animal products is relevant for food safety and authenticity. We assessed the suitability of AFLP molecular markers in the assignment of cattle individuals to their breed of origin. Three hundred and ninety-six animals belonging to 16 cattle breeds genotyped with 141 AFLP markers were used as reference data set. Assignment was performed with likelihood (aflpop) and Bayesian (structure) methods. The Bayesian approach was superior to the likelihood algorithm with respect to (i) the correct assignment of simulated individuals to their breed of origin (93% vs. 81% respectively), (ii) the correct assignment of 44 sampled Romagnola animals (91% vs. 45% respectively) and (iii) the correct classification of animals belonging to a breed that was not included within the reference dataset. Thus, AFLP profiling in combination with the Bayesian approach seems a useful tool for breed assignment.
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Affiliation(s)
- R Negrini
- Istituto di Zootecnica, Università Cattolica del S. Cuore, Piacenza, Italy.
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45
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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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46
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Ciampolini R, Cetica V, Ciani E, Mazzanti E, Fosella X, Marroni F, Biagetti M, Sebastiani C, Papa P, Filippini G, Cianci D, Presciuttini S. Statistical analysis of individual assignment tests among four cattle breeds using fifteen STR loci1. J Anim Sci 2006; 84:11-9. [PMID: 16361486 DOI: 10.2527/2006.84111x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Assignment tests based on multilocus genotypes are becoming increasingly important to certify quality and origin of livestock products and assure food safety and authenticity. The purpose of this study was to determine the potential of microsatellites (STR) for determining the breed origin of beef products among cattle breeds present in the market. We typed 19 STR in 269 animals from 4 cattle breeds. Based on Wright's F-statistics, 4 loci were discarded, and the remaining 15 loci (FIT = 0.101, FST = 0.089, and FIS = 0.013) were used to compute the likelihood that each multilocus genotype of the total sample was drawn from its true breed instead of another breed. To avoid occurrence of zero likelihood when one or more alleles were missing from a tested breed, sample allele frequencies were estimated assuming uniform prior distributions. Log-likelihood ratio [log(LR)] distributions of the individual assignments were determined for all possible breed contrasts, and their means and SD were used to infer the true-positive and false-positive rates at several values of the log(LR). The posterior probability that the animals of a presumed breed were actually drawn from that breed instead of any another breed was then calculated. Given an observed value of log(LR) > 0 and assuming equal priors, these probabilities were > 99.5% in 10 of 12 possible breed contrasts. For the 2 most closely related breeds (FST = 0.041), this probability was 96.3%, and the probability of excluding the origin of an animal from an alleged breed when it was actually derived from another breed was similar.
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Affiliation(s)
- R Ciampolini
- Dipartimento di Produzioni Animali, Viale delle Piagge 2, 56100 Pisa, Italy
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Wang W, Kirkness EF. Short interspersed elements (SINEs) are a major source of canine genomic diversity. Genome Res 2005; 15:1798-808. [PMID: 16339378 PMCID: PMC1356118 DOI: 10.1101/gr.3765505] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Accepted: 08/03/2005] [Indexed: 01/12/2023]
Abstract
SINEs are retrotransposons that have enjoyed remarkable reproductive success during the course of mammalian evolution, and have played a major role in shaping mammalian genomes. Previously, an analysis of survey-sequence data from an individual dog (a poodle) indicated that canine genomes harbor a high frequency of alleles that differ only by the absence or presence of a SINEC_Cf repeat. Comparison of this survey-sequence data with a draft genome sequence of a distinct dog (a boxer) has confirmed this prediction, and revealed the chromosomal coordinates for >10,000 loci that are bimorphic for SINEC_Cf insertions. Analysis of SINE insertion sites from the genomes of nine additional dogs indicates that 3%-5% are absent from either the poodle or boxer genome sequences--suggesting that an additional 10,000 bimorphic loci could be readily identified in the general dog population. We describe a methodology that can be used to identify these loci, and could be adapted to exploit these bimorphic loci for genotyping purposes. Approximately half of all annotated canine genes contain SINEC_Cf repeats, and these elements are occasionally transcribed. When transcribed in the antisense orientation, they provide splice acceptor sites that can result in incorporation of novel exons. The high frequency of bimorphic SINE insertions in the dog population is predicted to provide numerous examples of allele-specific transcription patterns that will be valuable for the study of differential gene expression among multiple dog breeds.
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Affiliation(s)
- Wei Wang
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
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48
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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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49
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Sundqvist AK, Björnerfeldt S, Leonard JA, Hailer F, Hedhammar A, Ellegren H, Vilà C. Unequal contribution of sexes in the origin of dog breeds. Genetics 2005; 172:1121-8. [PMID: 16219789 PMCID: PMC1456210 DOI: 10.1534/genetics.105.042358] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dogs (Canis familiaris) were domesticated from the gray wolf (Canis lupus) at least 14,000 years ago, and there is evidence of dogs with phenotypes similar to those in modern breeds 4000 years ago. However, recent genetic analyses have suggested that modern dog breeds have a much more recent origin, probably <200 years ago. To study the origin of contemporaneous breeds we combined the analysis of paternally inherited Y chromosome markers with maternally inherited mitochondrial DNA and biparentally inherited autosomal microsatellite markers in both domestic dogs and their wild ancestor, the gray wolf. Our results show a sex bias in the origin of breeds, with fewer males than females contributing genetically, which clearly differs from the breeding patterns in wild gray wolf populations where both sexes have similar contributions. Furthermore, a comparison of mitochondrial DNA and Y chromosome diversity in dog groups recognized by the World Canine Organization, as well as in groups defined by the breeds' genetic composition, shows that paternal lineages are more differentiated among groups than maternal lineages. This demonstrates a lower exchange of males than of females between breeds belonging to different groups, which illustrates how breed founders may have been chosen.
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Affiliation(s)
- A-K Sundqvist
- Department of Evolutionary Biology, Uppsala University, Sweden.
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50
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Schelling C, Gaillard C, Dolf G. Genetic variability of seven dog breeds based on microsatellite markers. J Anim Breed Genet 2005; 122 Suppl 1:71-7. [PMID: 16130460 DOI: 10.1111/j.1439-0388.2005.00515.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The present study, compared the genetic variability of seven dog breeds and a test sample from Switzerland by means of 26 microsatellite markers. Five loci were excluded from further analyses because one was monomorphic, one not in Hardy-Weinberg equilibrium in all breeds and three in linkage disequilibrium with linked loci. The proportion of shared alleles at the individual level of the remaining 21 microsatellite markers combined with the neighbour-joining method allowed for the clustering of the large majority of the individuals in accordance to their breed. The results were confirmed by analyses using a Bayesian approach for clustering and a Monte Carlo re-sampling method for individual assignment or exclusion to a given population.
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Affiliation(s)
- C Schelling
- Department of Animal Sciences, Swiss Federal Institute of Technology Zurich and Vetsuisse-Faculty, University of Zurich, Zurich, Switzerland
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