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Fossati P, Ruffo G. Purebred dogs and cats: A proposal for a better protection. J Vet Behav 2021. [DOI: 10.1016/j.jveb.2021.05.009] [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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Snegin EA, Kramarenko AS, Artemchuk OY, Kramarenko SS. Intra- and interbreed genetic heterogeneity and divergence in four commercial pig breeds based on microsatellite markers. REGULATORY MECHANISMS IN BIOSYSTEMS 2021. [DOI: 10.15421/022120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
In recent years, there has been an increasing amount of attention paid to the genetic health of domesticated animals and its relationship with the level of inbreeding and genetic diversity. At the same time, insufficient attention is still paid to the study of intrabreed genetic diversity and intrabreed stratification. The main goal of our work was to analyze the intra- and interbreed genetic diversity of commercial pig breeds on the basis of DNA microsatellite (MS-DNA) polymorphism. In total, the work used data for 3,308 pigs, which represented 11 herds. The animals belonged to four commercial pig breeds – Duroc (DR), Yorkshire (YR), Landrace (LN) and Large White (LW). 12 microsatellite loci recommended by ISAG-FAO and arranged in one multiplex panel (S0101, S0155, S0228, S0355, S0386, SW24, SW240, SW72, SW857, SW911, SW936, SW951) were used as DNA markers. When analyzing the intra- and interbreed variability of 11 herds, we found that all studied breeds significantly differed in terms of the proportion of both rare and the most common alleles. At the same time, the noted differences were determined, first of all, by the variability between individual herds within their breed. The location of herd centroids is random and is not consistent with their breed affiliation at all. When individuals belonging to the same breed are combined, the centroids of pig breeds in the space of first two axes from a Principal Coordinate Analysis form two clusters. The first one contains the only red pig breed (DR) used in the analysis, while the second one contains white pig breeds. In six pig herds the Ne estimates were below 50 inds., in two herds they were in the range of 50–100 inds., and finally in three herds the Ne estimates exceeded 100 inds. The analysis of the genetic variability of pigs of four commercial breeds showed that the high level of interbreed differences is caused, first of all, by the high variability among pig herds within each studied breed. Such intrabreed stratification can be formed due to the manifestation of many causes: different genetic basis of the founders of intrabreed genealogical groups, geographical isolation, different directions of selection within individual herds, exchange of animals between separate herds, the use of inbreeding in the practice of selection together with isolation, etc. Important consequences of intrabreed stratification are an increase in the level of interherd diversity (which is not lower than the level of interbreed diversity) against the background of a decrease in variability within individual herds, as well as a significant deficit of heterozygotes and an increase in the role of negative genetic and demographic processes. Thus, the existence of genetic heterogeneity within commercial pig breeds should be considered as an essential element in the history of their formation and breeding.
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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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Analysis of Genetic Diversity in the Czech Spotted Dog. Animals (Basel) 2020; 10:ani10081416. [PMID: 32823819 PMCID: PMC7459660 DOI: 10.3390/ani10081416] [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: 06/25/2020] [Revised: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 11/16/2022] Open
Abstract
Loss off genetic diversity negatively affects most of the modern dog breeds. However, no breed created strictly for laboratory purposes has been analyzed so far. In this paper, we sought to explore by pedigree analysis exactly such a breed-the Czech Spotted Dog (CSD). The pedigree contained a total of 2010 individuals registered since the second half of the 20th century. Parameters such as the mean average relatedness, coefficient of inbreeding, effective population size, effective number of founders, ancestors and founder genomes and loss of genetic diversity-which was calculated based on the reference population and pedigree completeness-were used to assess genetic variability. Compared to the founding population, the reference population lost 38.2% of its genetic diversity, of which 26% is due to random genetic drift and 12.2% is due to the uneven contribution of the founders. The reference population is highly inbred and related. The average inbreeding coefficient is 36.45%, and the mean average relatedness is 74.83%. The effective population size calculated based on the increase of inbreeding coefficient is 10.28. Thus, the Czech Spotted Dog suffered significant losses of genetic diversity that threaten its future existence.
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Wagner F, Ruf I. "Forever young"-Postnatal growth inhibition of the turbinal skeleton in brachycephalic dog breeds (Canis lupus familiaris). Anat Rec (Hoboken) 2020; 304:154-189. [PMID: 32462796 DOI: 10.1002/ar.24422] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/21/2020] [Accepted: 03/07/2020] [Indexed: 02/05/2023]
Abstract
In short snouted (brachycephalic) dogs (Canis lupus familiaris), several genetic mutations cause postnatal growth inhibition of the viscerocranium. Thus, for example, the pug keeps a snub nose like that observed in neonate dogs in general. However, little is known how far intranasal structures like the turbinal skeleton are also affected. In the present study, we provide the first detailed morphological and morphometric analyses on the turbinal skeleton of pug, Japanese chin, pekingese, King Charles spaniel, and Cavalier. In order to elucidate how a shortened snout affects turbinal shape, size, and density, our sample covers different degrees of brachycephaly. Macerated skulls of 1 juvenile and 17 adult individuals were investigated by μCT and virtual 3D reconstructions. In addition, histological serial sections of two prenatal and one neonate whippet were taken into account. All investigated postnatal stages show three frontoturbinals and three ethmoturbinals similar to longer snouted breeds, whereas the number of interturbinals is reduced. The shape of the entire turbinal skeleton simplifies with decreasing snout length, that is, within a minimized nasal cavity the turbinals decrease proportionally in surface area and surface density due to a looser arrangement. We interpret these apparent reductions as a result of spatial constraint which affects postnatal appositional bone growth and the position of the turbinals inside the nasal cavity. The turbinal skeleton of brachycephalic dogs arrests at an early ontogenetic stage, corresponding with previous studies on the dermal bones. Hence, we assume an association between the growth of intranasal structures and facial elongation.
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Affiliation(s)
- Franziska Wagner
- Abteilung Messelforschung und Mammalogie, Senckenberg Forschungsinstitut und Naturmuseum Frankfurt, Frankfurt am Main, Germany.,Museum für Tierkunde, Senckenberg Naturhistorische Sammlungen Dresden, Dresden, Germany
| | - Irina Ruf
- Abteilung Messelforschung und Mammalogie, Senckenberg Forschungsinstitut und Naturmuseum Frankfurt, Frankfurt am Main, Germany
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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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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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Wiener P, Sánchez-Molano E, Clements DN, Woolliams JA, Haskell MJ, Blott SC. Genomic data illuminates demography, genetic structure and selection of a popular dog breed. BMC Genomics 2017; 18:609. [PMID: 28806925 PMCID: PMC5557481 DOI: 10.1186/s12864-017-3933-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 07/09/2017] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Genomic methods have proved to be important tools in the analysis of genetic diversity across the range of species and can be used to reveal processes underlying both short- and long-term evolutionary change. This study applied genomic methods to investigate population structure and inbreeding in a common UK dog breed, the Labrador Retriever. RESULTS We found substantial within-breed genetic differentiation, which was associated with the role of the dog (i.e. working, pet, show) and also with coat colour (i.e. black, yellow, brown). There was little evidence of geographical differentiation. Highly differentiated genomic regions contained genes and markers associated with skull shape, suggesting that at least some of the differentiation is related to human-imposed selection on this trait. We also found that the total length of homozygous segments (runs of homozygosity, ROHs) was highly correlated with inbreeding coefficient. CONCLUSIONS This study demonstrates that high-density genomic data can be used to quantify genetic diversity and to decipher demographic and selection processes. Analysis of genetically differentiated regions in the UK Labrador Retriever population suggests the possibility of human-imposed selection on craniofacial characteristics. The high correlation between estimates of inbreeding from genomic and pedigree data for this breed demonstrates that genomic approaches can be used to quantify inbreeding levels in dogs, which will be particularly useful where pedigree information is missing.
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Affiliation(s)
- Pamela Wiener
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland UK
| | - Enrique Sánchez-Molano
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland UK
| | - Dylan N. Clements
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland UK
| | - John A. Woolliams
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland UK
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Breed, sex, and litter effects in 2-month old puppies' behaviour in a standardised open-field test. Sci Rep 2017; 7:1802. [PMID: 28496191 PMCID: PMC5431970 DOI: 10.1038/s41598-017-01992-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 03/28/2017] [Indexed: 11/25/2022] Open
Abstract
A considerable number of studies have reported differences among dog breeds with respect to their genetic profile, cognitive abilities or personality traits. Each dog breed is normally treated as a homogeneous group, however, researchers have recently questioned whether the behavioural profile of modern breeds still reflects their historical function or if the intense divergent selective pressures and geographical barriers have created a more fragmented picture. The majority of studies attempting to assess and compare modern breeds’ personality focused on the evaluation of adult dogs where the potential effects of environmental/human factors on the dogs’ behaviour are hard to discern from their genetic heritage. In the following study, we aimed at investigating between- and within-breed differences in the personality of two-months-old puppies by direct behavioural observation of 377 puppies from 12 breeds. Results showed that there was no effect of sex, however both breed and litter, significantly affected all personality traits. Breed on average explained 10% of the variance, whereas the effect of litter was noticeably higher, explaining on average 23% of the variance. Taken together, our results suggest that breed does have some influence on personality traits, but they also highlight the importance of taking litter effects into account.
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Dreger DL, Rimbault M, Davis BW, Bhatnagar A, Parker HG, Ostrander EA. Whole-genome sequence, SNP chips and pedigree structure: building demographic profiles in domestic dog breeds to optimize genetic-trait mapping. Dis Model Mech 2016; 9:1445-1460. [PMID: 27874836 PMCID: PMC5200897 DOI: 10.1242/dmm.027037] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/26/2016] [Indexed: 12/30/2022] Open
Abstract
In the decade following publication of the draft genome sequence of the domestic dog, extraordinary advances with application to several fields have been credited to the canine genetic system. Taking advantage of closed breeding populations and the subsequent selection for aesthetic and behavioral characteristics, researchers have leveraged the dog as an effective natural model for the study of complex traits, such as disease susceptibility, behavior and morphology, generating unique contributions to human health and biology. When designing genetic studies using purebred dogs, it is essential to consider the unique demography of each population, including estimation of effective population size and timing of population bottlenecks. The analytical design approach for genome-wide association studies (GWAS) and analysis of whole-genome sequence (WGS) experiments are inextricable from demographic data. We have performed a comprehensive study of genomic homozygosity, using high-depth WGS data for 90 individuals, and Illumina HD SNP data from 800 individuals representing 80 breeds. These data were coupled with extensive pedigree data analyses for 11 breeds that, together, allowed us to compute breed structure, demography, and molecular measures of genome diversity. Our comparative analyses characterize the extent, formation and implication of breed-specific diversity as it relates to population structure. These data demonstrate the relationship between breed-specific genome dynamics and population architecture, and provide important considerations influencing the technological and cohort design of association and other genomic studies. Summary: Successful application of whole-genome sequencing and genome-wide association studies for identifying both loci and mutations in canines is influenced by breed structure and demography, motivating researchers to generate breed-specific strategies for canine genetic studies.
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Affiliation(s)
- 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.,Institut de Génétique et Développement de Rennes, Rennes 35043, France
| | - Brian W Davis
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrienne Bhatnagar
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.,PIC North America, Hendersonville, TN 37075, USA
| | - Heidi G Parker
- 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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Pols S, Henneberg M, Norris R. Cranial Arterial Patterning in Greyhounds: Another Case of Internal Intraspecific Variation. Anat Histol Embryol 2016; 45:161-72. [DOI: 10.1111/ahe.12182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 04/24/2015] [Indexed: 11/27/2022]
Affiliation(s)
- S. Pols
- University of Adelaide; School of Animal and Veterinary Science; Mudla Wirra Road; Roseworthy SA 5371 Australia
| | - M. Henneberg
- University of Adelaide; School of Medical Sciences; Medical School South Building; Frome Road SA 5005 Australia
| | - R. Norris
- University of Adelaide; School of Animal and Veterinary Science; Mudla Wirra Road; Roseworthy SA 5371 Australia
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12
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Wijnrocx K, François L, Stinckens A, Janssens S, Buys N. Half of 23 Belgian dog breeds has a compromised genetic diversity, as revealed by genealogical and molecular data analysis. J Anim Breed Genet 2016; 133:375-83. [DOI: 10.1111/jbg.12203] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/30/2016] [Indexed: 11/27/2022]
Affiliation(s)
- K. Wijnrocx
- Department of Biosystems; KU Leuven, Livestock Genetics; 3001 Leuven Belgium
| | - L. François
- Department of Biosystems; KU Leuven, Livestock Genetics; 3001 Leuven Belgium
| | - A. Stinckens
- Department of Biosystems; KU Leuven, Livestock Genetics; 3001 Leuven Belgium
| | - S. Janssens
- Department of Biosystems; KU Leuven, Livestock Genetics; 3001 Leuven Belgium
| | - N. Buys
- Department of Biosystems; KU Leuven, Livestock Genetics; 3001 Leuven Belgium
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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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Farrell LL, Schoenebeck JJ, Wiener P, Clements DN, Summers KM. The challenges of pedigree dog health: approaches to combating inherited disease. Canine Genet Epidemiol 2015; 2:3. [PMID: 26401331 PMCID: PMC4579364 DOI: 10.1186/s40575-015-0014-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/13/2015] [Indexed: 01/29/2023] Open
Abstract
The issue of inherited disorders and poor health in pedigree dogs has been widely discussed in recent years. With the advent of genome-wide sequencing technologies and the increasing development of new diagnostic DNA disease tests, the full extent and prevalence of inherited disorders in pedigree dogs is now being realized. In this review we discuss the challenges facing pedigree dog breeds: the common pitfalls and problems associated with combating single gene mediated disorders, phenotypic selection on complex disorders, and ways of managing genetic diversity. Breeding strategies incorporating screening schemes have been shown to be successful in significantly reducing the prevalence of an inherited disorder and improving the overall health in certain breeds. However, with 215 breeds officially recognized by the Kennel Club in the United Kingdom and 396 inherited disorders currently identified, many breeds have reached the point at which successfully breeding away from susceptible individuals at a population-wide scale will require new genomic selection strategies in combination with currently available breeding schemes. Whilst DNA-based tests identifying disease causing mutation(s) remain the most informative and effective approach for single gene disorder disease management, they must be used along with current screening schemes, genomic selection, and pedigree information in breeding programs in the effort to maintain genetic diversity while also significantly reducing the number of inherited disorders in pedigree dogs.
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Affiliation(s)
- Lindsay L Farrell
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
| | - Jeffrey J Schoenebeck
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
| | - Pamela Wiener
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
| | - Dylan N Clements
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
| | - Kim M Summers
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
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Olsson M, Tintle L, Kierczak M, Perloski M, Tonomura N, Lundquist A, Murén E, Fels M, Tengvall K, Pielberg G, Dufaure de Citres C, Dorso L, Abadie J, Hanson J, Thomas A, Leegwater P, Hedhammar Å, Lindblad-Toh K, Meadows JRS. Thorough investigation of a canine autoinflammatory disease (AID) confirms one main risk locus and suggests a modifier locus for amyloidosis. PLoS One 2013; 8:e75242. [PMID: 24130694 PMCID: PMC3793984 DOI: 10.1371/journal.pone.0075242] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 08/13/2013] [Indexed: 12/04/2022] Open
Abstract
Autoinflammatory disease (AID) manifests from the dysregulation of the innate immune system and is characterised by systemic and persistent inflammation. Clinical heterogeneity leads to patients presenting with one or a spectrum of phenotypic signs, leading to difficult diagnoses in the absence of a clear genetic cause. We used separate genome-wide SNP analyses to investigate five signs of AID (recurrent fever, arthritis, breed specific secondary dermatitis, otitis and systemic reactive amyloidosis) in a canine comparative model, the pure bred Chinese Shar-Pei. Analysis of 255 DNA samples revealed a shared locus on chromosome 13 spanning two peaks of association. A three-marker haplotype based on the most significant SNP (p<2.6×10−8) from each analysis showed that one haplotypic pair (H13-11) was present in the majority of AID individuals, implicating this as a shared risk factor for all phenotypes. We also noted that a genetic signature (FST) distinguishing the phenotypic extremes of the breed specific Chinese Shar-Pei thick and wrinkled skin, flanked the chromosome 13 AID locus; suggesting that breed development and differentiation has played a parallel role in the genetics of breed fitness. Intriguingly, a potential modifier locus for amyloidosis was revealed on chromosome 14, and an investigation of candidate genes from both this and the chromosome 13 regions revealed significant (p<0.05) renal differential expression in four genes previously implicated in kidney or immune health (AOAH, ELMO1, HAS2 and IL6). These results illustrate that phenotypic heterogeneity need not be a reflection of genetic heterogeneity, and that genetic modifiers of disease could be masked if syndromes were not first considered as individual clinical signs and then as a sum of their component parts.
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Affiliation(s)
- Mia Olsson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- * E-mail: (MO); (KL-T); (JRSM)
| | - Linda Tintle
- Wurtsboro Veterinary Clinic, Wurtsboro, New York, United States of America
| | - Marcin Kierczak
- Computational Genetics Section, Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Michele Perloski
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, United States of America
| | - Noriko Tonomura
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, United States of America
- Department of Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, United States of America
| | - Andrew Lundquist
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, United States of America
| | - Eva Murén
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Max Fels
- Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Katarina Tengvall
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Gerli Pielberg
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | - Laetitia Dorso
- LUNAM University, Oniris, AMaROC Unit, Nantes, F-44307, France
| | - Jérôme Abadie
- LUNAM University, Oniris, AMaROC Unit, Nantes, F-44307, France
| | - Jeanette Hanson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Anne Thomas
- ANTAGENE Animal Genetics Laboratory, La Tour de Salvagny (69 Lyon), France
| | - Peter Leegwater
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, The Netherlands
| | - Åke Hedhammar
- Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA, United States of America
- * E-mail: (MO); (KL-T); (JRSM)
| | - Jennifer R. S. Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- * E-mail: (MO); (KL-T); (JRSM)
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17
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Wong AK, Ruhe AL, Biswas S, Robertson KR, Ali A, Akey JM, Neff MW. Marker panels for genealogy-based mapping, breed demographics, and inference-of-ancestry in the dog. Anim Biotechnol 2012; 23:241-52. [PMID: 23134304 DOI: 10.1080/10495398.2012.717151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Short tandem repeat polymorphisms (STRPs) are robust and informative markers for a range of genetic applications. STRPs are advantageous in experimental designs that derive power from sampling many individuals rather than many loci (e.g., pedigree-based studies, fine-scale mapping, and conservation genetics). STRPs have proven useful for vetting samples prior to costly high-density SNP analysis. Here we present validated STRPs (n = 1,012) spanning the canine genome (2.1 +/-1.4 Mb; 2.1 +/-2.1 cM). Standardized design, pre-multiplexing, M13-based dye-labeling, and selection for loci amenable to semi-automated allele-scoring minimize cost and facilitate efficient genotyping. The markers are leveraged from the canine linkage map, and thus are backed by genetic data useful for parametric multipoint analysis and assessment of empiric coverage. We demonstrate several applications with different marker subsets. The complete set provides a genome scan for linkage at ∼5 cM resolution. A subset of the markers measures molecular diversity between domestic and wild canid populations. Another subset reflects ancestry within breeds, uncovering hidden stratification and flagging genetic outliers prior to SNP genotyping. Thus, the markers described here add flexibility and cost effectiveness to several genetic applications in the dog that complement genome-wide SNP genotyping studies. Supplemental material is available for this article. Go to the publisher's online edition of Animal Biotechnology.
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Affiliation(s)
- Aaron K Wong
- Veterinary Genetics Laboratory, University of California, Davis, USA
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19
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Developmental validation of DogFiler, a novel multiplex for canine DNA profiling in forensic casework. Forensic Sci Int Genet 2012; 7:82-91. [PMID: 22832398 DOI: 10.1016/j.fsigen.2012.07.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 07/03/2012] [Accepted: 07/04/2012] [Indexed: 11/22/2022]
Abstract
While the analysis of human DNA has been the focus of large-scale collaborative endeavors, non-human forensic DNA analysis has not benefited from the same funding streams and coordination of effort. Consequently, the development of standard marker panels, allelic ladders and allele-specific sequence data comparable to those established for human forensic genetics has lagged. To meet that need for domestic dogs, we investigated sequence data provided by the published 7.6X dog genome for novel short tandem repeat markers that met our criteria for sensitivity, stability, robustness, polymorphic information content, and ease of scoring. Fifteen unlinked tetranucleotide repeat markers were selected from a pool of 3113 candidate markers and assembled with a sex-linked marker into a multiplex capable of generating a full profile with as little as 60pg of nuclear DNA. An accompanying allelic ladder was assembled and sequenced to obtain detailed repeat motif data. Validation was carried out according to SWGDAM guidelines, and the DogFiler panel has been integrated into forensic casework and accepted in courts across the U.S. Applying various formulae for calculating random match probabilities for inbred populations, estimates for this panel of markers have proven to be comparable to those obtained in human forensic genetics. The DogFiler panel and the associated allelic ladder represent the first published non-human profiling system to fully address all SWGDAM recommendations.
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20
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Pedersen NC, Liu H, McLaughlin B, Sacks BN. Genetic characterization of healthy and sebaceous adenitis affected Standard Poodles from the United States and the United Kingdom. ACTA ACUST UNITED AC 2012; 80:46-57. [PMID: 22512808 DOI: 10.1111/j.1399-0039.2012.01876.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The degree of heterogeneity associated with geographic origin and sebaceous adenitis (SA) status in Standard Poodles from the United States (US) and the United Kingdom (UK) was assessed. Healthy and SA-affected Standard Poodles from the US and the UK shared a major mitochondrial DNA (mtDNA) haplotype and a single Y chromosome haplotype. However, minor mtDNA haplotypes and frequencies were somewhat different between US and UK dogs and were significantly less associated with SA than major haplotypes across both populations. The US and UK populations exhibited recent divergence from a common gene pool, based on allele frequencies of 24 highly polymorphic short tandem repeats and principle coordinates and cluster analyses of genotype frequencies. However, there was no differentiation between SA affected and unaffected dogs. Over 90% of US and UK Poodles shared a common dog leukocyte antigen (DLA) class II haplotype, but showed some differentiation in minor haplotype frequency. No difference was observed in haplotype heterozygosity between SA affected and unaffected dogs from the same country and no disease association for SA was found within the DLA region by a high density single nucleotide polymorphism (SNP) scan. Zygosity mapping in the DLA region of Poodles indicated much lower site-specific diversity than in an outbred population of street dogs from Bali, Indonesia, reflecting the degree that breed associated historical bottlenecks have reduced diversity in a polymorphic region of the genome. This study shows possible pitfalls in more extensive genome-wide association studies, such as case and control numbers, population stratification, the involvement of multiple genes, and/or the possibility that SA susceptibility is fixed or nearly fixed within the breed, which can reduce power to detect genetic associations.
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Affiliation(s)
- N C Pedersen
- Center for Companion Animal Health, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.
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21
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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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22
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Genetic diversity, inbreeding and breeding practices in dogs: Results from pedigree analyses. Vet J 2011; 189:177-82. [DOI: 10.1016/j.tvjl.2011.06.016] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
This review assesses evidence from DNA analysis to determine whether there is sufficient genetic diversity within breeds to ensure that populations are sustainable in the absence of cross breeding and to determine whether genetic diversity is declining. On average, dog breeds currently retain approximately 87% of the available domestic canine genetic diversity. Requirements that breeding stock must be 'clear' for all genetic disorders may firstly place undue genetic pressure on animals tested as being 'clear' of known genetic disorders, secondly may contribute to loss of diversity and thirdly may result in the dissemination of new recessive disorders for which no genetic tests are available. Global exchange of genetic material may hasten the loss of alleles and this practice should be discussed in relation to the current effective population size of a breed and its expected future popularity. Genomic data do not always support the results from pedigree analysis and possible reasons for this are discussed.
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Affiliation(s)
- Claire M Wade
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia.
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24
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Pathirana IN, Tanaka K, Kawate N, Tsuji M, Hatoya S, Inaba T, Tamada H. Homozygosity of single nucleotide polymorphisms in the 3' region of the canine estrogen receptor 1 gene is greater in Toy Poodles than in Miniature Dachshunds and Chihuahuas. Anim Sci J 2011; 82:390-5. [PMID: 21615831 DOI: 10.1111/j.1740-0929.2010.00864.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Differences in the distribution of single nucleotide polymorphisms (SNPs) and haplotypes in the estrogen receptor α gene (ESR1) were examined in Miniature Dachshunds (n = 48), Chihuahuas (n = 20) and Toy Poodles (n = 18). Five DNA fragments located in the 40-kb region at the 3' end of ESR1 were amplified by polymerase chain reaction and were directly sequenced. We compared allele, genotype and estimated haplotype frequencies at each SNP in the 3' end of ESR1 for these three breeds of small dog. The frequency of the major allele and the genotype frequency of the major allele homozygotes, were significantly higher in Toy Poodles for five SNPs (SNP #5, #14-17) than in Miniature Dachshunds, and significantly higher in Toy Poodles than Chihuahuas for three SNPs (SNP #15-17). A common haplotype block was identified in an approximately 20-kb region encompassing four SNPs (SNPs # 14-17). The frequencies of the most abundant estimated haplotype (GTTG) and GTTG homozygotes were significantly higher in Toy Poodles than in the other two breeds. These results imply that homozygosity for the allele, genotype and haplotype distribution within the block at the 3' end of ESR1 is greater in Toy Poodles than in Miniature Dachshunds and Chihuahuas.
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Affiliation(s)
- Indunil N Pathirana
- Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Japan
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Parker HG, Shearin AL, Ostrander EA. Man's best friend becomes biology's best in show: genome analyses in the domestic dog. Annu Rev Genet 2011; 44:309-36. [PMID: 21047261 DOI: 10.1146/annurev-genet-102808-115200] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In the last five years, canine genetics has gone from map construction to complex disease deconstruction. The availability of a draft canine genome sequence, dense marker chips, and an understanding of the genome architecture has changed the types of studies canine geneticists can undertake. There is now a clear recognition that the dog system offers the opportunity to understand the genetics of both simple and complex traits, including those associated with morphology, disease susceptibility, and behavior. In this review, we summarize recent findings regarding canine domestication and review new information on the organization of the canine genome. We discuss studies aimed at finding genes controlling morphological phenotypes and provide examples of the way such paradigms may be applied to studies of behavior. We also discuss the many ways in which the dog has illuminated our understanding of human disease and conclude with a discussion on where the field is likely headed in the next five years.
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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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26
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Vila M, Marí-Mena N, Guerrero A, Schmitt T. Some butterflies do not care much about topography: a single genetic lineage of Erebia euryale (Nymphalidae) along the northern Iberian mountains. J ZOOL SYST EVOL RES 2010. [DOI: 10.1111/j.1439-0469.2010.00587.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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27
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Ke X, Kennedy LJ, Short AD, Seppälä EH, Barnes A, Clements DN, Wood SH, Carter SD, Happ GM, Lohi H, Ollier WER. Assessment of the functionality of genome-wide canine SNP arrays and implications for canine disease association studies. Anim Genet 2010; 42:181-90. [DOI: 10.1111/j.1365-2052.2010.02132.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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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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29
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Drake AG, Klingenberg CP. Large‐Scale Diversification of Skull Shape in Domestic Dogs: Disparity and Modularity. Am Nat 2010; 175:289-301. [PMID: 20095825 DOI: 10.1086/650372] [Citation(s) in RCA: 250] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Abby Grace Drake
- Faculty of Life Sciences, University of Manchester, Manchester, UK.
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30
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Summers JF, Diesel G, Asher L, McGreevy PD, Collins LM. Inherited defects in pedigree dogs. Part 2: Disorders that are not related to breed standards. Vet J 2009; 183:39-45. [PMID: 19963415 DOI: 10.1016/j.tvjl.2009.11.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 11/03/2009] [Accepted: 11/05/2009] [Indexed: 02/01/2023]
Abstract
Recent debate concerning health problems in pedigree animals has highlighted gaps in current knowledge of the prevalence, severity and welfare implications of deleterious inherited traits within the pedigree-dog population. In this second part of a two-part review, inherited disorders in the top 50 UK Kennel Club registered breeds were researched using systematic searches of existing databases. A set of inclusion and exclusion criteria, including an evidence strength scale (SEHB), were applied to search results. A total of 312 non-conformation linked inherited disorders was identified, with German shepherd dogs and Golden retrievers associated with the greatest number of disorders. The most commonly reported mode of inheritance was autosomal recessive (71%; 57 breed-disorder combinations), and the most common primarily affected body system was the nervous sensory system. To provide a true assessment of the scale of inherited disorders in the pedigree dogs studied more effort is required to collect accurate prevalence data.
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Affiliation(s)
- Jennifer F Summers
- Department of Veterinary Clinical Sciences, Royal Veterinary College, UK
| | - Gillian Diesel
- Department of Veterinary Clinical Sciences, Royal Veterinary College, UK
| | - Lucy Asher
- Department of Veterinary Clinical Sciences, Royal Veterinary College, UK
| | - Paul D McGreevy
- Faculty of Veterinary Science, University of Sydney, Australia
| | - Lisa M Collins
- Department of Veterinary Clinical Sciences, Royal Veterinary College, UK.
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31
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Oliehoek PA, Bijma P, van der Meijden A. History and structure of the closed pedigreed population of Icelandic Sheepdogs. Genet Sel Evol 2009; 41:39. [PMID: 19660133 PMCID: PMC2736928 DOI: 10.1186/1297-9686-41-39] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Accepted: 08/06/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dog breeds lose genetic diversity because of high selection pressure. Breeding policies aim to minimize kinship and therefore maintain genetic diversity. However, policies like mean kinship and optimal contributions might be impractical. Cluster analysis of kinship can elucidate the population structure, since this method divides the population in clusters of related individuals. Kinship-based analyses have been carried out on the entire Icelandic Sheepdog population, a sheep-herding breed. RESULTS Analyses showed that despite increasing population size and deliberately transferring dogs, considerable genetic diversity has been lost. When cluster analysis was based on kinships calculated seven generation backwards, as performed in previous studies, results differ markedly from those based on calculations going back to the founder-population, and thus invalidate recommendations based on previous research. When calculated back to the founder-population, kinship-based clustering reveals the distribution of genetic diversity, similarly to strategies using mean kinship. CONCLUSION Although the base population consisted of 36 Icelandic Sheepdog founders, the current diversity is equivalent to that of only 2.2 equally contributing founders with no loss of founder alleles in descendants. The maximum attainable diversity is 4.7, unlikely achievable in a non-supervised breeding population like the Icelandic Sheepdog. Cluster analysis of kinship coefficients can provide a supporting tool to assess the distribution of available genetic diversity for captive population management.
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Affiliation(s)
- Pieter A Oliehoek
- Animal Breeding and Genomics Centre, Wageningen University, the Netherlands.
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32
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KOBLMÜLLER STEPHAN, NORD MARIA, WAYNE ROBERTK, LEONARD JENNIFERA. Origin and status of the Great Lakes wolf. Mol Ecol 2009; 18:2313-26. [DOI: 10.1111/j.1365-294x.2009.04176.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hejjas K, Kubinyi E, Ronai Z, Szekely A, Vas J, Miklósi, Sasvari-Szekely M, Kereszturi E. Molecular and behavioral analysis of the intron 2 repeat polymorphism in the canine dopamine D4 receptor gene. GENES BRAIN AND BEHAVIOR 2009; 8:330-6. [DOI: 10.1111/j.1601-183x.2008.00475.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Castelhano MGP, Acland GM, Ciccone PA, Corey EE, Mezey JG, Schimenti JC, Todhunter RJ. Development and use of DNA archives at veterinary teaching hospitals to investigate the genetic basis of disease in dogs. J Am Vet Med Assoc 2009; 234:75-80. [PMID: 19119968 DOI: 10.2460/javma.234.1.75] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The DNA archives developed at veterinary medical teaching hospitals will be important resources for mapping disease loci and identifying underlying genes. The most important feature of a DNA archive is accurate identification or exclusion of diseases in each animal. Such archives will be complimentary resources to tissue banks that are currently available.
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Affiliation(s)
- Marta G P Castelhano
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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35
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Kukekova AV, Goldstein O, Johnson JL, Richardson MA, Pearce-Kelling SE, Swaroop A, Friedman JS, Aguirre GD, Acland GM. Canine RD3 mutation establishes rod-cone dysplasia type 2 (rcd2) as ortholog of human and murine rd3. Mamm Genome 2009; 20:109-23. [PMID: 19130129 PMCID: PMC2652121 DOI: 10.1007/s00335-008-9163-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Accepted: 11/19/2008] [Indexed: 10/21/2022]
Abstract
Rod-cone dysplasia type 2 (rcd2) is an autosomal recessive disorder that segregates in collie dogs. Linkage disequilibrium and meiotic linkage mapping were combined to take advantage of population structure within this breed and to fine map rcd2 to a 230-kb candidate region that included the gene C1orf36 responsible for human and murine rd3, and within which all affected dogs were homozygous for one haplotype. In one of three identified canine retinal RD3 splice variants, an insertion was found that cosegregates with rcd2 and is predicted to alter the last 61 codons of the normal open reading frame and further extend the open reading frame. Thus, combined meiotic linkage and LD mapping within a single canine breed can yield critical reduction of the disease interval when appropriate advantage is taken of within-breed population structure. This should permit a similar approach to tackle other hereditary traits that segregate in single closed populations.
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Affiliation(s)
- Anna V. Kukekova
- James A. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
| | - Orly Goldstein
- James A. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
| | - Jennifer L. Johnson
- James A. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
| | - Malcolm A. Richardson
- James A. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
- Department of Microbiology and Immunology, Dartmouth Medical School, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, 03766
| | - Susan E. Pearce-Kelling
- James A. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
| | - Anand Swaroop
- W. K. Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, 48105
- National Eye Institute/National Institutes of Health, Bethesda, Maryland, 20892
| | - James S. Friedman
- National Eye Institute/National Institutes of Health, Bethesda, Maryland, 20892
| | - Gustavo D. Aguirre
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Gregory M. Acland
- James A. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
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Nicholas TJ, Cheng Z, Ventura M, Mealey K, Eichler EE, Akey JM. The genomic architecture of segmental duplications and associated copy number variants in dogs. Genome Res 2009; 19:491-9. [PMID: 19129542 DOI: 10.1101/gr.084715.108] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of segmental duplications and associated copy number variants (CNVs) in the modern domesticated dog, Canis familiaris, which exhibits considerable morphological, physiological, and behavioral variation. Through computational analyses of the publicly available canine reference sequence, we estimate that segmental duplications comprise approximately 4.21% of the canine genome. Segmental duplications overlap 841 genes and are significantly enriched for specific biological functions such as immunity and defense and KRAB box transcription factors. We designed high-density tiling arrays spanning all predicted segmental duplications and performed aCGH in a panel of 17 breeds and a gray wolf. In total, we identified 3583 CNVs, approximately 68% of which were found in two or more samples that map to 678 unique regions. CNVs span 429 genes that are involved in a wide variety of biological processes such as olfaction, immunity, and gene regulation. Our results provide insight into mechanisms of canine genome evolution and generate a valuable resource for future evolutionary and phenotypic studies.
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Affiliation(s)
- Thomas J Nicholas
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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Intrabreed Stratification Related to Divergent Selection Regimes in Purebred Dogs May Affect the Interpretation of Genetic Association Studies. J Hered 2009; 100:S28-S36. [PMCID: PMC4176315 DOI: 10.1093/jhered/esp012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2008] [Revised: 02/13/2009] [Accepted: 02/25/2009] [Indexed: 12/22/2023] Open
Abstract
Until recently, canine genetic research has not focused on population structure within breeds, which may confound the results of case–control studies by introducing spurious correlations between phenotype and genotype that reflect population history. Intrabreed structure may exist when geographical origin or divergent selection regimes influence the choices of potential mates for breeding dogs. We present evidence for intrabreed stratification from a genome-wide marker survey in a sample of unrelated dogs. We genotyped 76 Border Collies, 49 Australian Shepherds, 17 German Shepherd Dogs, and 17 Portuguese Water Dogs for our primary analyses using Affymetrix Canine v2.0 single-nucleotide polymorphism (SNP) arrays. Subsets of autosomal markers were examined using clustering algorithms to facilitate assignment of individuals to populations and estimation of the number of populations represented in the sample. SNPs passing stringent quality control filters were employed for explicitly phylogenetic analyses reconstructing relationships between individuals using maximum parsimony and Bayesian methods. We used simulation studies to explore the possible effects of intrabreed stratification on genome-wide association studies. These analyses demonstrate significant stratification in at least one of our primary breeds of interest, the Border Collie. Demographic and pedigree data suggest that this population substructure may result from geographic isolation or divergent selection regimes practiced by breeders with different breeding program goals. Simulation studies indicate that such stratification could result in false discovery rates significant enough to confound genome-wide association analyses. Intrabreed stratification should be accounted for when designing and interpreting the results of case–control association studies using purebred dogs.
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