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Dutra L, Souza F, Friberg I, Araújo M, Vasconcellos A, Young R. Validating the use of oral swabs for telomere length assessment in dogs. J Vet Behav 2020. [DOI: 10.1016/j.jveb.2020.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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2
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Monge O, Dumas D, Baus I. Environmental DNA from avian residual saliva in fruits and its potential uses in population genetics. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-018-1074-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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3
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Long C, Lankford L, Kumar P, Grahn R, Borjesson DL, Farmer D, Wang A. Isolation and characterization of canine placenta-derived mesenchymal stromal cells for the treatment of neurological disorders in dogs. Cytometry A 2017; 93:82-92. [DOI: 10.1002/cyto.a.23171] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/19/2017] [Accepted: 06/27/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Connor Long
- Surgical Bioengineering Laboratory, Department of Surgery; University of California, Davis School of Medicine; Sacramento California
| | - Lee Lankford
- Surgical Bioengineering Laboratory, Department of Surgery; University of California, Davis School of Medicine; Sacramento California
| | - Priyadarsini Kumar
- Surgical Bioengineering Laboratory, Department of Surgery; University of California, Davis School of Medicine; Sacramento California
| | - Robert Grahn
- Veterinary Genetics Laboratory; University of California; Davis California
| | - Dori L. Borjesson
- Veterinary Institute for Regenerative Cures and Department of Pathology, Microbiology, Immunology; University of California, Davis School of Veterinary Medicine; Davis California
| | - Diana Farmer
- Surgical Bioengineering Laboratory, Department of Surgery; University of California, Davis School of Medicine; Sacramento California
| | - Aijun Wang
- Surgical Bioengineering Laboratory, Department of Surgery; University of California, Davis School of Medicine; Sacramento California
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A Novel Variant in CMAH Is Associated with Blood Type AB in Ragdoll Cats. PLoS One 2016; 11:e0154973. [PMID: 27171395 PMCID: PMC4865243 DOI: 10.1371/journal.pone.0154973] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/21/2016] [Indexed: 11/19/2022] Open
Abstract
The enzyme cytidine monophospho-N-acetylneuraminic acid hydroxylase is associated with the production of sialic acids on cat red blood cells. The cat has one major blood group with three serotypes; the most common blood type A being dominant to type B. A third rare blood type is known as AB and has an unclear mode of inheritance. Cat blood type antigens are defined, with N-glycolylneuraminic acid being associated with type A and N-acetylneuraminic acid with type B. Blood type AB is serologically characterized by agglutination using typing reagents directed against both A and B epitopes. While a genetic characterization of blood type B has been achieved, the rare type AB serotype remains genetically uncharacterized. A genome-wide association study in Ragdoll cats (22 cases and 15 controls) detected a significant association between blood type AB and SNPs on cat chromosome B2, with the most highly associated SNP being at position 4,487,432 near the candidate gene cytidine monophospho-N-acetylneuraminic acid hydroxylase. A novel variant, c.364C>T, was identified that is highly associated with blood type AB in Ragdoll cats and, to a lesser degree, with type AB in random bred cats. The newly identified variant is probably linked with blood type AB in Ragdoll cats, and is associated with the expression of both antigens (N-glycolylneuraminic acid and N-acetylneuraminic acid) on the red blood cell membrane. Other variants, not identified by this work, are likely to be associated with blood type AB in other breeds of cat.
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Breitenbuecher C, Belanger JM, Levy K, Mundell P, Fates V, Gershony L, Famula TR, Oberbauer AM. Protein expression and genetic variability of canine Can f 1 in golden and Labrador retriever service dogs. Canine Genet Epidemiol 2016; 3:3. [PMID: 27110374 PMCID: PMC4840867 DOI: 10.1186/s40575-016-0031-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 03/03/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Valued for trainability in diverse tasks, dogs are the primary service animal used to assist individuals with disabilities. Despite their utility, many people in need of service dogs are sensitive to the primary dog allergen, Can f 1, encoded by the Lipocalin 1 gene (LCN1). Several organizations specifically breed service dogs to meet special needs and would like to reduce allergenic potential if possible. In this study, we evaluated the expression of Can f 1 protein and the inherent variability of LCN1 in two breeds used extensively as service dogs. Saliva samples from equal numbers of male and female Labrador retrievers (n = 12), golden retrievers (n = 12), and Labrador-golden crosses (n = 12) were collected 1 h after the morning meal. Can f 1 protein concentrations in the saliva were measured by ELISA, and the LCN1 5' and 3' UTRs and exons sequenced. RESULTS There was no sex effect (p > 0.2) nor time-of-day effect; however, Can f 1 protein levels varied by breed with Labrador retrievers being lower than golden retrievers (3.18 ± 0.51 and 5.35 ± 0.52 μg/ml, respectively, p < 0.0075), and the Labrador-golden crosses having intermediate levels (3.77 ± 0.48 μg/ml). Although several novel SNPs were identified in LCN1, there were no significant breed-specific sequence differences in the gene and no association of LCN1 genotypes with Can f 1 expression. CONCLUSIONS As service dogs, Labrador retrievers likely have lower allergenic potential and, though there were no DNA sequence differences identified, classical genetic selection on the estimated breeding values associated with salivary Can f 1 expression may further reduce that potential.
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Affiliation(s)
| | - Janelle M Belanger
- Department of Animal Science, University of California, One Shields Ave, Davis, CA 95616 USA
| | - Kerinne Levy
- Canine Companions for Independence, Santa Rosa, CA USA
| | - Paul Mundell
- Canine Companions for Independence, Santa Rosa, CA USA
| | - Valerie Fates
- Department of Animal Science, University of California, One Shields Ave, Davis, CA 95616 USA
| | - Liza Gershony
- Department of Animal Science, University of California, One Shields Ave, Davis, CA 95616 USA
| | - Thomas R Famula
- Department of Animal Science, University of California, One Shields Ave, Davis, CA 95616 USA
| | - Anita M Oberbauer
- Department of Animal Science, University of California, One Shields Ave, Davis, CA 95616 USA
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6
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Koskinen LLE, Seppälä EH, Belanger JM, Arumilli M, Hakosalo O, Jokinen P, Nevalainen EM, Viitmaa R, Jokinen TS, Oberbauer AM, Lohi H. Identification of a common risk haplotype for canine idiopathic epilepsy in the ADAM23 gene. BMC Genomics 2015; 16:465. [PMID: 26084559 PMCID: PMC4470040 DOI: 10.1186/s12864-015-1651-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 05/20/2015] [Indexed: 12/17/2022] Open
Abstract
Background Idiopathic epilepsy is a common neurological disease in human and domestic dogs but relatively few risk genes have been identified to date. The seizure characteristics, including focal and generalised seizures, are similar between the two species, with gene discovery facilitated by the reduced genetic heterogeneity of purebred dogs. We have recently identified a risk locus for idiopathic epilepsy in the Belgian Shepherd breed on a 4.4 megabase region on CFA37. Results We have expanded a previous study replicating the association with a combined analysis of 157 cases and 179 controls in three additional breeds: Schipperke, Finnish Spitz and Beagle (pc = 2.9e–07, pGWAS = 1.74E-02). A targeted resequencing of the 4.4 megabase region in twelve Belgian Shepherd cases and twelve controls with opposite haplotypes identified 37 case-specific variants within the ADAM23 gene. Twenty-seven variants were validated in 285 cases and 355 controls from four breeds, resulting in a strong replication of the ADAM23 locus (praw = 2.76e–15) and the identification of a common 28 kb-risk haplotype in all four breeds. Risk haplotype was present in frequencies of 0.49–0.7 in the breeds, suggesting that ADAM23 is a low penetrance risk gene for canine epilepsy. Conclusions These results implicate ADAM23 in common canine idiopathic epilepsy, although the causative variant remains yet to be identified. ADAM23 plays a role in synaptic transmission and interacts with known epilepsy genes, LGI1 and LGI2, and should be considered as a candidate gene for human epilepsies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1651-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lotta L E Koskinen
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland. .,Department of Veterinary Biosciences and Department of Medical Genetics, University of Helsinki, Helsinki, Finland. .,Folkhälsan Institute of Genetics, Helsinki, Finland.
| | - Eija H Seppälä
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland. .,Department of Veterinary Biosciences and Department of Medical Genetics, University of Helsinki, Helsinki, Finland. .,Folkhälsan Institute of Genetics, Helsinki, Finland.
| | - Janelle M Belanger
- Department of Animal Science, University of California Davis, Davis, California, USA.
| | - Meharji Arumilli
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland. .,Department of Veterinary Biosciences and Department of Medical Genetics, University of Helsinki, Helsinki, Finland. .,Folkhälsan Institute of Genetics, Helsinki, Finland.
| | - Osmo Hakosalo
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland. .,Department of Veterinary Biosciences and Department of Medical Genetics, University of Helsinki, Helsinki, Finland. .,Folkhälsan Institute of Genetics, Helsinki, Finland.
| | - Päivi Jokinen
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland. .,Department of Veterinary Biosciences and Department of Medical Genetics, University of Helsinki, Helsinki, Finland. .,Folkhälsan Institute of Genetics, Helsinki, Finland.
| | - Elisa M Nevalainen
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland. .,Department of Veterinary Biosciences and Department of Medical Genetics, University of Helsinki, Helsinki, Finland. .,Folkhälsan Institute of Genetics, Helsinki, Finland.
| | - Ranno Viitmaa
- Department of Clinical Veterinary Sciences, University of Helsinki, Helsinki, Finland.
| | - Tarja S Jokinen
- Department of Clinical Veterinary Sciences, University of Helsinki, Helsinki, Finland.
| | - Anita M Oberbauer
- Department of Animal Science, University of California Davis, Davis, California, USA.
| | - Hannes Lohi
- Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland. .,Department of Veterinary Biosciences and Department of Medical Genetics, University of Helsinki, Helsinki, Finland. .,Folkhälsan Institute of Genetics, Helsinki, Finland.
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7
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Lit L, Belanger JM, Boehm D, Lybarger N, Oberbauer AM. Differences in behavior and activity associated with a poly(a) expansion in the dopamine transporter in Belgian Malinois. PLoS One 2013; 8:e82948. [PMID: 24376613 PMCID: PMC3871558 DOI: 10.1371/journal.pone.0082948] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 10/29/2013] [Indexed: 01/12/2023] Open
Abstract
In Belgian Malinois dogs, a 38-base pair variable number tandem repeat in the dopamine transporter gene (SLC6A3) is associated with behavior changes in Malinois. By additional sequencing in SLC6A3, we identified an intronic 12-nucleotide poly(A) insertion (“PolyA(22)”) before the terminal exon that was associated with seizure, “glazing over” behaviors, and episodic biting behaviors in a sample of 138 Malinois. We next investigated whether PolyA(22) was associated with 1) increased locomotor activity and 2) response to novelty. Using a sample of 22 Malinois and 25 dogs of other breeds, dogs’ activity was monitored in a novel and non-novel environment while wearing activity monitoring collars. All dogs were more active in novel compared with non-novel environments, and Malinois were more active overall than other breeds. There was an effect of PolyA(22) genotype on activity levels, and this effect appeared to underlie the difference detected between Malinois and other breeds. There was no effect of PolyA(22) genotype on the relative decrease in activity between novel and non-novel environments for either group or all dogs considered together. In addition to an association between PolyA(22) and owner reports of seizure, “glazing over” behaviors, and episodic biting behaviors, these findings support an effect of PolyA(22) on dopamine transporter function related to activity. Further investigation is required to confirm mechanistic effects of PolyA(22) on SLC6A3. The complex polygenic nature of behavior and the range of behaviors associated with this insertion predict that effects are likely also modified by additional genetic and environmental factors.
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Affiliation(s)
- Lisa Lit
- Department of Animal Science, University of California Davis, Davis, California, United States of America
- * E-mail:
| | - Janelle M. Belanger
- Department of Animal Science, University of California Davis, Davis, California, United States of America
| | - Debby Boehm
- Precision Canine, Phoenix, Arizona, United States of America
| | - Nathan Lybarger
- Left Coast K9, Marysville, California, United States of America
| | - Anita M. Oberbauer
- Department of Animal Science, University of California Davis, Davis, California, United States of America
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Lit L, Belanger JM, Boehm D, Lybarger N, Haverbeke A, Diederich C, Oberbauer AM. Characterization of a dopamine transporter polymorphism and behavior in Belgian Malinois. BMC Genet 2013; 14:45. [PMID: 23718893 PMCID: PMC3680094 DOI: 10.1186/1471-2156-14-45] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 05/22/2013] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The Belgian Malinois dog breed (MAL) is frequently used in law enforcement and military environments. Owners have reported seizures and unpredictable behavioral changes including dogs' eyes "glazing over," dogs' lack of response to environmental stimuli, and loss of behavioral inhibition including owner-directed biting behavior. Dogs with severe behavioral changes may be euthanized as they can represent a danger to humans and other dogs. In the dog, the dopamine transporter gene (DAT) contains a 38-base pair variable number tandem repeat (DAT-VNTR); alleles have either one or two copies of the 38-base pair sequence. The objective of this study was to assess frequency of DAT-VNTR alleles, and characterize the association between DAT-VNTR alleles and behavior in MAL and other breeds. RESULTS In an American sample of 280 dogs comprising 26 breeds, most breeds are predominantly homozygous for the DAT-VNTR two-tandem-repeat allele (2/2). The one-tandem-repeat allele is over-represented in American MAL (AM-MAL) (n = 144), both as heterozygotes (1/2) and homozygotes (1/1). All AM-MAL with reported seizures (n = 5) were 1/1 genotype. For AM-MAL with at least one "1" allele (1/1 or 1/2 genotype, n = 121), owners reported higher levels of attention, increased frequency of episodic aggression, and increased frequency of loss of responsiveness to environmental stimuli. In behavior observations, Belgian Military Working Dogs (MWD) with 1/1 or 1/2 genotypes displayed fewer distracted behaviors and more stress-related behaviors such as lower posture and increased yawning. Handlers' treatment of MWD varied with DAT-VNTR genotype as did dogs' responses to handlers' behavior. For 1/1 or 1/2 genotype MWD, 1) lower posture after the first aversive stimulus given by handlers was associated with poorer obedience performance; 2) increased aversive stimuli during protection exercises were associated with decreased performance; 3) more aversive stimuli during obedience were associated with more aversive stimuli during protection; and 4) handlers used more aversive stimuli in protection compared with obedience exercises. CONCLUSIONS The single copy allele of DAT-VNTR is associated with owner-reported seizures, loss of responsiveness to environmental stimuli, episodic aggression, and hyper-vigilance in MAL. Behavioral changes are associated with differential treatment by handlers. Findings should be considered preliminary until replicated in a larger sample.
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Affiliation(s)
- Lisa Lit
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA.
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9
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Neff MW, Beck JS, Koeman JM, Boguslawski E, Kefene L, Borgman A, Ruhe AL. Partial deletion of the sulfate transporter SLC13A1 is associated with an osteochondrodysplasia in the Miniature Poodle breed. PLoS One 2012; 7:e51917. [PMID: 23300579 PMCID: PMC3530542 DOI: 10.1371/journal.pone.0051917] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 11/14/2012] [Indexed: 11/18/2022] Open
Abstract
A crippling dwarfism was first described in the Miniature Poodle in Great Britain in 1956. Here, we resolve the genetic basis of this recessively inherited disorder. A case-control analysis (8:8) of genotype data from 173 k SNPs revealed a single associated locus on CFA14 (P(raw) <10(-8)). All affected dogs were homozygous for an ancestral haplotype consistent with a founder effect and an identical-by-descent mutation. Systematic failure of nine, nearly contiguous SNPs, was observed solely in affected dogs, suggesting a deletion was the causal mutation. A 130-kb deletion was confirmed both by fluorescence in situ hybridization (FISH) analysis and by cloning the physical breakpoints. The mutation was perfectly associated in all cases and obligate heterozygotes. The deletion ablated all but the first exon of SLC13A1, a sodium/sulfate symporter responsible for regulating serum levels of inorganic sulfate. Our results corroborate earlier findings from an Slc13a1 mouse knockout, which resulted in hyposulfatemia and syndromic defects. Interestingly, the metabolic disorder in Miniature Poodles appears to share more clinical signs with a spectrum of human disorders caused by SLC26A2 than with the mouse Slc13a1 model. SLC26A2 is the primary sodium-independent sulfate transporter in cartilage and bone and is important for the sulfation of proteoglycans such as aggregan. We propose that disruption of SLC13A1 in the dog similarly causes undersulfation of proteoglycans in the extracellular matrix (ECM), which impacts the conversion of cartilage to bone. A co-dominant DNA test of the deletion was developed to enable breeders to avoid producing affected dogs and to selectively eliminate the mutation from the gene pool.
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Affiliation(s)
- Mark W Neff
- Laboratory of Neurogenetics and Canine Behavior, Van Andel Research Institute, Grand Rapids, MI, USA.
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10
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Wong AK, Ruhe AL, Robertson KR, Loew ER, Williams DC, Neff MW. A de novo mutation in KIT causes white spotting in a subpopulation of German Shepherd dogs. Anim Genet 2012; 44:305-10. [PMID: 23134432 DOI: 10.1111/age.12006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2012] [Indexed: 11/30/2022]
Abstract
Although variation in the KIT gene is a common cause of white spotting among domesticated animals, KIT has not been implicated in the diverse white spotting observed in the dog. Here, we show that a loss-of-function mutation in KIT recapitulates the coat color phenotypes observed in other species. A spontaneous white spotting observed in a pedigree of German Shepherd dogs was mapped by linkage analysis to a single locus on CFA13 containing KIT (pairwise LOD = 15). DNA sequence analysis identified a novel 1-bp insertion in the second exon that co-segregated with the phenotype. The expected frameshift and resulting premature stop codons predicted a severely truncated c-Kit receptor with presumably abolished activity. No dogs homozygous for the mutation were recovered from multiple intercrosses (P = 0.01), suggesting the mutation is recessively embryonic lethal. These observations are consistent with the effects of null alleles of KIT in other species.
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Affiliation(s)
- A K Wong
- Veterinary Genetics Laboratory, University of California, Davis, CA 95616, USA
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11
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Brown SK, Pedersen NC, Jafarishorijeh S, Bannasch DL, Ahrens KD, Wu JT, Okon M, Sacks BN. Phylogenetic distinctiveness of Middle Eastern and Southeast Asian village dog Y chromosomes illuminates dog origins. PLoS One 2011; 6:e28496. [PMID: 22194840 PMCID: PMC3237445 DOI: 10.1371/journal.pone.0028496] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 11/09/2011] [Indexed: 12/04/2022] Open
Abstract
Modern genetic samples are commonly used to trace dog origins, which entails untested assumptions that village dogs reflect indigenous ancestry or that breed origins can be reliably traced to particular regions. We used high-resolution Y chromosome markers (SNP and STR) and mitochondrial DNA to analyze 495 village dogs/dingoes from the Middle East and Southeast Asia, along with 138 dogs from >35 modern breeds to 1) assess genetic divergence between Middle Eastern and Southeast Asian village dogs and their phylogenetic affinities to Australian dingoes and gray wolves (Canis lupus) and 2) compare the genetic affinities of modern breeds to regional indigenous village dog populations. The Y chromosome markers indicated that village dogs in the two regions corresponded to reciprocally monophyletic clades, reflecting several to many thousand years divergence, predating the Neolithic ages, and indicating long-indigenous roots to those regions. As expected, breeds of the Middle East and East Asia clustered within the respective regional village dog clade. Australian dingoes also clustered in the Southeast Asian clade. However, the European and American breeds clustered almost entirely within the Southeast Asian clade, even sharing many haplotypes, suggesting a substantial and recent influence of East Asian dogs in the creation of European breeds. Comparison to 818 published breed dog Y STR haplotypes confirmed this conclusion and indicated that some African breeds reflect another distinct patrilineal origin. The lower-resolution mtDNA marker consistently supported Y-chromosome results. Both marker types confirmed previous findings of higher genetic diversity in dogs from Southeast Asia than the Middle East. Our findings demonstrate the importance of village dogs as windows into the past and provide a reference against which ancient DNA can be used to further elucidate origins and spread of the domestic dog.
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Affiliation(s)
- Sarah K. Brown
- Canid Diversity and Conservation Laboratory, Center for Veterinary Genetics, University of California Davis, Davis, California, United States of America
- Veterinary Genetics Laboratory, University of California at Davis, Davis, California, United States of America
| | - Niels C. Pedersen
- Veterinary Genetics Laboratory, University of California at Davis, Davis, California, United States of America
- Center for Companion Animal Health, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Sardar Jafarishorijeh
- Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Danika L. Bannasch
- Veterinary Genetics Laboratory, University of California at Davis, Davis, California, United States of America
- Department of Population, Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Kristen D. Ahrens
- Canid Diversity and Conservation Laboratory, Center for Veterinary Genetics, University of California Davis, Davis, California, United States of America
- Biological Sciences Department, California State University Sacramento, Sacramento, California, United States of America
| | - Jui-Te Wu
- Department of Veterinary Medicine, National Chiayi University, Chiayi City, Taiwan, Republic of China
| | - Michaella Okon
- Ruah Midbar Kennel for Desert Bred Salukis, Herzliya, Israel
| | - Benjamin N. Sacks
- Canid Diversity and Conservation Laboratory, Center for Veterinary Genetics, University of California Davis, Davis, California, United States of America
- Veterinary Genetics Laboratory, University of California at Davis, Davis, California, United States of America
- Department of Population, Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
- Biological Sciences Department, California State University Sacramento, Sacramento, California, United States of America
- * E-mail:
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12
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Rincon G, Tengvall K, Belanger JM, Lagoutte L, Medrano JF, André C, Thomas A, Lawley CT, Hansen MS, Lindblad-Toh K, Oberbauer AM. Comparison of buccal and blood-derived canine DNA, either native or whole genome amplified, for array-based genome-wide association studies. BMC Res Notes 2011; 4:226. [PMID: 21718521 PMCID: PMC3145587 DOI: 10.1186/1756-0500-4-226] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 06/30/2011] [Indexed: 12/02/2022] Open
Abstract
Background The availability of array-based genotyping platforms for single nucleotide polymorphisms (SNPs) for the canine genome has expanded the opportunities to undertake genome-wide association (GWA) studies to identify the genetic basis for Mendelian and complex traits. Whole blood as the source of high quality DNA is undisputed but often proves impractical for collection of the large numbers of samples necessary to discover the loci underlying complex traits. Further, many countries prohibit the collection of blood from dogs unless medically necessary thereby restricting access to critical control samples from healthy dogs. Alternate sources of DNA, typically from buccal cytobrush extractions, while convenient, have been suggested to have low yield and perform poorly in GWA. Yet buccal cytobrushes provide a cost-effective means of collecting DNA, are readily accepted by dog owners, and represent a large resource base in many canine genetics laboratories. To increase the DNA quantities, whole genome amplification (WGA) can be performed. Thus, the present study assessed the utility of buccal-derived DNA as well as whole genome amplification in comparison to blood samples for use on the most recent iteration of the canine HD SNP array (Illumina). Findings In both buccal and blood samples, whether whole genome amplified or not, 97% of the samples had SNP call rates in excess of 80% indicating that the vast majority of the SNPs would be suitable to perform association studies regardless of the DNA source. Similarly, there were no significant differences in marker intensity measurements between buccal and blood samples for copy number variations (CNV) analysis. Conclusions All DNA samples assayed, buccal or blood, native or whole genome amplified, are appropriate for use in array-based genome-wide association studies. The concordance between subsets of dogs for which both buccal and blood samples, or those samples whole genome amplified, was shown to average >99%. Thus, the two DNA sources were comparable in the generation of SNP genotypes and intensity values to estimate structural variation indicating the utility for the use of buccal cytobrush samples and the reliability of whole genome amplification for genome-wide association and CNV studies.
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Affiliation(s)
- Gonzalo Rincon
- Department of Animal Science, University of California, Davis, CA 95616, USA.
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Tarditi CR, Grahn RA, Evans JJ, Kurushima JD, Lyons LA. Mitochondrial DNA sequencing of cat hair: an informative forensic tool. J Forensic Sci 2010; 56 Suppl 1:S36-46. [PMID: 21077873 DOI: 10.1111/j.1556-4029.2010.01592.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Approximately 81.7 million cats are in 37.5 million U.S. households. Shed fur can be criminal evidence because of transfer to victims, suspects, and/or their belongings. To improve cat hairs as forensic evidence, the mtDNA control region from single hairs, with and without root tags, was sequenced. A dataset of a 402-bp control region segment from 174 random-bred cats representing four U.S. geographic areas was generated to determine the informativeness of the mtDNA region. Thirty-two mtDNA mitotypes were observed ranging in frequencies from 0.6-27%. Four common types occurred in all populations. Low heteroplasmy, 1.7%, was determined. Unique mitotypes were found in 18 individuals, 10.3% of the population studied. The calculated discrimination power implied that 8.3 of 10 randomly selected individuals can be excluded by this region. The genetic characteristics of the region and the generated dataset support the use of this cat mtDNA region in forensic applications.
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Affiliation(s)
- Christy R Tarditi
- Department of Population Health and Reproduction, University of California, Davis, 95616, USA
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An ADAMTSL2 founder mutation causes Musladin-Lueke Syndrome, a heritable disorder of beagle dogs, featuring stiff skin and joint contractures. PLoS One 2010; 5. [PMID: 20862248 PMCID: PMC2941456 DOI: 10.1371/journal.pone.0012817] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 08/24/2010] [Indexed: 12/23/2022] Open
Abstract
Background Musladin-Lueke Syndrome (MLS) is a hereditary disorder affecting Beagle dogs that manifests with extensive fibrosis of the skin and joints. In this respect, it resembles human stiff skin syndrome and the Tight skin mouse, each of which is caused by gene defects affecting fibrillin-1, a major component of tissue microfibrils. The objective of this work was to determine the genetic basis of MLS and the molecular consequence of the identified mutation. Methodology and Principal Findings We mapped the locus for MLS by genome-wide association to a 3.05 Mb haplotype on canine chromosome 9 (CFA9 (50.11–54.26; praw <10−7)), which was homozygous and identical-by-descent among all affected dogs, consistent with recessive inheritance of a founder mutation. Sequence analysis of a candidate gene at this locus, ADAMTSL2, which is responsible for the human TGFβ dysregulation syndrome, Geleophysic Dysplasia (GD), uncovered a mutation in exon 7 (c.660C>T; p.R221C) perfectly associated with MLS (p-value = 10−12). Murine ADAMTSL2 containing the p.R221C mutation formed anomalous disulfide-bonded dimers when transiently expressed in COS-1, HEK293F and CHO cells, and was present in the medium of these cells at lower levels than wild-type ADAMTSL2 expressed in parallel. Conclusions/Significance The genetic basis of MLS is a founder mutation in ADAMTSL2, previously shown to interact with latent TGF-β binding protein, which binds fibrillin-1. The molecular effect of the founder mutation on ADAMTSL2 is formation of disulfide-bonded dimers. Although caused by a distinct mutation, and having a milder phenotype than human GD, MLS nevertheless offers a new animal model for study of GD, and for prospective insights on mechanisms and pathways of skin fibrosis and joint contractures.
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Oikawa M, Kuniba H, Kondoh T, Kinoshita A, Nagayasu T, Niikawa N, Yoshiura KI. Familial brain arteriovenous malformation maps to 5p13-q14, 15q11-q13 or 18p11: linkage analysis with clipped fingernail DNA on high-density SNP array. Eur J Med Genet 2010; 53:244-9. [PMID: 20601259 DOI: 10.1016/j.ejmg.2010.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 06/11/2010] [Indexed: 10/19/2022]
Abstract
Familial arteriovenous malformations (AVM) in the brain is a very rare disease. It is defined as its occurrence in two or more relatives (up to third-degree relatives) in a family without any associated disorders, such as hereditary hemorrhagic telangiectasia. We encountered a Japanese family with brain AVM in which four affected members in four successive generations were observed. One DNA sample extracted from leukocytes of the proband and ten DNA samples from clipped finger nails of other members were available. A genome-wide linkage analysis was performed on this pedigree using Affymetrix GeneCip 10K 2.0 Xba Array and MERLIN software. We obtained sufficient performance of SNP genotyping in the fingernail samples with the mean SNP call rate of 92.49%, and identified 18 regions with positive LOD scores. Haplotype and linkage analyses with microsatellite markers at these regions confirmed three possible disease-responsible regions, i.e., 5p13.2-q14.1, 15q11.2-q13.1 and 18p11.32-p11.22. Sequence analysis was conducted for ten selected candidate genes at 5p13.2-q14.1, such as MAP3K1, DAB2, OCLN, FGF10, ESM1, ITGA1, ITGA2, EGFLAM, ERBB2IP, and PIK3R1, but no causative genetic alteration was detected. This is the first experience of adoption of fingernail DNA to genome-wide, high-density SNP microarray analysis, showing candidate brain AVM susceptible regions.
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Affiliation(s)
- Masahiro Oikawa
- Departments of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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Oberbauer AM, Belanger JM, Grossman DI, Regan KR, Famula TR. Genome-wide linkage scan for loci associated with epilepsy in Belgian shepherd dogs. BMC Genet 2010; 11:35. [PMID: 20441595 PMCID: PMC2877138 DOI: 10.1186/1471-2156-11-35] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Accepted: 05/04/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Idiopathic epilepsy in the Belgian shepherd dog is known to have a substantial genetic component. The objective of this study was to identify genomic regions associated with the expression of generalized seizures in the Belgian Tervuren and Sheepdog. RESULTS DNA from 366 dogs, of which 74 were classified as epileptic, representing two extended families were subjected to a genome-wide linkage scan using 410 microsatellite markers yielding informative coverage averaging 5.95 +/- 0.21 Mb. Though previous studies based on pedigree analyses proposed a major gene of influence, the present study demonstrated the trait to be highly polygenic. Studies of complex disorders in humans indicate that a liberal composite evaluation of genetic linkage is needed to identify underlying quantitative trait loci (QTLs). Four chromosomes yielded tentative linkage based upon LOD scores in excess of 1.0. Possible QTLs within these regions were supported also by analyses of multipoint linkage, allele frequency, TDT, and transmission of haplotype blocks. CONCLUSIONS Taken together the data tentatively indicate six QTLs, three on CFA 2, and one on each of CFA 6, 12, and 37, that support fine mapping for mutations associated with epilepsy in the Belgian shepherd. The study also underscores the complexity of genomic linkage studies for polygenic disorders.
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Affiliation(s)
- Anita M Oberbauer
- Department of Animal Science, University of California, Davis, CA, USA.
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Wong AK, Ruhe AL, Dumont BL, Robertson KR, Guerrero G, Shull SM, Ziegle JS, Millon LV, Broman KW, Payseur BA, Neff MW. A comprehensive linkage map of the dog genome. Genetics 2010; 184:595-605. [PMID: 19966068 PMCID: PMC2828735 DOI: 10.1534/genetics.109.106831] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Accepted: 11/30/2009] [Indexed: 12/15/2022] Open
Abstract
We have leveraged the reference sequence of a boxer to construct the first complete linkage map for the domestic dog. The new map improves access to the dog's unique biology, from human disease counterparts to fascinating evolutionary adaptations. The map was constructed with approximately 3000 microsatellite markers developed from the reference sequence. Familial resources afforded 450 mostly phase-known meioses for map assembly. The genotype data supported a framework map with approximately 1500 loci. An additional approximately 1500 markers served as map validators, contributing modestly to estimates of recombination rate but supporting the framework content. Data from approximately 22,000 SNPs informing on a subset of meioses supported map integrity. The sex-averaged map extended 21 M and revealed marked region- and sex-specific differences in recombination rate. The map will enable empiric coverage estimates and multipoint linkage analysis. Knowledge of the variation in recombination rate will also inform on genomewide patterns of linkage disequilibrium (LD), and thus benefit association, selective sweep, and phylogenetic mapping approaches. The computational and wet-bench strategies can be applied to the reference genome of any nonmodel organism to assemble a de novo linkage map.
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Affiliation(s)
- Aaron K. Wong
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Alison L. Ruhe
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Beth L. Dumont
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Kathryn R. Robertson
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Giovanna Guerrero
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Sheila M. Shull
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Janet S. Ziegle
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Lee V. Millon
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Karl W. Broman
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Bret A. Payseur
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Mark W. Neff
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California 95616, Applied Biosystems, Foster City, California 94404, Department of Biostatistics and Medical Informatics and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
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Abstract
The size, shape, and behavior of the modern domesticated dog has been sculpted by artificial selection for at least 14,000 years. The genetic substrates of selective breeding, however, remain largely unknown. Here, we describe a genome-wide scan for selection in 275 dogs from 10 phenotypically diverse breeds that were genotyped for over 21,000 autosomal SNPs. We identified 155 genomic regions that possess strong signatures of recent selection and contain candidate genes for phenotypes that vary most conspicuously among breeds, including size, coat color and texture, behavior, skeletal morphology, and physiology. In addition, we demonstrate a significant association between HAS2 and skin wrinkling in the Shar-Pei, and provide evidence that regulatory evolution has played a prominent role in the phenotypic diversification of modern dog breeds. Our results provide a first-generation map of selection in the dog, illustrate how such maps can rapidly inform the genetic basis of canine phenotypic variation, and provide a framework for delineating the mechanistic basis of how artificial selection promotes rapid and pronounced phenotypic evolution.
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Mitsouras K, Faulhaber EA. Saliva as an alternative source of high yield canine genomic DNA for genotyping studies. BMC Res Notes 2009; 2:219. [PMID: 19874604 PMCID: PMC2781016 DOI: 10.1186/1756-0500-2-219] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Accepted: 10/29/2009] [Indexed: 11/10/2022] Open
Abstract
Background The domestic dog presents an attractive model system for the study of the genetic basis of disease. The development of resources such as the canine genome sequence and SNP genotyping platforms has allowed for the implementation of canine genetic studies. Successful implementation of such studies depends not only on the quality of individual DNA samples, but also on the number of samples obtained. The latter can be maximized using a non-invasive DNA collection method that can increase study participation. We compared the DNA yield and quality obtained from blood and buccal swabs to those obtained using a non-invasive saliva collection kit (Oragene ®•ANIMAL kit). We also assessed the success rate of PCR amplification and genotyping accuracy of DNA isolated using these collection methods. Findings Comparison of DNA yields from matched saliva, blood and buccal swab samples showed that yields from saliva were significantly higher than those from blood (p = 0.0198) or buccal swabs (p = 0.0008). Electrophoretic analysis revealed that blood and saliva produced higher quality DNA than buccal swabs. In addition, a 1.1-kb PCR fragment was successfully amplified using the paired DNA samples and genotyping by PCR-RFLP yielded identical results. Conclusion We demonstrate that DNA yields from canine saliva are higher than those from blood or buccal swabs. The quality of DNA extracted from saliva is sufficient for successful amplification of a 1.1-kb fragment and for accurate SNP genotyping by PCR-RFLP. We conclude that saliva presents a non-invasive alternative source of high quantities of canine genomic DNA suitable for genotyping studies.
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Affiliation(s)
- Katherine Mitsouras
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, USA.
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20
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Smith LB, Bannasch DL, Young AE, Grossman DI, Belanger JM, Oberbauer AM. Canine fibroblast growth factor receptor 3 sequence is conserved across dogs of divergent skeletal size. BMC Genet 2008; 9:67. [PMID: 18940000 PMCID: PMC2576350 DOI: 10.1186/1471-2156-9-67] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Accepted: 10/21/2008] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Fibroblast growth factor receptor 3 (FGFR3) is expressed in the growth plate of endochondral bones and serves as a negative regulator of linear bone elongation. Activating mutations severely limit bone growth, resulting in dwarfism, while inactivating mutations significantly enhance bone elongation and overall skeletal size. Domesticated dogs exhibit the greatest skeletal size diversity of any species and, given the regulatory role of FGFR3 on growth plate proliferation, we asked whether sequence differences in FGFR3 could account for some of the size differences. METHODS All exons, the promoter region, and 60 bp of the 3' flanking region of the canine FGFR3 gene were sequenced for nine different dog breeds representing a spectrum of skeletal size. The resultant sequences were compared to the reference Boxer genome sequence. RESULTS There was no variation in sequence for any FGFR3 exons, promoter region, or 3' flanking sequence across all breeds evaluated. CONCLUSION The results suggest that, regardless of domestication selection pressure to develop breeds having extreme differences in skeletal size, the FGFR3 gene is conserved. This implies a critical role for this gene in normal skeletal integrity and indicates that other genes account for size variability in dogs.
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Affiliation(s)
- Logan B Smith
- Department of Animal Science, University of California, Davis, CA, USA
| | - Danika L Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine University of California, Davis, CA, USA
| | - Amy E Young
- Department of Population Health and Reproduction, School of Veterinary Medicine University of California, Davis, CA, USA
| | | | | | - Anita M Oberbauer
- Department of Animal Science, University of California, Davis, CA, USA
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Oberbauer AM, Hollingsworth SR, Belanger JM, Regan KR, Famula TR. Inheritance of cataracts and primary lens luxation in Jack Russell Terriers. Am J Vet Res 2008; 69:222-7. [PMID: 18241019 DOI: 10.2460/ajvr.69.2.222] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To characterize heritability and mode of inheritance of cataracts and primary lens luxation in Jack Russell Terriers. ANIMALS 872 Jack Russell Terriers from which buccal epithelial cells were collected and phenotypes for cataracts and lens luxation were determined and an additional 1,898 Jack Russell Terriers without phenotypic information used to complete pedigree relationships and that were included in the analyses. PROCEDURES Narrow-sense heritabilities and genetic correlation for cataracts and lens luxation were modeled by use of threshold analysis, whereas complex segregation analysis was used to characterize mode of inheritance. For the analyses, dogs < 6 years old, unless confirmed as having cataracts or lens luxation, were classified as an unknown phenotype. The possible involvement of an HSF4 mutation in cataracts was determined by DNA sequencing. RESULTS Cataracts and primary lens luxation were highly heritable and genetically correlated, and neither was controlled by a single gene. Cataracts were not associated with an HSF4 mutation. CONCLUSIONS AND CLINICAL RELEVANCE Analysis of the data indicated that concerted selection against both cataracts and primary lens luxation when choosing breeding animals can be used to improve ocular health in Jack Russell Terriers.
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Affiliation(s)
- Anita M Oberbauer
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, CA 95616, USA
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22
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Clements DN, Wood S, Carter SD, Ollier WER. Assessment of the quality and quantity of genomic DNA recovered from canine blood samples by three different extraction methods. Res Vet Sci 2007; 85:74-9. [PMID: 18031774 DOI: 10.1016/j.rvsc.2007.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2007] [Accepted: 09/08/2007] [Indexed: 01/05/2023]
Abstract
The ideal method for genomic DNA (gDNA) extraction should recover high quantities of pure, integral gDNA from the original sample source with minimal co-extraction of inhibitors of downstream processes. Canine ethylenediamine tetra-acetic acid (EDTA) treated and clotted blood samples were extracted by three different methods (a silica column method, a phenol-chloroform method and a modified salt precipitation method). Phenol-chloroform and modified salt precipitation based extractions demonstrated similar relative recovery of gDNA with EDTA preserved blood, but were less efficient at recovering gDNA from clotted blood. Spectrophotometer measurement of phenol-chloroform based extractions tended to overestimate the quantity of gDNA recovered from extractions, and was associated with the greater co-extraction of PCR inhibitors. The silica column method recovered gDNA with equal efficiency, purity and integrity irrespective of the sample type or method of quantification.
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Affiliation(s)
- Dylan N Clements
- Musculoskeletal Research Group, c/o Department of Veterinary Pathology, Faculty of Veterinary Science, University of Liverpool, Liverpool L69 3BX, UK.
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23
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Runstadler JA, Angles JM, Pedersen NC. Dog leucocyte antigen class II diversity and relationships among indigenous dogs of the island nations of Indonesia (Bali), Australia and New Guinea. ACTA ACUST UNITED AC 2006; 68:418-26. [PMID: 17092255 DOI: 10.1111/j.1399-0039.2006.00696.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The genetic polymorphism at the dog leucocyte antigen (DLA) class II loci DQA1, DQB1 and DRB1 was studied in a large genetically diverse population of feral and wild-type dogs from the large island nations of Indonesia (Bali), Australia and New Guinea (Bali street dog, dingo and New Guinea singing dog, respectively). Sequence-based typing (SBT) of the hypervariable region of DLA-DRB1, -DQA1 and -DQB1 alleles was used to determine genetic diversity. No new DQA1 alleles were recognized among the three dog populations, but five novel DLA-DRB1 and 2 novel DLA-DQB1 allele sequences were detected. Additional unknown alleles were postulated to exist in Bali street dogs, as indicated by the large percentage of individuals (15%-33%) that had indeterminate DRB1, DQA1 and DQB1 alleles by SBT. All three groups of dogs possessed alleles that were relatively uncommon in conventional purebreds. The New Guinea singing dog and dingo shared alleles that were not present in the Bali street dogs. These findings suggested that the dingo was more closely related to indigenous dogs from New Guinea. Feral dog populations, in particular large ones such as that of Bali, show genetic diversity that existed prior to phenotypic selection for breeds originating from their respective regions. This diversity needs to be identified and maintained in the face of progressive Westernization. These populations deserve further study as potential model populations for the evolution of major histocompatibility complex alleles, for the study of canine genetic diversity, for the development of dog breeds and for studies on the comigration of ancestral human and dog populations.
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Affiliation(s)
- J A Runstadler
- Center for Veterinary Genetics, School of Veterinary Medicine, University of California, Davis, CA, USA.
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25
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Lyons LA, Bailey SJ, Baysac KC, Byrns G, Erdman CA, Fretwell N, Froenicke L, Gazlay KW, Geary LA, Grahn JC, Grahn RA, Karere GM, Lipinski MJ, Rah H, Ruhe MT, Bach LH. The Tabby cat locus maps to feline chromosome B1. Anim Genet 2006; 37:383-6. [PMID: 16879352 PMCID: PMC1619149 DOI: 10.1111/j.1365-2052.2006.01458.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The Tabby markings of the domestic cat are unique coat patterns for which no causative candidate gene has been inferred from other mammals. In this study, a genome scan was performed on a large pedigree of cats that segregated for Tabby coat markings, specifically for the Abyssinian (Ta-) and blotched (tbtb) phenotypes. There was linkage between the Tabby locus and eight markers on cat chromosome B1. The most significant linkage was between marker FCA700 and Tabby (Z = 7.56, θ = 0.03). Two additional markers in the region supported linkage, although not with significant LOD scores. Pairwise analysis of the markers supported the published genetic map of the cat, although additional meioses are required to refine the region. The linked markers cover a 17-cM region and flank an evolutionary breakpoint, suggesting that the Tabby gene has a homologue on either human chromosome 4 or 8. Alternatively, Tabby could be a unique locus in cats.
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Affiliation(s)
- L A Lyons
- Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616, USA.
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Imes DL, Geary LA, Grahn RA, Lyons LA. Albinism in the domestic cat (Felis catus) is associated with a tyrosinase (TYR) mutation. Anim Genet 2006; 37:175-8. [PMID: 16573534 PMCID: PMC1464423 DOI: 10.1111/j.1365-2052.2005.01409.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Albino phenotypes are documented in a variety of species including the domestic cat. As albino phenotypes in other species are associated with tyrosinase (TYR) mutations, TYR was proposed as a candidate gene for albinism in cats. An Oriental and Colourpoint Shorthair cat pedigree segregating for albinism was analysed for association with TYR by linkage and sequence analyses. Microsatellite FCA931, which is closely linked to TYR and TYR sequence variants were tested for segregation with the albinism phenotype. Sequence analysis of genomic DNA from wild-type and albino cats identified a cytosine deletion in TYR at position 975 in exon 2, which causes a frame shift resulting in a premature stop codon nine residues downstream from the mutation. The deletion mutation in TYR and an allele of FCA931 segregated concordantly with the albino phenotype. Taken together, our results suggest that the TYR gene corresponds to the colour locus in cats and its alleles, from dominant to recessive, are as follows: C (full colour) > c(b) (burmese) > or = c(s) (siamese) > c (albino).
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Affiliation(s)
- D L Imes
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis 95616, USA
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Cooper MP, Fretwell N, Bailey SJ, Lyons LA. White spotting in the domestic cat (Felis catus) maps near KIT on feline chromosome B1. Anim Genet 2006; 37:163-5. [PMID: 16573531 PMCID: PMC1464422 DOI: 10.1111/j.1365-2052.2005.01389.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Five feline-derived microsatellite markers were genotyped in a large pedigree of cats that segregates for ventral white spotting. Both KIT and EDNRB cause similar white spotting phenotypes in other species. Thus, three of the five microsatellite markers chosen were on feline chromosome B1 in close proximity to KIT; the other two markers were on feline chromosome A1 near EDNRB. Pairwise linkage analysis supported linkage of the white spotting with the three chromosome B1 markers but not with the two chromosome A1 markers. This study indicates that KIT, or another gene within the linked region, is a candidate for white spotting in cats. Platelet-derived growth factor alpha (PDGFRA) is also a strong candidate, assuming that the KIT-PDGFRA linkage group, which is conserved in many mammalian species, is also conserved in the cat.
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Affiliation(s)
- M P Cooper
- Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616, USA
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28
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Cooper MP, Fretwell N, Bailey SJ, Lyons LA. White spotting in the domestic cat (Felis catus) maps near KIT on feline chromosome B1. Anim Genet 2005. [DOI: 10.1111/j.1365-2052.2005.01389test.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Angles JM, Famula TR, Pedersen NC. Uveodermatologic (VKH-like) syndrome in American Akita dogs is associated with an increased frequency of DQA1*00201. ACTA ACUST UNITED AC 2005; 66:656-65. [PMID: 16305682 DOI: 10.1111/j.1399-0039.2005.00508.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Akita breed of dog is affected by a number of distinct immune-mediated diseases, including thyroiditis, sebaceous adenitis, pemphigus foliaceus, uveitis, polyarthritis, myasthenia gravis, and uveodermatologic (UV) syndrome. UV syndrome is manifested by progressive uveitis and depigmenting dermatitis that closely resembles the human Vogt - Koyanagi - Harada syndrome. This study examined the allelic diversity of the three DLA class II loci (DRB1, DQA1, and DQB1) in the American Akita dog, and the relationship of specific DLA class II alleles to the UV. Low allelic variation was demonstrated within genes of DLA class II. American Akita dogs possessed six of the reported 16 DQA1 alleles, but only eight of 61 reported alleles in DRB1 and nine of 47 reported alleles in DQB1. Almost one-half of American Akita dogs were homozygous for a single allele at DQA1 and up to a quarter at DRB1 and DQB1. DLA-DQA1*00201 was associated with a significantly higher relative risk (RR = 15.3) or odds ratio (OR = 15.99) for UV syndrome than other DLA class II alleles. No significant association was noted with haplotypes of DRB1, DQB1, and DQA1 alleles; DRB1*03201-DQA1*00201 trended toward significance. This study confirmed loss of DLA genetic diversity in the American Akita dog in common with other pure breeds of dog and suggested a role for certain DLA class II gene alleles in the pathogenesis of UV.
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Affiliation(s)
- J M Angles
- Koret Center for Veterinary Genetics and Center for Companion Animal Health, University of California, One Shields Drive, Davis, CA 95616, USA
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Angles JM, Kennedy LJ, Pedersen NC. Frequency and distribution of alleles of canine MHC-II DLA-DQB1, DLA-DQA1 and DLA-DRB1 in 25 representative American Kennel Club breeds. ACTA ACUST UNITED AC 2005; 66:173-84. [PMID: 16101828 DOI: 10.1111/j.1399-0039.2005.00461.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The frequency and distribution of dog leucocyte antigens (DLA) class II -DQA1, -DQB1 and -DRB1 alleles were determined for 25 American Kennel Club (AKC) registered dog breeds, representing 360 dogs from each of the seven major performance categories. Six to twenty-eight (average n=11) dogs were studied per group, with the exception of the Akita dog (n=94). All dogs were unrelated with no common grandparents based on AKC pedigree records (F-value <0.125). DLA class II allelic diversity was broad across breeds; 31/61 published DLA-DRB1 alleles, 11/18 published DLA-DQA1 alleles and 31/47 published DLA-DQB1 alleles were found among the 25 breeds. However, allelic diversity was severely limited within a breed. Seventeen of the DLA-DRB1 alleles were each found in only a single breed, and only seven alleles were shared by seven or more breeds. DLA-DRB1*00101 and DLA-DRB1*01501 were shared by 16 and 19 breeds, respectively. DLA-DQA1*00101 and DLA-DQA1*00601 alleles were shared by many breeds. The Rough Collie (DLA-DQA1*00901), English Setter (DLA-DQA1*00101) and Scottish Terrier (DLA-DQA1*00101) were monoallelic for DLA-DQA1. Eleven DLA-DQB1 alleles were each found only in a single breed and only seven alleles were shared by six or more breeds. DLA-DQB1*00201 and DLA-DQB1*02301 were shared by 17 and 18 breeds, respectively. Forty per cent of dogs typed were homozygous at DLA-DRB1, 52% at DLA-DQA1 and 44% at DLA-DQB1. Nine new DLA class II alleles were identified; three for DRB1 and six for DQB1. Comparison of our study of North American purebred dogs to previous European DLA surveys showed a similar use of common alleles consistent with known founder effects. However, more alleles were detected in European breeds, compared to their North American descendents, indicating that additional DLA class II diversity was lost when European breeds were established in North America.
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Affiliation(s)
- J M Angles
- Koret Center for Veterinary Genetics and Center for Companion Animal Health, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
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Bannasch DL, Bannasch MJ, Ryun JR, Famula TR, Pedersen NC. Y chromosome haplotype analysis in purebred dogs. Mamm Genome 2005; 16:273-80. [PMID: 15965788 DOI: 10.1007/s00335-004-2435-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2004] [Accepted: 01/14/2005] [Indexed: 10/25/2022]
Abstract
In order to evaluate the genetic structure of purebred dogs, six Y chromosome microsatellite markers were used to analyze DNA samples from 824 unrelated dogs from 50 recognized breeds. A relatively small number of haplotypes (67) were identified in this large sample set due to extensive sharing of haplotypes between breeds and low haplotype diversity within breeds. Fifteen breeds were characterized by a single Y chromosome haplotype. Breed-specific haplotypes were identified for 26 of the 50 breeds, and haplotype sharing between some breeds indicated a common history. A molecular variance analysis (AMOVA) demonstrated significant genetic variation across breeds (63.7%) and with geographic origin of the breeds (11.5%). A network analysis of the haplotypes revealed further relationships between the breeds as well as deep rooting of many of the breed-specific haplotypes, particularly among breeds of African origin.
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Affiliation(s)
- Danika L Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California 95616, USA.
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Neff MW, Robertson KR, Wong AK, Safra N, Broman KW, Slatkin M, Mealey KL, Pedersen NC. Breed distribution and history of canine mdr1-1Delta, a pharmacogenetic mutation that marks the emergence of breeds from the collie lineage. Proc Natl Acad Sci U S A 2004; 101:11725-30. [PMID: 15289602 PMCID: PMC511012 DOI: 10.1073/pnas.0402374101] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mutation in the canine multidrug resistance gene, MDR1, has previously been associated with drug sensitivities in two breeds from the collie lineage. We exploited breed phylogeny and reports of drug sensitivity to survey other purebred populations that might be genetically at risk. We found that the same allele, mdr1-1Delta, segregated in seven additional breeds, including two sighthounds that were not expected to share collie ancestry. A mutant haplotype that was conserved among affected breeds indicated that the allele was identical by descent. Based on breed histories and the extent of linkage disequilibrium, we conclude that all dogs carrying mdr1-1Delta are descendants of a dog that lived in Great Britain before the genetic isolation of breeds by registry (ca. 1873). The breed distribution and frequency of mdr1-1Delta have applications in veterinary medicine and selective breeding, whereas the allele's history recounts the emergence of formally recognized breeds from an admixed population of working sheepdogs.
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Affiliation(s)
- Mark W Neff
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA.
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