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Posbergh CJ, Kalla SE, Sutter NB, Tennant BC, Huson HJ. Mutation responsible for congenital photosensitivity and hyperbilirubinemia in Southdown sheep. Am J Vet Res 2018; 79:538-545. [PMID: 29688779 DOI: 10.2460/ajvr.79.5.538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To identify the genetic cause for congenital photosensitivity and hyperbilirubinemia (CPH) in Southdown sheep. ANIMALS 73 Southdown sheep from a CPH research flock and 48 sheep of various breeds from commercial flocks without CPH. PROCEDURES Whole-genome sequencing was performed for a phenotypically normal Southdown sheep heterozygous for CPH. Heterozygous variants within Slco1b3 coding exons were identified, and exons that contained candidate mutations were amplified by PCR assay methods for Sanger sequencing. Blood samples from the other 72 Southdown sheep of the CPH research flock were used to determine plasma direct and indirect bilirubin concentrations. Southdown sheep with a plasma total bilirubin concentration < 0.3 mg/dL were classified as controls, and those with a total bilirubin concentration ≥ 0.3 mg/dL and signs of photosensitivity were classified as mutants. Sanger sequencing was used to determine the Slco1b3 genotype for all sheep. Genotypes were compared between mutants and controls of the CPH research flock and among all sheep. Protein homology was measured across 8 species to detect evolutionary conservation of Slco1b. RESULTS A nonsynonymous mutation at ovine Chr3:193,691,195, which generated a glycine-to-arginine amino acid change within the predicted Slco1b3 protein, was significantly associated with hyperbilirubinemia and predicted to be deleterious. That amino acid was conserved across 7 other mammalian species. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested a nonsynonymous mutation in Slco1b3 causes CPH in Southdown sheep. This disease appears to be similar to Rotor syndrome in humans. Sheep with CPH might be useful animals for Rotor syndrome research.
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Al Abri MA, Posbergh C, Palermo K, Sutter NB, Eberth J, Hoffman GE, Brooks SA. Genome-Wide Scans Reveal a Quantitative Trait Locus for Withers Height in Horses Near the ANKRD1 Gene. J Equine Vet Sci 2018. [DOI: 10.1016/j.jevs.2017.05.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Staiger EA, Al Abri MA, Pflug KM, Kalla SE, Ainsworth DM, Miller D, Raudsepp T, Sutter NB, Brooks SA. Skeletal variation in Tennessee Walking Horses maps to the LCORL/NCAPG gene region. Physiol Genomics 2016; 48:325-35. [PMID: 26931356 DOI: 10.1152/physiolgenomics.00100.2015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/19/2016] [Indexed: 11/22/2022] Open
Abstract
Conformation has long been a driving force in horse selection and breed creation as a predictor for performance. The Tennessee Walking Horse (TWH) ranges in size from 1.5 to 1.7 m and is often used as a trail, show, and pleasure horse. To investigate the contribution of genetics to body conformation in the TWH, we collected DNA samples, body measurements, and gait/training information from 282 individuals. We analyzed the 32 body measures with a principal component analysis. Principal component (PC)1 captured 28.5% of the trait variance, while PC2 comprised just 9.5% and PC3 6.4% of trait variance. All 32 measures correlated positively with PC1, indicating that PC1 describes overall body size. We genotyped 109 horses using the EquineSNP70 bead chip and marker association assessed the data using PC1 scores as a phenotype. Mixed-model linear analysis (EMMAX) revealed a well-documented candidate locus on ECA3 (raw P = 3.86 × 10(-9)) near the LCORL gene. A custom genotyping panel enabled fine-mapping of the PC1 body-size trait to the 3'-end of the LCORL gene (P = 7.09 × 10(-10)). This position differs from other reports suggesting single nucleotide polymorphisms (SNPs) upstream of the LCORL coding sequence regulate expression of the gene and, therefore, body size in horses. Fluorescent in situ hybridization analysis defined the position of a highly homologous 5 kb retrogene copy of LCORL (assigned to unplaced contigs of the EquCab 2.0 assembly) at ECA9 q12-q13. This is the first study to identify putative causative SNPs within the LCORL transcript itself, which are associated with skeletal size variation in horses.
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Affiliation(s)
- E A Staiger
- Department of Animal Science, Cornell University, Ithaca, New York
| | - M A Al Abri
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - K M Pflug
- Department of Animal Science, University of Florida, Gainesville, Florida
| | - S E Kalla
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - D M Ainsworth
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - D Miller
- Baker Institute for Animal Health, Cornell University, Ithaca, New York
| | - T Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas; and
| | - N B Sutter
- Department of Biology, La Sierra University, Riverside, California
| | - S A Brooks
- Department of Animal Science, University of Florida, Gainesville, Florida;
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Rimbault M, Beale HC, Schoenebeck JJ, Hoopes BC, Allen JJ, Kilroy-Glynn P, Wayne RK, Sutter NB, Ostrander EA. Derived variants at six genes explain nearly half of size reduction in dog breeds. Genome Res 2013; 23:1985-95. [PMID: 24026177 PMCID: PMC3847769 DOI: 10.1101/gr.157339.113] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Selective breeding of dogs by humans has generated extraordinary diversity in body size. A number of multibreed analyses have been undertaken to identify the genetic basis of this diversity. We analyzed four loci discovered in a previous genome-wide association study that used 60,968 SNPs to identify size-associated genomic intervals, which were too large to assign causative roles to genes. First, we performed fine-mapping to define critical intervals that included the candidate genes GHR, HMGA2, SMAD2, and STC2, identifying five highly associated markers at the four loci. We hypothesize that three of the variants are likely to be causative. We then genotyped each marker, together with previously reported size-associated variants in the IGF1 and IGF1R genes, on a panel of 500 domestic dogs from 93 breeds, and identified the ancestral allele by genotyping the same markers on 30 wild canids. We observed that the derived alleles at all markers correlated with reduced body size, and smaller dogs are more likely to carry derived alleles at multiple markers. However, breeds are not generally fixed at all markers; multiple combinations of genotypes are found within most breeds. Finally, we show that 46%–52.5% of the variance in body size of dog breeds can be explained by seven markers in proximity to exceptional candidate genes. Among breeds with standard weights <41 kg (90 lb), the genotypes accounted for 64.3% of variance in weight. This work advances our understanding of mammalian growth by describing genetic contributions to canine size determination in non-giant dog breeds.
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Affiliation(s)
- Maud Rimbault
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Makvandi-Nejad S, Hoffman GE, Allen JJ, Chu E, Gu E, Chandler AM, Loredo AI, Bellone RR, Mezey JG, Brooks SA, Sutter NB. Four loci explain 83% of size variation in the horse. PLoS One 2012; 7:e39929. [PMID: 22808074 PMCID: PMC3394777 DOI: 10.1371/journal.pone.0039929] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 05/29/2012] [Indexed: 01/09/2023] Open
Abstract
Horse body size varies greatly due to intense selection within each breed. American Miniatures are less than one meter tall at the withers while Shires and Percherons can exceed two meters. The genetic basis for this variation is not known. We hypothesize that the breed population structure of the horse should simplify efforts to identify genes controlling size. In support of this, here we show with genome-wide association scans (GWAS) that genetic variation at just four loci can explain the great majority of horse size variation. Unlike humans, which are naturally reproducing and possess many genetic variants with weak effects on size, we show that horses, like other domestic mammals, carry just a small number of size loci with alleles of large effect. Furthermore, three of our horse size loci contain the LCORL, HMGA2 and ZFAT genes that have previously been found to control human height. The LCORL/NCAPG locus is also implicated in cattle growth and HMGA2 is associated with dog size. Extreme size diversification is a hallmark of domestication. Our results in the horse, complemented by the prior work in cattle and dog, serve to pinpoint those very few genes that have played major roles in the rapid evolution of size during domestication.
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Affiliation(s)
- Shokouh Makvandi-Nejad
- Department of Clinical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Gabriel E. Hoffman
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Jeremy J. Allen
- Department of Clinical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Erin Chu
- Department of Clinical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Esther Gu
- Department of Clinical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Alyssa M. Chandler
- Department of Clinical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Ariel I. Loredo
- Department of Clinical Sciences, Cornell University, Ithaca, New York, United States of America
- Biology Department, La Sierra University, Riverside, California, United States of America
| | - Rebecca R. Bellone
- Department of Biology, University of Tampa, Tampa, Florida, United States of America
| | - Jason G. Mezey
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Samantha A. Brooks
- Department of Animal Science, Cornell University, Ithaca, New York, United States of America
| | - Nathan B. Sutter
- Department of Clinical Sciences, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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Balmus G, Zhu M, Mukherjee S, Lyndaker AM, Hume KR, Lee J, Riccio ML, Reeves AP, Sutter NB, Noden DM, Peters RM, Weiss RS. Disease severity in a mouse model of ataxia telangiectasia is modulated by the DNA damage checkpoint gene Hus1. Hum Mol Genet 2012; 21:3408-20. [PMID: 22575700 DOI: 10.1093/hmg/dds173] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The human genomic instability syndrome ataxia telangiectasia (A-T), caused by mutations in the gene encoding the DNA damage checkpoint kinase ATM, is characterized by multisystem defects including neurodegeneration, immunodeficiency and increased cancer predisposition. ATM is central to a pathway that responds to double-strand DNA breaks, whereas the related kinase ATR leads a parallel signaling cascade that is activated by replication stress. To dissect the physiological relationship between the ATM and ATR pathways, we generated mice defective for both. Because complete ATR pathway inactivation causes embryonic lethality, we weakened the ATR mechanism to different degrees by impairing HUS1, a member of the 911 complex that is required for efficient ATR signaling. Notably, simultaneous ATM and HUS1 defects caused synthetic lethality. Atm/Hus1 double-mutant embryos showed widespread apoptosis and died mid-gestationally. Despite the underlying DNA damage checkpoint defects, increased DNA damage signaling was observed, as evidenced by H2AX phosphorylation and p53 accumulation. A less severe Hus1 defect together with Atm loss resulted in partial embryonic lethality, with the surviving double-mutant mice showing synergistic increases in genomic instability and specific developmental defects, including dwarfism, craniofacial abnormalities and brachymesophalangy, phenotypes that are observed in several human genomic instability disorders. In addition to identifying tissue-specific consequences of checkpoint dysfunction, these data highlight a robust, cooperative configuration for the mammalian DNA damage response network and further suggest HUS1 and related genes in the ATR pathway as candidate modifiers of disease severity in A-T patients.
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Affiliation(s)
- Gabriel Balmus
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
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Powell JA, Allen J, Sutter NB. DOG-SPOT database for comprehensive management of dog genetic research data. Source Code Biol Med 2010; 5:10. [PMID: 21159202 PMCID: PMC3009958 DOI: 10.1186/1751-0473-5-10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 12/15/2010] [Indexed: 11/25/2022]
Abstract
Research laboratories studying the genetics of companion animals have no database tools specifically designed to aid in the management of the many kinds of data that are generated, stored and analyzed. We have developed a relational database, "DOG-SPOT," to provide such a tool. Implemented in MS-Access, the database is easy to extend or customize to suit a lab's particular needs. With DOG-SPOT a lab can manage data relating to dogs, breeds, samples, biomaterials, phenotypes, owners, communications, amplicons, sequences, markers, genotypes and personnel. Such an integrated data structure helps ensure high quality data entry and makes it easy to track physical stocks of biomaterials and oligonucleotides.
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Affiliation(s)
- Julie As Powell
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, 14853, USA.
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Boyko AR, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD, Lohmueller KE, Zhao K, Brisbin A, Parker HG, vonHoldt BM, Cargill M, Auton A, Reynolds A, Elkahloun AG, Castelhano M, Mosher DS, Sutter NB, Johnson GS, Novembre J, Hubisz MJ, Siepel A, Wayne RK, Bustamante CD, Ostrander EA. A simple genetic architecture underlies morphological variation in dogs. PLoS Biol 2010; 8:e1000451. [PMID: 20711490 PMCID: PMC2919785 DOI: 10.1371/journal.pbio.1000451] [Citation(s) in RCA: 335] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 07/02/2010] [Indexed: 02/08/2023] Open
Abstract
The largest genetic study to date of morphology in domestic dogs identifies genes
controlling nearly 100 morphological traits and identifies important trends in
phenotypic variation within this species. Domestic dogs exhibit tremendous phenotypic diversity, including a greater
variation in body size than any other terrestrial mammal. Here, we generate a
high density map of canine genetic variation by genotyping 915 dogs from 80
domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across
60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource
with external measurements from breed standards and individuals as well as
skeletal measurements from museum specimens, we identify 51 regions of the dog
genome associated with phenotypic variation among breeds in 57 traits. The
complex traits include average breed body size and external body dimensions and
cranial, dental, and long bone shape and size with and without allometric
scaling. In contrast to the results from association mapping of quantitative
traits in humans and domesticated plants, we find that across dog breeds, a
small number of quantitative trait loci (≤3) explain the majority of
phenotypic variation for most of the traits we studied. In addition, many
genomic regions show signatures of recent selection, with most of the highly
differentiated regions being associated with breed-defining traits such as body
size, coat characteristics, and ear floppiness. Our results demonstrate the
efficacy of mapping multiple traits in the domestic dog using a database of
genotyped individuals and highlight the important role human-directed selection
has played in altering the genetic architecture of key traits in this important
species. Dogs offer a unique system for the study of genes controlling morphology. DNA
from 915 dogs from 80 domestic breeds, as well as a set of feral dogs, was
tested at over 60,000 points of variation and the dataset analyzed using novel
methods to find loci regulating body size, head shape, leg length, ear position,
and a host of other traits. Because each dog breed has undergone strong
selection by breeders to have a particular appearance, there is a strong
footprint of selection in regions of the genome that are important for
controlling traits that define each breed. These analyses identified new regions
of the genome, or loci, that are important in controlling body size and shape.
Our results, which feature the largest number of domestic dogs studied at such a
high level of genetic detail, demonstrate the power of the dog as a model for
finding genes that control the body plan of mammals. Further, we show that the
remarkable diversity of form in the dog, in contrast to some other species
studied to date, appears to have a simple genetic basis dominated by genes of
major effect.
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Affiliation(s)
- Adam R. Boyko
- Department of Genetics, Stanford School of Medicine, Stanford,
California, United States of America
- Department of Biological Statistics and Computational Biology, Cornell
University, Ithaca, New York, United States of America
| | - Pascale Quignon
- Cancer Genetic Branch, National Human Genome Research Institute, National
Institutes of Health, Bethesda, Maryland, United States of America
| | - Lin Li
- Department of Biological Statistics and Computational Biology, Cornell
University, Ithaca, New York, United States of America
| | - Jeffrey J. Schoenebeck
- Cancer Genetic Branch, National Human Genome Research Institute, National
Institutes of Health, Bethesda, Maryland, United States of America
| | - Jeremiah D. Degenhardt
- Department of Biological Statistics and Computational Biology, Cornell
University, Ithaca, New York, United States of America
| | - Kirk E. Lohmueller
- Department of Biological Statistics and Computational Biology, Cornell
University, Ithaca, New York, United States of America
| | - Keyan Zhao
- Department of Genetics, Stanford School of Medicine, Stanford,
California, United States of America
- Department of Biological Statistics and Computational Biology, Cornell
University, Ithaca, New York, United States of America
| | - Abra Brisbin
- Department of Biological Statistics and Computational Biology, Cornell
University, Ithaca, New York, United States of America
| | - Heidi G. Parker
- Cancer Genetic Branch, National Human Genome Research Institute, National
Institutes of Health, Bethesda, Maryland, United States of America
| | - Bridgett M. vonHoldt
- Department of Ecology and Environmental Biology, University of
California, Los Angeles, California, United States of America
| | - Michele Cargill
- Affymetrix Corporation, Santa Clara, California, United States of
America
| | - Adam Auton
- Department of Biological Statistics and Computational Biology, Cornell
University, Ithaca, New York, United States of America
| | - Andy Reynolds
- Department of Biological Statistics and Computational Biology, Cornell
University, Ithaca, New York, United States of America
| | - Abdel G. Elkahloun
- Cancer Genetic Branch, National Human Genome Research Institute, National
Institutes of Health, Bethesda, Maryland, United States of America
| | - Marta Castelhano
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell
University, Ithaca, New York, United States of America
| | - Dana S. Mosher
- Cancer Genetic Branch, National Human Genome Research Institute, National
Institutes of Health, Bethesda, Maryland, United States of America
| | - Nathan B. Sutter
- Department of Biological Statistics and Computational Biology, Cornell
University, Ithaca, New York, United States of America
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell
University, Ithaca, New York, United States of America
| | - Gary S. Johnson
- Department of Veterinary Pathobiology, University of Missouri, Columbia,
Missouri, United States of America
| | - John Novembre
- Department of Ecology and Environmental Biology, University of
California, Los Angeles, California, United States of America
| | - Melissa J. Hubisz
- Department of Biological Statistics and Computational Biology, Cornell
University, Ithaca, New York, United States of America
| | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell
University, Ithaca, New York, United States of America
| | - Robert K. Wayne
- Department of Ecology and Environmental Biology, University of
California, Los Angeles, California, United States of America
| | - Carlos D. Bustamante
- Department of Genetics, Stanford School of Medicine, Stanford,
California, United States of America
- Department of Biological Statistics and Computational Biology, Cornell
University, Ithaca, New York, United States of America
- * E-mail: (CDB); (EAO)
| | - Elaine A. Ostrander
- Cancer Genetic Branch, National Human Genome Research Institute, National
Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (CDB); (EAO)
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Gray MM, Sutter NB, Ostrander EA, Wayne RK. The IGF1 small dog haplotype is derived from Middle Eastern grey wolves. BMC Biol 2010; 8:16. [PMID: 20181231 PMCID: PMC2837629 DOI: 10.1186/1741-7007-8-16] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 02/24/2010] [Indexed: 11/26/2022] Open
Abstract
Background A selective sweep containing the insulin-like growth factor 1 (IGF1) gene is associated with size variation in domestic dogs. Intron 2 of IGF1 contains a SINE element and single nucleotide polymorphism (SNP) found in all small dog breeds that is almost entirely absent from large breeds. In this study, we surveyed a large sample of grey wolf populations to better understand the ancestral pattern of variation at IGF1 with a particular focus on the distribution of the small dog haplotype and its relationship to the origin of the dog. Results We present DNA sequence data that confirms the absence of the derived small SNP allele in the intron 2 region of IGF1 in a large sample of grey wolves and further establishes the absence of a small dog associated SINE element in all wild canids and most large dog breeds. Grey wolf haplotypes from the Middle East have higher nucleotide diversity suggesting an origin there. Additionally, PCA and phylogenetic analyses suggests a closer kinship of the small domestic dog IGF1 haplotype with those from Middle Eastern grey wolves. Conclusions The absence of both the SINE element and SNP allele in grey wolves suggests that the mutation for small body size post-dates the domestication of dogs. However, because all small dogs possess these diagnostic mutations, the mutations likely arose early in the history of domestic dogs. Our results show that the small dog haplotype is closely related to those in Middle Eastern wolves and is consistent with an ancient origin of the small dog haplotype there. Thus, in concordance with past archeological studies, our molecular analysis is consistent with the early evolution of small size in dogs from the Middle East. See associated opinion by Driscoll and Macdonald: http://jbiol.com/content/9/2/10
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Affiliation(s)
- Melissa M Gray
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.
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Ostrander EA, Boyko A, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD, Lohmueller KE, Zhao K, Brisbin A, Parker HG, Von Holdt BM, Cargill M, Auton A, Reynolds A, Elkahloun AG, Mosher DS, Sutter NB, Novembre J, Hubisz MJ, Siepel A, Wayne RK, Bustamante CD. Tracking genes and finding mutations: finding genes for complex traits in the domestic dog (Canis familiaris). Genome Biol 2010. [DOI: 10.1186/1465-6906-11-s1-i23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Ostrander EA, Boyko A, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD, Lohmueller KE, Zhao K, Brisbin A, Parker HG, Von Holdt BM, Cargill M, Auton A, Reynolds A, Elkahloun AG, Mosher DS, Sutter NB, Novembre J, Hubisz MJ, Siepel A, Wayne RK, Bustamante CD. Tracking genes and finding mutations: finding genes for complex traits in the domestic dog ( Canis familiaris). Genome Biol 2010. [PMCID: PMC3026216 DOI: 10.1186/gb-2010-11-s1-i23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda MD, USA
| | - Adam Boyko
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Pascale Quignon
- National Human Genome Research Institute, National Institutes of Health, Bethesda MD, USA
| | - Lin Li
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Jeffrey J Schoenebeck
- National Human Genome Research Institute, National Institutes of Health, Bethesda MD, USA
| | - Jeremiah D Degenhardt
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Kurt E Lohmueller
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Keyan Zhao
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA ,Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Abra Brisbin
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, Bethesda MD, USA
| | - Bridgett M Von Holdt
- Department of Ecology and Environmental Biology, University of California, Los Angeles, CA, USA
| | | | - Adam Auton
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Andy Reynolds
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Abdel G Elkahloun
- National Human Genome Research Institute, National Institutes of Health, Bethesda MD, USA
| | - Dana S Mosher
- National Human Genome Research Institute, National Institutes of Health, Bethesda MD, USA
| | - Nathan B Sutter
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - John Novembre
- Department of Ecology and Environmental Biology, University of California, Los Angeles, CA, USA
| | - Melissa J Hubisz
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Robert K Wayne
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Carlos D Bustamante
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA ,Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
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Parker HG, VonHoldt BM, Quignon P, Margulies EH, Shao S, Mosher DS, Spady TC, Elkahloun A, Cargill M, Jones PG, Maslen CL, Acland GM, Sutter NB, Kuroki K, Bustamante CD, Wayne RK, Ostrander EA. An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs. Science 2009; 325:995-8. [PMID: 19608863 DOI: 10.1126/science.1173275] [Citation(s) in RCA: 245] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Retrotransposition of processed mRNAs is a common source of novel sequence acquired during the evolution of genomes. Although the vast majority of retroposed gene copies, or retrogenes, rapidly accumulate debilitating mutations that disrupt the reading frame, a small percentage become new genes that encode functional proteins. By using a multibreed association analysis in the domestic dog, we demonstrate that expression of a recently acquired retrogene encoding fibroblast growth factor 4 (fgf4) is strongly associated with chondrodysplasia, a short-legged phenotype that defines at least 19 dog breeds including dachshund, corgi, and basset hound. These results illustrate the important role of a single evolutionary event in constraining and directing phenotypic diversity in the domestic dog.
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Affiliation(s)
- Heidi G Parker
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Mosher DS, Quignon P, Bustamante CD, Sutter NB, Mellersh CS, Parker HG, Ostrander EA. A mutation in the myostatin gene increases muscle mass and enhances racing performance in heterozygote dogs. PLoS Genet 2007; 3:e79. [PMID: 17530926 PMCID: PMC1877876 DOI: 10.1371/journal.pgen.0030079] [Citation(s) in RCA: 530] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2007] [Accepted: 04/04/2007] [Indexed: 11/18/2022] Open
Abstract
Double muscling is a trait previously described in several mammalian species including cattle and sheep and is caused by mutations in the myostatin (MSTN) gene (previously referred to as GDF8). Here we describe a new mutation in MSTN found in the whippet dog breed that results in a double-muscled phenotype known as the “bully” whippet. Individuals with this phenotype carry two copies of a two-base-pair deletion in the third exon of MSTN leading to a premature stop codon at amino acid 313. Individuals carrying only one copy of the mutation are, on average, more muscular than wild-type individuals (p = 7.43 × 10−6; Kruskal-Wallis Test) and are significantly faster than individuals carrying the wild-type genotype in competitive racing events (Kendall's nonparametric measure, τ = 0.3619; p ≈ 0.00028). These results highlight the utility of performance-enhancing polymorphisms, marking the first time a mutation in MSTN has been quantitatively linked to increased athletic performance. An individual's genetic profile can play a role in defining their natural skills and talents. The canine species presents an excellent system in which to find such associative genes. The purebred dog has a long history of selective breeding, which has produced specific breeds of extraordinary strength, intelligence, and speed. We have discovered a mutation in the canine myostatin gene, a negative regulator of muscle mass, which affects muscle composition, and hence racing speed, in whippets. Dogs that possess a single copy of this mutation are more muscled than normal and are among the fastest dogs in competitive racing events. However, dogs with two copies of the same mutation are grossly overmuscled, superficially resembling double-muscled cattle known to possess similar mutations. This result is the first to quantitatively link a mutation in the myostatin gene to athletic performance. Further, it emphasizes what is sure to be a growing area of research for performance-enhancing polymorphisms in competitive athletics. Future implications include screening for myostatin mutations among elite athletes. However, as little is known about the health issues and potential risks associated with being a myostatin-mutation carrier, research in this arena should proceed with extreme caution.
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Affiliation(s)
- Dana S Mosher
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Pascale Quignon
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Carlos D Bustamante
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Nathan B Sutter
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cathryn S Mellersh
- Animal Health Trust, Center for Preventive Medicine, Newmarket, United Kingdom
| | - Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail:
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15
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Sutter NB, Bustamante CD, Chase K, Gray MM, Zhao K, Zhu L, Padhukasahasram B, Karlins E, Davis S, Jones PG, Quignon P, Johnson GS, Parker HG, Fretwell N, Mosher DS, Lawler DF, Satyaraj E, Nordborg M, Lark KG, Wayne RK, Ostrander EA. A single IGF1 allele is a major determinant of small size in dogs. Science 2007; 316:112-5. [PMID: 17412960 PMCID: PMC2789551 DOI: 10.1126/science.1137045] [Citation(s) in RCA: 426] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The domestic dog exhibits greater diversity in body size than any other terrestrial vertebrate. We used a strategy that exploits the breed structure of dogs to investigate the genetic basis of size. First, through a genome-wide scan, we identified a major quantitative trait locus (QTL) on chromosome 15 influencing size variation within a single breed. Second, we examined genetic variation in the 15-megabase interval surrounding the QTL in small and giant breeds and found marked evidence for a selective sweep spanning a single gene (IGF1), encoding insulin-like growth factor 1. A single IGF1 single-nucleotide polymorphism haplotype is common to all small breeds and nearly absent from giant breeds, suggesting that the same causal sequence variant is a major contributor to body size in all small dogs.
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Affiliation(s)
- Nathan B. Sutter
- National Human Genome Research Institute, Building 50, Room 5349, 50 South Drive MSC 8000, Bethesda, MD 20892–8000, USA
| | - Carlos D. Bustamante
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA
| | - Kevin Chase
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Melissa M. Gray
- Department of Ecology and Environmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Keyan Zhao
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Lan Zhu
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA
| | - Badri Padhukasahasram
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA
| | - Eric Karlins
- National Human Genome Research Institute, Building 50, Room 5349, 50 South Drive MSC 8000, Bethesda, MD 20892–8000, USA
| | - Sean Davis
- National Human Genome Research Institute, Building 50, Room 5349, 50 South Drive MSC 8000, Bethesda, MD 20892–8000, USA
| | - Paul G. Jones
- The WALTHAM Centre for Pet Nutrition, Waltham on the Wolds, Leicestershire, LE14 4RT, UK
| | - Pascale Quignon
- National Human Genome Research Institute, Building 50, Room 5349, 50 South Drive MSC 8000, Bethesda, MD 20892–8000, USA
| | - Gary S. Johnson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Heidi G. Parker
- National Human Genome Research Institute, Building 50, Room 5349, 50 South Drive MSC 8000, Bethesda, MD 20892–8000, USA
| | - Neale Fretwell
- The WALTHAM Centre for Pet Nutrition, Waltham on the Wolds, Leicestershire, LE14 4RT, UK
| | - Dana S. Mosher
- National Human Genome Research Institute, Building 50, Room 5349, 50 South Drive MSC 8000, Bethesda, MD 20892–8000, USA
| | | | | | - Magnus Nordborg
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - K. Gordon Lark
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Robert K. Wayne
- Department of Ecology and Environmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Elaine A. Ostrander
- National Human Genome Research Institute, Building 50, Room 5349, 50 South Drive MSC 8000, Bethesda, MD 20892–8000, USA
- To whom correspondence should be addressed.
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16
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Lark KG, Chase K, Sutter NB. Genetic architecture of the dog: sexual size dimorphism and functional morphology. Trends Genet 2006; 22:537-44. [PMID: 16934357 PMCID: PMC2785546 DOI: 10.1016/j.tig.2006.08.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2006] [Revised: 05/11/2006] [Accepted: 08/04/2006] [Indexed: 10/24/2022]
Abstract
Purebred dogs are a valuable resource for genetic analysis of quantitative traits. Quantitative traits are complex, controlled by many genes that are contained within regions of the genome known as quantitative trait loci (QTL). The genetic architecture of quantitative traits is defined by the characteristics of these genes: their number, the magnitude of their effects, their positions in the genome and their interactions with each other. QTL analysis is a valuable tool for exploring genetic architecture, and highlighting regions of the genome that contribute to the variation of a trait within a population.
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Affiliation(s)
- Karl G Lark
- Department of Biology, University of Utah, Salt Lake City, UT 84112-0840, USA.
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17
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Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, Ponting CP, Galibert F, Smith DR, DeJong PJ, Kirkness E, Alvarez P, Biagi T, Brockman W, Butler J, Chin CW, Cook A, Cuff J, Daly MJ, DeCaprio D, Gnerre S, Grabherr M, Kellis M, Kleber M, Bardeleben C, Goodstadt L, Heger A, Hitte C, Kim L, Koepfli KP, Parker HG, Pollinger JP, Searle SMJ, Sutter NB, Thomas R, Webber C, Baldwin J, Abebe A, Abouelleil A, Aftuck L, Ait-Zahra M, Aldredge T, Allen N, An P, Anderson S, Antoine C, Arachchi H, Aslam A, Ayotte L, Bachantsang P, Barry A, Bayul T, Benamara M, Berlin A, Bessette D, Blitshteyn B, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Brown A, Cahill P, Calixte N, Camarata J, Cheshatsang Y, Chu J, Citroen M, Collymore A, Cooke P, Dawoe T, Daza R, Decktor K, DeGray S, Dhargay N, Dooley K, Dooley K, Dorje P, Dorjee K, Dorris L, Duffey N, Dupes A, Egbiremolen O, Elong R, Falk J, Farina A, Faro S, Ferguson D, Ferreira P, Fisher S, FitzGerald M, Foley K, Foley C, Franke A, Friedrich D, Gage D, Garber M, Gearin G, Giannoukos G, Goode T, Goyette A, Graham J, Grandbois E, Gyaltsen K, Hafez N, Hagopian D, Hagos B, Hall J, Healy C, Hegarty R, Honan T, Horn A, Houde N, Hughes L, Hunnicutt L, Husby M, Jester B, Jones C, Kamat A, Kanga B, Kells C, Khazanovich D, Kieu AC, Kisner P, Kumar M, Lance K, Landers T, Lara M, Lee W, Leger JP, Lennon N, Leuper L, LeVine S, Liu J, Liu X, Lokyitsang Y, Lokyitsang T, Lui A, Macdonald J, Major J, Marabella R, Maru K, Matthews C, McDonough S, Mehta T, Meldrim J, Melnikov A, Meneus L, Mihalev A, Mihova T, Miller K, Mittelman R, Mlenga V, Mulrain L, Munson G, Navidi A, Naylor J, Nguyen T, Nguyen N, Nguyen C, Nguyen T, Nicol R, Norbu N, Norbu C, Novod N, Nyima T, Olandt P, O'Neill B, O'Neill K, Osman S, Oyono L, Patti C, Perrin D, Phunkhang P, Pierre F, Priest M, Rachupka A, Raghuraman S, Rameau R, Ray V, Raymond C, Rege F, Rise C, Rogers J, Rogov P, Sahalie J, Settipalli S, Sharpe T, Shea T, Sheehan M, Sherpa N, Shi J, Shih D, Sloan J, Smith C, Sparrow T, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Stone S, Sykes S, Tchuinga P, Tenzing P, Tesfaye S, Thoulutsang D, Thoulutsang Y, Topham K, Topping I, Tsamla T, Vassiliev H, Venkataraman V, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Yang S, Yang X, Young G, Yu Q, Zainoun J, Zembek L, Zimmer A, Lander ES. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 2005; 438:803-19. [PMID: 16341006 DOI: 10.1038/nature04338] [Citation(s) in RCA: 1677] [Impact Index Per Article: 88.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 10/11/2005] [Indexed: 12/12/2022]
Abstract
Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
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Affiliation(s)
- Kerstin Lindblad-Toh
- Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA.
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18
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Lohi H, Young EJ, Fitzmaurice SN, Rusbridge C, Chan EM, Vervoort M, Turnbull J, Zhao XC, Ianzano L, Paterson AD, Sutter NB, Ostrander EA, André C, Shelton GD, Ackerley CA, Scherer SW, Minassian BA. Expanded Repeat in Canine Epilepsy. Science 2005; 307:81. [PMID: 15637270 DOI: 10.1126/science.1102832] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Epilepsy afflicts 1% of humans and 5% of dogs. We report a canine epilepsy mutation and evidence for the existence of repeat-expansion disease outside humans. A canid-specific unstable dodecamer repeat in the Epm2b (Nhlrc1) gene recurrently expands, causing a fatal epilepsy and contributing to the high incidence of canine epilepsy. Tracing the repeat origins revealed two successive events, starting 50 million years ago, unique to canid evolution. A genetic test, presented here, will allow carrier and presymptomatic diagnosis and disease eradication. Clinicopathologic characterization establishes affected animals as a model for Lafora disease, the most severe teenage-onset human epilepsy.
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Affiliation(s)
- Hannes Lohi
- The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
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19
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Abstract
Purebred dogs are providing invaluable information about morphology, behaviour and complex diseases, both of themselves and humans, by supplying tractable populations in which to map genes that control those processes. The diversification of dog breeds has led to the development of breeds enriched for particular genetic disorders, the mapping and cloning of which have been facilitated by the availability of the canine genome map and sequence. These tools have aided our understanding of canine population genetics, linkage disequilibrium and haplotype sharing in the dog, and have informed ongoing efforts of the need to identify quantitative trait loci that are important in complex traits.
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Affiliation(s)
- Nathan B Sutter
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, MSC8002, Building 50, Room 5222, Bethesda, Maryland 20892, USA
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20
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Sutter NB, Eberle MA, Parker HG, Pullar BJ, Kirkness EF, Kruglyak L, Ostrander EA. Extensive and breed-specific linkage disequilibrium in Canis familiaris. Genome Res 2004; 14:2388-96. [PMID: 15545498 PMCID: PMC534662 DOI: 10.1101/gr.3147604] [Citation(s) in RCA: 228] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The 156 breeds of registered dogs in the United States offer a unique opportunity to map genes important in disease susceptibility, morphology, and behavior. Linkage disequilibrium (LD) is of current interest for its application in whole genome association mapping, since the extent of LD determines the feasibility of such studies. We have measured LD at five genomic intervals, each 5 Mb in length and composed of five clusters of sequence variants spaced 800 kb-1.6 Mb apart. These intervals are located on canine chromosomes 1, 2, 3, 34, and 37, and none is under obvious selective pressure. Approximately 20 unrelated dogs were assayed from each of five breeds: Akita, Bernese Mountain Dog, Golden Retriever, Labrador Retriever, and Pekingese. At each genomic interval, SNPs and indels were discovered and typed by resequencing. Strikingly, LD in canines is much more extensive than in humans: D' falls to 0.5 at 400-700 kb in Golden Retriever and Labrador Retriever, 2.4 Mb in Akita, and 3-3.2 Mb in Bernese Mountain Dog and Pekingese. LD in dog breeds is up to 100x more extensive than in humans, suggesting that a correspondingly smaller number of markers will be required for association mapping studies in dogs compared to humans. We also report low haplotype diversity within regions of high LD, with 80% of chromosomes in a breed carrying two to four haplotypes, as well as a high degree of haplotype sharing among breeds.
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Affiliation(s)
- Nathan B Sutter
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA
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21
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Parker HG, Kim LV, Sutter NB, Carlson S, Lorentzen TD, Malek TB, Johnson GS, DeFrance HB, Ostrander EA, Kruglyak L. Genetic structure of the purebred domestic dog. Science 2004; 304:1160-4. [PMID: 15155949 DOI: 10.1126/science.1097406] [Citation(s) in RCA: 448] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We used molecular markers to study genetic relationships in a diverse collection of 85 domestic dog breeds. Differences among breeds accounted for approximately 30% of genetic variation. Microsatellite genotypes were used to correctly assign 99% of individual dogs to breeds. Phylogenetic analysis separated several breeds with ancient origins from the remaining breeds with modern European origins. We identified four genetic clusters, which predominantly contained breeds with similar geographic origin, morphology, or role in human activities. These results provide a genetic classification of dog breeds and will aid studies of the genetics of phenotypic breed differences.
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Affiliation(s)
- Heidi G Parker
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Post Office Box 19024, 1100 Fairview Avenue North, D4-100, Seattle, WA 98109-1024, USA
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22
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Sutter NB, Scalzo D, Fiering S, Groudine M, Martin DIK. Chromatin insulation by a transcriptional activator. Proc Natl Acad Sci U S A 2003; 100:1105-10. [PMID: 12547916 PMCID: PMC298734 DOI: 10.1073/pnas.242732999] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2002] [Indexed: 11/18/2022] Open
Abstract
In eukaryotic genomes, transcriptionally active regions are interspersed with silent chromatin that may repress genes in its vicinity. Chromatin insulators are elements that can shield a locus from repressive effects of flanking chromatin. Few such elements have been characterized in higher eukaryotes, but transcriptional activating elements are an invariant feature of active loci and have been shown to suppress transgene silencing. Hence, we have assessed the ability of a transcriptional activator to cause chromatin insulation, i.e., to relieve position effects at transgene integration sites in cultured cells. The transgene contained a series of binding sites for the metal-inducible transcriptional activator MTF, linked to a GFP reporter. Clones carrying single integrated transgenes were derived without selection for expression, and in most clones the transgene was silent. Induction of MTF resulted in transition of the transgene from the silent to the active state, prolongation of the active state, and a marked narrowing of the range of expression levels at different genomic sites. At one genomic site, prolonged induction of MTF resulted in suppression of transgene silencing that persisted after withdrawal of the induction stimulus. These results are consistent with MTF acting as a chromatin insulator and imply that transcriptional activating elements can insulate active loci against chromatin repression.
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Affiliation(s)
- Nathan B Sutter
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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